Classification and quantification of bacteriophage taxa in human gut metagenomes

Waller, Alison S.; Yamada, Takuji; Kristensen, David M.; Kultima, Jens Roat; Sunagawa, Shinichi; Koonin, Eugene V.; Bork, Peer

doi:10.1038/ismej.2014.30

Cited by 140 publications

(159 citation statements)

References 54 publications

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“…More subtle competition occurs by monitoring and manipulating signalling molecules of competitors, which appears to occur for the quorum-sensing molecule autoinducer-2 (AI-2) 64 . Bacteriophages (or phages) are also abundant in the gut 65 and can impact microbial competition and promote diversity; phages tend to spread easily through host bacteria that are plentiful, which can give rarer species an advantage 14 . Finally, phages drive horizontal gene transfer (HGT).…”

Section: Microbe To Microbe: Surviving the Microbiome Junglementioning

confidence: 99%

The evolution of the host microbiome as an ecosystem on a leash

Foster

Schluter

Coyte

et al. 2017

Nature

719

617

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The human body carries vast communities of microbes that provide many benefits. Our microbiome is complex and challenging to understand, but evolutionary theory provides a universal framework with which to analyse its biology and health impacts. Here we argue that to understand a given microbiome feature, such as colonization resistance, host nutrition or immune development, we must consider how hosts and symbionts evolve. Symbionts commonly evolve to compete within the host ecosystem, while hosts evolve to keep the ecosystem on a leash. We suggest that the health benefits of the microbiome should be understood, and studied, as an interplay between microbial competition and host control.

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Section: Microbe To Microbe: Surviving the Microbiome Junglementioning

confidence: 99%

The evolution of the host microbiome as an ecosystem on a leash

Foster

Schluter

Coyte

et al. 2017

Nature

719

617

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“…In the absence of disease, enteric bacteriophage populations exhibit significant diversity between individuals and are temporally stable (Minot et al, 2013; Reyes et al, 2010). Bacteriophages in the healthy human intestine are predominantly temperate dsDNA Caudovirales or ssDNA Microviridae that latently infect their bacterial hosts and generate few viral progeny that may infect and kill other bacteria (Minot et al, 2013; Minot et al, 2011; Reyes et al, 2010; Waller et al, 2014). However, environmental stimuli, such as nitric oxide and antibiotics, induce the production of infectious bacteriophages that lyse their bacterial host and infect neighboring cells bearing specific receptors (Lindsay et al, 1998; Maiques et al, 2006; Zhang et al, 2000; Zhang and LeJeune, 2008).…”

Section: Introductionmentioning

confidence: 99%

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Norman

Handley

Baldridge

et al. 2015

Cell

1,048

1,058

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SUMMARY Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn’s disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease- and cohort-specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.

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“…ORFs were predicted using the WebMGA server. Proteins longer than 100 aa with less than 1% of the length of ambiguities were queried against ACLAME database (e value < 1e-10) and contigs were classified based on Waller (28).…”

Section: Methodsmentioning

confidence: 99%

Healthy human gut phageome

Manrique

Bolduc

Walk

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

455

447

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The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.

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Classification and quantification of bacteriophage taxa in human gut metagenomes

Cited by 140 publications

References 54 publications

The evolution of the host microbiome as an ecosystem on a leash

The evolution of the host microbiome as an ecosystem on a leash

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Healthy human gut phageome

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