Effects of live yeast on differential genetic and functional attributes of rumen microbiota in beef cattle

Springer Science and Business Media LLC - Tập 10 - Trang 1-7 - 2019
Ibukun M. Ogunade1, Jerusha Lay1, Kenneth Andries1, Christina J. McManus1, Frederick Bebe1
1College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, USA

Tóm tắt

Several studies have evaluated the effects of live yeast supplementation on rumen microbial population; however, its effect on differential microbial genes and their functional potential has not been described. Thus, this study applied shotgun metagenomic sequencing to evaluate the effects of live yeast supplementation on genetic and functional potential of the rumen microbiota in beef cattle. Eight rumen-cannulated Holstein steers were randomly assigned to two treatments in a cross-over design with two 25-day experimental periods and a 10-day wash-out between the two periods. The steers were housed in individual pens and fed 50% concentrate-mix and 50% red clover/orchard hay ad libitum. Treatments were (1) control (CON; basal diet without additive) and (2) yeast (YEA; basal diet plus 15 g/d of live yeast product). Rumen fluid samples were collected at 3, 6, and 9 h after feeding on the last d of each period. Sequencing was done on an Illumina HiSeq 2500 platform. Dietary yeast supplementation increased the relative abundance of carbohydrate-fermenting bacteria (such as Ruminococcus albus, R. champanellensis, R. bromii, and R. obeum) and lactate-utilizing bacteria (such as Megasphaera elsdenii, Desulfovibrio desulfuricans, and D. vulgaris). A total of 154 differentially abundant genes (DEGs) were obtained (false discovery rate < 0.01). Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of the DEGs revealed that 10 pathways, including amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, lipopolysaccharide biosynthesis, pantothenate and coenzyme A biosynthesis, glutathione metabolism, beta-alanine metabolism, polyketide sugar unit biosynthesis, protein export, ribosome, and bacterial secretory system, were enriched in steers fed YEA. Annotation analysis of the DEGs in the carbohydrate-active enzymes (CAZy) database revealed that the abundance of genes coding for enzymes belonging to glycoside hydrolases, glycosyltransferases, and carbohydrate binding modules were enriched in steers fed YEA. These results confirm the effectiveness of a live S. cerevisiae product for improving rumen function in beef steers by increasing the abundance of cellulolytic bacteria, lactic acid-utilizing bacteria, and carbohydrate-active enzymes in the rumen.

Tài liệu tham khảo

Chaucheyras-Durand F, Chevaux E, Martin C, Forano E. Use of yeast probiotics in ruminants: Effects and mechanisms of action on rumen pH, fiber degradation, and microbiota according to the diet. In: Rigobelo E, editor. Probiotic in Animals. Rijeka, Croatia: IntechOpen; 2012. p. 119–52. https://doi.org/10.5772/50192.

Nisbet DJ, Martin SA. The effect of Saccharomyces cerevisiae culture on lactate utilization by the ruminal bacterium Selenomonas ruminantium. J Anim Sci. 1991;69:4628–33.

Ercolini D. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl Environ Microbiol. 2013;79:3148–55.

Jiang Y, Ogunade IM, Qi S, Hackmann TJ, Staples CR, Adesogan AT. Effects of the dose and viability of Saccharomyces cerevisiae. 1. Diversity of ruminal microbes as analyzed by Illumina MiSeq sequencing and quantitative PCR. J Dairy Sci. 2017;100:325–42.

Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S. Metatranscriptome sequencing reveals insights into the gene expression and functional potential of rumen wall bacteria. Front Microbiol. 2018;9:43.

Ogunade I, Schweickart H, McCoun M, Cannon K, McManus C. Integrating 16S rRNA sequencing and LC–MS-based metabolomics to evaluate the effects of live yeast on rumen function in beef cattle. Animals. 2019;9(1):28.

Ogunade IM, Schweickart H, Andries K, Lay J. Monensin alters the functional and metabolomics profile of rumen microbiota in beef cattle. Animals. 2018;8:211.

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.

Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.

Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–5.

Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:46.

Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38:132.

Li W, Godzik A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.

Anders S, Huber W. Differential expression of RNA-Seq data at the gene level–the DESeq package. Heidelberg: European Molecular Biology Laboratory (EMBL); 2012.

Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol. 2008;6:121–31.

Reichardt N, Duncan SH, Young P, Belenguer A, Leitch CM, Scott KP, et al. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J. 2014;8:1323.

Vita N, Valette O, Brasseur G, Lignon S, Denis Y, Ansaldi M, et al. The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol. 2015;6:606.

Iannotti EL, Kafkewitz D, Wolin MJ, Bryant MP. Glucose fermentation products of Ruminococcus albus grown in continuous culture with Vibrio succinogenes: changes caused by interspecies transfer of H2. J Bacteriol. 1973;114:1231–40.

Chassard C, Delmas E, Robert C, Bernalier-Donadille A. The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol. 2010;74:205–13.

Loor JJ, Elolimy AA, McCann JC. Dietary impacts on rumen microbiota in beef and dairy production. Anim Front. 2016;6:22–9.

Hook SE, Wright ADG, McBride BW. Methanogens: methane producers of the rumen and mitigation strategies. Archaea. 2010;2010:945785.

Chaucheyras-Durand F, Fonty G, Bertin G, Gouet P. In vitro H2 utilization by a ruminal acetogenic bacterium cultivated alone or in association with an archaea methanogen is stimulated by a probiotic strain of Saccharomyces cerevisiae. Appl Environ Microbiol. 1995;61:3466–7.

Newbold CJ, Rode LM. Dietary additives to control methanogenesis in the rumen. Int Congr Ser. 2006;1293:138–47.

Beattie DS, Jenkins HC, Howton MM. Biochemical evidence for the orientation of cytochrome b in the yeast mitochondrial membrane in the eight-helix model. Arch Biochem Biophys. 1994;312:292–300.

Chaucheyras-Durand F, Walker ND, Bach A. Effects of active dry yeasts on the rumen microbial ecosystem: past, present and future. Anim Feed Sci Technol. 2008;145:5–26.

Kondo KI, Doi H, Adachi H, Nishimura Y. Synergistic effect of CMP/KDO synthase inhibitors with antimicrobial agents on inhibition of production and release of vero toxin by enterohaemorrhagic Escherichia coli O157: H7. Bioorg Med Chem Lett. 2004;14:467–70.

Krause DO, Nagaraja TG, Wright AD, Callaway TR. Board invited review: rumen microbiology: leading the way in microbial ecology. J Anim Sci. 2013;91:331–41.

Volker D, Hüther L, Daş G, Abel H. Pantothenic acid supplementation to support rumen microbes? Arch Anim Nutr. 2011;65:163–73.

NRC. Nutrient Requirements of Dairy Cattle. 7th rev. ed. Washington, DC: National Academies Press; 2001.

White WH, Gunyuzlu PL, Toyn JH. Saccharomyces cerevisiae is capable of de novo pantothenic acid biosynthesis involving a novel pathway of beta-alanine production from spermine. J Biol Chem. 2001;276:10794–800.

Wolin MJ, Miller TL. Microbe-microbe interactions. In: Hobson PN, editor. The rumen microbial ecosystem. London: Elsevier Applied Science; 1988. p. 343–59.

Luan Y, Xu W. The structure and main functions of aminopeptidase N. Curr Med Chem. 2007;14:639–47.

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. The Endoplasmic Reticulum. In Molecular Biology of the Cell. 4th ed. New York: Garland Science; 2002.

Bryant MP, Robinson IM. Studies on the nitrogen requirements of some ruminal cellulolytic bacteria. Appl Microbiol. 1961;9:96–103.

Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):1–18.

Lairson LL, Henrissat B, Davies GJ, Withers SG. Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem. 2008;77:521–55.

Thông tin
Thông tin xuất bản

Springer Science and Business Media LLC

Tập 10

1-7

Thông tin tác giả