Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria

Scientific Reports
E H HartA H Kingston-Smith

Abstract

The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most ab...Continue Reading

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Citations

Apr 11, 2020·Frontiers in Microbiology·Rosalind A GilbertEleanor Jameson
Oct 7, 2020·Animals : an Open Access Journal From MDPI·Shih-Te ChuangMing-Ju Chen
Aug 8, 2020·Methods : a Companion to Methods in Enzymology·Thea Os AndersenPhillip B Pope

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Methods Mentioned

BETA
protein folding

Software Mentioned

iPATH pathways explorer
Metaproteome analyser
UniPept
Samtools idxstats
MGKIT
Bowtie2
DIAMOND
Velvet
Mass Hunter Qualitative Analysis
MASCOT

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