Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

Guerin, Emma; Shkoporov, Andrey N.; Stockdale, Stephen R.; Clooney, Adam G.; Ryan, Feargal J.; Sutton, Thomas D.S.; Draper, Lorraine A.; González-Tortuero, Enrique; Ross, R. Paul; Hill, Colin

doi:10.1016/j.chom.2018.10.002

Cited by 236 publications

(272 citation statements)

References 63 publications

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“…Although p-crAssphage is highly abundant in the adult gut microbiome 5,14 and has been detected in infant gut microbiomes, it is unclear when or how it is acquired. Consistent with previous studies describing low relative abundance or absence of p-crAssphage in the infant gut microbiome 7,22 , we found 0 out of 22 infants have ≥ 1,000 p-crAssphage reads in samples collected within 24 hours of birth (Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…Guerin et al 5 assembled 249 complete or near-complete crAss-like phage genomes out of metagenomic sequencing datasets, which were then classified into 4 subfamilies (Alpha, Beta, Gamma, Delta) and 10 clusters (1-10) based on shared protein coding genes. P-crAssphage is a member of cluster Alpha 01.…”

Section: Resultsmentioning

confidence: 99%

“…Raw sequencing reads from Bäckhed et al 15 and Yassour et al 16 were downloaded from SRA from each sample and preprocessed in a consistent way: TrimGalore version 0.5.0 43 For classification of crAss-like phages, we added to the viral database, replacing the original "crAss-like viruses" clade with genomes in the proposed subfamily and cluster hierarchy described in Guerin et al 5 . Kraken2 was used with default classification parameters on pairedend reads.…”

Section: Sequence Read Preprocessingmentioning

confidence: 99%

Section: Main Text Introductionmentioning

confidence: 99%

“…More recent investigations have shown that crAssphage is one member of a wide range of crAss-like phages that exist in the human microbiome 5,12 . In this manuscript, we adopt the taxonomic classification system for crAss-like phages by Guerin et al 5 , which proposed 4 subfamily (Alpha, Beta, Gamma, Delta) and 10 cluster (1-10) designations based on shared protein coding genes. The crAssphage first described by Dutilh et al 4 belongs to the Alpha subfamily, cluster 1 and is given the designation prototypical crAssphage (p-crAssphage); we use p-crAssphage in all further designations to avoid ambiguity.…”

Section: Main Text Introductionmentioning

confidence: 99%

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Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Siranosian

Tamburini

Sherlock

et al. 2018

Preprint

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CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Strain diversity in the p-crAssphage population in mothers is generally low, with a median of 50 variable sites in the 97kb genome. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation. These results enhance our understanding of the acquisition, individual-level strain diversity, and transmission of crAss-like phages, which have emerged as some of the most successful human-associated microbes.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Sequence Read Preprocessingmentioning

confidence: 99%

Section: Main Text Introductionmentioning

confidence: 99%

Section: Main Text Introductionmentioning

confidence: 99%

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Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Siranosian

Tamburini

Sherlock

et al. 2018

Preprint

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Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors

et al. 2021

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The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial co-factors of colorectal cancer (CRC) carcinogenesis or progression. We analyzed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs.The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. λ48. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues,and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co-)risk factors of CRC, and extend putative suggestions on critical microbiome species in CRC metastasis.

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Bacteriophage and Viral Ecology in the “Omics Age”

Chopyk

Nasko

Sakowski

2021

Studies in Viral Ecology

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Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

Cited by 236 publications

References 63 publications

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors

Bacteriophage and Viral Ecology in the “Omics Age”

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