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    Gut microbiota and colorectal cancer: insights into pathogenesis for novel therapeutic strategies. Kang Yongbo,Pan Wei,Cai Yue Zeitschrift fur Gastroenterologie Colorectal cancer (CRC), as a leading cause of cancer-related death, is triggered by the complex interplay of host genetics and environmental factors. Mounting evidence has shed light on the association of the gut microbiota dysbiosis with CRC. In CRC experimental models, certain gut microbial strains have been shown to inhibit or attenuate immune responses, indicating that specific species among intestinal commensal bacteria may play either a pathogenic or a protective role in the development of CRC. Oral intake of probiotics/prebiotics can therefore serve as a therapeutic approach for CRC treatment. Microbiota studies in cancer, however, are still at the early stage, lack of quantitative data for clinic application. Fortunately, sequencing-based technologies are a boon to further investigation on the association of the intestinal bacterial flora and human diseases. This review considers the evidence for the role of the gut microbiota in CRC development and progression, responsiveness to immune system, and the related therapeutic applications of probiotics/prebiotics. 10.1055/s-0043-116387
    Polyphenols-gut microbiota interplay and brain neuromodulation. Filosa Stefania,Di Meo Francesco,Crispi Stefania Neural regeneration research Increasing evidence suggests that food ingested polyphenols can have beneficial effects in neuronal protection acting against oxidative stress and inflammatory injury. Moreover, polyphenols have been reported to promote cognitive functions. Biotransformation of polyphenols is needed to obtain metabolites active in brain and it occurs through their processing by gut microbiota. Polyphenols metabolites could directly act as neurotransmitters crossing the blood-brain barrier or indirectly by modulating the cerebrovascular system. The microbiota-gut-brain axis is considered a neuroendocrine system that acts bidirectionally and plays an important role in stress responses. The metabolites produced by microbiota metabolism can modulate gut bacterial composition and brain biochemistry acting as neurotransmitters in the central nervous system. Gut microbiota composition can be influenced by dietary ingestion of natural bioactive molecules such as probiotics, prebiotics and polyphenol. Microbiota composition can be altered by dietary changes and gastrointestinal dysfunctions are observed in neurodegenerative diseases. In addition, several pieces of evidence support the idea that alterations in gut microbiota and enteric neuroimmune system could contribute to onset and progression of these age-related disorders. The impact of polyphenols on microbiota composition strengthens the idea that maintaining a healthy microbiome by modulating diet is essential for having a healthy brain across the lifespan. Moreover, it is emerging that they could be used as novel therapeutics to prevent brain from neurodegeneration. 10.4103/1673-5374.241429
    Bacterial interspecies quorum sensing in the mammalian gut microbiota. Bivar Xavier Karina Comptes rendus biologies The mammalian gastrointestinal tract harbors a diverse and complex resident bacterial community, which interacts with the host in many beneficial processes required for optimal host health. We are studying the importance of bacterial cell-cell communication mediated by the interspecies quorum-sensing signal autoinducer-2 (AI-2) in the beneficial properties of the gut microbiota. Our recent work provided the first evidence that AI-2 produced by Escherichia coli can influence the species composition of this community in the mouse gut. We showed that, under conditions of microbiota imbalances induced by antibiotic treatments, E. coli, which increases intestinal AI-2 levels, not only had an effect on the overall structure of the microbiota community, but specifically favored the expansion of the Firmicutes phylum. Because the Firmicutes are very important for many gut functions and were the group of bacteria most severely affected by antibiotic treatment with streptomycin, we are addressing the possibility that AI-2 can influence the balance of the major bacterial groups in the gut and promote recovery of gut homeostasis. Overall, we want to understand how bacterial chemical signaling shapes the multi-species bacterial communities in the mammalian gut and how these communities affect host physiology. 10.1016/j.crvi.2018.03.006
    Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Dimidi Eirini,Cox Selina Rose,Rossi Megan,Whelan Kevin Nutrients Fermented foods are defined as foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action. In recent years, fermented foods have undergone a surge in popularity, mainly due to their proposed health benefits. The aim of this review is to define and characterise common fermented foods (kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, sourdough bread), their mechanisms of action (including impact on the microbiota), and the evidence for effects on gastrointestinal health and disease in humans. Putative mechanisms for the impact of fermented foods on health include the potential probiotic effect of their constituent microorganisms, the fermentation-derived production of bioactive peptides, biogenic amines, and conversion of phenolic compounds to biologically active compounds, as well as the reduction of anti-nutrients. Fermented foods that have been tested in at least one randomised controlled trial (RCT) for their gastrointestinal effects were kefir, sauerkraut, natto, and sourdough bread. Despite extensive in vitro studies, there are no RCTs investigating the impact of kombucha, miso, kimchi or tempeh in gastrointestinal health. The most widely investigated fermented food is kefir, with evidence from at least one RCT suggesting beneficial effects in both lactose malabsorption and eradication. In summary, there is very limited clinical evidence for the effectiveness of most fermented foods in gastrointestinal health and disease. Given the convincing in vitro findings, clinical high-quality trials investigating the health benefits of fermented foods are warranted. 10.3390/nu11081806
    Are the Gut Bacteria Telling Us to Eat or Not to Eat? Reviewing the Role of Gut Microbiota in the Etiology, Disease Progression and Treatment of Eating Disorders. Lam Yan Y,Maguire Sarah,Palacios Talia,Caterson Ian D Nutrients Traditionally recognized as mental illnesses, eating disorders are increasingly appreciated to be biologically-driven. There is a growing body of literature that implicates a role of the gut microbiota in the etiology and progression of these conditions. Gut bacteria may act on the gut-brain axis to alter appetite control and brain function as part of the genesis of eating disorders. As the illnesses progress, extreme feeding patterns and psychological stress potentially feed back to the gut ecosystem that can further compromise physiological, cognitive, and social functioning. Given the established causality between dysbiosis and metabolic diseases, an altered gut microbial profile is likely to play a role in the co-morbidities of eating disorders with altered immune function, short-chain fatty acid production, and the gut barrier being the key mechanistic links. Understanding the role of the gut ecosystem in the pathophysiology of eating disorders will provide critical insights into improving current treatments and developing novel microbiome-based interventions that will benefit patients with eating disorders. 10.3390/nu9060602
    The gut microbiota and host health: a new clinical frontier. Marchesi Julian R,Adams David H,Fava Francesca,Hermes Gerben D A,Hirschfield Gideon M,Hold Georgina,Quraishi Mohammed Nabil,Kinross James,Smidt Hauke,Tuohy Kieran M,Thomas Linda V,Zoetendal Erwin G,Hart Ailsa Gut Over the last 10-15 years, our understanding of the composition and functions of the human gut microbiota has increased exponentially. To a large extent, this has been due to new 'omic' technologies that have facilitated large-scale analysis of the genetic and metabolic profile of this microbial community, revealing it to be comparable in influence to a new organ in the body and offering the possibility of a new route for therapeutic intervention. Moreover, it might be more accurate to think of it like an immune system: a collection of cells that work in unison with the host and that can promote health but sometimes initiate disease. This review gives an update on the current knowledge in the area of gut disorders, in particular metabolic syndrome and obesity-related disease, liver disease, IBD and colorectal cancer. The potential of manipulating the gut microbiota in these disorders is assessed, with an examination of the latest and most relevant evidence relating to antibiotics, probiotics, prebiotics, polyphenols and faecal microbiota transplantation. 10.1136/gutjnl-2015-309990
    Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota. Karl J Philip,Hatch Adrienne M,Arcidiacono Steven M,Pearce Sarah C,Pantoja-Feliciano Ida G,Doherty Laurel A,Soares Jason W Frontiers in microbiology Stress, a ubiquitous part of daily human life, has varied biological effects which are increasingly recognized as including modulation of commensal microorganisms residing in the gastrointestinal tract, the gut microbiota. In turn, the gut microbiota influences the host stress response and associated sequelae, thereby implicating the gut microbiota as an important mediator of host health. This narrative review aims to summarize evidence concerning the impact of psychological, environmental, and physical stressors on gut microbiota composition and function. The stressors reviewed include psychological stress, circadian disruption, sleep deprivation, environmental extremes (high altitude, heat, and cold), environmental pathogens, toxicants, pollutants, and noise, physical activity, and diet (nutrient composition and food restriction). Stressors were selected for their direct relevance to military personnel, a population that is commonly exposed to these stressors, often at extremes, and in combination. However, the selected stressors are also common, alone or in combination, in some civilian populations. Evidence from preclinical studies collectively indicates that the reviewed stressors alter the composition, function and metabolic activity of the gut microbiota, but that effects vary across stressors, and can include effects that may be beneficial or detrimental to host health. Translation of these findings to humans is largely lacking at present. This gap precludes concluding with certainty that transient or cumulative exposures to psychological, environmental, and physical stressors have any consistent, meaningful impact on the human gut microbiota. However, provocative preclinical evidence highlights a need for translational research aiming to elucidate the impact of stressors on the human gut microbiota, and how the gut microbiota can be manipulated, for example by using nutrition, to mitigate adverse stress responses. 10.3389/fmicb.2018.02013
    Intestinal IgA as a modulator of the gut microbiota. Okai Shinsaku,Usui Fumihito,Ohta Misa,Mori Hiroshi,Kurokawa Ken,Matsumoto Satoshi,Kato Tamotsu,Miyauchi Eiji,Ohno Hiroshi,Shinkura Reiko Gut microbes Accumulating evidence suggests that dysbiosis plays a role in the pathogenesis of intestinal diseases including inflammatory bowel disease (IBD) as well as extra-intestinal disorders. As a modulator of the intestinal microbiota, we isolated a mouse monoclonal IgA antibody (clone W27) with high affinities for multiple commensal bacteria, but not for beneficial bacteria such as Lactobacillus casei (L. casei). Via specific recognition of an epitope in serine hydroxymethyltransferase (SHMT), a bacterial metabolic enzyme, W27 IgA selectively inhibited the in vitro growth of bound bacteria, including Escherichia coli (E. coli), while having no effect on unbound beneficial bacteria such as L. casei. By modulating the gut microbiota in vivo, oral administration of W27 IgA effectively prevented development of colitis in several mouse models. Here we discuss how intestinal IgA modulates the gut microbiota through recognition of SHMT. 10.1080/19490976.2017.1310357
    Stress and the gut microbiota-brain axis. Molina-Torres Guadalupe,Rodriguez-Arrastia Miguel,Roman Pablo,Sanchez-Labraca Nuria,Cardona Diana Behavioural pharmacology Stress is a nonspecific response of the body to any demand imposed upon it, disrupting the body homoeostasis and manifested with symptoms such as anxiety, depression or even headache. These responses are quite frequent in the present competitive world. The aim of this review is to explore the effect of stress on gut microbiota. First, we summarize evidence of where the microbiota composition has changed as a response to a stressful situation, and thereby the effect of the stress response. Likewise, we review different interventions that can modulate microbiota and could modulate the stress according to the underlying mechanisms whereby the gut-brain axis influences stress. Finally, we review both preclinical and clinical studies that provide evidence of the effect of gut modulation on stress. In conclusion, the influence of stress on gut microbiota and gut microbiota on stress modulation is clear for different stressors, but although the preclinical evidence is so extensive, the clinical evidence is more limited. A better understanding of the mechanism underlying stress modulation through the microbiota may open new avenues for the design of therapeutics that could boost the pursued clinical benefits. These new designs should not only focus on stress but also on stress-related disorders such as anxiety and depression, in both healthy individuals and different populations. 10.1097/FBP.0000000000000478
    The gut microbiota in internal medicine: implications for health and disease. Lankelma J M,Nieuwdorp M,de Vos W M,Wiersinga W J The Netherlands journal of medicine The human gut microbiota may be viewed as an organ, executing numerous functions in metabolism, development of the immune system and host defence against pathogens. It may therefore be involved in the development of a range of diseases such as gastrointestinal infections, inflammatory bowel disease, allergy and diabetes mellitus. Reversely, certain therapies that are often used, such as antibiotics and chemotherapy, may negatively affect the composition and function of the gut microbiota and thereby the wellbeing of patients. As the microbiota research field is currently moving from association studies to intervention studies and even clinical trials, implementation of this new knowledge into clinical practice is coming near. Several therapeutic interventions that target the gut microbiota are being evaluated, ranging from supplementation of food components to transplantation of faecal microbiota. In this review we provide an overview of current literature on the gut microbiota in both a healthy state and a range of diseases that are relevant for internal medicine. In anticipation of gut microbiota-targeted therapies, it is important to realise the key function of the gut microbiota in physiological processes and the collateral damage that may be caused when disrupting this ecosystem within us.
    Probiotics, gut microbiota, and their influence on host health and disease. Sánchez Borja,Delgado Susana,Blanco-Míguez Aitor,Lourenço Anália,Gueimonde Miguel,Margolles Abelardo Molecular nutrition & food research The gastrointestinal tract of mammals hosts a high and diverse number of different microorganisms, known as intestinal microbiota. Many probiotics were originally isolated from the gastrointestinal tract, and they were defined by the Food and Agriculture Organization of the United Nations (FAO)/WHO as "live microorganisms which when administered in adequate amounts confer a health benefit on the host." Probiotics exert their beneficial effects on the host through four main mechanisms: interference with potential pathogens, improvement of barrier function, immunomodulation and production of neurotransmitters, and their host targets vary from the resident microbiota to cellular components of the gut-brain axis. However, in spite of the wide array of beneficial mechanisms deployed by probiotic bacteria, relatively few effects have been supported by clinical data. In this regard, different probiotic strains have been effective in antibiotic-associated diarrhea or inflammatory bowel disease for instance. The aim of this review was to compile the molecular mechanisms underlying the beneficial effects of probiotics, mainly through their interaction with the intestinal microbiota and with the intestinal mucosa. The specific benefits discussed in this paper include among others those elicited directly through dietary modulation of the human gut microbiota. 10.1002/mnfr.201600240
    Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease. Pickard Joseph M,Zeng Melody Y,Caruso Roberta,Núñez Gabriel Immunological reviews The intestinal tract of mammals is colonized by a large number of microorganisms including trillions of bacteria that are referred to collectively as the gut microbiota. These indigenous microorganisms have co-evolved with the host in a symbiotic relationship. In addition to metabolic benefits, symbiotic bacteria provide the host with several functions that promote immune homeostasis, immune responses, and protection against pathogen colonization. The ability of symbiotic bacteria to inhibit pathogen colonization is mediated via several mechanisms including direct killing, competition for limited nutrients, and enhancement of immune responses. Pathogens have evolved strategies to promote their replication in the presence of the gut microbiota. Perturbation of the gut microbiota structure by environmental and genetic factors increases the risk of pathogen infection, promotes the overgrowth of harmful pathobionts, and the development of inflammatory disease. Understanding the interaction of the microbiota with pathogens and the immune system will provide critical insight into the pathogenesis of disease and the development of strategies to prevent and treat inflammatory disease. 10.1111/imr.12567
    Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Lazar Veronica,Ditu Lia-Mara,Pircalabioru Gratiela Gradisteanu,Gheorghe Irina,Curutiu Carmen,Holban Alina Maria,Picu Ariana,Petcu Laura,Chifiriuc Mariana Carmen Frontiers in immunology The microbiota consists of a dynamic multispecies community of bacteria, fungi, archaea, and protozoans, bringing to the host organism a dowry of cells and genes more numerous than its own. Among the different non-sterile cavities, the human gut harbors the most complex microbiota, with a strong impact on host homeostasis and immunostasis, being thus essential for maintaining the health condition. In this review, we outline the roles of gut microbiota in immunity, starting with the background information supporting the further presentation of the implications of gut microbiota dysbiosis in host susceptibility to infections, hypersensitivity reactions, autoimmunity, chronic inflammation, and cancer. The role of diet and antibiotics in the occurrence of dysbiosis and its pathological consequences, as well as the potential of probiotics to restore eubiosis is also discussed. 10.3389/fimmu.2018.01830
    The gut microbiota: A treasure for human health. Li Daotong,Wang Pan,Wang Pengpu,Hu Xiaosong,Chen Fang Biotechnology advances The interplay between the host and host-associated gut microbiota is an area of increasing interest during the recent decade. From young infants to elderly people, from primitive tribes to modern societies, accumulating evidence has suggested the association of critical physiological roles of gut microbiota in the pathogenesis of a variety of human metabolic, immunological and neurological diseases. Importantly, it appears that the relationship between the gut microbiota and disease is bidirectional, instead of causal or consequential. Personalized nutritional and therapeutic strategies targeting the gut microbiota such as prebiotics, probiotics, drugs and fecal microbiota transplantation may create a new era in the human health. 10.1016/j.biotechadv.2016.08.003
    Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. Rosen Connor E,Palm Noah W BioEssays : news and reviews in molecular, cellular and developmental biology The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of "functional" classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease. 10.1002/bies.201700032
    Gut microbiota modulates drug pharmacokinetics. Zhang Juanhong,Zhang Junmin,Wang Rong Drug metabolism reviews Gut microbiota, one of the determinants of pharmacokinetics, has long been underestimated. It is now generally accepted that the gut microbiota plays an important role in drug metabolism during enterohepatic circulation either before drug absorption or through various microbial enzymatic reactions in the gut. In addition, some drugs are metabolized by the intestinal microbiota to specific metabolites that cannot be formed in the liver. More importantly, metabolizing drugs through the gut microbiota prior to absorption can alter the systemic bioavailability of certain drugs. Therefore, understanding intestinal flora-mediated drug metabolism is critical to interpreting changes in drug pharmacokinetics. Here, we summarize the effects of gut microbiota on drug pharmacokinetics, and propose that the influence of intestinal flora on pharmacokinetics should be organically related to the therapeutic effects and side effects of drugs. More importantly, we could rationally perform the strategy of intestinal microflora-mediated metabolism to design drugs. 10.1080/03602532.2018.1497647
    The Gut Microbiota and Healthy Aging: A Mini-Review. Kim Sangkyu,Jazwinski S Michal Gerontology The gut microbiota shows a wide inter-individual variation, but its within-individual variation is relatively stable over time. A functional core microbiome, provided by abundant bacterial taxa, seems to be common to various human hosts regardless of their gender, geographic location, and age. With advancing chronological age, the gut microbiota becomes more diverse and variable. However, when measures of biological age are used with adjustment for chronological age, overall richness decreases, while a certain group of bacteria associated with frailty increases. This highlights the importance of considering biological or functional measures of aging. Studies using model organisms indicate that age-related gut dysbiosis may contribute to unhealthy aging and reduced longevity. The gut microbiome depends on the host nutrient signaling pathways for its beneficial effects on host health and lifespan, and gut dysbiosis disrupting the interdependence may diminish the beneficial effects or even have reverse effects. Gut dysbiosis can trigger the innate immune response and chronic low-grade inflammation, leading to many age-related degenerative pathologies and unhealthy aging. The gut microbiota communicates with the host through various biomolecules, nutrient signaling-independent pathways, and epigenetic mechanisms. Disturbance of these communications by age-related gut dysbiosis can affect the host health and lifespan. This may explain the impact of the gut microbiome on health and aging. 10.1159/000490615
    Probiotic Species in the Modulation of Gut Microbiota: An Overview. Azad Md Abul Kalam,Sarker Manobendro,Li Tiejun,Yin Jie BioMed research international Probiotics are microbial strains that are beneficial to health, and their potential has recently led to a significant increase in research interest in their use to modulate the gut microbiota. The animal gut is a complex ecosystem of host cells, microbiota, and available nutrients, and the microbiota prevents several degenerative diseases in humans and animals via immunomodulation. The gut microbiota and its influence on human nutrition, metabolism, physiology, and immunity are addressed, and several probiotic species and strains are discussed to improve the understanding of modulation of gut microbiota. This paper provides a broad review of several spp., spp., and other coliform bacteria as the most promising probiotic species and their role in the prevention of degenerative diseases, such as obesity, diabetes, cancer, cardiovascular diseases, malignancy, liver disease, and inflammatory bowel disease. This review also discusses a recent study of spp. in which inflammation was prevented by promotion of proinflammatory immune function via the production of short-chain fatty acids. A summary of gut microbiota alteration with future perspectives is also provided. 10.1155/2018/9478630
    The gut microbiota of wild rodents: Challenges and opportunities. Viney Mark Laboratory animals The gut microbiota can have important, wide-ranging effects on its host. To date, laboratory animals, particularly mice, have been the major study system for microbiota research. It is now becoming increasingly clear that laboratory animals often poorly model aspects of the biology of wild animals, and this concern extends to the study of the gut microbiota. Here, the relatively few studies of the microbiota of wild rodents are reviewed, including a critical assessment of how the gut microbiota differs between laboratory and wild rodents. Finally, the many potential advantages and opportunities of wild-animal systems for research into the gut microbiota are considered. 10.1177/0023677218787538
    Role of Gut Microbiota in the Development and Treatment of Colorectal Cancer. Lin Caizhao,Cai Xiaolu,Zhang Jing,Wang Weibing,Sheng Qinsong,Hua Hanju,Zhou Xile Digestion Human guts harbor abundant microbes that regulate many aspects of host physiology. However, bacterial imbalance or dysbiosis in the gut due to the dietary or environmental changes may cause colorectal cancer (CRC). Increasing studies show that gut microbiota plays an important role in the occurrence and development of CRC, as a result of virulence factors, bacterial metabolites, or inflammatory pathways. In the future, probiotics or targeting the microbiota will probably be a powerful weapon in the battle against CRC. This review seeks to outline the relationship between gut microbiota and the development of CRC as well as the potential mechanisms of microbiota involved in treatment of CRC, so as to provide some references for research on the development, prevention, and treatment of this disease. 10.1159/000494052
    The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease. Zuo Tao,Ng Siew C Frontiers in microbiology In the twenty first century, the changing epidemiology of inflammatory bowel disease (IBD) globally with increasing disease incidence across many countries relates to the altered gut microbiota, due to a combinatorial effect of environmental factors, human immune responses and genetics. IBD is a gastrointestinal disease associated with a gut microbial dysbiosis, including an expansion of facultative anaerobic bacteria of the family Enterobacteriaceae. Advances in high-throughput sequencing enable us to entangle the gut microbiota in human health and IBD beyond the gut bacterial microbiota, expanding insights into the mycobiota, virobiota and helminthes. (viruses) and , and (fungi) are revealed to be increased in IBD. The deconvolution of the gut microbiota in IBD lays the basis for unveiling the roles of these various gut microbiota components in IBD pathogenesis and being conductive to instructing on future IBD diagnosis and therapeutics. Here we comprehensively elucidate the alterations in the gut microbiota in IBD, discuss the effect of diets in the gut microbiota in relation to IBD, and illustrate the potential of manipulation of gut microbiota for IBD therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in IBD. 10.3389/fmicb.2018.02247
    Interplay between food and gut microbiota in health and disease. Danneskiold-Samsøe Niels Banhos,Dias de Freitas Queiroz Barros Helena,Santos Rosangela,Bicas Juliano Lemos,Cazarin Cinthia Baú Betim,Madsen Lise,Kristiansen Karsten,Pastore Glaucia Maria,Brix Susanne,Maróstica Júnior Mário Roberto Food research international (Ottawa, Ont.) Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease. 10.1016/j.foodres.2018.07.043
    [Ulcerative colitis: Does the modulation of gut microbiota induce long-lasting remission?] Stallmach Andreas,Grunert Philip,Pieper Dietmar,Steube Arndt Zeitschrift fur Gastroenterologie Although the pathogenesis of ulcerative colitis (UC) remains elusive, substantial progress in understanding its development and progression has been achieved in the past decades, and novel effective treatment strategies have been developed. Changes in gut microbiota, environmental triggers, deregulation of immunological responses, and genetic predisposition have been identified as pathogenic key factors. There are several lines of clinical observations, which support a close connection of altered gut microbiota with the development and course of UC. Despite a plethora of microbiota alterations in UC, it is currently unclear whether the observed changes in inflammation are cause or effect of the altered microbiota state.Fecal microbiota transplantation (FMT) provides a novel, perhaps complementary, strategy to restore gut microbial diversity, bacterial richness, and microbial homeostasis in UC. FMT is an already established treatment option for recurrent Clostridioides difficile infection, and several case series and randomized controlled trials have described its use in UC. In this review, we evaluate recent efficacy and safety data on FMT for UC, discuss possible pitfalls and show possible areas of future development. Although FMT could become a promising treatment modality for UC, based on currently available data, FMT should be only performed in clinical trials as controlled studies focusing on long-term outcomes and safety are warranted. 10.1055/a-0874-6603
    Tackling probiotic and gut microbiota functionality through proteomics. Ruiz Lorena,Hidalgo Claudio,Blanco-Míguez Aitor,Lourenço Anália,Sánchez Borja,Margolles Abelardo Journal of proteomics UNLABELLED:Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Many strains exert their beneficial effects after transiently colonizing the human gut, where they interact with the rest of the intestinal microorganisms and with the host mucosa. Indeed the human gut harbours a huge number of microorganisms also known as gut microbiota. Imbalances in the relative abundances of the individual components of the gut microbiota may determine the health status of the host and alterations in specific groups have been related to different diseases and metabolic disorders. Proteomics provide a set of high-throughput methodologies for protein identification that are extremely useful for studying probiotic functionality and helping in the assessment of specific health-promoting activities, such as their immunomodulatory activity, the intestinal colonization processes, and the crosstalk mechanisms with the host. Furthermore, proteomics have been used to identify markers of technological performance and stress adaptation, which helps to predict traits such as behaviour into food matrices and ability to survive passage through the gastrointestinal tract. The aim of this review is to compile studies in which proteomics have been used to assess probiotic functionality and to identify molecular players supporting their mechanisms of action. SIGNIFICANCE:Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Molecular basis underlying the functional properties of probiotic bacteria responsible for the health promoting effects have been in the background for many years. Breakthrough of omics technologies in the probiotic and microbiota fields has had a very relevant impact in the elucidation of probiotic mechanisms and in the procedures to select these microorganisms, based on solid scientific evidence. It is unquestionable that, in the near future, the evolution of proteomic techniques will play a pivotal role in the generation of knowledge about the functions of probiotics and gut commensals, still a pending issue in the field of intestinal microbiomics. 10.1016/j.jprot.2016.03.023
    Impact of human aging and modern lifestyle on gut microbiota. Valle Gottlieb Maria Gabriela,Closs Vera Elizabeth,Junges Vilma Maria,Schwanke Carla Helena Augustin Critical reviews in food science and nutrition Human evolution and lifestyle changes caused by the agricultural and industrial revolutions have led to great advances in medicine and increased life expectancy, whilst also profoundly altering the ecological relationships and disease patterns of populations. Studies involving populations that still enjoy a rural way of life and with traits similar to the Paleolithic period reveal them to present a more robust, resistant and diverse gut microbiota, in comparison to highly industrialized civilizations. The human diet has expanded and broadened to include the consumption of high-calorie foods, particularly from animal sources such as game meat and eggs. For some time, authors have been alert to the fact that a modern lifestyle leads to reduced intake of beneficial bacteria, suggesting that nonpathogenic bacteria are being eradicated. Furthermore, therapeutic procedures, including the use of probiotics and prebiotics, have been proposed to lead to recovery of this microbiota, which is altered due to both the ageing process and lifestyle related aspects. Accordingly, this article aims to review the impact of human aging and modern lifestyle on gut microbiota, within an evolutionary, ecological, epidemiological and therapeutic context. 10.1080/10408398.2016.1269054
    The gut microbiota: cause and cure of gut diseases. White Lauren S,Van den Bogaerde Johan,Kamm Michael The Medical journal of Australia The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.
