Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea

Zhao, Guoyan; Droit, Lindsay; Gilbert, Margaret H.; Schiro, Faith; Didier, Peter J.; Si, Xuemei; Paredes, Anne M.; Handley, Scott A.; Virgin, Herbert W.; Bohm, Rudolf P.; Wang, David

doi:10.1016/j.virol.2018.10.001

Cited by 24 publications

(26 citation statements)

References 46 publications

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“…Indeed, examination of the virome along different sites of the GIT in non-human primates found that the virome of the large intestine and rectum were similar but distinct from the ileum. These findings indicate that feces provide a good representation of the colon specifically rather than the gut as a whole (Zhao et al, 2019 ). Another example of sampling site variation was observed in the identification of microbial signatures associated with Crohn's disease in children.…”

Section: Current Methodologies Challenges and Potential Solutionsmentioning

confidence: 95%

“…This creates a gradient of conditions from the mouth to the large intestine resulting in microbial niche specificity (Pereira and Berry, 2017 ; Bauer et al, 2018 ). In addition to longitudinal variation, the GIT varies radially due to features such as the lumen, mucosa, villi and crypts (Donaldson et al, 2016 ; Zhao et al, 2019 ). Within this complex ecosystem bacteriophages can partake in intricate dynamics with bacteria and can influence microbiome homeostasis.…”

Section: The Human Gut Phageomementioning

confidence: 99%

“…The environmental conditions of the gut have an important role in this due to the impact they can have on the metabolic state and stress levels in bacteria ( Figures 2B,C ). These conditions include the physical and anatomical variation along the radial and longitudinal axes of the GIT, mucous, bile acids, pH, oxygen, water levels, nutrient levels, peristalsis and dietary components (Koziolek et al, 2015 ; Vandeputte et al, 2016 ; Shkoporov and Hill, 2019 ; Zhao et al, 2019 ).…”

Section: Phage-host Interactionsmentioning

confidence: 99%

See 2 more Smart Citations

Shining Light on Human Gut Bacteriophages

Guerin

Hill

2020

Front. Cell. Infect. Microbiol.

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Section: Current Methodologies Challenges and Potential Solutionsmentioning

confidence: 95%

Section: The Human Gut Phageomementioning

confidence: 99%

Section: Phage-host Interactionsmentioning

confidence: 99%

See 1 more Smart Citation

Shining Light on Human Gut Bacteriophages

Guerin

Hill

2020

Front. Cell. Infect. Microbiol.

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“…Site-specific differences in the intestinal virome have been explored in mice (Kim and Bae, 2016) and in rhesus macaques, where viromes from the terminal ileum (TI) were distinct from those of the colon and rectum (Zhao et al, 2019). Early research on the human intestinal virome characterized ileal and cecal viral particles, but these studies lacked modern high-throughput sequencing approaches (Lepage et al, 2008;Wagner et al, 2013;Hoyles et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

Butcher

Mack

Stintzi

2020

Front. Cell. Infect. Microbiol.

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While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.

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“…Although a significant number of metagenomic datasets from various species have been published (28)(29)(30)(31), the vast majority of these studies focus on detection and interpretation of the animal viruses sequences, and bacteriophages have not been given significant attention. Only a few studies give emphasis to bacteriophage diversity in these samples, although this is limited to identifying differences between health and disease states in rhesus monkeys (32,33) or specifically focusing on the diversity of ssDNA viruses (34).…”

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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Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea

Cited by 24 publications

References 46 publications

Shining Light on Human Gut Bacteriophages

Shining Light on Human Gut Bacteriophages

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

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

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