Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics
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Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks’ age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks’ growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.
Abstract
Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks’ age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks’ growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.
참고문헌 (31)
- Qiu Q, "The yak genome and adaptation to life at high altitude", Nat Genet, 44, pp.946~949 (2012)
- Flint HJ, "Microbial degradation of complex carbohydrates in the gut", Gut microbes, 3, pp.289~306 (2012)
- Wei YQ, "Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau", Anaerobe, 39, pp.158~164 (2016)
- Backhed F, "Host-bacterial mutualism in the human intestine", Science, 307, pp.1915~1920 (2005)
- Hooper LV, "Analyzing the molecular foundations of commensalism in the mouse intestine", Curr Opin Microbiol, 3, pp.79~85 (2000)
- Zhu L, "Evidence of cellulose metabolism by the giant panda gut microbiome", Proc Natl Acad Sci USA, 108, pp.17714~17719 (2011)
- Eckburg PB, "Diversity of the human intestinal microbial flora", Science, 308, pp.1635~1638 (2005)
- Asano R, "Development and analysis of microbial characteristics of an acidulocomposting system for the treatment of garbage and cattle manure", J Biosci Bioeng, 110, pp.419~425 (2010)
- Qin JJ, "A human gut microbial gene catalogue established by metagenomic sequencing", Nature, 464, pp.U59~U70 (2010)
- Jung JY, "Metagenomic analysis of kimchi, a traditional Korean fermented food", Appl Environ Microbiol, 77, pp.2264~2274 (2011)
- Patel V, "Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet", Appl Microbiol Biotechnol, 98, pp.9749~9761 (2014)
- Walter J, "Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers", Appl Environ Microbiol, 66, pp.297~303 (2000)
- Muyzer G, "Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA", Appl Environ Microbiol, 59, pp.695~700 (1993)
- Fromin N, "Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns", Environ Microbiol, 4, pp.634~643 (2002)
- Li RQ, "De novo assembly of human genomes with massively parallel short read sequencing", Genome Res, 20, pp.265~272 (2010)
- Altschul SF, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res, 25, pp.3389~3402 (1997)
- Huson DH, "MEGAN analysis of metagenomic data", Genome Res, 17, pp.377~386 (2007)
- Parks DH, "Identifying biologically relevant differences between metagenomic communities", Bioinformatics, 26, pp.715~721 (2010)
- Wang X, "Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis", J Appl Microbiol, 95, pp.508~520 (2003)
- Durso LM, "Animal-to-animal variation in fecal microbial diversity among beef cattle", Appl Environ Microb, 76, pp.4858~4862 (2010)
- DeLong EF, "Community genomics among stratified microbial assemblages in the ocean's interior", Science, 311, pp.496~503 (2006)
- Le Chatelier E, "Richness of human gut microbiome correlates with metabolic markers", Nature, 500, pp.541~546 (2013)
- Qin JJ, "A metagenome-wide association study of gut microbiota in type 2 diabetes", Nature, 490, pp.55~60 (2012)
- Zhao W, "The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments", PLoS ONE, 10, pp.e0117441~ (2015)
- Dowd SE, "Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)", BMC Microbiol, 8, pp.208~213 (2008)
- Ozutsumi Y, "Culture-independent analysis of fecal microbiota in cattle", Biosci Biotechnol Biochem, 69, pp.1793~1797 (2005)
- Ziemer CJ, "Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides", Appl Environ Microbiol, 80, pp.574~585 (2014)
- Cotta MA, "Isolation, characterization and comparison of bacteria from swine feces and manure storage pits", Environ Microbiol, 5, pp.737~745 (2003)
- Wexler HM, "Bacteroides: the good, the bad, and the nitty-gritty", Clin Microbiol Rev, 20, pp.593~621 (2007)
- Li MJ, "Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis", Vet Microbiol, 155, pp.72~80 (2012)
- Ley RE, "Evolution of mammals and their gut microbes", Science, 320, pp.1647~1651 (2008)