A human gut phage catalog correlates the gut phageome with type 2 diabetes

Ma, Yingfei; You, Xiao-Yan; Mai, Guoqin; Tokuyasu, Taku A.; Liu, Chenli

doi:10.1186/s40168-018-0410-y

Cited by 175 publications

(159 citation statements)

References 47 publications

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“…Most GM studies focus on the bacterial gut component, whereas the archaeal, yeast, fungal, and viral (virome) components of the GM have been more sparsely investigated [3,4]. However, recently gut virome dysbiosis have been associated with flares of Crohn’s disease and ulcerative colitis [5], Clostridium difficile associated diarrhoea [6] and type-2-diabetes [7] highlighting the importance of the virome in health and disease. The gut virome is predominated by prokaryotic viruses [8], also called bacteriophages (phages) which are viruses attacking bacteria in a host-specific manner.…”

Section: Introductionmentioning

confidence: 99%

Mouse vendor influence on the bacterial and viral gut composition exceeds the effect of diet

Rasmussen

Vries

Kot

et al. 2019

Preprint

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Often physiological studiess using mice from one vendor show different outcome when being 16 reproduced using mice from another vendor. These divergent phenotypes between similar mouse strains 17 from different vendors have been assigned to differences in the gut microbiome. During recent years, 18 evidence has mounted that the gut viral community plays a key role in shaping the gut microbiome and may 19 thus also influence mouse phenotype. However, to date inter-vendor variation in the murine gut virome has 20 not been studied. Using a metavirome approach, combined with 16S rRNA gene sequencing, we here 21 compare the composition of the viral and bacterial gut community of C57BL/6N mice from three different 22 vendors exposed to either a chow-based low-fat diet or high-fat diet. Interestingly, both the bacterial and the 23 viral component of the gut community differed significantly between vendors. The different diets also 24 strongly influenced both the viral and bacterial gut community, but surprisingly the effect of vendor 25 exceeded the effect of diet. In conclusion, the vendor effect is substantial on not only the gut bacterial 26 community, but also strongly influences viral community composition. Given the effect of GM on mice 27 phenotype this is essential to consider, for increasing reproducibility of mouse studies. 28 29

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Section: Introductionmentioning

confidence: 99%

Mouse vendor influence on the bacterial and viral gut composition exceeds the effect of diet

Rasmussen

Vries

Kot

et al. 2019

Preprint

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“…For example, enriched phage communities in human intestinal mucus can act as an acquired immune system by limiting mucosal bacterial populations (2), while dysbiotic gut phageomes are associated with diseases such as type II diabetes (3), colitis (4), and stunting (5). Transplantation of healthy viral filtrates restored health in Clostridium difficile patients (6), while in vitro studies suggest phages from stunted children shape bacterial populations differently than those of healthy children (5), supporting a direct link between phageome composition and disease.…”

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confidence: 99%

Primate phageomes are structured by superhost phylogeny and environment

Gogarten

Rühlemann

Archie

et al. 2020

Preprint

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The evolutionary origins of human-associated bacteriophage communities are poorly understood.To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations, and find relatives of the majority of human-associated phages. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost co-divergence is detected for 44 individual phages. Within species, neighboring social groups harbor evolutionarily and compositionally distinct phageomes, structured by superhost social behavior. However, captive non-human primate phageomes are more similar to humans than their wild counterparts, revealing replacement of wild-associated phages with human-associated ones. Together, our results suggest that potentially labile primate-phage associations persisted across millions of years of evolution, potentially facilitated by transmission between groupmates. One Sentence Summary:Relatives of human-associated phages in wild primates reveal ancient but dynamic superhostphage associations shaped by social transmission. Main Text:Mammals harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. Gut bacterial communities in turn host diverse bacteriophage communities that influence their structure, function, colonization patterns, and ultimately superhost health (the superhost is the host for bacteria that in turn host the bacteriophages; 1).

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“…Despite the genome of phages could be DNA or RNA, we focused on the abundant DNA phageome in this study. The study above based on metagenomic analysis revealed an increase in the number of gut phages and an elevation of the relative pOTU number in the T2D group [36]. Using the VLP isolation-based method in our study, no changes in abundance of the 5 phage families were found between the T2D group and Ctrl group (Fig.…”

Section: Discussionmentioning

confidence: 40%

“…When it comes to the technical routes for investigating phageome, a metagenome-dependent method and a VLP isolation-dependent method are in use [32][33][34][35]. A previous study using the metagenomic data analysis has investigated the comprehensive DNA phageome containing both the genomes of phage particles and the genetic elements of prophages in patients with T2D for the first time [36]. In present study, we used a method based on virus-like particles isolation and focused on the extracellular phages, which could directly regulate the microbiota, thus to affect the physiology of the human host.…”

Section: Discussionmentioning

confidence: 99%

Enteric phageome alternations in Type 2 diabetes disease

Chen¹,

Ma²,

Li³

et al. 2019

Preprint

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Background Type 2 diabetes (T2D) is a complex metabolic disease and has been proved to involve in the alternation of the gut microbiota. The previous studies primarily focused on the changes in bacteriome while ignoring the phage community composition. The extracellular phages could lyse the host bacteria, and thus influence the microbiota through the positive or negative interactions with bacteria. We investigated the change of extracellular phageome and explored its role in T2D pathogenesis.Results We used a sequencing-based approach to identify the bacteriophage after isolation of VLPs from the fecal samples. We identified 330 phages according to the predicted host bacteria. The phageome characteristics were highly diverse among individuals. In the T2D group, the intestinal phage population is altered and the abundance of 7 identified phages specific to Enterobacteriaceae hosts were found increased markedly. Additionally, the abundance of Enterobacteriaceae bacteria in gut was significantly increased and the systemic LPS elevation was observed in T2D group. Several phage consortia were found to have significant correlations with T2D disease indicators.Conclusions The alteration of bacteriophages predicted to infect Enterobacteriaceae in the gut was observed in this study, which was expected to be a new source of systemic LPS in T2D patients, and may contribute to the pathogenesis of the disease. The data present in this study revealed the similar variation trend in enteric bacteriome and the correlated bacteriophages, which is likely to shed considerable light on overall understanding the interactions between microbiome and metabolic diseases.

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A human gut phage catalog correlates the gut phageome with type 2 diabetes

Cited by 175 publications

References 47 publications

Mouse vendor influence on the bacterial and viral gut composition exceeds the effect of diet

Mouse vendor influence on the bacterial and viral gut composition exceeds the effect of diet

Primate phageomes are structured by superhost phylogeny and environment

Enteric phageome alternations in Type 2 diabetes disease

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