Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese

Scientific Reports
Sergei V DrovetskiGary R Graves

Abstract

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition,...Continue Reading

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Citations

Jan 17, 2020·Molecular Ecology·Darien C CapunitanSarah M Hird
Mar 29, 2020·Royal Society Open Science·Kirsten GrondSarah M Hird
Aug 28, 2018·Frontiers in Microbiology·Kasun H BodawattaMichael Poulsen
Nov 5, 2020·Poultry Science·Nadia A AndreaniMatthew Goddard
Jan 28, 2021·Animal Microbiome·Gary R GravesSergei V Drovetski
Feb 20, 2021·Animal Microbiome·Kasun H BodawattaKnud A Jønsson

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Methods Mentioned

BETA
lavage
PCR
Assay

Software Mentioned

Quantitative Insights Into Microbial Ecology ( QIIME )
R package Vegan
LEfSe
ADONIS
Calypso
R
ChimeraSlayer

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