In vivo competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens and Ruminoccus albus in a gnotobiotic sheep model revealed by multi-omic analyses

Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon cellulolytic biomass. Yet their molecular interactions in vivo have not hereunto been examined. Two gnotobiotically-raised lambs harboring a 17h-old immature microbiota devoid of culturable cellulolytics and methanogens were inoculated with F. succinogenes S85 and Methanobrevibacter spp. 87.7 and five months later with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in noticeable alterations in CAZyme gene expression, including an increase in GH 9 and GH 48 family glycoside hydrolases, an increase in CMCase and xylanase activities, and increases in acetate and butyrate at the expense of propionate. Yet, these changes were not accompanied by greater degradation of in sacco incubated lucerne or wheat straw. Instead, DM disappearance varied between animals, and by substrate suggesting that factors other than total CMCase and xylanase enzyme activities affect the efficiency of fiber degradation.