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World Journal of Microbiology and Biotechnology

, Volume 29, Issue 9, pp 1585–1595 | Cite as

Intestinal microbiota of gibel carp (Carassius auratus gibelio) and its origin as revealed by 454 pyrosequencing

  • Shan-Gong Wu
  • Jing-Yun Tian
  • François-Joël Gatesoupe
  • Wen-Xiang Li
  • Hong Zou
  • Bao-Juan Yang
  • Gui-Tang WangEmail author
Original Paper

Abstract

The intestinal microbiota has received increasing attention, as it influences growth, feed conversion, epithelial development, immunity as well as the intrusion of pathogenic microorganisms in the intestinal tract. In this study, pyrosequencing was used to explore the bacterial community of the intestine in gibel carp (Carassius auratus gibelio), and the origin of these microorganisms. The results disclosed great bacterial diversities in the carp intestines and cultured environments. The gibel carp harbored characteristic intestinal microbiota, where Proteobacteria were predominant, followed by Firmicutes. The analysis on the 10 most abundant bacterial operational taxonomic units (OTUs) revealed a majority of Firmicutes in the intestinal content (by decreasing order: Veilonella sp., Lachnospiraceae, Lactobacillales, Streptococcus sp., and Lactobacillus sp.). The second most abundant OTU was Rothia sp. (Actinobacteria). The most likely potential probiotics (Lactobacillus sp., and Bacillus sp.) and opportunists (Aeromonas sp., and Acinetobacter sp.) were not much abundant. Bacterial community comparisons showed that the intestinal community was closely related to that of the sediment, indicating the importance of sediment as source of gut bacteria in gibel carp. However, 37.95 % of the OTUs detected in feed were retrieved in the intestine, suggesting that food may influence markedly the microbiota of gibel carp, and therefore may be exploited for oral administration of probiotics.

Keywords

Gibel carp Intestine Microbiota Pyrosequencing 

Notes

Acknowledgments

The research was financially supported by grants from National Natural Science Foundation of China (No. 31272706), National Basic Research Program of China (No. 2009CB118705), the Natural Science Foundation of Hubei Province (No. 2009CDB331), and the earmarked fund for China Agriculture Research System (No. CARS-46-08).

Supplementary material

11274_2013_1322_MOESM1_ESM.tif (915 kb)
Fig. S1 Hierarchically clustered heatmap of the bacterial distribution of different communities. Row represents the relative percentage of each bacterial family, and column stands for different samples. Clusterings based upon the distance of the different libraries along the X-axis and the bacterial families along the Y-axis are indicated in the upper and left of the figure, respectively. The relative values for each bacterial family are depicted by color intensity with the legend indicated at the upper left of the figure. The Z-score denoted a measure of distance, in standard deviations, away from the mean (TIFF 914kb)
11274_2013_1322_MOESM2_ESM.tif (249 kb)
Fig. S2 Venn diagram denoting the number of unique and shared OTUs (97%) in the different libraries (TIFF 248kb)

