Skip to main content

Advertisement

SpringerLink
Log in

Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene

  • Applied genetics and molecular biotechnology
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Akbari M, Hansen MD, Halgunset J, Skorpen F, Krokan HE (2005) Low copy number DNA template can render polymerase chain reaction error prone in a sequence-dependent manner. JMD 7(1):36–39

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andersone Z, Ozolins J (2004) Food habits of wolves (Canis lupus) in Latvia. Acta Theriol 49(3):357–367

  • Becker AA, Hesta M, Hollants J, Janssens GP, Huys G (2014) Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae. BMC Microbiol 14:43. doi:10.1186/1471-2180-14-43

    Article  PubMed  PubMed Central  Google Scholar 

  • Bian G, Ma L, Su Y, Zhu W (2013) The microbial community in the feces of the white rhinoceros (Ceratotherium simum) as determined by barcoded pyrosequencing analysis. PLoS One 8(7):e70103. doi:10.1371/journal.pone.0070103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanback R (2014) Individual diet has sex-dependent effects on vertebrate gut microbiota. Nat Commun 5:4500. doi:10.1038/ncomms5500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Capitani C, Bertelli I, Varuzza P, Scandura M, Apollonio M (2004) A comparative analysis of wolf (Canis lupus) diet in three different Italian ecosystems. Mammalian Biology - Zeitschrift für S01ugetierkunde 69:1–10

    Article  Google 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):267–278

    Google 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

    Article  CAS  PubMed  Google Scholar 

  • Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6(11):e280. doi:10.1371/journal.pbio.0060280

    Article  PubMed  PubMed Central  Google Scholar 

  • Dominianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, Ahn J (2015) Sex, body mass index, and dietary fiber intake influence the human gut microbiome. PLoS One 10(4):e0124599. doi:10.1371/journal.pone.0124599

    Article  PubMed  PubMed Central  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (Oxford, England) 27(16):2194–2200. doi:10.1093/bioinformatics/btr381

    Article  CAS  Google Scholar 

  • Ghosh TS, Gupta SS, Bhattacharya T, Yadav D, Barik A, Chowdhury A, Das B, Mande SS, Nair GB (2014) Gut microbiomes of Indian children of varying nutritional status. PLoS One 9(4):e95547. doi:10.1371/journal.pone.0095547

    Article  PubMed  PubMed Central  Google Scholar 

  • Gu S, Chen D, Zhang JN, Lv X, Wang K, Duan LP, Nie Y, Wu XL (2013) Bacterial community mapping of the mouse gastrointestinal tract. PLoS One 8(10):e74957. doi:10.1371/journal.pone.0074957

    Article  CAS  PubMed  PubMed Central  Google 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Jami E, Mizrahi I (2012) Composition and similarity of bovine rumen microbiota across individual animals. PLoS One 7(3):e33306. doi:10.1371/journal.pone.0033306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Köchling T, Sanz JL, Gavazza S, Florencio L (2015) Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing. Appl Microbiol Biotechnol 99:5657–5668

    Article  PubMed  Google Scholar 

  • Karanth KU, Sunquist ME (1995) Prey selection by tiger, leopard and dhole in tropical forests. J Anim Ecol 64(4):439–450

    Article  Google Scholar 

  • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79(17):5112–5120

    Article  CAS  PubMed  PubMed Central  Google 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillen S, Vila C (2002) Ancient DNA evidence for old world origin of new world dogs. Science (New York, NY) 298(5598):1613–1616. doi:10.1126/science.1076980

    Article  CAS  Google Scholar 

  • Liang J, Sha SM, Wu KC (2014) Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases. J Dig Dis 15(12):641–646

    Article  CAS  PubMed  Google 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):355–355

    Google 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):65–65

    Google Scholar 

  • Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38. doi:10.1186/1471-2105-12-38

    Article  PubMed  PubMed Central  Google Scholar 

  • Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T (2002) Genetic evidence for an East Asian origin of domestic dogs. Science 298(5598):1610–1613. doi:10.1126/science.1073906

    Article  CAS  PubMed  Google Scholar 

  • Srivathsa A, Karanth KK, Jathanna D, Kumar NS, Karanth KU (2014) On a dhole trail: examining ecological and anthropogenic correlates of dhole habitat occupancy in the Western ghats of India. PLoS One 9(6):e98803. doi:10.1371/journal.pone.0098803

    Article  PubMed  PubMed Central  Google 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

  • Thinley P, Kamler JF, Wang SW, Lham K, Stenkewitz U, Macdonald DW (2011) Seasonal diet of dholes (Cuon alpinus) in northwestern Bhutan. Mammalian Biology - Zeitschrift für S01ugetierkunde 76(4):518–520

    Article  Google Scholar 

  • Tun HM, Brar MS, Khin N, Li J, Hui KH, Dowd SE, Leung CC (2012) Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. J Microbiol Methods 88(3):369–376

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams C, Ponten F, Moberg C, Soderkvist P, Uhlen M, Ponten J, Sitbon G, Lundeberg J (1999) A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am J Pathol 155(5):1467–1471. doi:10.1016/s0002-9440(10)65461-2

    Article  CAS  PubMed  PubMed Central  Google 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Chen L (2010) Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus). Mol Biol Rep 37(8):4013–4022. doi:10.1007/s11033-010-0060-z

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Chen L (2011) The complete mitochondrial genome of dhole Cuon alpinus: phylogenetic analysis and dating evolutionary divergence within canidae. Mol Biol Rep 38(3):1651–1660. doi:10.1007/s11033-010-0276-y

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

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.

Author information

Authors and Affiliations

  1. College of Life Science, Qufu Normal University, Jingxuan West Street No. 57, Qufu, Shandong, 273165, China

    Xiaoyang Wu, Honghai Zhang, Jun Chen, Shuai Shang, Qinguo Wei, Jiakuo Yan & Xiangyu Tu

Authors
  1. Xiaoyang Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Honghai Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shuai Shang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qinguo Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jiakuo Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiangyu Tu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Honghai Zhang.

Ethics declarations

Funding

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.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wu, X., Zhang, H., Chen, J. et al. Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. Appl Microbiol Biotechnol 100, 3577–3586 (2016). https://doi.org/10.1007/s00253-015-7257-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-015-7257-y

Keywords

Search

Navigation