crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes

Bryan P Brown; Denis Chopera; Enock Havyarimana; Jerome Wendoh; Shameem Jaumdally; Donald D Nyangahu; Clive M Gray; Darren P Martin; Arvind Varsani; Heather B Jaspan

doi:10.1016/j.virusres.2020.198219

crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes

Virus Res. 2021 Jan 15:292:198219. doi: 10.1016/j.virusres.2020.198219. Epub 2020 Nov 1.

Authors

Affiliations

¹ Seattle Children's Research Institute, Seattle, WA, USA; Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA.
² Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.
³ Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
⁴ Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁵ The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa. Electronic address: [email protected].
⁶ Seattle Children's Research Institute, Seattle, WA, USA; Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA; Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa. Electronic address: [email protected].

Abstract

crAssphages are a broad group of diverse bacteriophages in the order Caudovirales that have been found to be highly abundant in the human gastrointestinal tract. Despite their high prevalence, we have an incomplete understanding of how crAssphages shape and respond to ecological and evolutionary dynamics in the gut. Here, we report genomes of crAssphages from feces of one South African woman and three infants. Across the complete genome sequences of the South African crAssphages described here, we identify particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, contrasted against purifying selection, genome-wide. We further validate these findings against a crAssphage genome from previous studies. Together, our results suggest hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.

Keywords: Bacteriophage; Selection; South Africa; Tail protein; crAssphage.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adult
Bacteriophages / classification
Bacteriophages / genetics
Bacteriophages / isolation & purification*
Caudovirales / classification
Caudovirales / genetics
Caudovirales / isolation & purification*
Feces / virology*
Female
Gastrointestinal Microbiome
Genome, Viral*
Genomics
Humans
Infant
Infant, Newborn
Male
Phylogeny
Viral Tail Proteins / genetics*
Young Adult

Substances

Viral Tail Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding