CrAssphage and its bacterial host in cat feces

Yanpeng Li,Amanda Idle,Alexander L Greninger,Xutao Deng,Ryan C Shean,Emilia Gordon,Eric Delwart

doi:10.1038/s41598-020-80076-9

Abstract

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages’ cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat’s feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.

Highlights

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus
Pool 4 was re-sequenced on the MiSeq and in order to generate even more viral reads the same cat SB2894 random RT-PCR viral-like particles (VLP) library was sequenced on a HiSeq4000 (SAMN16266525)
In order to focus the sequencing on DNA alone enriched VLP associated nucleic acids from SB2894 and pool 4 were amplified using PhiX174 DNA polymerase using random primers in a multiple displacement amplification (MDA) followed by use of the Illumina Nextera XT prior to deep sequencing using the HiSeq4000 platform

Summary

Introduction

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphage has been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. We describe crAssphage DNA in a feline fecal sample. We report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal. The circular crAssphage DNA genome of ~ 100 Kb was initially assembled in 2014 from human feces metagenomics data[1] and is considered the most abundant human gut phage[2]. In order to follow up on this unexpected find in a non-human sample we performed further deep sequencing and assembled and annotated 95% of a crAssphage genome, confirmed the feline origin of the fecal sample, and identified DNA of its putative bacterial host. We demonstrate the first genomeconfirmed detection of crAssphage in the gut of a non-primate animal, here a cat

Methods

Results

Conclusion