    Neurotransmitter modulation by the gut microbiota. Strandwitz Philip Brain research The gut microbiota - the trillions of bacteria that reside within the gastrointestinal tract - has been found to not only be an essential component immune and metabolic health, but also seems to influence development and diseases of the enteric and central nervous system, including motility disorders, behavioral disorders, neurodegenerative disease, cerebrovascular accidents, and neuroimmune-mediated disorders. By leveraging animal models, several different pathways of communication have been identified along the "gut-brain-axis" including those driven by the immune system, the vagus nerve, or by modulation of neuroactive compounds by the microbiota. Of the latter, bacteria have been shown to produce and/or consume a wide range of mammalian neurotransmitters, including dopamine, norepinephrine, serotonin, or gamma-aminobutyric acid (GABA). Accumulating evidence in animals suggests that manipulation of these neurotransmitters by bacteria may have an impact in host physiology, and preliminary human studies are showing that microbiota-based interventions can also alter neurotransmitter levels. Nonetheless, substantially more work is required to determine whether microbiota-mediated manipulation of human neurotransmission has any physiological implications, and if so, how it may be leveraged therapeutically. In this review this exciting route of communication along the gut-brain-axis, and accompanying data, are discussed. 10.1016/j.brainres.2018.03.015
    Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases. Codella Roberto,Luzi Livio,Terruzzi Ileana Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver Limited animal and human research findings suggests that exercise might have a beneficial role for health gut. Cardiorespiratory fitness correlates with health-associated gut parameters such as taxonomic diversity and richness. Physical exercise may augment intestinal microbial diversity through several mechanisms including promotion of an anti-inflammatory state. Disease-associated microbial functions were linked to distinct taxa in previous studies of familial type 1 diabetes mellitus (T1D). An integrated multi-approach in the study of T1D, including physical exercise, is advocated. The present review explores how exercise might modulate gut microbiota and microbiome characteristics in chronic and immune-based diseases, given the demonstrated relationship between gut function and human health. 10.1016/j.dld.2017.11.016
    Role of the normal gut microbiota. Jandhyala Sai Manasa,Talukdar Rupjyoti,Subramanyam Chivkula,Vuyyuru Harish,Sasikala Mitnala,Nageshwar Reddy D World journal of gastroenterology Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual's life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool. 10.3748/wjg.v21.i29.8787
    The role of gut microbiota in Clostridium difficile infection. Samarkos Michael,Mastrogianni Elpida,Kampouropoulou Olga European journal of internal medicine Clostridium difficile infection has emerged as a major health problem. Because it is a spore-forming microorganism, C. difficile is difficult to eradicate and recurrences of the infection are frequent. The strong association of CDI with prior use of antibiotics led to the recognition that disturbances in the gut microbiota apparently plays a central role in CDI. Except for antibiotics, several other risk factors for CDI have been recognised, such as advanced age and use of proton pump inhibitors. The common characteristic of these factors is that they are associated with changes in the composition of gut microbiota. Data from human studies have shown that the presence of C. difficile, either as a colonizer or as a pathogen, is associated with reduced microbiota diversity. C. difficile infection per se seems to be associated with changes in the representation of specific microbial populations (e.g. taxa) which either may act protectively against C. difficile colonization of the gut or may increase susceptibility for C. difficile infection. Therapeutic gut microbiota manipulation can be achieved by faecal microbiota transplantation, which is highly effective for the treatment of CDI. 10.1016/j.ejim.2018.02.006
    Gut microbiota and cancer: How gut microbiota modulates activity, efficacy and toxicity of antitumoral therapy. Gori Stefania,Inno Alessandro,Belluomini Lorenzo,Bocus Paolo,Bisoffi Zeno,Russo Antonio,Arcaro Guido Critical reviews in oncology/hematology Gut microbiota is involved in gastrointestinal carcinogenesis. Also, it modulates the activity, efficacy and toxicity of several chemotherapy agents, such as gemcitabine, cyclophosphamide, irinotecan, cisplatin and 5-Fluorouracil, and target therapy, such as tyrosine kinase inhibitors. More recently, accumulating data suggest that the composition of gut microbiota may also affect efficacy and toxicity of cancer immunotherapy. Therefore, the manipulation of gut microbiota through antibiotics, probiotics, prebiotics or fecal transplantation has been investigating with the aim to improve efficacy and mitigate toxicity of anticancer drugs. 10.1016/j.critrevonc.2019.09.003
    Inter-kingdom signaling between gut microbiota and their host. Li Qing,Ren Yixing,Fu Xiangsheng Cellular and molecular life sciences : CMLS The crosstalk between prokaryotic bacteria and eukaryotic gut epithelial cells has opened a new field for research. Quorum sensing system (QS) molecules employed by gut microbiota may play an essential role in host-microbial symbioses of the gut. Recent studies on the gut microbiome will unveil evolved mechanisms of the host to affect bacterial QS and shape bacterial composition. Bacterial autoinducers (AIs) could talk to the host's gut by eliciting proinflammatory effects and modulating the activities of T lymphocyte, macrophage, dendritic cells, and neutrophils. In addition, the gut mucosa could interfere with bacterial AIs by degrading them or secreting AI mimics. Moreover, bacterial AIs and gut hormones epinephrine and noradrenaline may be interchangeable in the crosstalk between the microbiota and human gut. Therefore, inter-kingdom signaling between gut microbiota and host may provide a novel target in the management of gut microbiota-related conditions or diseases in the future. 10.1007/s00018-019-03076-7
    The role of diet on gut microbiota composition. Bibbò S,Ianiro G,Giorgio V,Scaldaferri F,Masucci L,Gasbarrini A,Cammarota G European review for medical and pharmacological sciences Gut microbiota is characterized by an inter-individual variability due to genetic and environmental factors. Among the environmental ones, dietary habits play a key role in the modulation of gut microbiota composition. There are main differences between the intestinal microbiota of subjects fed with prevalent Western diet and that of subjects with a diet rich in fibers. Specific changes in the composition of gut microbiota have been demonstrated among subjects according to a different dietary intake. A particular diet may promote the growth of specific bacterial strains, driving hosts to a consequent alteration of fermentative metabolism, with a direct effect on intestinal pH, which can be responsible for the development of a pathogenic flora. Moreover, a high-fat diet can promote the development of a pro-inflammatory gut microbiota, with a consequent increase of intestinal permeability and, consequently, of circulating levels of lipopolysaccharides. In this review, we discuss the direct role of the diet in the composition of gut microbiota and about the possible clinical consequences.
    Gut microbiota and malnutrition. Million Matthieu,Diallo Aldiouma,Raoult Didier Microbial pathogenesis Malnutrition is the leading cause of death worldwide in children under the age of five, and is the focus of the first World Health Organization (WHO) Millennium Development Goal. Breastfeeding, food and water security are major protective factors against malnutrition and critical factors in the maturation of healthy gut microbiota, characterized by a transient bifidobacterial bloom before a global rise in anaerobes. Early depletion in gut Bifidobacterium longum, a typical maternal probiotic, known to inhibit pathogens, represents the first step in gut microbiota alteration associated with severe acute malnutrition (SAM). Later, the absence of the Healthy Mature Anaerobic Gut Microbiota (HMAGM) leads to deficient energy harvest, vitamin biosynthesis and immune protection, and is associated with diarrhea, malabsorption and systemic invasion by microbial pathogens. A therapeutic diet and infection treatment may be unable to restore bifidobacteria and HMAGM. Besides refeeding and antibiotics, future trials including non-toxic missing microbes and nutrients necessary to restore bifidobacteria and HMAGM, including prebiotics and antioxidants, are warranted in children with severe or refractory disease. 10.1016/j.micpath.2016.02.003
    Diet and Gut Microbiota in Health and Disease. Shen Ting-Chin David Nestle Nutrition Institute workshop series Gut microbiota plays an important role in host health maintenance and disease pathogenesis. The development of a stable and diverse gut microbiota is essential to various host physiologic functions such as immunoregulation, pathogen prevention, energy harvest, and metabolism. At the same time, a dysbiotic gut microbiota associated with disease is altered in structure and function, and often characterized by a decrease in species richness and proliferation of pathogenic bacterial taxa. As a shared substrate between the host and the gut microbiota, diet significantly impacts the health and disease states of the host both directly and through gut microbial metabolite production. This is demonstrated in the examples of short-chain fatty acid and trimethylamine production via bacterial metabolism of dietary complex carbohydrates and choline, respectively. In disorders related to mucosal immune dysregulation such as inflammatory bowel disease, the dysbiotic gut microbiota and diet contribute to its pathogenesis. Reversal of dysbiosis through fecal microbiota transplantation and dietary interventions may thus represent important strategies to modify the gut microbiota and its metabolite production for health maintenance as well as disease prevention and management. 10.1159/000455220
    Gut microbiota and aging. Mangiola F,Nicoletti A,Gasbarrini A,Ponziani F R European review for medical and pharmacological sciences The hypothesis of an important role of gut microbiota in maintaining physiological state into the gastrointestinal (GI) system is supported by qualitative and quantitative alteration of the intestinal flora in a number of physiological and pathological condition as shown in several studies. The evidence of the inflammatory state alteration, highlighted in neurodegenerative diseases such as Parkinson's and Alzheimer's strongly recalls the microbiota disturbance, highly suggesting a link between the gastrointestinal system and cognitive functions. Given this perspective, looking at the mutual influence between microbiota products, inflammation mediators and immune system, the modulation of gut microbiota may help to facilitate a physiological and non-pathological aging process and, perhaps, to contrast the progression of degenerating mechanisms. Some studies have already characterized gut microbiota in elderly, with promising results. Future studies should be designed to better understand the correlation between the gut microbiota, the ageing process and degenerative diseases typical of the elderly. 10.26355/eurrev_201811_16280
    Introduction to the human gut microbiota. Thursby Elizabeth,Juge Nathalie The Biochemical journal The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host-microbe interactions. 10.1042/BCJ20160510
    Visceral pain: gut microbiota, a new hope? Pusceddu Matteo M,Gareau Melanie G Journal of biomedical science BACKGROUND:Visceral pain is a complex and heterogeneous disorder, which can range from the mild discomfort of indigestion to the agonizing pain of renal colic. Regulation of visceral pain involves the spinal cord as well as higher order brain structures. Recent findings have linked the microbiota to gastrointestinal disorders characterized by abdominal pain suggesting the ability of microbes to modulate visceral hypersensitivity and nociception to pain. MAIN BODY:In this review we describe the neuroanatomical basis of visceral pain signaling and the existing evidence of its manipulation exerted by the gut microbiota. We included an updated overview of the potential therapeutic effects of dietary intervention, specifically probiotics and prebiotics, in alleviating hypersensitivity to visceral pain stimuli. CONCLUSIONS:The gut microbiota dramatically impacts normal visceral pain sensation and affects the mechanisms mediating visceral nociception. Furthermore, manipulation of the gut microbiota using prebiotics and probiotics plays a potential role in the regulation of visceral pain disorders. 10.1186/s12929-018-0476-7
    An update on the role of gut microbiota in chronic inflammatory diseases, and potential therapeutic targets. Laing Bobbi,Barnett Matthew P G,Marlow Gareth,Nasef Noha Ahmed,Ferguson Lynnette R Expert review of gastroenterology & hepatology INTRODUCTION:The human microbiome plays a critical role in human health, having metabolic, protective, and trophic functions, depending upon its' exact composition. This composition is affected by a number of factors, including the genetic background of the individual, early life factors (including method of birth, length of breastfeeding) and nature of the diet and other environmental exposures (including cigarette smoking) and general life habits. It plays a key role in the control of inflammation, and in turn, its' composition is significantly influenced by inflammation. Areas covered: We consider metabolic, protective, and trophic functions of the microbiome and influences through the lifespan from post-partum effects, to diet later in life in healthy older adults, the effects of aging on both its' composition, and influence on health and potential therapeutic targets that may have anti-inflammatory effects. Expert commentary: The future will see the growth of more effective therapies targeting the microbiome particularly with respect to the use of specific nutrients and diets personalized to the individual. 10.1080/17474124.2018.1505497
    Impact of gut microbiota on gut-distal autoimmunity: a focus on T cells. Sprouse Maran L,Bates Nicholas A,Felix Krysta M,Wu Hsin-Jung Joyce Immunology The immune system is essential for maintaining a delicate balance between eliminating pathogens and maintaining tolerance to self-tissues to avoid autoimmunity. An enormous and complex community of gut microbiota provides essential health benefits to the host, particularly by regulating immune homeostasis. Many of the metabolites derived from commensals can impact host health by directly regulating the immune system. Many autoimmune diseases arise from an imbalance between pathogenic effector T cells and regulatory T (Treg) cells. Recent interest has emerged in understanding how cross-talk between gut microbiota and the host immune system promotes autoimmune development by controlling the differentiation and plasticity of T helper and Treg cells. At the molecular level, our recent study, along with others, demonstrates that asymptomatic colonization by commensal bacteria in the gut is capable of triggering autoimmune disease by molecular mimicking self-antigen and skewing the expression of dual T-cell receptors on T cells. Dysbiosis, an imbalance of the gut microbiota, is involved in autoimmune development in both mice and humans. Although it is well known that dysbiosis can impact diseases occurring within the gut, growing literature suggests that dysbiosis also causes the development of gut-distal/non-gut autoimmunity. In this review, we discuss recent advances in understanding the potential molecular mechanisms whereby gut microbiota induces autoimmunity, and the evidence that the gut microbiota triggers gut-distal autoimmune diseases. 10.1111/imm.13037
