Insights Into Culturomics of the Rumen Microbiome

Frontiers in Microbiology
Tamar ZehaviItzhak Mizrahi

Abstract

Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a ...Continue Reading

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Citations

Mar 7, 2020·Frontiers in Microbiology·Francisco PascoalRodrigo Costa
Feb 21, 2021·Applied and Environmental Microbiology·Paul E MooteG Douglas Inglis
Nov 12, 2020·FEMS Microbiology Ecology·Francisco PascoalCatarina Magalhães
May 14, 2021·Nature Reviews. Microbiology·Itzhak MizrahiSarah Moraïs
Jul 1, 2021·Communications Biology·Christopher L Anderson, Samodha C Fernando

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Datasets Mentioned

BETA
SRP153190

Methods Mentioned

BETA
scraping
PCR
amplicon sequencing

Software Mentioned

UCLUST
phyloT
fasta
Rstudio
Casava
Shiny
iTOL
eulerr
QIIME
PERMANOVA

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