crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads

Abstract

word count: 241 24 Main text word count: 4,667 25 26 Abstract 29crAssphages are a class of bacteriophages that are highly abundant in the human 30 gastrointestinal tract. Accordingly, crAssphage genomes have been identified in most 31human fecal viral metagenome studies. However, we currently have an incomplete 32 understanding of factors impacting the transmission frequencies of these phages 33 between mothers and infants, and the evolutionary pressures associated with such 34 transmissions. Here, we use metagenome sequencing of stool-associated virus-like 35 particles to identify the prevalence of crAssphage across ten South African mother-36 infant dyads that are discordant for HIV infection. We report the identification of a 37 complete 97kb crAssphage genome, parts of which are detected at variable levels 38 across each mother-infant dyad. We observed average nucleotide sequence identities 39 of >99% for crAssphages from related mother-infant pairs but ~97% identities between 40 crAssphages from unrelated mothers and infants: a finding strongly suggestive of 41 vertical mother to infant transmission. We further analyzed patterns of nucleotide 42 diversity across the crAssphage sequences described here, identifying particularly 43 elevated positive selection in RNA polymerase and phage tail protein encoding genes, 44 which we validated against a crAssphage genome from previous studies. Using 16S 45 rRNA gene sequencing, we found that the relative abundances of Bacteroides 46 thetaiotaomicron and Parabacteroides merdae (Order: Bacteroidales) were differentially 47 Importance 53 crAssphages are an ubiquitous member of the human gut microbiome and modulate 54 interactions with key bacterial associates within the order Bacteroidales. However, the 55 role of this interaction in the genomic evolution of crAssphage remains unclear. Across 56 a longitudinally sampled cohort of ten South African mother-infant dyads, we use 57 metagenome sequencing of the fecal virome and 16S rRNA gene sequencing of the 58 fecal bacterial microbiota to elucidate the ecological and evolutionary dynamics of these 59interactions. Here, we demonstrate elevated levels of crAssphage average nucleotide 60 identity between related mother-infant dyads as compared to unrelated individuals, 61suggesting vertical transmission. We report strong positive selection in crAssphage 62 RNA polymerase and phage tail protein genes. Finally, we demonstrate that 63 crAssphage abundance is linearly correlated (P < 0.014) with the abundance of two 64 bacterial taxa, Bacteroides thetaiotaomicron and Parabacteroides merdae. These 65 results suggest that phage-bacterial interactions may help shape ecological and 66 evolutionary dynamics in the gut. 67 68

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

“…Phage tail proteins are responsible for host tropism; [29][30][31] therefore maintaining multiple functionally different alleles in the population may be beneficial to expand the host range of p-crAssphage. Increased variation in tail fiber genes was also found in an analysis of p-crAssphage genomes from South Africa 32 . The genes that were least likely to have nonsynonymous multiallelic sites appear to be those that are critical for phage function, such as "putative portal protein", "putative major capsid protein" and putative RNA polymerase subunits.…”

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

“…To this aim, we identified 880 viral genes under positive selection (Table S6), for which non-synonymous polymorphisms were more likely to be retained than rejected. This included 30 tail fibre genes, which have previously been shown to be positively selected among gut phages as evidence of their adaptive evolution [134, 135]. Phage tail fibre proteins are involved in host tropism [94, 95], thus the carriage of genetically diverse tail fibre genes may expand a population’s host range.…”

“…To this aim, we identified 880 viral genes under positive selection (Table S6), for which non-synonymous polymorphisms were more likely to be retained than rejected. This included 30 tail fibre genes, which have previously been shown to be positively selected among gut phages as evidence of their adaptive evolution [134,135].…”