Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Abstract

The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

Bovine host genome acts on specific metabolism, communication and genetic processes of rumen microbes host-genomically linked to methane emissions

“…2, Supplementary Table 4). This approach revealed co-abundance clusters of bacterial and fungal genera 71 with strong r gCH4 and methanogenic archaea, e.g. fungal Metschnikowia (r gCH4 =0.77, P 0 =0.96) and archaeal Methanosarcina (cluster 9 in Fig.…”

An efficient enzyme-triggered controlled release system for colon-targeted oral delivery to combat dextran sodium sulfate (DSS)-induced colitis in mice

“…Recently, advanced stimuli-responsive controlled release systems have received increasing attention for drug delivery (Descalzo et al., 2006 ), which can regulate the release of entrapped drug molecules by specific external stimuli such as light (Schroeder et al., 2012 ), temperature (Ruiz et al., 2020 ), magnetic fields (Tasciotti, 2018 ) or by internal enzymes (Zhang et al., 2014 ). Gut microbiota are microorganisms coexist peacefully with the host in their gut and secret several carbohydrate-active and reductive metabolizing enzymes (Peng et al., 2021 ). Intestinal enzymes are unique stimuli that are increasingly being used as triggers in controlled release systems due to their high substrate specificity (Mura et al., 2013 ).…”

New insights from 33,813 publicly available metagenome-assembled-genomes (MAGs) assembled from the rumen microbiome

“…As globally important food-producing animals, ruminants are the subject of intense research, particularly as the microbiome in the rumen is primarily responsible for the breakdown of recalcitrant plant material into nutrients that the host can absorb. Peng et al 1 and Gharechahi et al 2 both recently published hundreds of rumen-derived MAGs, and compared them to 4941 rumen MAGs from Stewart et al 3 , and a previously published culture collection 4 . However, many more rumen-derived MAGs are publicly available, including 15 MAGs released by Hess et al 5 , 79 from Solden et al 6 , 99 from Svartstrom et al 7 , 251 from Parks et al 8 (which analysed rumen data from Wallace et al 9 and Shi et al 10 ), 1200 from Wilkinson et al 11 , 4199 released by Glendinning et al 12 (391 of which were the subject of the publication), and 20469 released by Stewart et al 3 (4941 of which were the subject of the publication).…”