    Gut microbiota in colorectal cancer: mechanisms of action and clinical applications. Wong Sunny H,Yu Jun Nature reviews. Gastroenterology & hepatology Colorectal cancer (CRC) accounts for about 10% of all new cancer cases globally. Located at close proximity to the colorectal epithelium, the gut microbiota comprises a large population of microorganisms that interact with host cells to regulate many physiological processes, such as energy harvest, metabolism and immune response. Sequencing studies have revealed microbial compositional and ecological changes in patients with CRC, whereas functional studies in animal models have pinpointed the roles of several bacteria in colorectal carcinogenesis, including Fusobacterium nucleatum and certain strains of Escherichia coli and Bacteroides fragilis. These findings give new opportunities to take advantage of our knowledge on the gut microbiota for clinical applications, such as gut microbiota analysis as screening, prognostic or predictive biomarkers, or modulating microorganisms to prevent cancer, augment therapies and reduce adverse effects of treatment. This Review aims to provide an overview and discussion of the gut microbiota in colorectal neoplasia, including relevant mechanisms in microbiota-related carcinogenesis, the potential of utilizing the microbiota as CRC biomarkers, and the prospect for modulating the microbiota for CRC prevention or treatment. These scientific findings will pave the way to clinically translate the use of gut microbiota for CRC in the near future. 10.1038/s41575-019-0209-8
    The developing gut microbiota and its consequences for health. Butel M-J,Waligora-Dupriet A-J,Wydau-Dematteis S Journal of developmental origins of health and disease The developmental origin of health and disease highlights the importance of the period of the first 1000 days (from the conception to the 2 years of life). The process of the gut microbiota establishment is included in this time window. Various perinatal determinants, such as cesarean section delivery, type of feeding, antibiotics treatment, gestational age or environment, can affect the pattern of bacterial colonization and result in dysbiosis. The alteration of the early bacterial gut pattern can persist over several months and may have long-lasting functional effects with an impact on disease risk later in life. As for example, early gut dysbiosis has been involved in allergic diseases and obesity occurrence. Besides, while it was thought that the fetus developed under sterile conditions, recent data suggested the presence of a microbiota in utero, particularly in the placenta. Even if the origin of this microbiota and its eventual transfer to the infant are nowadays unknown, this placental microbiota could trigger immune responses in the fetus and would program the infant's immune development during fetal life, earlier than previously considered. Moreover, several studies demonstrated a link between the composition of placental microbiota and some pathological conditions of the pregnancy. All these data show the evidence of relationships between the neonatal gut establishment and future health outcomes. Hence, the use of pre- and/or probiotics to prevent or repair any early dysbiosis is increasingly attractive to avoid long-term health consequences. 10.1017/S2040174418000119
    Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Xiong Weili,Abraham Paul E,Li Zhou,Pan Chongle,Hettich Robert L Proteomics The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults. 10.1002/pmic.201400571
    Gut microbiota-mediated inflammation in obesity: a link with gastrointestinal cancer. Cani Patrice D,Jordan Benedicte F Nature reviews. Gastroenterology & hepatology Overweight and obesity are associated with increased risk of developing metabolic disorders such as diabetes and cardiovascular diseases. However, besides these metabolic diseases, excess body weight is also associated with different cancers, including gastrointestinal cancers, such as liver, pancreatic and colon cancers. Inflammation is a common feature of both obesity and cancer; however, the origin of this inflammation has been largely debated. Over the past decade, growing evidence has shown that the composition of the gut microbiota and its activity might be associated not only with the onset of inflammation but also with metabolic disorders and cancer. Here, we review the links between the gut microbiota, gut barrier function and the onset of low-grade inflammation in the development of gastrointestinal cancer. We also describe the mechanisms by which specific microorganism-associated molecular patterns crosstalk with the immune system and how the metabolic activity of bacteria induces specific signalling pathways beyond the gut that eventually trigger carcinogenesis. 10.1038/s41575-018-0025-6
    Time for food: The impact of diet on gut microbiota and human health. Zhang Na,Ju Zhongjie,Zuo Tao Nutrition (Burbank, Los Angeles County, Calif.) There is growing recognition of the role of diet on modulating the composition and metabolic activity of the human gut microbiota, which in turn influence health. Dietary ingredients and food additives have a substantial impact on the gut microbiota and hence affect human health. Updates on current understanding of the gut microbiota in diseases and metabolic disorders are addressed in this review, providing insights into how this can be transferred from bench to bench side as gut microbes are integrated with food. The potency of microbiota-targeted biomarkers as a state-of-art tool for diagnosis of diseases was also discussed, and it would instruct individuals with healthy dietary consumption. Herein, recent advances in understanding the effect of diet on gut microbiota from an ecological perspective, and how these insights might promote health by guiding development of prebiotic and probiotic strategies and functional foods, were explored. 10.1016/j.nut.2017.12.005
    Gut microbiota functions: metabolism of nutrients and other food components. Rowland Ian,Gibson Glenn,Heinken Almut,Scott Karen,Swann Jonathan,Thiele Ines,Tuohy Kieran European journal of nutrition The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays. 10.1007/s00394-017-1445-8
    Pathogenic role of the gut microbiota in gastrointestinal diseases. Nagao-Kitamoto Hiroko,Kitamoto Sho,Kuffa Peter,Kamada Nobuhiko Intestinal research The gastrointestinal (GI) tract is colonized by a dense community of commensal microorganisms referred to as the gut microbiota. The gut microbiota and the host have co-evolved, and they engage in a myriad of immunogenic and metabolic interactions. The gut microbiota contributes to the maintenance of host health. However, when healthy microbial structure is perturbed, a condition termed dysbiosis, the altered gut microbiota can trigger the development of various GI diseases including inflammatory bowel disease, colon cancer, celiac disease, and irritable bowel syndrome. There is a growing body of evidence suggesting that multiple intrinsic and extrinsic factors, such as genetic variations, diet, stress, and medication, can dramatically affect the balance of the gut microbiota. Therefore, these factors regulate the development and progression of GI diseases by inducing dysbiosis. Herein, we will review the recent advances in the field, focusing on the mechanisms through which intrinsic and extrinsic factors induce dysbiosis and the role a dysbiotic microbiota plays in the pathogenesis of GI diseases. 10.5217/ir.2016.14.2.127
    Inflammasomes in the gastrointestinal tract: infection, cancer and gut microbiota homeostasis. Man Si Ming Nature reviews. Gastroenterology & hepatology Inflammasome signalling is an emerging pillar of innate immunity and has a central role in the regulation of gastrointestinal health and disease. Activation of the inflammasome complex mediates both the release of the pro-inflammatory cytokines IL-1β and IL-18 and the execution of a form of inflammatory cell death known as pyroptosis. In most cases, these mediators of inflammation provide protection against bacterial, viral and protozoal infections. However, unchecked inflammasome activities perpetuate chronic inflammation, which underpins the molecular and pathophysiological basis of gastritis, IBD, upper and lower gastrointestinal cancer, nonalcoholic fatty liver disease and obesity. Studies have also highlighted an inflammasome signature in the maintenance of gut microbiota and gut-brain homeostasis. Harnessing the immunomodulatory properties of the inflammasome could transform clinical practice in the treatment of acute and chronic gastrointestinal and extragastrointestinal diseases. This Review presents an overview of inflammasome biology in gastrointestinal health and disease and describes the value of experimental and pharmacological intervention in the treatment of inflammasome-associated clinical manifestations. 10.1038/s41575-018-0054-1
    Gut Microbiota: The Conductor in the Orchestra of Immune-Neuroendocrine Communication. El Aidy Sahar,Dinan Timothy G,Cryan John F Clinical therapeutics PURPOSE:It is well established that mammals are so-called super-organisms that coexist with a complex microbiota. Growing evidence points to the delicacy of this host-microbe interplay and how disruptive interventions could have lifelong consequences. The goal of this article was to provide insights into the potential role of the gut microbiota in coordinating the immune-neuroendocrine cross-talk. METHODS:Literature from a range of sources, including PubMed, Google Scholar, and MEDLINE, was searched to identify recent reports regarding the impact of the gut microbiota on the host immune and neuroendocrine systems in health and disease. FINDINGS:The immune system and nervous system are in continuous communication to maintain a state of homeostasis. Significant gaps in knowledge remain regarding the effect of the gut microbiota in coordinating the immune-nervous systems dialogue. Recent evidence from experimental animal models found that stimulation of subsets of immune cells by the gut microbiota, and the subsequent cross-talk between the immune cells and enteric neurons, may have a major impact on the host in health and disease. IMPLICATIONS:Data from rodent models, as well as from a few human studies, suggest that the gut microbiota may have a major role in coordinating the communication between the immune and neuroendocrine systems to develop and maintain homeostasis. However, the underlying mechanisms remain unclear. The challenge now is to fully decipher the molecular mechanisms that link the gut microbiota, the immune system, and the neuroendocrine system in a network of communication to eventually translate these findings to the human situation, both in health and disease. 10.1016/j.clinthera.2015.03.002
    Human gut microbiota plays a role in the metabolism of drugs. Jourova Lenka,Anzenbacher Pavel,Anzenbacherova Eva Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia BACKGROUND AND AIMS:The gut microbiome, an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract, is now known to play a critical role in human health and predisposition to disease. It is also involved in the biotransformation of xenobiotics and several recent studies have shown that the gut microbiota can affect the pharmacokinetics of orally taken drugs with implications for their oral bioavailability. METHODS:Review of Pubmed, Web of Science and Science Direct databases for the years 1957-2016. RESULTS AND CONCLUSIONS:Recent studies make it clear that the human gut microbiota can play a major role in the metabolism of xenobiotics and, the stability and oral bioavailability of drugs. Over the past 50 years, more than 30 drugs have been identified as a substrate for intestinal bacteria. Questions concerning the impact of the gut microbiota on drug metabolism, remain unanswered or only partially answered, namely (i) what are the molecular mechanisms and which bacterial species are involved? (ii) What is the impact of host genotype and environmental factors on the composition and function of the gut microbiota, (iii) To what extent is the composition of the intestinal microbiome stable, transmissible, and resilient to perturbation? (iv) Has past exposure to a given drug any impact on future microbial response, and, if so, for how long? Answering such questions should be an integral part of pharmaceutical research and personalised health care. 10.5507/bp.2016.039
    Current understanding of the gut microbiota shaping mechanisms. Chang Cherng-Shyang,Kao Cheng-Yuan Journal of biomedical science Increasing evidences have shown strong associations between gut microbiota and many human diseases, and understanding the dynamic crosstalks of host-microbe interaction in the gut has become necessary for the detection, prevention, or therapy of diseases. Many reports have showed that diet, nutrient, pharmacologic factors and many other stimuli play dominant roles in the modulation of gut microbial compositions. However, it is inappropriate to neglect the impact of host factors on shaping the gut microbiota. In this review, we highlighted the current findings of the host factors that could modulate the gut microbiota. Particularly the epithelium-associated factors, including the innate immune sensors, anti-microbial peptides, mucus barrier, secretory IgAs, epithelial microvilli, epithelial tight junctions, epithelium metabolism, oxygen barrier, and even the microRNAs are discussed in the context of the microbiota shaping. With these shaping factors, the gut epithelial cells could select the residing microbes and affect the microbial composition. This knowledge not only could provide the opportunities to better control many diseases, but may also be used for predicting the success of fecal microbiota transplantation clinically. 10.1186/s12929-019-0554-5
    [Gut microbiota: Description, role and pathophysiologic implications]. Landman C,Quévrain E La Revue de medecine interne The human gut contains 10(14) bacteria and many other micro-organisms such as Archaea, viruses and fungi. Studying the gut microbiota showed how this entity participates to gut physiology and beyond this to human health, as a real "hidden organ". In this review, we aimed to bring information about gut microbiota, its structure, its roles and its implication in human pathology. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to four major phyla. The use of culture independent methods and more recently the development of high throughput sequencing allowed to depict precisely gut microbiota structure and diversity as well as its alteration in diseases. Gut microbiota is implicated in the maturation of the host immune system and in many fundamental metabolic pathways including sugars and proteins fermentation and metabolism of bile acids and xenobiotics. Imbalance of gut microbial populations or dysbiosis has important functional consequences and is implicated in many digestive diseases (inflammatory bowel diseases, colorectal cancer, etc.) but also in obesity and autism. These observations have led to a surge of studies exploring therapeutics which aims to restore gut microbiota equilibrium such as probiotics or fecal microbiota transplantation. But recent research also investigates biological activity of microbial products which could lead to interesting therapeutics leads. 10.1016/j.revmed.2015.12.012
