Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene
- 1.9k Downloads
Intestinal microbes are part of a complex ecosystem. They have a mutual relationship with the host and play an essential role in maintaining the host’s health. To optimize the feeding strategies and improve the health status of the dhole, which is an endangered species, we analyzed the structure of fecal microbes in four captive dholes using high-throughput Illumina sequencing targeting the V3–V4 region of the 16S rRNA gene. The diversity indexes and rarefaction curves indicated high microbial diversity in the intestines of the four dholes. The average number of operational taxonomical units (OTUs) in the four samples was 1196, but the number of OTUs common to all libraries was 126, suggesting only a few dominant species. Phylogenetic analysis identified 19 prokaryotic phyla from the 16S rRNA gene sequences, of which only 5 phyla were core microbiota: Bacteroidetes (21.63–38.97 %), Firmicutes (20.97–44.01 %), Proteobacteria (9.33–17.60 %), Fusobacteria (9.11–17.90 %), and Actinobacteria (1.22–2.87 %). These five phyla accounted for 97 % of the bacteria in all the dholes apart from one, in which 78 % of the bacteria were from these phyla. The results of our study provide an effective theoretical basis from which to reach an understanding of the biological mechanisms relevant to the protection of this endangered species.
KeywordsDhole (Cuon alpinus) Fecal microbes 16S rRNA Illumina MiSeq sequencing
This research was supported by the Special Fund for Forest Scientific Research in the Public Welfare (201404420), the National Natural Science Fund of China (31372220, 31172119), the Natural Science Fund of Shandong Province of China (ZR2011CM009), and the Ph.D. Programs Foundation of Ministry of Education of China (20113705110001). The authors thank all the supports.
Compliance with ethical standards
This study was funded by the Special Fund for Forest Scientific Research in the Public Welfare (201404420), the National Natural Science Fund of China (31372220, 31172119), the Natural Science Fund of Shandong Province of China (ZR2011CM009), and the Ph.D. Programs Foundation of Ministry of Education of China (20113705110001).
Conflict of interest
All of the authors declare that they have no conflict of interest.
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.
- Andersone Z, Ozolins J (2004) Food habits of wolves (Canis lupus) in Latvia. Acta Theriol 49(3):357–367Google Scholar
- Costa MC, Arroyo LG, Allen-Vercoe E, Stӓmpfli HR, Kim PT, Sturgeon A, Weese JS (2012) Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene. PLoS One 7(7):267–278Google Scholar
- Daly K, Proudman CJ, Duncan SH, Flint HJ, Dyer J, Shirazi-Beechey SP (2012) Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease. The British Journal of Nutrition 107(7):989–995. doi: 10.1017/s0007114511003825 CrossRefPubMedGoogle Scholar
- Guard BC, Barr JW, Reddivari L, Klemashevich C, Jayaraman A, Steiner JM, Vanamala J, Suchodolski JS (2015) Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea. PLoS One 10(5):e0127259. doi: 10.1371/journal.pone.0127259 CrossRefPubMedPubMedCentralGoogle Scholar
- Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortes ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499(7457):214–218. doi: 10.1038/nature12213 CrossRefPubMedPubMedCentralGoogle Scholar
- Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. Biomed Research International 2012(3):355–355Google Scholar
- Nam YD, Jung MJ, Roh SW, Kim MS, Bae JW (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6(7):65–65Google Scholar
- Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey Jr GC (2011) Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. The ISME Journal 5(4):639–649. doi: 10.1038/ismej.2010.162
- Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV (2008) Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455(7216):1109–1113. doi: 10.1038/nature07336 CrossRefPubMedPubMedCentralGoogle Scholar
- Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA (2012) Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res 40(14):e107. doi: 10.1093/nar/gks299 CrossRefPubMedPubMedCentralGoogle Scholar