Rapid evolution of the human gut virome

Minot, Samuel S.; Bryson, Alexandra; Chehoud, Christel; Wu, Gary D.; Lewis, James D.; Bushman, Frederic D.

doi:10.1073/pnas.1300833110

Cited by 523 publications

(605 citation statements)

References 41 publications

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“…We also observed the same phages in the skin microbiota when the individuals were sampled 14-21 weeks later (Supplementary Table S2). Our findings are consistent with the intra-individual temporal stability found in the human oral and gut viromes (Pride et al, 2012;Minot et al, 2013). Further studies at multiple time points are needed to determine the dynamics of P. acnes phage populations in the skin microbiota.…”

Section: Phage Strainssupporting

confidence: 86%

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

et al. 2015

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The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.

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Section: Phage Strainssupporting

confidence: 86%

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

et al. 2015

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“…nih.gov/refseq/; Supplementary Figure 3). Similar to results found for viromes from different environments (Desnues et al, 2008;Minot et al, 2011;Roux et al, 2012;Wommack et al, 2012;Minot et al, 2013;Yoshida et al, 2013), the majority of the contigs had no known viral homologues. Approximately 32.7±5.9% (range from 20.3 to 48.0%) of the virome contigs were homologous to known viruses, depending on the subject and time point analyzed (Supplementary Figure 3).…”

Section: Identification Of Virusessupporting

confidence: 78%

“…Many of the viruses in these communities are bacteriophage (Breitbart et al, 2003;Minot et al, 2011;Willner et al, 2011;Pride et al, 2012a;Minot et al, 2013), likely secondary to the abundance of bacterial cells compared with eukaryote cells in these communities. Viruses likely have a key role in microbial population structures by altering the composition of bacterial communities (Duerkop et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…In a more recent study of gut viromes, six individuals were sampled at four time points over a relatively short 8-day period and demonstrated substantial individuality in their virome compositions (Minot et al, 2011). In another study, a healthy individual's colonic microbiome was sampled 16 times over 2.4 years, demonstrating that much of the viral taxonomy of the gut was persistent (Minot et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Human oral viruses are personal, persistent and gender-consistent

et al. 2014

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Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem.

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“…[54][55][56] Yet outcomes from these studies suggest differing models of the roles of viruses and range of normal diversity. Some work suggests that there are components of a shared healthy virome, while others suggest that increased phage diversity was seen in patients with IBD.…”

Section: Screening For Non-bacterial Members Of the Gut Microbiotamentioning

confidence: 99%

Challenges in fecal donor selection and screening for fecal microbiota transplantation: A review

et al. 2017

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Fecal microbiota transplantation is best understood as an effective and inexpensive therapy for recurrent Clostridium difficile infection but fecal donor selection and screening should be periodically revised. Here, we review current recommendations for selection and screening of fecal donors for fecal microbiota transplantation. We recommend considering diabetes mellitus, prior cardiovascular events, and clinical healthcare exposure as fecal donor exclusion criteria until more is known about the association of these conditions with the human gut microbiome. We review the non-bacterial members of the human gut microbiome, associations of the gut microbiome with colorectal malignancies, the human gut resistome and how these may impact future donor screening recommendations. Collaboration between clinicians, clinical laboratory scientists, industry and regulatory agencies will be critically important for continued improvement in donor selection and screening.

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Rapid evolution of the human gut virome

Cited by 523 publications

References 41 publications

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

Human oral viruses are personal, persistent and gender-consistent

Challenges in fecal donor selection and screening for fecal microbiota transplantation: A review

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