Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues
Citation
Tingley, J.P., Low, K.E., Xing, X., Abbott, D.W. (2021). Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues, 14(1), http://dx.doi.org/10.1186/s13068-020-01869-8
Plain language summary
In order to digest dietary fiber, animals rely on their gut microbiome, a community of microorganisms inhabiting the gastrointestinal tract. Complex carbohydrates influence the structure, function, and diversity of the gut microbiome, which has further implications for human health. The advance of high-throughput sequencing methods has helped us to determine which microorganisms are found in the gut microbiome; however, efforts to unravel how carbohydrate digestion is performed are still in early stages. Here we review contemporary methods to study carbohydrate digestion pathways, which includes: determining the structure of dietary carbohydrates; characterizing the digestive role of the gut microbiome using next-generation sequencing and improving our ability to predict enzyme function; and implementing advanced approaches to determine how bacterial cells respond and interact within a community. Together, these approaches will continue to advance our knowledge of how diet can be used to shape the structure, function, and diversity of the gut microbiome.
Abstract
© 2021, The Author(s).The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common “-omics”-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.