Massive expansion of human gut bacteriophage diversity

Camarillo-Guerrero, Luis F.; Almeida, Alexandre; Rangel-Piñeros, Guillermo; Finn, Robert D.; Lawley, Trevor D.

doi:10.1101/2020.09.03.280214

Cited by 29 publications

(41 citation statements)

References 57 publications

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“…Using de novo assembly and viral discovery approaches, we identified a huge number of viruses from the subjects’ fecal samples, including 31,341 non-redundant complete and partial DNA viral genomes and 579 non-redundant RNA viruses, particularly the number of DNA vOTUs increased over eightfold compared with the isolated viral sequences in RefSeq database. The majority of viruses were unclassified even at the family level, in agreement with previous observations of extensive novelty of viral world in multiple environments as well as in the human gut ( Reyes et al 2012 ; Paez-Espino et al 2016 ; Rampelli et al 2017 ; Camarillo-Guerrero et al 2021 ).…”

Section: Discussionsupporting

confidence: 90%

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Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis

et al. 2021

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Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

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Section: Discussionsupporting

confidence: 90%

“…These studies suggest a significant role of gut virome in human disease and health. Besides of that, several recent studies had revealed the important role of host properties, including geography, lifestyle, and environment, in shaping the healthy gut virome ( Hannigan et al 2018 ; Zuo et al 2020 ; Camarillo-Guerrero et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis

et al. 2021

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“…Almost all VCs (2,532) were linked to one host phylum, though a notable minority of 43 VCs exhibited very wide predicted host ranges that spanned two or three phyla. This agrees with previously published estimates of cross-phyla phage host range 27 .…”

Section: Resultssupporting

confidence: 93%

Members of a highly widespread bacteriophage family are hallmarks of metabolic syndrome gut microbiomes

Jonge

Wortelboer

Scheithauer

et al. 2021

Preprint

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There is significant interest in altering the course of cardiometabolic disease development via the gut microbiome. Nevertheless, the highly abundant viral members -which impact gut bacteria- of the complex gut ecosystem remain understudied. Here, we characterized gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease. MetS gut virome populations exhibited decreased richness and diversity, but larger inter-individual variation. These populations were enriched in phages infecting Bacteroidaceae and depleted in those infecting Ruminococcaeae. Differential abundance analysis identified eighteen viral clusters (VCs) as significantly associated with either MetS or healthy viromes. Among these are a MetS-associated Roseburia VC that is related to healthy control-associated Faecalibacterium and Oscillibacter VCs. Further analysis of these VCs revealed the Candidatus Heliusviridae, a highly widespread gut phage lineage found in 90+% of the participants. The temperate Ca. Heliusviridae are important novel research targets for understanding the role of the microbiome in human cardiometabolic health and developing microbiome-targeted interventions.

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“…Virus discovery can be aided through re-analysis of the petabases of high-throughput sequencing data available in public databases such as the Sequence Read Archive (SRA) [1,[7][8][9][10][11][12]. This data spans millions of ecologically diverse biological samples, many of which capture viral transcripts incidental to the goals of the original studies [13].…”

Section: Introductionmentioning

confidence: 99%

Petabase-scale sequence alignment catalyses viral discovery

Edgar¹,

Taylor²,

Lin³

et al. 2020

Preprint

117

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Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, `Serratus`, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community (https://serratus.io). Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.

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Massive expansion of human gut bacteriophage diversity

Cited by 29 publications

References 57 publications

Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis

Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis

Members of a highly widespread bacteriophage family are hallmarks of metabolic syndrome gut microbiomes

Petabase-scale sequence alignment catalyses viral discovery

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