Studying the gut virome in the metagenomic era: challenges and perspectives

Garmaeva, Sanzhima; Sinha, Trishla; Kurilshikov, Alexander; Fu, Jingyuan; Wijmenga, Cisca; Zhernakova, Alexandra

doi:10.1186/s12915-019-0704-y

Cited by 124 publications

(96 citation statements)

References 141 publications

(191 reference statements)

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“…Microbiome changes are widely accepted to have a significant association with human health, while metagenomic analysis of viruses, one of the most poorly understood components of the human gut microbiome, has recently revolutionized our view of gut microbiome 20,[38][39][40] , highlighting the critical role of the interrelationships between gut phages and bacteria in health and disease.…”

Section: Discussionmentioning

confidence: 99%

Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity

Bikel

López-Leal

Cornejo‐Granados

et al. 2020

Preprint

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Changes in the composition of the human gut microbiome are recognized to have a significant association with obesity and metabolic syndrome. Mexico leads worldwide childhood-obesity rankings representing an epidemic problem for public health. To this date, it is still unclear how the gut phageome, the bacteriophage component of the virome, influences childhood obesity and obesity with metabolic syndrome. We characterized the gut phageome of 28 school-age children with healthy normal-weight (NW), obese (O), and obese with metabolic syndrome (OMS) profiles, using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. Viromes derived from VLPs were mainly dominated by Caudovirales, and only Inoviridae family was significantly increased in obesity. The three groups showed a similar number of VLPs, while a significant increase in phage richness and diversity was found in obesity groups compared NW. Few phage contigs dominated the phageome composition in NW, being increased in obesity groups. Interestingly, the majority of the phageome was shared among all individuals, establishing a core and common phageome, which abundances correlated with anthropometric and biochemical traits and bacteria previously associated with obesity and metabolic syndrome. We also established a healthy core phageome shared in >80% of NW samples, with a decreased prevalence in the O and OMS groups. Our data support that changes in the gut phageome may contribute to obesity and metabolic syndrome development via bacterial dysbiosis. We consider the phageome characterization provides the basis for novel diagnostic and therapeutic strategies for managing obesity and preventing metabolic syndrome development in obese children through potential phage manipulation. To the best of our knowledge, this study represents the most in-depth sequenced dataset of human bacteriophages, demonstrating for the first time that alterations of the gut phageome characterize obesity.

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Section: Discussionmentioning

confidence: 99%

Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity

Bikel

López-Leal

Cornejo‐Granados

et al. 2020

Preprint

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“…The virome includes double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), as well as RNA viruses. Significant research effort in recent years was devoted to characterize this diverse community and appraise its impact on the host wellbeing [70][71][72]. Viruses are found in numerous human body sites, with the intestine being the most extensively populated and studied niche.…”

Section: Human Viromementioning

confidence: 99%

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

Matijašić

Meštrović

Paljetak

et al. 2020

IJMS

189

110

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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.

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“…Bacteriophage diversity, biogeography and dynamics in the human gut has been investigated in depth in numerous studies using metagenomic approaches (16,17,21); see also reviews (17,22,23). It has to be mentioned, however, that in almost all of the studies the viral community of the feces was used as a proxy of the intestinal viromes.…”

Section: Introductionmentioning

confidence: 99%

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

Babenko

Millard

Kulikov

et al. 2020

Preprint

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The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.Short abstract (needed in some journals as eLife)The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways.Importance. (needed for mBio)The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.

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Studying the gut virome in the metagenomic era: challenges and perspectives

Cited by 124 publications

References 141 publications

Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity

Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

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