    Gut microbiota-mediated protection against diarrheal infections. Vogt Stefanie L,Finlay B Brett Journal of travel medicine Background:The mammalian gut microbiota is a highly abundant and diverse microbial community that resides in the gastrointestinal tract. One major benefit that the gut microbiota provides to its host is colonization resistance-the ability to prevent colonization by foreign microbes, including diarrheal pathogens such as Clostridium difficile , Salmonella enterica serovar Typhimurium and diarrheagenic Escherichia coli . Methods:We conducted a literature review of the effects of the gut microbiota on infection by diarrheal pathogens. We used PubMed to search for relevant articles published before July 2016, as well as incorporated data from our laboratory. Results:The gut microbiota provides protection from diarrheal infections both by direct inhibition of pathogens and by indirect effects on host functions. Direct effects of the microbiota on diarrheal pathogens include competing for nutrients and producing metabolites that inhibit pathogen growth or virulence. Indirect effects of the gut microbiota include promoting maintenance of the gut mucosal barrier and stimulating innate and adaptive immunity. Conclusions:Human epidemiological studies and experimental infections of laboratory animals both demonstrate that antibiotic treatment can alter the gut microbial community and thereby reduce colonization resistance against diarrheal pathogens. Further research might lead to the development of next-generation probiotics that could be used to bolster colonization resistance and thus prevent travellers' diarrheal. Introduction: 10.1093/jtm/taw086
    Modulation of the gut microbiota: a focus on treatments for irritable bowel syndrome. Harris Lucinda A,Baffy Noemi Postgraduate medicine Irritable bowel syndrome (IBS), which is characterized by recurrent abdominal pain and disordered bowel habits, is one of the most common functional bowel disorders. IBS is a substantial burden on both patient health-related quality of life and healthcare costs. Several pathophysiologic mechanisms have been postulated for the occurrence of IBS, including altered gastrointestinal motility, visceral hypersensitivity, changes in gut permeability, immune activation, gut-brain dysregulation, central nervous system dysfunction, and changes in the gut microbiota. Of note, both qualitative and quantitative differences have been observed in the gut microbiota of a population with IBS versus a healthy population. Because of the substantial interest in the gut microbiota and its role as a therapeutic target in IBS, this article provides an overview of specific interventions with the potential to modulate the gut microbiota in IBS, including elimination diets, prebiotics, probiotics, synbiotics, and nonsystemic antibiotics. Although probiotics and synbiotics are generally well tolerated, differences in the composition and concentration of different bacterial species and inclusion or exclusion of prebiotic components varies widely across studies and has prevented strong recommendations on their use in IBS. For nonsystemic antibiotics, rifaximin is indicated in the United States for the treatment of IBS with diarrhea in adults and has been shown to be efficacious and well tolerated in well-designed clinical trials. Overall, more consistent evidence is needed regarding the efficacy and safety of elimination diets, prebiotics, probiotics, and synbiotics for the treatment of patients with IBS. Furthermore, additional well-designed studies are needed that examine alterations in the gut microbiota that occur with these interventions and their potential associations with clinical symptoms of IBS. 10.1080/00325481.2017.1383819
    Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis. Zhuang Xiaojun,Xiong Lishou,Li Li,Li Manying,Chen Minhu Journal of gastroenterology and hepatology BACKGROUND AND AIMS:Alterations of gut microbiota were assumed to be the etiology and pathogenesis of irritable bowel syndrome (IBS) in some studies. However, alterations of gut microbiota in IBS patients had not been systematically assessed with a meta-analysis. We performed a mate-analysis to explore and compare the alterations of gut microbiota in IBS patients from China and other regions around the world. METHODS:Case-control studies detecting gut microbiota in IBS patients were identified through English and Chinese databases. The standardized mean difference (SMD) with 95% confidence interval (CI) of bacterial counts was calculated. RESULTS:Ten studies from China and seven studies from other regions around the world were included in our study. As compared with healthy controls, the SMDs of Bifidobacteria, Lactobacillus, Escherichia Coli, and Enterobacter in Chinese IBS patients were -1.42 (CI: -2.10, -0.75), -0.91 (95% CI: -1.31, -0.52), 0.83 (95% CI: 0.26, 1.40), and 0.57 (95% CI: 0.33, 0.82), respectively. But the SMDs of Bacteroides and Enterococcus were found no significant differences in Chinese IBS patients. However, the SMDs of Bifidobacteria and Bacteroides in IBS patients from other regions were -0.76 (CI: -1.43, -0.09) and 1.17 (CI: 0.00, 2.35), while the SMDs of Lactobacillus, E. Coli, Enterobacter, and Enterococcus were found no significant differences. CONCLUSIONS:There were alterations of gut microbiota in IBS patients, and it implied that alterations of gut microbiota might be involved in the pathogenesis of IBS. However, the species-specific alterations of gut microbiota were different between IBS patients from China and other regions. 10.1111/jgh.13471
    Study Insights into Gastrointestinal Cancer through the Gut Microbiota. Kong Fanli,Cai Yi BioMed research international The gut microbiome in human is recognized as a "microbial organ" for its roles and contributions in regulating the human homeostasis and metabolism. Gastrointestinal (GI) cancers, especially colorectal cancer (CRC), rank as the most common cancer-related deaths worldwide. Evidences have suggested that the disorder of gut microbiota, also named as "dysbiosis," is related to the development of a variety of diseases such as inflammatory bowel disease (IBD) and the CRC. However, detailed mechanisms between disease and gut microbiota remain largely unknown. This review introduced the correlation between gastrointestinal diseases and the microbiota in human gut from the recent studies, as well as the roles of microbiota in manipulating the CRC and IBDs development, in order to facilitate future studies and to develop novel methods for the precaution, diagnosis, or even cure of gastrointestinal diseases. Additionally, we also elucidated the possibility of probiotics in treatment against CRC. 10.1155/2019/8721503
    The influence of gut microbiota on drug metabolism and toxicity. Li Houkai,He Jiaojiao,Jia Wei Expert opinion on drug metabolism & toxicology INTRODUCTION:Gut microbiota plays critical roles in drug metabolism. The variation of gut microbiota contributes to the interindividual differences toward drug therapy including drug-induced toxicity and efficacy. Accordingly, the investigation and elucidation of gut microbial impacts on drug metabolism and toxicity will not only facilitate the way of personalized medicine, but also improve rational drug design. AREAS COVERED:This review provides an overview of the microbiota-host co-metabolism on drug metabolism and summarizes 30 clinical drugs that are co-metabolized by host and gut microbiota. Moreover, this review is specifically focused on elucidating the gut microbial modulation of some clinical drugs, in which the gut microbial influences on drug metabolism, drug-induced toxicity and efficacy are discussed. EXPERT OPINION:The gut microbial contribution to drug metabolism and toxicity is increasingly recognized, but remains largely unexplored due to the extremely complex relationship between gut microbiota and host. The mechanistic elucidation of gut microbiota in drug metabolism is critical before any practical progress in drug design or personalized medicine could be made by modulating human gut microbiota. Analytical technique innovation is urgently required to strengthen our capability in recognizing microbial functions, including metagenomics, metabolomics and the integration of multidisciplinary knowledge. 10.1517/17425255.2016.1121234
    Impact of Omega-3 Fatty Acids on the Gut Microbiota. Costantini Lara,Molinari Romina,Farinon Barbara,Merendino Nicolò International journal of molecular sciences Long-term dietary habits play a crucial role in creating a host-specific gut microbiota community in humans. Despite the many publications about the effects of carbohydrates (prebiotic fibers), the impact of dietary fats, such as omega-3 polyunsaturated fatty acids (PUFAs), on the gut microbiota is less well defined. The few studies completed in adults showed some common changes in the gut microbiota after omega-3 PUFA supplementation. In particular, a decrease in , often associated with an increase in the and butyrate-producing bacteria belonging to the family, has been observed. Coincidentally, a dysbiosis of these taxa is found in patients with inflammatory bowel disease. Omega-3 PUFAs can exert a positive action by reverting the microbiota composition in these diseases, and increase the production of anti-inflammatory compounds, like short-chain fatty acids. In addition, accumulating evidence in animal model studies indicates that the interplay between gut microbiota, omega-3 fatty acids, and immunity helps to maintain the intestinal wall integrity and interacts with host immune cells. Finally, human and animal studies have highlighted the ability of omega-3 PUFAs to influence the gut-brain axis, acting through gut microbiota composition. From these findings, the importance of the omega-3 connection to the microbiota emerges, encouraging further studies. 10.3390/ijms18122645
    Interindividual variability in gut microbiota and host response to dietary interventions. Healey Genelle R,Murphy Rinki,Brough Louise,Butts Christine A,Coad Jane Nutrition reviews Dysbiosis is linked to human disease; therefore, gut microbiota modulation strategies provide an attractive means of correcting microbial imbalance to enhance human health. Because diet has a major influence on the composition, diversity, and metabolic capacity of the gut microbiota, numerous dietary intervention studies have been conducted to manipulate the gut microbiota to improve host outcomes and reduce disease risk. Emerging evidence suggests that interindividual variability in gut microbiota and host responsiveness exists, making it difficult to predict gut microbiota and host response to a given dietary intervention. This may, in turn, have implications on the consistency of results among studies and the perceived success or true efficacy of a dietary intervention in eliciting beneficial changes to the gut microbiota and human health. 10.1093/nutrit/nux062
    The influence of proton pump inhibitors and other commonly used medication on the gut microbiota. Imhann Floris,Vich Vila Arnau,Bonder Marc Jan,Lopez Manosalva Ailine G,Koonen Debby P Y,Fu Jingyuan,Wijmenga Cisca,Zhernakova Alexandra,Weersma Rinse K Gut microbes Proton pump inhibitors (PPIs), used to treat gastro-esophageal reflux and prevent gastric ulcers, are among the most widely used drugs in the world. The use of PPIs is associated with an increased risk of enteric infections. Since the gut microbiota can, depending on composition, increase or decrease the risk of enteric infections, we investigated the effect of PPI-use on the gut microbiota. We discovered profound differences in the gut microbiota of PPI users: 20% of their bacterial taxa were statistically significantly altered compared with those of non-users. Moreover, we found that it is not only PPIs, but also antibiotics, antidepressants, statins and other commonly used medication were associated with distinct gut microbiota signatures. As a consequence, commonly used medications could affect how the gut microbiota resist enteric infections, promote or ameliorate gut inflammation, or change the host's metabolism. More studies are clearly needed to understand the role of commonly used medication in altering the gut microbiota as well as the subsequent health consequences. 10.1080/19490976.2017.1284732
    A critical review on the impacts of β-glucans on gut microbiota and human health. Jayachandran Muthukumaran,Chen Jiali,Chung Stephen Sum Man,Xu Baojun The Journal of nutritional biochemistry The β-glucans are the glucose polymers present in the cells walls of yeast, fungi and cereals. β-Glucans are the major compositions of various nutritional diets such as oats, barley, seaweeds and mushrooms. Various biological activities of β-glucans have been reported such as anticancer, antidiabetic, anti-inflammatory and immune-modulating effects. The importance of β-glucans in food processing industries such as bread preparation, yogurt and pasta have been well elucidated. In recent findings on food science research gut microbiota plays a significant role and vastly studied for its intermediate role in regulating health. Several reports have suggested that β-glucans should have a significant impact on the gut microbiota changes and in turn on human health. The review was aimed to accumulate the evidence on types of β-glucans, their functional properties and the mechanism by how the β-glucans regulate the gut microbiota and human health. The various in vitro, in vivo and clinical studies, have been summarized, in particular, the changes happening upon the β-glucans supplementation on the gut microbiota. Overall, this review updates the recent studies on β-glucans and gut microbiota and also inputs the demanding questions to be addressed in β-glucans-microbiota research in the future. 10.1016/j.jnutbio.2018.06.010
    Challenges of metabolomics in human gut microbiota research. Smirnov Kirill S,Maier Tanja V,Walker Alesia,Heinzmann Silke S,Forcisi Sara,Martinez Inés,Walter Jens,Schmitt-Kopplin Philippe International journal of medical microbiology : IJMM The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine. 10.1016/j.ijmm.2016.03.006
    Human Gut Microbiota and Gastrointestinal Cancer. Meng Changting,Bai Chunmei,Brown Thomas D,Hood Leroy E,Tian Qiang Genomics, proteomics & bioinformatics Human gut microbiota play an essential role in both healthy and diseased states of humans. In the past decade, the interactions between microorganisms and tumors have attracted much attention in the efforts to understand various features of the complex microbial communities, as well as the possible mechanisms through which the microbiota are involved in cancer prevention, carcinogenesis, and anti-cancer therapy. A large number of studies have indicated that microbial dysbiosis contributes to cancer susceptibility via multiple pathways. Further studies have suggested that the microbiota and their associated metabolites are not only closely related to carcinogenesis by inducing inflammation and immune dysregulation, which lead to genetic instability, but also interfere with the pharmacodynamics of anticancer agents. In this article, we mainly reviewed the influence of gut microbiota on cancers in the gastrointestinal (GI) tract (including esophageal, gastric, colorectal, liver, and pancreatic cancers) and the regulation of microbiota by diet, prebiotics, probiotics, synbiotics, antibiotics, or the Traditional Chinese Medicine. We also proposed some new strategies in the prevention and treatment of GI cancers that could be explored in the future. We hope that this review could provide a comprehensive overview of the studies on the interactions between the gut microbiota and GI cancers, which are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention, diagnosis, and treatment. 10.1016/j.gpb.2017.06.002
