Not Just a Passing Phage.
Sutcliffe Steven G,Maurice Corinne F
Cell host & microbe
The viral fraction of the human gut microbiota, or virome, has been studied in a limited capacity. In this issue of Cell Host & Microbe, Shkoporov et al. (2019) perform a longitudinal study with database-independent clustering of bacteriophage genomes and de novo taxonomic classification, increasing our understanding of the virome.
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.
Guerin Emma,Shkoporov Andrey,Stockdale Stephen R,Clooney Adam G,Ryan Feargal J,Sutton Thomas D S,Draper Lorraine A,Gonzalez-Tortuero Enrique,Ross R Paul,Hill Colin
Cell host & microbe
CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.
Yutin Natalya,Makarova Kira S,Gussow Ayal B,Krupovic Mart,Segall Anca,Edwards Robert A,Koonin Eugene V
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.
Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome.
Shkoporov Andrey N,Hill Colin
Cell host & microbe
The human gut microbiome is a dense and taxonomically diverse consortium of microorganisms. While the bacterial components of the microbiome have received considerable attention, comparatively little is known about the composition and physiological significance of human gut-associated bacteriophage populations (phageome). By extrapolating our knowledge of phage-host interactions from other environments, one could expect that >10 viruses reside in the human gut, and we can predict that they play important roles in regulating the complex microbial networks operating in this habitat. Before delving into their function, we need to first overcome the challenges associated with studying and characterizing the phageome. In this Review, we summarize the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome. We also discuss the main challenges in the field and identify promising avenues for future research.
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.
Edwards Robert A,Vega Alejandro A,Norman Holly M,Ohaeri Maria,Levi Kyle,Dinsdale Elizabeth A,Cinek Ondrej,Aziz Ramy K,McNair Katelyn,Barr Jeremy J,Bibby Kyle,Brouns Stan J J,Cazares Adrian,de Jonge Patrick A,Desnues Christelle,Díaz Muñoz Samuel L,Fineran Peter C,Kurilshikov Alexander,Lavigne Rob,Mazankova Karla,McCarthy David T,Nobrega Franklin L,Reyes Muñoz Alejandro,Tapia German,Trefault Nicole,Tyakht Alexander V,Vinuesa Pablo,Wagemans Jeroen,Zhernakova Alexandra,Aarestrup Frank M,Ahmadov Gunduz,Alassaf Abeer,Anton Josefa,Asangba Abigail,Billings Emma K,Cantu Vito Adrian,Carlton Jane M,Cazares Daniel,Cho Gyu-Sung,Condeff Tess,Cortés Pilar,Cranfield Mike,Cuevas Daniel A,De la Iglesia Rodrigo,Decewicz Przemyslaw,Doane Michael P,Dominy Nathaniel J,Dziewit Lukasz,Elwasila Bashir Mukhtar,Eren A Murat,Franz Charles,Fu Jingyuan,Garcia-Aljaro Cristina,Ghedin Elodie,Gulino Kristen M,Haggerty John M,Head Steven R,Hendriksen Rene S,Hill Colin,Hyöty Heikki,Ilina Elena N,Irwin Mitchell T,Jeffries Thomas C,Jofre Juan,Junge Randall E,Kelley Scott T,Khan Mirzaei Mohammadali,Kowalewski Martin,Kumaresan Deepak,Leigh Steven R,Lipson David,Lisitsyna Eugenia S,Llagostera Montserrat,Maritz Julia M,Marr Linsey C,McCann Angela,Molshanski-Mor Shahar,Monteiro Silvia,Moreira-Grez Benjamin,Morris Megan,Mugisha Lawrence,Muniesa Maite,Neve Horst,Nguyen Nam-Phuong,Nigro Olivia D,Nilsson Anders S,O'Connell Taylor,Odeh Rasha,Oliver Andrew,Piuri Mariana,Prussin Ii Aaron J,Qimron Udi,Quan Zhe-Xue,Rainetova Petra,Ramírez-Rojas Adán,Raya Raul,Reasor Kim,Rice Gillian A O,Rossi Alessandro,Santos Ricardo,Shimashita John,Stachler Elyse N,Stene Lars C,Strain Ronan,Stumpf Rebecca,Torres Pedro J,Twaddle Alan,Ugochi Ibekwe MaryAnn,Villagra Nicolás,Wandro Stephen,White Bryan,Whiteley Andy,Whiteson Katrine L,Wijmenga Cisca,Zambrano Maria M,Zschach Henrike,Dutilh Bas E
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome.
Koonin Eugene V,Yutin Natalya
Trends in microbiology
Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were predicted, including unusual ones such as giant RNA polymerase polyproteins. The host range of the crAss-like phages consists of various members of the bacterial phylum Bacteroidetes as demonstrated by CRISPR spacer analysis and by analysis of genes acquired by phages from the hosts. New metagenomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancient association with primates. The first members of the crAss-like group was recently isolated and shown to infect the bacterium Bacteroides intestinales. Characterization of this phage validated the predicted podovirus-like virion structure and the identity of the major capsid protein and other predicted virion proteins, including three RNA polymerase subunits.
Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes.
Nakatsu Geicho,Zhou Haokui,Wu William Ka Kei,Wong Sunny Hei,Coker Olabisi Oluwabukola,Dai Zhenwei,Li Xiangchun,Szeto Chun-Ho,Sugimura Naoki,Lam Thomas Yuen-Tung,Yu Allen Chi-Shing,Wang Xiansong,Chen Zigui,Wong Martin Chi-Sang,Ng Siew Chien,Chan Matthew Tak Vai,Chan Paul Kay Sheung,Chan Francis Ka Leung,Sung Joseph Jao-Yiu,Yu Jun
BACKGROUND & AIMS:Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome. METHODS:We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times. RESULTS:The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls. CONCLUSIONS:In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.
Rapid evolution of the human gut virome.
Minot Samuel,Bryson Alexandra,Chehoud Christel,Wu Gary D,Lewis James D,Bushman Frederic D
Proceedings of the National Academy of Sciences of the United States of America
Humans are colonized by immense populations of viruses, which metagenomic analysis shows are mostly unique to each individual. To investigate the origin and evolution of the human gut virome, we analyzed the viral community of one adult individual over 2.5 y by extremely deep metagenomic sequencing (56 billion bases of purified viral sequence from 24 longitudinal fecal samples). After assembly, 478 well-determined contigs could be identified, which are inferred to correspond mostly to previously unstudied bacteriophage genomes. Fully 80% of these types persisted throughout the duration of the 2.5-y study, indicating long-term global stability. Mechanisms of base substitution, rates of accumulation, and the amount of variation varied among viral types. Temperate phages showed relatively lower mutation rates, consistent with replication by accurate bacterial DNA polymerases in the integrated prophage state. In contrast, Microviridae, which are lytic bacteriophages with single-stranded circular DNA genomes, showed high substitution rates (>10(-5) per nucleotide each day), so that sequence divergence over the 2.5-y period studied approached values sufficient to distinguish new viral species. Longitudinal changes also were associated with diversity-generating retroelements and virus-encoded Clustered Regularly Interspaced Short Palindromic Repeats arrays. We infer that the extreme interpersonal diversity of human gut viruses derives from two sources, persistence of a small portion of the global virome within the gut of each individual and rapid evolution of some long-term virome members.
The human gut virome: inter-individual variation and dynamic response to diet.
Minot Samuel,Sinha Rohini,Chen Jun,Li Hongzhe,Keilbaugh Sue A,Wu Gary D,Lewis James D,Bushman Frederic D
Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human "virome") in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet.
Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins.
Moreno-Gallego J Leonardo,Chou Shao-Pei,Di Rienzi Sara C,Goodrich Julia K,Spector Timothy D,Bell Jordana T,Youngblut Nicholas D,Hewson Ian,Reyes Alejandro,Ley Ruth E
Cell host & microbe
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage. Microbiome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns are driven by bacteriophages, not eukaryotic viruses. Collectively, these observations support a strong role of the microbiome in patterning for the virome.
The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.
Legoff Jérôme,Resche-Rigon Matthieu,Bouquet Jerome,Robin Marie,Naccache Samia N,Mercier-Delarue Séverine,Federman Scot,Samayoa Erik,Rousseau Clotilde,Piron Prescillia,Kapel Nathalie,Simon François,Socié Gérard,Chiu Charles Y
Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46-4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.
Choice of assembly software has a critical impact on virome characterisation.
Sutton Thomas D S,Clooney Adam G,Ryan Feargal J,Ross R Paul,Hill Colin
BACKGROUND:The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. DESIGN:This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes. RESULTS:Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.
Studying the gut virome in the metagenomic era: challenges and perspectives.
Garmaeva Sanzhima,Sinha Trishla,Kurilshikov Alexander,Fu Jingyuan,Wijmenga Cisca,Zhernakova Alexandra
The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
Gut Microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD.
Matijašić Mario,Meštrović Tomislav,Paljetak Hana Čipčić,Perić Mihaela,Barešić Anja,Verbanac Donatella
International journal of molecular sciences
The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.
The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches.
