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

Siranosian, Benjamin A.; Tamburini, Fiona B.; Sherlock, Gavin; Bhatt, Ami S.

doi:10.1038/s41467-019-14103-3

Cited by 57 publications

(36 citation statements)

References 53 publications

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“…intestinalis pair as a model. We observed that, similarly to metagenomic findings from the human gut (6,8), a monoxenic mouse model was able to support long term and stable persistence of ΦcrAss001. Bacterial clones recovered from colonised mice showed varied degree of resistance to phage, but no obvious cost with regards to bacterial population density was associated with phage colonisation.…”

Section: Discussionsupporting

confidence: 70%

“…A recent longitudinal study of the human gut virome highlighted long-term (months and even years) high-level persistence of different combinations of crAss-like phages across individuals (6). When vertically transmitted from mothers to their infants or transplanted into in the course of faecal microbial transplantation (FMT), crAss-like phage engraft successfully and stably persist for many months (7,8). CrAss-like phages can also persist in pure bacterial culture in vitro over many serial passages without any significant effect on the density of host population (9).…”

Section: Introductionmentioning

confidence: 99%

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Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

Shkoporov

Хохлова

Stephens

et al. 2020

Preprint

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The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate unexplained long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we demonstrate that rapid phase variation of alternate capsular polysaccharides plays an important role in dynamic equilibrium between phage sensitivity and resistance in B. intestinalis cultures, allowing phage and bacteria to multiply in parallel. The data also suggests the role of concomitant phage persistence mechanisms associated with delayed lysis of infected cells, such as carrier state infection. From an ecological and evolutionary standpoint this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other 'benign' forms of phage infection when the host is stably present at high abundance.

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Section: Discussionsupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

Shkoporov

Хохлова

Stephens

et al. 2020

Preprint

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“…The group of crAss-like phages and their high prevalence and abundance across human gut viromes have been described extensively [37], [76], [99], [100]. Although not as widespread as the crAss-like phages, the newly discovered LoVEphage seems to be rather common as well, with a prevalence of 28.6% in the healthy Danish subjects, and 14.4% in the SRA viromes (Fig.…”

Section: Discussionmentioning

confidence: 93%

A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue

Espen

Bak

Beller

et al. 2021

Preprint

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Background: Gut viruses are important players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies is steadily increasing, however we are still only scratching the surface of the immense viral diversity as many wet lab and bio-informatics challenges remain. In this study, 254 virus-enriched faecal metagenomes from 204 Danish subjects were used to generate a Danish Enteric Virome Catalogue (DEVoC) of 12,986 non-redundant viral genome sequences encoding 190,029 viral genes, which formed 67,921 orthologous groups. The DEVoC was used to characterize the composition of the healthy DEVoC gut viromes from 46 children and adolescents (6-18 years old) and 45 adults (40 -73 years old).Results: The majority of DEVoC viral sequences (67.3 %) and proteins (61.6 %) were not present in other (human gut) viral genome databases. Gut viromes of healthy Danish subjects mostly consisted of phages. While 39 phage genomes (PGs) were present in more than 10 healthy subjects, the degree of viral individuality was high. Among the 39 prevalent PGs, one was significantly more prevalent in the paediatric cohort, whereas two were more prevalent in adults. In 1,880 gut virome samples of 27 studies from across the world, the 39 prevalent PGs reveal several age-, geography- and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide – a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, genus I; and a previously undescribed circular temperate phage (14.4% prevalence), named LoVEphage (because it encodes Lots of Viral Elements). A de novo assembly of selected public datasets generated an additional 18 circular LoVEphage-like genomes (67.9-72.4 kb). CRISPR spacer analysis suggested Bacteroides as a host genus for the LoVEphage, and a closely related prophage was identified in Bacteroides dorei, further confirming the host.Conclusions: The DEVoC, the largest human gut virome catalogue generated from consistently processed faecal samples, facilitated analysis of healthy Danish human gut viromes and we foresee that it will benefit future analysis on the roles of gut viruses in human health and disease. The identification of a previously undescribed prevalent phage illustrates the usefulness of developing a virome catalogue.

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“…The presence of CrAssphage in the gut appears to begin in infancy (McCann et al, 2018;Edwards et al, 2019;). It appears to be transmitted vertically, with homology found between isolates from mother and child (Siranosian et al, 2020), which also corresponds with the presence of its Bacteroides host (Tanaka and Nakayama, 2017). However, there is again a large degree of inter-individual variation in the presence and abundance of CrAssphage.…”

Section: Identification Of Novel Human Phagesmentioning

confidence: 98%

The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

Townsend

Kelly

Muscatt

et al. 2021

Front. Cell. Infect. Microbiol.

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The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.

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

Cited by 57 publications

References 53 publications

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue

The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

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