    Potential for Monitoring Gut Microbiota for Diagnosing Infections and Graft-versus-Host Disease in Cancer and Stem Cell Transplant Patients. Koh Andrew Y Clinical chemistry BACKGROUND:Gut microbiota, the collective community of microorganisms inhabiting the intestine, have been shown to provide many beneficial functions for the host. Recent advances in next-generation sequencing and advanced molecular biology approaches have allowed researchers to identify gut microbiota signatures associated with disease processes and, in some cases, establish causality and elucidate underlying mechanisms. CONTENT:This report reviews 3 commonly used methods for studying the gut microbiota and microbiome (the collective genomes of the gut microorganisms): 16S rRNA gene sequencing, bacterial group or species-specific quantitative polymerase chain reaction (qPCR), and metagenomic shotgun sequencing (MSS). The technical approaches and resources needed for each approach are outlined, and advantages and disadvantages for each approach are summarized. The findings regarding the role of the gut microbiota in the health of patients with cancer and stem cell transplant (SCT) patients (specifically in modulating the development of gut-derived bacterial infections and a posttransplant immune-mediated complication known as graft-vs-host-disease) are reviewed. Finally, there is discussion of the potential viability of these approaches in the actual clinical treatment of cancer and SCT patients. SUMMARY:Advances in next-generation sequencing have revolutionized our understanding of the importance of the gut microbiome to human health. Both 16S rRNA gene sequencing and MSS are currently too labor-intensive or computationally burdensome to incorporate into real-time clinical monitoring of gut microbiomes. Yet, the lessons learned from these technologies could be adapted to currently used methods (e.g., qPCR) that could then be rigorously tested in the clinical care of these patients. 10.1373/clinchem.2016.259499
    A Review on Gut Remediation of Selected Environmental Contaminants: Possible Roles of Probiotics and Gut Microbiota. Feng Pengya,Ye Ze,Kakade Apurva,Virk Amanpreet Kaur,Li Xiangkai,Liu Pu Nutrients Various environmental contaminants including heavy metals, pesticides and antibiotics can contaminate food and water, leading to adverse effects on human health, such as inflammation, oxidative stress and intestinal disorder. Therefore, remediation of the toxicity of foodborne contaminants in human has become a primary concern. Some probiotic bacteria, mainly have received a great attention due to their ability to reduce the toxicity of several contaminants. For instance, can reduce the accumulation and toxicity of selective heavy metals and pesticides in animal tissues by inhibiting intestinal absorption of contaminants and enhancing intestinal barrier function. Probiotics have also shown to decrease the risk of antibiotic-associated diarrhea possibly via competing and producing antagonistic compounds against pathogenic bacteria. Furthermore, probiotics can improve immune function by enhancing the gut microbiota mediated anti-inflammation. Thus, these probiotic bacteria are promising candidates for protecting body against foodborne contaminants-induced toxicity. Study on the mechanism of these beneficial bacterial strains during remediation processes and particularly their interaction with host gut microbiota is an active field of research. This review summarizes the current understanding of the remediation mechanisms of some probiotics and the combined effects of probiotics and gut microbiota on remediation of foodborne contaminants in vivo. 10.3390/nu11010022
    Gut microbiota and its implications in small bowel transplantation. Wang Chenyang,Li Qiurong,Li Jieshou Frontiers of medicine The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice. 10.1007/s11684-018-0617-0
    Interaction between gut microbiota and toll-like receptor: from immunity to metabolism. Yiu Jensen H C,Dorweiler Bernhard,Woo Connie W Journal of molecular medicine (Berlin, Germany) The human gut contains trillions of commensal bacteria, and similar to pathogenic bacteria, the gut microbes and their products can be recognized by toll-like receptors (TLRs). It is well acknowledged that the interaction between gut microbiota and the local TLRs help to maintain the homeostasis of intestinal immunity. High-fat intake or obesity can weaken gut integrity leading to the penetration of gut microbiota or their bacterial products into the circulation, leading to the activation of TLRs on immune cells and subsequently low-grade systemic inflammation in host. Metabolic cells including hepatocytes and adipocytes also express TLRs. Although they are able to produce and secrete inflammatory molecules, the effectiveness remains low compared with the immune cells embedded in the liver and adipose tissue. The interaction of TLRs in these metabolic cells or organs with gut microbiota remains unclear, but a few studies have suggested that the functions of these TLRs are related to metabolism. Alteration of the gut microbiota is associated with body weight change and adiposity in human, and the interaction between the commensal gut microbiota and TLRs may possibly involve both metabolic and immunological regulation. In this review, we will summarize the current findings on the relationship between TLRs and gut microbiota with a focus on metabolic regulation and discuss how such interaction participates in host metabolism. 10.1007/s00109-016-1474-4
    Irritable bowel syndrome: a gut microbiota-related disorder? Bhattarai Yogesh,Muniz Pedrogo David A,Kashyap Purna C American journal of physiology. Gastrointestinal and liver physiology Irritable bowel syndrome (IBS) is one of the most common gastrointestinal (GI) disorders. Despite its prevalence, the pathophysiology of IBS is not well understood although multiple peripheral and central factors are implicated. Recent studies suggest a role for alterations in gut microbiota in IBS. Significant advances in next-generation sequencing technology and bioinformatics and the declining cost have now allowed us to better investigate the role of gut microbiota in IBS. In the following review, we propose gut microbiota as a unifying factor in the pathophysiology of IBS. We first describe how gut microbiota can be influenced by factors predisposing individuals to IBS such as host genetics, stress, diet, antibiotics, and early life experiences. We then highlight the known effects of gut microbiota on mechanisms implicated in the pathophysiology of IBS including disrupted gut brain axis (GBA), visceral hypersensitivity (VH), altered GI motility, epithelial barrier dysfunction, and immune activation. While there are several gaps in the field that preclude us from connecting the dots to establish causation, we hope this overview will allow us to identify and fill in the voids. 10.1152/ajpgi.00338.2016
    Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry? Swanson Hollie I Drug metabolism and disposition: the biological fate of chemicals The importance of the gut microbiome in determining not only overall health, but also in the metabolism of drugs and xenobiotics, is rapidly emerging. It is becoming increasingly clear that the gut microbiota can act in concert with the host cells to maintain intestinal homeostasis, cometabolize drugs and xenobiotics, and alter the expression levels of drug-metabolizing enzymes and transporters and the expression and activity levels of nuclear receptors. In this myriad of activities, the impact of the microbiota may be beneficial or detrimental to the host. Given that the interplay between the gut microbiota and host cells is likely subject to high interindividual variability, this work has tremendous implications for our ability to predict accurately a particular drug's pharmacokinetics and a given patient population's response to drugs. In this issue of Drug Metabolism and Disposition, a series of articles is presented that illustrate the progress and challenges that lie ahead as we unravel the intricacies associated with drug and xenobiotic metabolism by the gut microbiota. These articles highlight the underlying mechanisms that are involved and the use of in vivo and in vitro approaches that are currently available for elucidating the role of the gut microbiota in drug and xenobiotic metabolism. These articles also shed light on exciting new avenues of research that may be pursued as we consider the role of the gut microbiota as an endocrine organ, a component of the brain-gut axis, and whether the gut microbiota is an appropriate and amenable target for new drugs. 10.1124/dmd.115.065714
    Interactions of gut microbiota with dietary polyphenols and consequences to human health. Tomás-Barberán Francisco A,Selma María V,Espín Juan C Current opinion in clinical nutrition and metabolic care PURPOSE OF REVIEW:Dietary (poly)phenolic compounds have received attention over the last 20 years as antioxidants with preventive properties against chronic diseases. However, the evidence of these effects in clinical trials is weak, mainly because of a considerable interindividual variability. Polyphenols bioavailability is low, and gut microbiota metabolize them into simpler metabolites. As gut microbiota vary among individuals, such interindividual variability should be considered as a moderating factor in clinical trials. In this review, we show evidence of interactions with gut microbiota that help understanding polyphenols' health effects. RECENT FINDINGS:Recent studies indicate that dietary polyphenols are relevant in the modulation of gut microbiota and that these microorganisms convert polyphenols into active and bioavailable metabolites; hence, variations in gut microbiota can affect polyphenol activity. SUMMARY:The results show that study participants' stratification by their polyphenol-metabolizing phenotypes would be necessary for clinical trials as specific metabotypes produce the bioactive metabolites responsible for the health effects. Metabotypes can also reflect the gut microbiota composition and metabolic status, and could be biomarkers of the potential polyphenol health effects mediated through gut microbiota. 10.1097/MCO.0000000000000314
    [Gut microbiota and immune crosstalk in metabolic disease]. Burcelin Rémy Biologie aujourd'hui The aim of the review is to discuss about the role played by the defence crosstalk between the gut microbiota and the intestinal immune system, in the development of metabolic disease focusing on obesity and diabetes. Starting from physiological and pathological stand points and based on the latest published data, this review is addressing how the concept of the hologenome theory of evolution can drive the fate of metabolic disease. The notion of "metabolic infection" to explain the "metabolic inflammation" is discussed. This imply comments about the process of bacterial translocation and impaired intestinal immune defense against commensals. Eventually this review sets the soil for personalized medicine. The monthly increase in the number of publications on the gut microbiota to intestinal immune defense and the control of metabolism demonstrate the importance of this field of investigation. The notion of commensal as "self or non-self" has to be reevaluated in the light of the current data. Furthermore, data demonstrate the major role played by short chain fatty acids, secondary bile acids, LPS, peptidoglycans, indole derivatives, and other bacteria-related molecules on the shaping of cells involved in the intestinal protection against commensals is now becoming a central player in the incidence of metabolic diseases. The literature demonstrates that the onset of metabolic diseases and some specific co-morbidities can be explained by a gut microbiota to intestinal immune system crosstalk. Therefore, one should now consider this avenue of investigation as a putative source of biomarkers and therapeutic targets to personalize the treatment of metabolic disease and its co-morbidities. Gut microbiota is considered as a major regulator of metabolic disease. This reconciles the notion of metabolic inflammation and the epidemic development of the disease. In addition to evidence showing that a specific gut microbiota characterizes patients with obesity, type 2 diabetes, and hepatic steatosis, the mechanisms causal to the disease could be related to the translocation of microbiota from the gut to the tissues, which induces inflammation. The mechanisms regulating such a process are based on the crosstalk between the gut microbiota and the host immune system. The hologenome theory of evolution supports this concept and implies that therapeutic strategies aiming to control glycemia should take into account both the gut microbiota and the host immune system. This review discusses the latest evidence regarding the bidirectional impact of the gut microbiota on host immune system crosstalk for the control of metabolic disease, hyperglycemia, and obesity. To avoid redundancies with the literature, we will focus our attention on the intestinal immune system, identifying evidence for the generation of novel therapeutic strategies, which could be based on the control of the translocation of gut bacteria to tissues. Such novel strategies should hamper the role played by gut microbiota dysbiosis on the development of metabolic inflammation. Recent evidence in rodents allows us to conclude that an impaired intestinal immune system characterizes and could be causal in the development of metabolic disease. The fine understanding of the molecular mechanisms should allow for the development of a first line of treatment for metabolic disease and its co-morbidities. 10.1051/jbio/2017008
    Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs. Noh Keumhan,Kang You Ra,Nepal Mahesh Raj,Shakya Rajina,Kang Mi Jeong,Kang Wonku,Lee Sangkyu,Jeong Hye Gwang,Jeong Tae Cheon Archives of pharmacal research The intestinal mucosa and liver have long been considered as the main sites of drug metabolism, and the contribution of gut microbiota to drug metabolism has been under-estimated. However, it is now generally accepted that the gut microbiota plays an important role in drug metabolism prior to drug absorption or during enterohepatic circulation via various microbial enzymatic reactions in the intestine. Moreover, some drugs are metabolized by gut microbiota to specific metabolite(s) that cannot be formed in the liver. More importantly, the metabolism of drugs by gut microbiota prior to absorption can alter the systemic bioavailability of certain drugs. Therefore, understanding drug metabolism by gut microbiota is critical for explaining changes in the pharmacokinetics of drugs, which may cause significant alterations in drug-induced pharmacodynamics and toxicities. In this review, we describe recent progress with regard to the role of metabolism by gut microbiota in some drug-induced alterations of either pharmacological or toxicological effects to emphasize the clinical importance of gut microbiota for safe and effective use of drugs. 10.1007/s12272-017-0986-y