Ungaro Federica,Massimino Luca,D'Alessio Silvia,Danese Silvio
United European gastroenterology journal
The association of intestinal dysbiosis with the pathogenesis of inflammatory bowel disease has been well established. Besides bacteria, microbiota comprises yeasts, archaea, protists and viruses, neglected actors in inflammatory bowel disease-associated microbiota. In the past, a great limitation in studying microbiota composition was the low sensitivity of sequencing technologies and that few computational approaches were sufficient to thoroughly analyse the whole microbiome. However, new cutting-edge technologies in nucleic acid sequencing, -omics analysis and the innovative statistics and bioinformatics pipelines made possible more sensitive and accurate metagenomics, ultimately identifying novel players in intestinal inflammation, including prokaryotic and eukaryotic viruses, that together form the gut virome. The discovery of peculiar inflammatory bowel disease-associated microbial strains will not only shed new light on inflammatory bowel disease aetiogenesis, they may also support the development of novel therapeutic strategies not merely treating symptoms, but precisely counteracting the primary cause of chronic intestinal inflammation.
Early life dynamics of the human gut virome and bacterial microbiome in infants.
Lim Efrem S,Zhou Yanjiao,Zhao Guoyan,Bauer Irma K,Droit Lindsay,Ndao I Malick,Warner Barbara B,Tarr Phillip I,Wang David,Holtz Lori R
The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.
Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin.
Rampelli Simone,Turroni Silvia,Schnorr Stephanie L,Soverini Matteo,Quercia Sara,Barone Monica,Castagnetti Andrea,Biagi Elena,Gallinella Giorgio,Brigidi Patrizia,Candela Marco
It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co-occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome-host co-evolutionary process.
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease.
Clooney Adam G,Sutton Thomas D S,Shkoporov Andrey N,Holohan Ross K,Daly Karen M,O'Regan Orla,Ryan Feargal J,Draper Lorraine A,Plevy Scott E,Ross R Paul,Hill Colin
Cell host & microbe
The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn's disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.
CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.
Soto-Perez Paola,Bisanz Jordan E,Berry Joel D,Lam Kathy N,Bondy-Denomy Joseph,Turnbaugh Peter J
Cell host & microbe
Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model.
Rasmussen Torben Sølbeck,Mentzel Caroline Märta Junker,Kot Witold,Castro-Mejía Josué Leonardo,Zuffa Simone,Swann Jonathan Richard,Hansen Lars Hestbjerg,Vogensen Finn Kvist,Hansen Axel Kornerup,Nielsen Dennis Sandris
OBJECTIVE:Development of obesity and type 2 diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. The antagonistic behaviour of phages has the potential to alter the GM. As a proof-of-concept, we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice. DESIGN:The FVT consisted of viromes with distinct profiles extracted from the caecal content of mice from different vendors that were fed a low-fat (LF) diet for 14 weeks. Male C57BL/6NTac mice were divided into five groups: LF (as diet control), high-fat (HF) diet, HF+ampicillin (Amp), HF+Amp+FVT and HF+FVT. At weeks 6 and 7 of the study, the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with Amp 24 hours prior to first FVT treatment. RESULTS:Six weeks after first FVT, the HF+FVT mice showed a significant decrease in weight gain compared with the HF group. Further, glucose tolerance was comparable between the LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome and expression levels of genes associated with obesity and T2D development. CONCLUSIONS:Transfer of caecal viral communities from mice with a lean phenotype into mice with an obese phenotype led to reduced weight gain and normalised blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes.
What is (not) known about the dynamics of the human gut virome in health and disease.
Beller Leen,Matthijnssens Jelle
Current opinion in virology
The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.
Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease.
Ungaro Federica,Massimino Luca,Furfaro Federica,Rimoldi Valeria,Peyrin-Biroulet Laurent,D'Alessio Silvia,Danese Silvio
Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.
Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut.
Santiago-Rodriguez Tasha M,Hollister Emily B
The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.
Shkoporov Andrey N,Clooney Adam G,Sutton Thomas D S,Ryan Feargal J,Daly Karen M,Nolan James A,McDonnell Siobhan A,Khokhlova Ekaterina V,Draper Lorraine A,Forde Amanda,Guerin Emma,Velayudhan Vimalkumar,Ross R Paul,Hill Colin
Cell host & microbe
The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.
The Human Gut Virome in Hypertension.
Han Maozhen,Yang Pengshuo,Zhong Chaofang,Ning Kang
Frontiers in microbiology
Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.
The gut virome: the 'missing link' between gut bacteria and host immunity?
Mukhopadhya Indrani,Segal Jonathan P,Carding Simon R,Hart Ailsa L,Hold Georgina L
Therapeutic advances in gastroenterology
The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease.
Gut mucosal virome alterations in ulcerative colitis.
Zuo Tao,Lu Xiao-Juan,Zhang Yu,Cheung Chun Pan,Lam Siu,Zhang Fen,Tang Whitney,Ching Jessica Y L,Zhao Risheng,Chan Paul K S,Sung Joseph J Y,Yu Jun,Chan Francis K L,Cao Qian,Sheng Jian-Qiu,Ng Siew C
OBJECTIVE:The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC. DESIGN:Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2. RESULTS:In UC, there was an expansion of mucosa viruses, particularly bacteriophages, and a decrease in mucosa diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. and were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC. CONCLUSION:We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.