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      Microbiome-Metabolome Responses in Ruminal Content and Feces of Lactating Dairy Cows With N-Carbamylglutamate Supplementation Under Heat Stress

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          Abstract

          The objective of the present study was to investigate the effects of N-carbamylglutamate (NCG) supplementation on metabolic profile and microbiota in ruminal content and feces of lactating dairy cows under heat stress (HS). Forty-eight lactating Holstein cows (154 ± 13.6 days in milk) were assigned randomly to four treatments ( n = 12), to receive 0, 15, 20, or 25 g/day of commercial NCG (proportion: 97.7%) for the period of 60 days. The recorded ambient temperature–humidity index (THI) suggested that the cows were exposed to HS for almost the entire experimental period (average THI: 80.6). Samples of ruminal content and feces were collected at the end of the trial (day 60) to determine the biological effects of NCG supplementation on metabolome and microbiota using mass spectrometry-based metabolomics and 16S rRNA gene sequencing techniques, respectively. Results showed that NCG supplementation enhanced the levels of ruminal microbial protein, total volatile fatty acids (VFAs), and the molar proportion of propionate in the rumen, but lowered the ruminal pH, ammonia nitrogen (NH 3-N), and the ratio of acetate to propionate. NCG at doses of 20 and 25 g/day reduced the community richness and diversity of ruminal microbiota with the decrease of Shannon and Simpson diversity. Compositions of ruminal and fecal microbiotas were altered by NCG, and the PICRUSt results revealed that metabolic pathways of the bacteria, such as amino acid metabolism, energy metabolism, and pyruvate metabolism, were enriched in NCG groups. Distinct changes in the metabolomic profile of ruminal fluid were observed between the control and NCG groups. Changes of 26 metabolites mainly involved in arginine metabolism, glutamate metabolism, and nitrogen metabolism were observed associated with NCG supplementation. These results provided new insights into the effects of NCG on metabolomic profile and microbiota in ruminal content and feces, and the optimal dose of NCG supplemented to dairy cows was 20 g/hd/day, which contributed to understanding the effects of NCG on HS in lactating dairy cows.

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          Most cited references55

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

            Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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              Automated simultaneous determination of ammonia and total amino acids in ruminal fluid and in vitro media.

              Catalyzed phenol-hypochlorite and ninhydrin colorimetric procedures were adapted to the Technicon AutoAnalyzer for simultaneous determination of ammonia and total amino acids in ruminal fluid or ruminal in vitro media. The manifold developed was compatible with a sampling rate of 40/h without significant sample-to-sample carryover. With proper storage, reagents for both the phenol-hypochlorite and the air-stable ninhydrin systems were stable for 8 mo or more. Response of individual amino acids in the phenol-hypochlorite system were generally 1% or less than equimolar amounts of ammonia. Certain amino acids inhibited ammonia color yield 10 to 15% when with equimolar amounts of ammonia; however, the inhibitory effect of casein amino acids was only 2 to 3%. Although ninhydrin response, relative to leucine, of individual alpha-amino acids ranged from 62 (valine) to 151% (histidine), recoveries of casein amino acids from ruminal fluid had coefficients of variation of 1% or less. Coefficients of variation for ammonia recoveries from ruminal fluid by the phenol-hypochlorite procedure were about half of those for the Conway microdiffusion technique. Intraclass correlations for the adapted procedures indicated high degrees of accuracy and precision for both ammonia and amino acid analyses.
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                Author and article information

                Contributors
                Journal
                Front Vet Sci
                Front Vet Sci
                Front. Vet. Sci.
                Frontiers in Veterinary Science
                Frontiers Media S.A.
                2297-1769
                23 June 2022
                2022
                : 9
                : 902001
                Affiliations
                [1] 1College of Veterinary Medicine, Veterinary Biological Technology Innovation Center of Hebei Province, Hebei Agricultural University , Baoding, China
                [2] 2College of Animal Science and Technology, Hebei Agricultural University , Baoding, China
                [3] 3Hebei Technology Innovation Center of Cattle and Sheep Embryo , Baoding, China
                [4] 4Hebei Research Institute of Dairy Industry Technology , Shijiazhuang, China
                Author notes

                Edited by: Tugay Ayasan, Osmaniye Korkut Ata University, Turkey

                Reviewed by: Pongsatorn Gunun, Rajamangala University of Technology Isan, Thailand; Gercino Ferreira Virgínio Júnior, University of São Paulo, Brazil; Yosra Ahmed Soltan, Alexandria University, Egypt

                *Correspondence: Jianguo Li 1181935094@ 123456qq.com

                This article was submitted to Animal Nutrition and Metabolism, a section of the journal Frontiers in Veterinary Science

                †These authors have contributed equally to this work

                Article
                10.3389/fvets.2022.902001
                9260145
                35812889
                8ae95bc2-6958-463a-8640-e70d0b6fec0c
                Copyright © 2022 Li, Ma, Ren, Wang, Hu, Shen, Cao, Li, Li and Gao.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 22 March 2022
                : 30 May 2022
                Page count
                Figures: 4, Tables: 2, Equations: 0, References: 55, Pages: 12, Words: 8403
                Funding
                Funded by: Earmarked Fund for China Agriculture Research System, doi 10.13039/501100010038;
                Categories
                Veterinary Science
                Original Research

                cow,metabonomics,microbiota,n-carbamylglutamate,rumen
                cow, metabonomics, microbiota, n-carbamylglutamate, rumen

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