Multi-omic Directed Discovery of Cellulosomes, Polysaccharide Utilization Loci, and Lignocellulases from an Enriched Rumen Anaerobic Consortium

The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries.

fraction of PLs sequences in the anaerobic consortium were predicted as PLs, 12 out of 19 PLs families (defined by CAZy) were encountered (Table 1 and Additional file 2).
The auxiliary activity families contain oxidative ligninolytic enzymes and lytic polysaccharide monoxygenases. The AA families were categorized into five families, of which AA6 (1,4-benzoquinone reductase) was the most prevalent. Even though most microorganisms identified in this consortium are strictly anaerobic, the prediction of oxidative AA families was also previously observed from metagenomic anaerobic samples, including camel rumen camel (5) and landfill (6).
Non-GH CAZy members, such as CBMs, are protein domains found in carbohydrate-active enzymes that can potentiate the activity of the associate catalytic domains (7). The set of predicted CBMs ERAC comprised 43 families, of which surprisingly CBM50, predicted to bind peptidoglycan-like and chitin-derived oligosaccharides (8), was the most prevalent encountered in the metagenome dataset (Table 1). The CBM50 were predominantly predicted in association to GH23 and GH73, both families related with peptidoglycan degradation. Similar abundance was also found in the moose rumen microbiome (9) and camel rumen (5). In our study, genes encoding CBMs that bind on xylan (CBM4, CBM9, CBM16, CBM22, CBM35, and CBM36), cellulose (CBM2, CBM3, CBM6, CBM11, CBM13, CBM30, and CBM63), starch (CBM20, CBM26, CBM34, and CBM69), pullulan (CBM41 and CBM68), and glucans (CBM 56, CBM65, CBM 76, CBM 79, and CBM 80) were predicted (Table 1 and Additional file 2). Overall, the ERAC is composed of microorganisms encoding a wide variety of carbohydrate degrading genes with the potential to produce a broad range of enzymatic activities for deconstructing the whole component plant cell wall.
Although studies of enrichment strategies have been reported, to our knowledge, our study is the first to apply multi-omics strategies (and other comprehensive analyses), to study anaerobic-enriched microbial community. In addition, our study is unique as it reveals the secreted CAZymes, cellulosomes, PULs, as well several nearly complete genomes from lignocellulolytic microbes. For example, the ZCTH02 consortium reported six near-complete reconstructed genomes (11) ( Table S12). The moose rumen-and beaver dropping-derived anaerobic consortia reported dockerin-or cohesin-containing proteins and PULs (4), nonetheless, the presence of cellulosomes in metagenomic data is unclear.
Furthermore, when compared to the three composting-derived consortia established under static condition (APACMC, ZCTH02, and EMSD5), ERAC is the second in terms of CAZyme abundance numbers and diversity (Table S12). The ERAC encodes approximately half of CDS (142,703) compared to APACMC (220,767), which encode  After quality filtering reads, merged sequences and removal of chimeric sequences. 3 Operational Taxonomic Units (OTUs) 4 OTUs featuring reads counts of less than 0.01 % of the total reads were removed from OUT table.     Peptidase-SLH-SLH 4 Peptidase-SLH-SLH-SLH 2 Cthe-SLH-SLH 1 SLH-DUF3373 3 SLH-SLH_DUF5077 1 1 -Except the domain organizations of CBM-SLH, which are indicated in Table S5.