Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen

Abstract

Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle’s diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.

Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse

“…), Ruminococcaceae, Spirochaetaceae (Treponema spp.) (Vital et al, 2015;Gharechahi et al, 2020;Vacca et al, 2020) and Rikenellaceae (Vital et al, 2015). The bioavailability of butyrate is obviously related to endurance performance because of the role played by this molecule in energy metabolism (Mollica et al, 2017).…”

Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

“…The results show that Firmicutes and Bacteroides are dominant and their sum of relative abundance reached more than 90% in the intestine of Suhuai pigs ( Figure 1 ), which is consistent with the research of Adhikari et al (2019) on PIC genetics nursery pigs and the research of Niu et al (2019 , 2020) on Sutai pigs and Suhuai pigs. Previous studies have found that Firmicutes and Bacteroides were capable of degrading many carbohydrate polymers in different ruminants, including cattle ( Stewart et al, 2018 , 2019 ; Gharechahi et al, 2021 ), camels ( Gharechahi and Salekdeh, 2018 ), and moose ( Svartström et al, 2017 ). The proportion of Firmicutes in the intestinal tract of pigs with low digestibility (L_NDF: 85.85%; L_ADF: 86.31%) was higher than that of high digestibility (H_NDF: 79.88; H_ADF: 78.76%) and the proportion of Bacteroidetes in the intestinal tract of pigs with high digestibility (H_NDF: 12.14%; H_ADF: 12.08%) was higher than that of low digestibility (L_NDF: 7.16%; L_ADF: 6.89%), which indicated that the community competition between Firmicutes and Bacteroidetes may be related to the fiber degradation ability of pigs ( Figure 1 ).…”

Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance

“…), Ruminococcaceae , Spirochaetaceae ( Treponema spp.) (Vital et al , 2015; Vacca et al , 2020; Gharechahi et al , 2020) and Rikenellaceae (Vital et al , 2015). The bioavailability of butyrate is obviously related to endurance performance because of the role played by this molecule in energy metabolism (Mollica et al , 2017).…”