    Metabolome analysis for investigating host-gut microbiota interactions. Chen Michael X,Wang San-Yuan,Kuo Ching-Hua,Tsai I-Lin Journal of the Formosan Medical Association = Taiwan yi zhi Dysbiosis of the gut microbiome is associated with host health conditions. Many diseases have shown to have correlations with imbalanced microbiota, including obesity, inflammatory bowel disease, cancer, and even neurodegeneration disorders. Metabolomics studies targeting small molecule metabolites that impact the host metabolome and their biochemical functions have shown promise for studying host-gut microbiota interactions. Metabolome analysis determines the metabolites being discussed for their biological implications in host-gut microbiota interactions. To facilitate understanding the critical aspects of metabolome analysis, this article reviewed (1) the sample types used in host-gut microbiome studies; (2) mass spectrometry (MS)-based analytical methods and (3) useful tools for MS-based data processing/analysis. In addition to the most frequently used sample type, feces, we also discussed others biosamples, such as urine, plasma/serum, saliva, cerebrospinal fluid, exhaled breaths, and tissues, to better understand gut metabolite systemic effects on the whole organism. Gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and capillary electrophoresis-mass spectrometry (CE-MS), three powerful tools that can be utilized to study host-gut microbiota interactions, are included with examples of their applications. After obtaining big data from MS-based instruments, noise removal, peak detection, missing value imputation, and data analysis are all important steps for acquiring valid results in host-gut microbiome research. The information provided in this review will help new researchers aiming to join this field by providing a global view of the analytical aspects involved in gut microbiota-related metabolomics studies. 10.1016/j.jfma.2018.09.007
    Gut Microbiota as a Therapeutic Target for Metabolic Disorders. Okubo Hirofumi,Nakatsu Yusuke,Kushiyama Akifumi,Yamamotoya Takeshi,Matsunaga Yasuka,Inoue Masa-Ki,Fujishiro Midori,Sakoda Hideaki,Ohno Haruya,Yoneda Masayasu,Ono Hiraku,Asano Tomoichiro Current medicinal chemistry BACKGROUND:Gut microbiota play a vital role not only in the digestion and absorption of nutrients, but also in homeostatic maintenance of host immunity, metabolism and the gut barrier. Recent evidence suggests that gut microbiota alterations contribute to the pathogenesis of metabolic disorders. OBJECTIVE AND METHOD:In this review, we discuss the association between the gut microbiota and metabolic disorders, such as obesity, type 2 diabetes mellitus and non-alcoholic fatty liver disease, and the contribution of relevant modulating interventions, focusing on recent human studies. RESULTS:Several studies have identified potential causal associations between gut microbiota and metabolic disorders, as well as the underlying mechanisms. The effects of modulating interventions, such as prebiotics, probiotics, fecal microbiota transplantation, and other new treatment possibilities on these metabolic disorders have also been reported. CONCLUSION:A growing body of evidence highlights the role of gut microbiota in the development of dysbiosis, which in turn influences host metabolism and disease phenotypes. Further studies are required to elucidate the precise mechanisms by which gut microbiota-derived mediators induce metabolic disorders and modulating interventions exert their beneficial effects in humans. The gut microbiota represents a novel potential therapeutic target for a range of metabolic disorders. 10.2174/0929867324666171009121702
    Our gut microbiota: a long walk to homeostasis. Dicks L M T,Geldenhuys J,Mikkelsen L S,Brandsborg E,Marcotte H Beneficial microbes The microbiome of the human gastrointestinal tract (GIT) consists of billions of bacteria, fungi and viruses, of which bacteria play the most important role in nutrition, immune development, production of vitamins and maintaining a well-balanced (homeostatic) microbial population. Many papers have been published on the microbiota in the human GIT, but little is known about the first group of bacteria that colonises an infant. The intestinal tract of an unborn is, despite general belief, not sterile, but contains bacteria that have been transferred from the mother. This opens a new research field and may change our understanding about the role bacteria play in early life, the selection of strains with probiotic properties and the treatment of diseases related to bacterial infections. Differences in bacterial populations isolated from meconia may provide answers to the prevention of certain forms of diabetes. More research is now focusing on the effect that a genetically diverse group, versus a much simpler microbial population, may have on the development of a homeostatic gut microbiome. The effect different bacterial species have on the gut-associated lymphoid tissue and cascade of immune responses has been well researched, but we still fail in identifying the ideal group of intestinal bacteria and if we do, it will certainly not be possible to maintain homeostasis with so many challenges the gut faces. Changes in diet, antibiotics, food preservatives and stress are some of the factors we would like to control, but more than often fail to do so. The physiology and genetics of the GIT changes with age and so the microbiome. This review summarises factors involved in the regulation of a gut microbiome. 10.3920/BM2017.0066
    Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes. Clavel Thomas,Gomes-Neto João Carlos,Lagkouvardos Ilias,Ramer-Tait Amanda E Immunological reviews The community of microorganisms in the mammalian gastrointestinal tract, referred to as the gut microbiota, influences host physiology and immunity. The last decade of microbiome research has provided significant advancements for the field and highlighted the importance of gut microbes to states of both health and disease. Novel molecular techniques have unraveled the tremendous diversity of intestinal symbionts that potentially influence the host, many proof-of-concept studies have demonstrated causative roles of gut microbial communities in various pathologies, and microbiome-based approaches are beginning to be implemented in the clinic for diagnostic purposes or for personalized treatments. However, several challenges for the field remain: purely descriptive reports outnumbering mechanistic studies and slow translation of experimental results obtained in animal models into the clinics. Moreover, there is a dearth of knowledge regarding how gut microbes, including novel species that have yet to be identified, impact host immune responses. The sheer complexity of the gut microbial ecosystem makes it difficult, in part, to fully understand the microbiota-host networks that regulate immunity. In the present manuscript, we review key findings on the interactions between gut microbiota members and the immune system. Because culturing microbes allows performing functional studies, we have emphasized the impact of specific taxa or communities thereof. We also highlight underlying molecular mechanisms and discuss opportunities to implement minimal microbiome-based strategies. 10.1111/imr.12578
    Metformin and gut microbiota: their interactions and their impact on diabetes. Vallianou Natalia G,Stratigou Theodora,Tsagarakis Stylianos Hormones (Athens, Greece) The ratio of human to bacterial cells in the human body (microbiota) is around 1:1. As a result of co-evolution of the host mucosal immune system and the microbiota, both have developed multiple mechanisms to maintain homeostasis. However, dissociations between the composition of the gut microbiota and the human host may play a crucial role in the development of type 2 diabetes. Metformin, the most frequently administered medication to treat patients with type 2 diabetes, has only recently been suggested to alter gut microbiota composition through the increase in mucin-degrading Akkermansia muciniphila, as well as several SCFA-producing (short-chain fatty acid) microbiota. The gut microbiota of participants on metformin has exerted alterations in gut metabolomics with increased ability to produce butyrate and propionate, substances involved in glucose homeostasis. Thus, metformin appears to affect the microbiome, and an individual's metformin tolerance or intolerance may be influenced by their microbiome. In this review, we will focus on the effects of metformin in gut microbiota among patients with T2DM. 10.1007/s42000-019-00093-w
    The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile. Biagi Elena,Rampelli Simone,Turroni Silvia,Quercia Sara,Candela Marco,Brigidi Patrizia Mechanisms of ageing and development The changing physiology and lifestyle of elderly people affect the gut microbiota composition, the changes of which can, in turn, affect the health maintenance of the ageing host. In a co-evolutionary vision of the relationship between gut microbiota and ageing as an adaptive process of the human superorganism, long-living individuals who get to "successfully" age might be the ones whose microbiota manages to continuously re-establish a mutualistic relationship with the host, adapting to the progressive endogenous and environmental changes. The study of the gut microbiota of long-living people might provide insights on whether and how the gut microbiota can contribute to health maintenance and survival. Here, we provide the state of the art on the study of the gut microbiota in ageing and longevity, with particular attention to the perspective and direction this peculiar field of the microbiota research should take, in order to be a starting point for future mechanistic, pharmacological and clinical studies in ageing research. In particular, longevous people having different genetic, environmental, and cultural background must be analyzed and compared in the attempt to describe "universal" longevity dynamics, useful to unravel how the gut microbial ecosystem can help in expanding human healthspan. 10.1016/j.mad.2016.12.013
    Gut Microbiota-Dependent Modulation of Energy Metabolism. Heiss Christina N,Olofsson Louise E Journal of innate immunity The gut microbiota has emerged as an environmental factor that modulates the host's energy balance. It increases the host's ability to harvest energy from the digested food, and produces metabolites and microbial products such as short-chain fatty acids, secondary bile acids, and lipopolysaccharides. These metabolites and microbial products act as signaling molecules that modulate appetite, gut motility, energy uptake and storage, and energy expenditure. Several findings suggest that the gut microbiota can affect the development of obesity. Germ-free mice are leaner than conventionally raised mice and they are protected against diet-induced obesity. Furthermore, obese humans and rodents have an altered gut microbiota composition with less phylogeneic diversity compared to lean controls, and transplantation of the gut microbiota from obese subjects to germ-free mice can transfer the obese phenotype. Taken together, these findings indicate a role for the gut microbiota in obesity and suggest that the gut microbiota could be targeted to improve metabolic diseases like obesity. This review focuses on the role of the gut microbiota in energy balance regulation and its potential role in obesity. 10.1159/000481519
    Gut microbiota and mTOR signaling: Insight on a new pathophysiological interaction. Noureldein Mohamed H,Eid Assaad A Microbial pathogenesis The gut microbiota plays a substantial role in regulating the host metabolic and immune functions. Dysbiosis, resulting from disruption of gut microbiota, predisposes many morbid pathologies like obesity and its associated comorbidities, diabetes and inflammatory conditions including some types of cancer. There are numerous proposed signaling pathways through which alterations in gut microbiota and its metabolites can disturb the host's normal physiological functions. Interestingly, many of these processes happen to be controlled by the mammalian target of rapamycin (mTOR). The mTOR pathway responds to environmental changes and regulates accordingly many intracellular processes such as transcription, translation, cell growth, cytoskeletal organization and autophagy. In this review, we aim to highlight the cross-talk between the gut microbiota and the mTOR pathway and discuss how this emerging field of research gives a beautiful insight into how the mentioned cross-talk impacts the body's homeostasis thus leading to undesirable complications including obesity, diabetes, colon and pancreatic cancer, immune system malfunctioning and ageing. Although there are a limited number of studies investigating the crosstalk between the gut microbiota and the mTOR pathway, the results obtained so far are enough to elucidate the key role of the mTOR signaling in microbiota-associated metabolic and immune regulations. 10.1016/j.micpath.2018.03.021
    Gut microbiota in common elderly diseases affecting activities of daily living. Shimizu Yukihiro World journal of gastroenterology Gut microbiota are involved in the development or prevention of various diseases such as type 2 diabetes, fatty liver, and malignancy such as colorectal cancer, breast cancer and hepatocellular carcinoma. Alzheimer's disease, osteoporosis, sarcopenia, atherosclerotic stroke and cardiovascular disease are major diseases associated with decreased activities of daily living (ADL), especially in elderly people. Recent analyses have revealed the importance of gut microbiota in the control of these diseases. The composition or diversity of these microbiota is different between patients with these conditions and healthy controls, and administration of probiotics or prebiotics has been shown effective in the treatment of these diseases. Gut microbiota may affect distant organs through mechanisms that include regulating the absorption of nutrients and/or the production of microbial metabolites, regulating and interacting with the systemic immune system, and translocating bacteria/bacterial products through disrupted mucosal barriers. Thus, the gut microbiota may be important regulators in the development of diseases that affect ADL. Although adequate exercise and proper diet are important for preventing these diseases, their combination with interventions that manipulate the composition and/or diversity of gut microbiota could be a promising strategy for maintaining health condition and preserving ADL. This review thus summarizes current understanding of the role of gut microbiota in the development or prevention of diseases closely associated with the maintenance of ADL. 10.3748/wjg.v24.i42.4750
    Diet, gut microbiota and cognition. Proctor Cicely,Thiennimitr Parameth,Chattipakorn Nipon,Chattipakorn Siriporn C Metabolic brain disease The consumption of a diet high in fat and sugar can lead to the development of obesity, type 2 diabetes mellitus (T2DM), cardiovascular disease and cognitive decline. In the human gut, the trillions of harmless microorganisms harboured in the host's gastrointestinal tract are called the 'gut microbiota'. Consumption of a diet high in fat and sugar changes the healthy microbiota composition which leads to an imbalanced microbial population in the gut, a phenomenon known as "gut dysbiosis". It has been shown that certain types of gut microbiota are linked to the pathogenesis of obesity. In addition, long-term consumption of a high fat diet is associated with cognitive decline. It has recently been proposed that the gut microbiota is part of a mechanistic link between the consumption of a high fat diet and the impaired cognition of an individual, termed "microbiota-gut-brain axis". In this complex relationship between the gut, the brain and the gut microbiota, there are several types of gut microbiota and host mechanisms involved. Most of these mechanisms are still poorly understood. Therefore, this review comprehensively summarizes the current evidence from mainly in vivo (rodent and human) studies of the relationship between diet, gut microbiota and cognition. The possible mechanisms that the diet and the gut microbiota have on cognition are also presented and discussed. 10.1007/s11011-016-9917-8
