Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion

Abstract

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

“…In humans, the relative abundance of this phage family in the gut can be as high as 90% of the total viral load in some individuals. The geographical spread of this phage family has also been confirmed with p-crAssphage for example, being largely absent from hunter-gatherer gut populations compared to industrialized populations [ 19 , 22 – 24 ]. This may be due to differences in dietary habits and bacteriome compositions.…”

Microbial and Viral Indicators of Pathogens and Human Health Risks from Recreational Exposure to Waters Impaired by Fecal Contamination

“…In terms of geographical variation in crAssphage concentrations, Farkas et al (2019) found lower, but still measurable, concentrations of crAssphage in WWTP influent in the United Kingdom than were found in Tampa, Florida (Ahmed et al 2018b), andSpain (García-Aljaro et al 2017). Geographic differences in crAssphage concentrations in untreated sewage had been noted in earlier studies (Stachler and Bibby 2014), potentially due to geographic differences in viral distributions (Stachler and Bibby 2014), levels of industrialization, or diet (Honap et al 2020).…”

Superior performance of human wastewater-associated viral markers compared to bacterial markers in tropical environments

“…Neither wastewater treatment capacity nor wastewater volume received affected the concentrations of HPyVs and crAssphage, as previously stated (Crank et al, 2020). However, differences in reported quantity could result from intrinsic factors, such as different gut microbial levels due to diets and lifestyles (Honap et al, 2020; Mah et al, 2008; Turnbaugh et al, 2009), and extrinsic factors, such as temperature, sewer pipe condition, and retention time (Ahmed et al, 2019c; Okadera et al, 2020). Comparisons among different studies could also present confounding biases due to different field and laboratory protocols, analytical instruments, and data analysis methods, which could affect each virus at different levels (Agetsuma-Yanagihara et al, 2017; Crank et al, 2020; Kongprajug et al, 2020; Petcharat et al, 2020; Shanks et al, 2012).…”