Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses

Ajay Badhan; Kristin E Low; Darryl R Jones; Xiaohui Xing; Mohammad Raza Marami Milani; Rodrigo Ortega Polo; Leeann Klassen; Sivasankari Venketachalam; Michael G Hahn; D Wade Abbott; Tim A McAllister

doi:10.1016/j.csbj.2021.12.009

Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses

Comput Struct Biotechnol J. 2021 Dec 9:20:148-164. doi: 10.1016/j.csbj.2021.12.009. eCollection 2022.

Authors

Affiliations

¹ Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
² Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
³ Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Abstract

There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.

Keywords: AB, arabinan; ADF, acid detergent fibre; AG, arabinogalactan; AGP, arabinogalactan protein; AIR, alcohol insoluble residue; AO, ammonium oxalate; AX, arabinoxylan; BS, barley straw; CAZyme, carbohydrate active enzyme; CAZymes; CE, carbohydrate esterase; CH, chlorite; DE, differentially expressed; Dietary polysaccharides; Differential gene expression; ELISA, enzyme-linked immunosorbent assay; FID, flame ionization detection GC, gas chromatography; GH, glycosyl hydrolase; Glycome profiling; Glycoside hydrolase; HG, homogalacturonan; HPAEC-PAD, high performance anion exchange chromatography coupled with pulsed amperometric detection; HX, heteroxylan; Linkage analysis; MS, mass spectrometry; NDF, neutral detergent fibre; Nutrient utilization; PC, post-chlorite; PL, polysaccharide lyase; RG, rhamnogalacturonan; Rumen microbiome; SC, sodium carbonate; TTIR, total tract indigestible residue; Transcriptome; XG, xyloglucan; mAbs, monoclonal antibodies.