Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation

In vitro ruminal fermentation is considered
an
efficient way to degrade crop residue. To better understand the microbial
communities and their functions during in vitro ruminal
fermentation,
the microbiome and short chain fatty acid (SCFA) production were investigated
using the metagenomic sequencing and rumen simulation technique (RUSITEC)
system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed,
and 298 MAGs were found copresenting in metagenomic data of the current
work and 58 previously ruminal representative samples. Additionally,
the domains related to pectin and xylan degradation were overrepresented
in the copresent MAGs compared with total MAGs. Among the copresent
MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively
correlated with SCFA concentrations. The MAGs obtained from this study
enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation
and show promise for pointing out directions for further research
on in vitro ruminal fermentation.