References

  1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169Google Scholar
  2. Asfie M, Yoshijima T, Sugita H (2003) Characterization of the goldfish fecal microflora by the fluorescent in situ hybridization method. Fish Sci 69:21–26CrossRefGoogle Scholar
  3. Cahill MM (1990) Bacterial flora of fishes: a review. Microb Ecol 19:21–41CrossRefGoogle Scholar
  4. Feng X, Wu ZX, Zhu DM, Wang Y, Pang SF, Yu YM, Mei XH, Chen XX (2008) Study on digestive enzyme-producing bacteria from the digestive tract of Ctenopharyngodon idellus and Carassius auratus gibelio. Freshw Fish 38:51–57Google Scholar
  5. Han SF, Liu YC, Zhou ZG, He SX, Cao YA, Shi PJ, Yao B, Ringø E (2010) Analysis of bacterial diversity in the intestine of grass carp (Ctenopharyngodon idellus) based on 16S rDNA gene sequences. Aquac Res 42:47–56CrossRefGoogle Scholar
  6. Heuer H, Krsek M, Baker P, Smalla K, Wellington EMH (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233–3241Google Scholar
  7. Kim DH, Brunt J, Austin B (2007) Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 102:1654–1664CrossRefGoogle Scholar
  8. Kovach W (1999) MVSP-a multivariate statistical package for Windows, ver. 3.1. Kovach Computing services, PentraethGoogle Scholar
  9. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123CrossRefGoogle Scholar
  10. Lee C, Cho JC, Lee SH, Lee DG, Kim SJ (2002) Distribution of Aeromonas spp. as identified by 16S rDNA restriction fragment length polymorphism analysis in a trout farm. J Appl Microbiol 93:976–985CrossRefGoogle Scholar
  11. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776–788CrossRefGoogle Scholar
  12. Li XB, Huang WF (2003) Study on the bacterial septicemia of Carassius auratus of penze (♀) × Cyprinus actidorsalis (♂) I-isolation and identification of the pathogen. Microbiology 30:56–60Google Scholar
  13. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104:11436–11440CrossRefGoogle Scholar
  14. Lu WH, Chen H, Zou Y, Yang YJ, Wang XD, Huang CG (2010) Identification and drug sensitive test of the pathogen in Acinetobacter disease from hybrid crucian carp (Carassius auratus gibelio ♀ × Cyprinus carpio ♂). Fish Sci 29:156–161Google Scholar
  15. MacMillan JR, Santucci T (1990) Seasonal trendy in intestinal bacterial flora of farm raised channel catfish. J Aquat Anim Health 2:217–222CrossRefGoogle Scholar
  16. Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquac Res 41:1553–1573CrossRefGoogle Scholar
  17. Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci USA 101:4596–4601CrossRefGoogle Scholar
  18. Reid HI, Treasurer JW, Adam B, Birkbeck TH (2009) Analysis of bacterial populations in the gut of developing cod larvae and identification of Vibrio logei, Vibrio anguillarum and Vibrio splendidus as pathogens of cod larvae. Aquaculture 288:36–43CrossRefGoogle Scholar
  19. Ringø E, Birkbeck TH (1999) Intestinal microflora of fish larvae and fry. Aquac Res 30:73–93CrossRefGoogle Scholar
  20. Ringø E, Strom E (1994) Microflora of arctic charr, Salvilinus alpinus (L). Gastrointestinal microflora of free living fish and effect of diet and salinity on intestinalmicroflora. Aquac Fish Manag 25:623–629Google Scholar
  21. Ringø E, Sperstad S, Myklebust R, Refstie S, Krogdahl A (2006) Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.)—the effect of fish meal, standard soybean meal and a bioprocessed soybean meal. Aquaculture 261:829–841CrossRefGoogle Scholar
  22. Ringø E, Olsen RE, Gifstad TO, Dalmo RA, Amlund H, Hemre GI, Bakke AM (2010) Prebiotics in aquaculture: a review. Aquac Nutr 16:117–136CrossRefGoogle Scholar
  23. Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J. doi: 10.1038/ismej.2011.1038 Google Scholar
  24. Romero J, Navarrete P (2006) 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch). Microb Ecol 51:422–430CrossRefGoogle Scholar
  25. Russell J, Bottje W, Cotta M (1981) Degradation of protein by mixed cultures of rumen bacteria: identification of Streptococcus bovis as an actively proteolytic rumen bacterium. J Anim Sci 53:242Google Scholar
  26. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537CrossRefGoogle Scholar
  27. Shi CY, Zhu XL, Lu QZ (1998) Studies on the hemostatic disorder in crucian carp induced by bacterial septicemia. Acta Hydrobiol Sin 22:367–370Google Scholar
  28. Silva FC, Nicoli JR, Zambonino-Infante JL, Kaushik S, Gatesoupe FJ (2011) Influence of the diet on microbial diversity of faecal and gastrointestinal contents in gilthead sea bream (Sparus aurata) and intestinal contents in goldfish (Carassius auratus). FEMS Microbiol Ecol 78:285–296Google Scholar
  29. Van Elsas JD, Van Overbeek LS (1993) Bacterial responses to soil stimuli. In: Kjelleberg S (ed) Starvation in bacteria. Plenum Press, New York, pp 55–80CrossRefGoogle Scholar
  30. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W (2000) Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev 64:655–671CrossRefGoogle Scholar
  31. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703Google Scholar
  32. Wu SG, Gao TH, Zheng YZ, Wang WW, Cheng YY, Wang GT (2010) Microbial diversity of intestinal contents and mucus in yellow catfish (Pelteobagrus fulvidraco). Aquaculture 303:1–7CrossRefGoogle Scholar
  33. Xu J, Gordon JI (2003) Honor thy symbionts. Proc Natl Acad Sci USA 100:10452–10459CrossRefGoogle Scholar
  34. Yu Z, Morrison M (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36:808–812Google Scholar
  35. Zu GZ, Yu WY, Li JN (2000) Epidemiological investigation and diagnosis of the bacterial septicemia of grass carp (Ctenopharyngodon idellus). Freshw Fish 30:35–37Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Shan-Gong Wu
    • 1
  • Jing-Yun Tian
    • 2
  • François-Joël Gatesoupe
    • 3
  • Wen-Xiang Li
    • 1
  • Hong Zou
    • 1
  • Bao-Juan Yang
    • 1
  • Gui-Tang Wang
    • 1
    Email author
  1. 1.State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of HydrobiologyChinese Academy of SciencesWuhanPeople’s Republic of China
  2. 2.National Oceanographic CenterQingdaoPeople’s Republic of China
  3. 3.INRA, UR 1067 Nutrition Metabolism and Aquaculture, IfremerPlouzanéFrance

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