Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides

Low, Kristin E.; Xing, Xiaohui; Moote, Paul E.; Inglis, G. Douglas; Venketachalam, Sivasankari; Hahn, Michael G.; King, Marissa L.; Tétard‐Jones, Catherine; Jones, Darryl R.; Willats, William G. T.; Slominski, B. A.; Abbott, D. Wade

doi:10.3390/microorganisms8121888

Cited by 17 publications

(15 citation statements)

References 78 publications

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“…Birds were maintained in a sanitized facility, as one goal of the current study was to ascertain the impact of CM on the structure and function of the enteric microbiota. We observed that the diversity of the microbiota (Shannon’s index of ≈6.8) was comparative to that of ceca harvested from broilers in commercial production settings [ 35 ]. Moreover, the structure of the microbiota amongst broilers maintained in replicate housing enclosures was consistent, which indicated that the establishing a diverse cecal microbiota via the administration of bacteria from a donor bird was successful.…”

Section: Discussionmentioning

confidence: 99%

Expeller-Pressed Canola (Brassica napus) Meal Modulates the Structure and Function of the Cecal Microbiota, and Alters the Metabolome of the Pancreas, Liver, and Breast Muscle of Broiler Chickens

Inglis

Wright

Sheppard

et al. 2021

Animals

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The inoculation of one-day-old broiler chicks with the cecal contents from a mature broiler breeder resulted in a highly diverse and uniform cecal bacterial community. CM did not affect feed consumption, weight gain, nor the richness, evenness, or diversity of the cecal bacterial community. However, the structure of the bacterial community was altered in birds fed the CM diet. Although the CM diet was formulated to contain equivalent metabolizable energy to the control diet, it contained more dietary fiber. The abundance of bacterial families, including those that are known to contain species able to metabolize fiber was altered (e.g., bacteria within the families, Methanobacteriaceae, Atopobiaceae, Prevotellaceae, Clostridiales Family XIII, Peptostreptococcaceae, and Succinivibrionaceae), and concentrations of SCFAs were higher in the ceca of birds fed the CM diet. Moreover, concentrations of isoleucine, isobutyrate, glutamate, and 2-oxoglutarate were higher, whereas concentrations of phenyllactic acid, indole, glucose, 3-phenylpropionate, and 2-oxobutyrate were lower in the digesta of chickens that were fed CM. The metabolic profiles of pancreas, liver, and breast muscle tissues of birds fed the CM diet differed from control birds. Metabolites that were associated with energy production, protection against oxidative stress, and pathways of amino acid and glycerophospholipid metabolism had altered concentrations in these tissues. Some of the observed changes in metabolite levels may indicate an increased disease risk in birds fed the CM diet (e.g., pancreatitis), and others suggested that birds mounted metabolic response to offset the adverse impacts of CM (e.g., oxidative stress in the liver).

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Section: Discussionmentioning

confidence: 99%

Expeller-Pressed Canola (Brassica napus) Meal Modulates the Structure and Function of the Cecal Microbiota, and Alters the Metabolome of the Pancreas, Liver, and Breast Muscle of Broiler Chickens

Inglis

Wright

Sheppard

et al. 2021

Animals

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“…The pre-treated wheat straw and resulting growth cultures were analyzed using HPAEC-PAD to determine which CAZymes induced the differential expression patterns between pre-treatment methods. Furthermore, the combination of MAPP, linkage analysis, and metagenomics has recently been used to determine the CAZymes responsible for the digestion of non-soluble polysaccharides in chickens—an approach highly portable to anaerobic digesters [ 224 ]. As the field of biofuels progresses, a multi-disciplinary approach will be needed to fine-tune and standardize methods to optimize production, as diversity in microorganisms in combination with feedstocks and feedstock pre-treatments can drastically alter saccharification and fermentation efficiencies.…”

Section: Glycomic and Multi-omic Integrationmentioning

confidence: 99%

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

Tingley

Low

Xing

et al. 2021

Biotechnol Biofuels

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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.

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“…The acetyl-mannosamine transferase GT26 was only present in clade III strains. Only three types of carbohydrate esterases (CEs) were identified across all C. innocuum strains, all involved in plant cell degradation, CE6 (acetyl xylan esterase), CE4 (chitin deacetylase), and CE9 ( N -acetylglucosamine 6-phosphate deacetylase) ( 62 , 63 ). Four carbohydrate-binding modules were also observed across all clades, including CBM66, part of the LPXTG cell wall anchor domain-containing protein that degrades fructoside residues in fructans, and CBM48, associated with the GH13 family of CAZymes responsible for degrading starches ( 64 ).…”

Section: Resultsmentioning

confidence: 99%

Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota

Bhattacharjee

Flores

Woelfel-Monsivais

et al. 2023

mSphere

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Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides

Cited by 17 publications

References 78 publications

Expeller-Pressed Canola (Brassica napus) Meal Modulates the Structure and Function of the Cecal Microbiota, and Alters the Metabolome of the Pancreas, Liver, and Breast Muscle of Broiler Chickens

Expeller-Pressed Canola (Brassica napus) Meal Modulates the Structure and Function of the Cecal Microbiota, and Alters the Metabolome of the Pancreas, Liver, and Breast Muscle of Broiler Chickens

Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota

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