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

View ORCID ProfileBryan P. Brown, Jerome Wendoh, Denis Chopera, Enock Havyarimana, Shameem Jaumdally, Donald D. Nyangahu, Clive M. Gray, Darren P. Martin, Arvind Varsani, Heather B. Jaspan
doi: https://doi.org/10.1101/582015
Bryan P. Brown
aSeattle Children’s Research Institute, Seattle, Washington, USA
bSchools of Medicine and Public Health, University of WA, Seattle, WA, USA
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  • ORCID record for Bryan P. Brown
  • For correspondence: Arvind.varsani@asu.edu bryan.brown@seattlechildrens.org
Jerome Wendoh
cDepartment of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Denis Chopera
dAfrica Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
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Enock Havyarimana
cDepartment of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Shameem Jaumdally
cDepartment of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Donald D. Nyangahu
aSeattle Children’s Research Institute, Seattle, Washington, USA
bSchools of Medicine and Public Health, University of WA, Seattle, WA, USA
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Clive M. Gray
cDepartment of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Darren P. Martin
eStructural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
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Arvind Varsani
fThe Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, Arizona, USA
gDepartment of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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  • For correspondence: Arvind.varsani@asu.edu bryan.brown@seattlechildrens.org
Heather B. Jaspan
aSeattle Children’s Research Institute, Seattle, Washington, USA
bSchools of Medicine and Public Health, University of WA, Seattle, WA, USA
cDepartment of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Abstract

crAssphages are a class of bacteriophages that are highly abundant in the human gastrointestinal tract. Accordingly, crAssphage genomes have been identified in most human fecal viral metagenome studies. However, we currently have an incomplete understanding of factors impacting the transmission frequencies of these phages between mothers and infants, and the evolutionary pressures associated with such transmissions. Here, we use metagenome sequencing of stool-associated virus-like particles to identify the prevalence of crAssphage across ten South African mother-infant dyads that are discordant for HIV infection. We report the identification of a complete 97kb crAssphage genome, parts of which are detected at variable levels across each mother-infant dyad. We observed average nucleotide sequence identities of >99% for crAssphages from related mother-infant pairs but ∼97% identities between crAssphages from unrelated mothers and infants: a finding strongly suggestive of vertical mother to infant transmission. We further analyzed patterns of nucleotide diversity across the crAssphage sequences described here, identifying particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, which we validated against a crAssphage genome from previous studies. Using 16S rRNA gene sequencing, we found that the relative abundances of Bacteroides thetaiotaomicron and Parabacteroides merdae (Order: Bacteroidales) were differentially correlated with crAssphage abundance. Together, our results reveal that crAssphages may be vertically transmitted from mothers to their infants and that hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.

Importance crAssphages are an ubiquitous member of the human gut microbiome and modulate interactions with key bacterial associates within the order Bacteroidales. However, the role of this interaction in the genomic evolution of crAssphage remains unclear. Across a longitudinally sampled cohort of ten South African mother-infant dyads, we use metagenome sequencing of the fecal virome and 16S rRNA gene sequencing of the fecal bacterial microbiota to elucidate the ecological and evolutionary dynamics of these interactions. Here, we demonstrate elevated levels of crAssphage average nucleotide identity between related mother-infant dyads as compared to unrelated individuals, suggesting vertical transmission. We report strong positive selection in crAssphage RNA polymerase and phage tail protein genes. Finally, we demonstrate that crAssphage abundance is linearly correlated (P < 0.014) with the abundance of two bacterial taxa, Bacteroides thetaiotaomicron and Parabacteroides merdae. These results suggest that phage-bacterial interactions may help shape ecological and evolutionary dynamics in the gut.

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Posted March 19, 2019.
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crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads
Bryan P. Brown, Jerome Wendoh, Denis Chopera, Enock Havyarimana, Shameem Jaumdally, Donald D. Nyangahu, Clive M. Gray, Darren P. Martin, Arvind Varsani, Heather B. Jaspan
bioRxiv 582015; doi: https://doi.org/10.1101/582015
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crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads
Bryan P. Brown, Jerome Wendoh, Denis Chopera, Enock Havyarimana, Shameem Jaumdally, Donald D. Nyangahu, Clive M. Gray, Darren P. Martin, Arvind Varsani, Heather B. Jaspan
bioRxiv 582015; doi: https://doi.org/10.1101/582015

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