    [Gut microbiota: What impact on colorectal carcinogenesis and treatment?] Bruneau Antoine,Baylatry Minh-Tam,Joly Anne Christine,Sokol Harry Bulletin du cancer The gut microbiota, composed of 10 microorganisms, is now considered as a "hidden organ", regarding to its digestive, metabolic and immune functions, which are helpful to its host. For the last 15 years, advances in molecular biology have highlighted the association of gut microbiota dysbiosis with several diseases, including colorectal cancer. An increased abundance of some bacteria (including Fusobacterium nucleatum, Bacteroides fragilis, Escherichia coli) is associated with cancer, whereas others seem to be protective (Faecalibacterium prausnitzii). Several mechanisms, which are species-specific, are involved in colorectal carcinogenesis. Most of the time, bacterial toxins are involved in pro-inflammatory processes and in activation of angiogenesis and cellular proliferation pathways. The identification of these bacteria leads to envisage the gut microbiota as potential screening tool for colorectal cancer. Recent studies showed a relation between the gut microbiota and the efficacy and toxicity of chemotherapies (oxaliplatin, irinotecan) and immunotherapies (including ipilimumab). Therapeutic approaches targeting the gut microbiota are now available (probiotics, fecal microbiota transplantation…). New therapeutic strategy combining both chemotherapy and/or immunotherapy with an adjuvant treatment targeting the gut microbiota can now be developed in order to improve treatment response and tolerance. 10.1016/j.bulcan.2017.10.025
    Gut microbiota: an Indicator to Gastrointestinal Tract Diseases. Patel Trupti,Bhattacharya Priyanjali,Das Suvrajit Journal of gastrointestinal cancer PURPOSE:Gut microbiota is predicted to play a key role in manifestation of gastrointestinal tract cancers. The human gastrointestinal tract is a complex and abundant network of microbial community. Gut microbiota depicts the microbe population living in our intestine. Humans harbour more than 10(14) microbes in the gut, and the diversity and densities of the microbiota increase from stomach to colon. METHODS:The beneficial relationship between endogenous microbiota and the eukaryotic hosts helps in maintaining various metabolic activities of the body as well as temperature and pH balance. Studies using culturing methods have suggested that the oesophagus is either sterile or contains only a few transient microbes that originates from the oropharynx by swallowing or from the stomach by gastroesophageal reflux. However, metagenomics suggest that large numbers of uncultured organisms are harboured in the human gut. RESULTS:Observations suggest that research directed towards manipulation of the gut microbiota can be employed in prevention as well as treatment of these conditions. Well-designed, randomized, placebo-controlled human studies using probiotics and/or prebiotics are necessary to formulate the directions for prevention and therapy. CONCLUSIONS:Change in gut microbes in gastrointestinal (GI) tract may have major implication in gastric cancer, the fifth most occurring malignancy in the world. Affected population manifests multiple conditions and diseases, which majorly includes inflammatory bowel disease and colorectal malignancy. 10.1007/s12029-016-9820-x
    Gut microbiota in the pathogenesis of inflammatory bowel disease. Nishida Atsushi,Inoue Ryo,Inatomi Osamu,Bamba Shigeki,Naito Yuji,Andoh Akira Clinical journal of gastroenterology Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is a chronic and relapsing inflammatory disorder of the intestine. Although its incidence is increasing globally, the precise etiology remains unclear and a cure for IBD has yet to be discovered. The most accepted hypothesis of IBD pathogenesis is that complex interactions between genetics, environmental factors, and the host immune system lead to aberrant immune responses and chronic intestinal inflammation. The human gut harbors a complex and abundant aggregation of microbes, collectively referred to as the gut microbiota. The gut microbiota has physiological functions associated with nutrition, the immune system, and defense of the host. Recent advances in next-generation sequencing technology have identified alteration of the composition and function of the gut microbiota, which is referred to as dysbiosis, in IBD. Clinical and experimental data suggest dysbiosis may play a pivotal role in the pathogenesis of IBD. This review is focused on the physiological function of the gut microbiota and the association between the gut microbiota and pathogenesis in IBD. In addition, we review the therapeutic options for manipulating the altered gut microbiota, such as probiotics and fecal microbiota transplantation. 10.1007/s12328-017-0813-5
    Whole cereal grains and potential health effects: Involvement of the gut microbiota. Gong Lingxiao,Cao Wenyan,Chi Hailin,Wang Jing,Zhang Huijuan,Liu Jie,Sun Baoguo Food research international (Ottawa, Ont.) The intakes of whole cereal grains (WCGs) have long been linked to decreased risks of metabolic syndromes (MetS) and several chronic diseases. Owing to the complex range of components of cereals, which may show synergistic activities to mediate these protective effects, the mechanisms by which the benefits of whole cereals arise are not fully understood. The gut microbiota has recently become a new focus of research at the intersection of diet and metabolic health. Moreover, cereals contain various ingredients known as microbiota-accessible substrates that resist digestion in the upper gastrointestinal tract, including resistant starch and non-starch polysaccharides such as β-glucan and arabinoxylans, making them an important fuel for the microbiota. Thus, WCGs may manipulate the ecophysiology of gut microbiota. In this review, the scientific evidence supporting the hypothesis that WCGs prevent MetS by modulating gut microbiota composition and functions are discussed, with focuses on cereal intake-related mechanisms by which gut microbiota contributes to human health and scientific evidences for the effects of WCGs on modulating gut microbiota. Once strong support for the association among WCGs, gut microbiota and host metabolic health can be demonstrated, particular cereals, their processing technologies, or cereal-based foods might be better utilized to prevent and possibly even treat metabolic disease. 10.1016/j.foodres.2017.10.025
    An insight into gut microbiota and its functionalities. Adak Atanu,Khan Mojibur R Cellular and molecular life sciences : CMLS Gut microbiota has evolved along with their hosts and is an integral part of the human body. Microbiota acquired at birth develops in parallel as the host develops and maintains its temporal stability and diversity through adulthood until death. Recent developments in genome sequencing technologies, bioinformatics and culturomics have enabled researchers to explore the microbiota and in particular their functions at more detailed level than before. The accumulated evidences suggest that though a part of the microbiota is conserved, the dynamic members vary along the gastrointestinal tract, from infants to elderly, primitive tribes to modern societies and in different health conditions. Though the gut microbiota is dynamic, it performs some basic functions in the immunological, metabolic, structural and neurological landscapes of the human body. Gut microbiota also exerts significant influence on both physical and mental health of an individual. An in-depth understanding of the functioning of gut microbiota has led to some very exciting developments in therapeutics, such as prebiotics, probiotics, drugs and faecal transplantation leading to improved health. 10.1007/s00018-018-2943-4
    The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders. Thumann Timo A,Pferschy-Wenzig Eva-Maria,Moissl-Eichinger Christine,Bauer Rudolf Journal of ethnopharmacology ETHNOPHARMACOLOGICAL RELEVANCE:Many medicinal plants have been traditionally used for the treatment of gastrointestinal disorders. According to the monographs published by the Committee on Herbal Medicinal Products (HMPC) at the European Medicines Agency, currently 44 medicinal plants are recommended in the European Union for the treatment of gastrointestinal disorders based on traditional use. The main indications are functional and chronic gastrointestinal disorders, such as functional dyspepsia and irritable bowel syndrome (IBS), and typical effects of these plants are stimulation of gastric secretion, spasmolytic and carminative effects, soothing effects on the gastrointestinal mucosa, laxative effects, adstringent or antidiarrheal activities, and anti-inflammatory effects. A possible interaction with human gut microbiota has hardly been considered so far, although it is quite likely. AIM OF THE STUDY:In this review, we aimed to identify and evaluate published studies which have investigated interactions of these plants with the gut microbiome. RESULTS:According to this survey, only a minor portion of the 44 medicinal plants considered in EMA monographs for the treatment of gastrointestinal diseases has been studied so far with regard to potential interactions with gut microbiota. We could identify eight relevant in vitro studies that have been performed with six of these medicinal plants, 17 in vivo studies performed in experimental animals involving seven of the medicinal plants, and three trials in humans performed with two of the plants. The most robust evidence exists for the use of inulin as a prebiotic, and in this context also the prebiotic activity of chicory root has been investigated quite intensively. Flaxseed dietary fibers are also known to be fermented by gut microbiota to short chain fatty acids, leading to prebiotic effects. This could cause a health-beneficial modulation of gut microbiota by flaxseed supplementation. In flaxseed, also other compound classes like lignans and polyunsaturated fatty acids are present, that also have been shown to interact with gut microbiota. Drugs rich in tannins and anthocyanins also interact intensively with gut microbiota, since these compounds reach the colon at high levels in unchanged form. Tannins and anthocyanins are intensively metabolized by certain gut bacteria, leading to the generation of small, bioavailable and potentially bioactive metabolites. Moreover, interaction with these compounds may exert a prebiotic-like effect on gut microbiota. Gut microbial metabolization has also been shown for certain licorice constituents, but their potential effects on gut microbiota still need to be investigated in detail. Only a limited amount of studies investigated the interactions of essential oil- and secoiridoid-containing drugs with human gut microbiota. However, other constituents present in some of these drugs, like curcumin (curcuma), shogaol (ginger), and rosmarinic acid have been shown to be metabolized by human gut microbiota, and preliminary data also indicate potential gut microbiome modulatory effects. To conclude, the interaction with gut microbiota is still not fully investigated for many herbal drugs traditionally used for gastrointestinal disorders, which offers a vast field for future research. 10.1016/j.jep.2019.112153
    Impact of a Healthy Dietary Pattern on Gut Microbiota and Systemic Inflammation in Humans. Telle-Hansen Vibeke H,Holven Kirsten B,Ulven Stine M Nutrients Gut microbiota have recently been suggested to play a part in low-grade systemic inflammation, which is considered a key risk factor for cardiometabolic disorders. Diet is known to affect gut microbiota; however, the effects of diet and dietary components on gut microbiota and inflammation are not fully understood. In the present review, we summarize recent research on human dietary intervention studies, investigating the effects of healthy diets or dietary components on gut microbiota and systemic inflammation. We included 18 studies that reported how different dietary components altered gut microbiota composition, short-chain fatty acid levels, and/or inflammatory markers. However, the heterogeneity among the intervention studies makes it difficult to conclude whether diets or dietary components affect gut microbiota homeostasis and inflammation. More appropriately designed studies are needed to better understand the effects of diet on the gut microbiota, systemic inflammation, and risk of cardiometabolic disorders. 10.3390/nu10111783
    Gut microbiota and functional diseases of the gastrointestinal tract. Imperatore Nicola,Tortora Raffaella,Morisco Filomena,Caporaso Nicola Minerva gastroenterologica e dietologica INTRODUCTION:Functional gastrointestinal disorders (FGIDs) are a common group of chronic gastrointestinal (GI) diseases defined by symptom-based diagnostic criteria, which consider chronic or recurrent symptoms of the GI tract in the absence of other organic or biochemical reasons. Recent evidences have been highlighted the role of gut microbiota in the pathophysiology of the FGIDs. EVIDENCE ACQUISITION:A critical analysis of the existing literature on the role of gut microbiota in FGIDs was performed by evaluating the differences of composition, functions and role of intestinal flora in FGIDs of the upper and lower gastrointestinal tract. Moreover, we focused on recent evidences about gut microbiota and celiac disease (CD), especially in CD patients who are symptomatic despite gluten-free diet (GFD), and who seem to share similar features of FGIDs subjects. In this setting, we conducted an additional PubMed search for guidelines, systematic reviews (SR) and primary studies published after the last search update of the most recent reviews. EVIDENCE SYNTHESIS:Some data suggest that, in a significant percentage of patients, the microbiota plays an important role in the genesis and maintenance of FGIDs. Probiotic supplementation and antibiotic treatment appear to be of therapeutic value, although the clinical data remain controversial. CONCLUSIONS:Despite the exciting and growing research on the role of gut microbiota in FGIDs, our knowledge remains fairly limited. Further studies are needed to measure the diversity, function and resistance to antibiotics of the intestinal microbiota in FGIDs. 10.23736/S1121-421X.16.02336-9
    New frontiers in nanotoxicology: Gut microbiota/microbiome-mediated effects of engineered nanomaterials. Pietroiusti Antonio,Magrini Andrea,Campagnolo Luisa Toxicology and applied pharmacology It has been recently recognized that the gut microbiota, the community of organisms living within the gastrointestinal tract is an integral part of the human body, and that its genoma (the microbiome) interacts with the genes expressed by the cells of the host organism. Several important physiological functions require the cooperation of microbiota/microbiome, whose alterations play an important role in several human diseases. On this basis, it is probable that microbiota/microbiome may in part be involved in many biological effects of engineered nanomaterials (ENMs). There are still few reports on the possible toxicological effects of ENMs on microbiota/microbiome, and on their possible clinical consequences. Available data suggest that several ENMs, including carbon nanotubes (CNTs), titanium dioxide, cerium dioxide, zinc oxide, nanosilica and nanosilver may affect the microbiota and that clinical disorders such as colitis, obesity and immunological dysfunctions might follow. On the other hand, other ENMs such as iron nanoparticles may show advantages over traditional iron-based supplemental treatment because they do not interfere with the microbiota/microbiome, and some ENM-based therapeutic interventions might be employed for treating intestinal infections, while sparing the microbiota. The final section of the review is focused on the possible future developments of the research in this field: new in vitro and in vivo models, possible biomarkers and new pathophysiological pathways are proposed and discussed, as well as the possibility that metabolic changes following ENMs/microbiota interactions might be exploited as a fingerprint of ENM exposure. The potential toxicological relevance of physico-chemical modifications of ENMs induced by the microbiota is also highlighted. 10.1016/j.taap.2015.12.017