Skip to main content

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats

Indian Journal of Microbiology volume 57, pages 235–240 (2017)Cite this article

Abstract

Tilapia ( Oreochromis mossambicus ) is one of the most invasive fish found throughout the World and emerged as a major threat to the indigenous fishes in many countries. Investigating the gut microbial diversity of such fishes is one of the ways to understand its physiology. In the present study, we have explored the gut microbial community structure of tilapia using 16S rRNA gene sequencing on the Illumina Miseq platform. Our study showed significant differences in tilapia gut microbiota collected from different habitats (i.e. river and lakes) suggesting the influence of habitat on the gut microbial diversity of tilapia. This study gives a first insight into the mossambicus tilapia gut microbiota and provides a reference for future studies.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  1. Singh AK, Lakra WS (2011) Risk and benefit assessment of alien fish species of the aquaculture and aquarium trade into India. Rev Aquac 3:3–18

    Article  Google Scholar 

  2. Pullin RSV, Palomares ML, Casal CV, Dey MM, Pauly D (1997) Environmental impacts of tilapias. In: Fitzsimmons K (ed) Tilapia aquaculture—proceedings from the fourth international symposium on Tilapia in aquaculture. Northeast Regional Agricultural Engineering Service Cooperative Extension, Ithaca, New York pp 554–570

  3. Huang YK, Lin KH, Chen HW, Chen-Chen C, Chen-Wuing L, Mo-Hsiung Y, Yu-Mei H (2003) Arsenic species contents at aquaculture farm and in farmed mouthbreeder (Oreochromis mossambicus) in blackfoot disease hyperendemic areas. Food Chem Toxicol 41:1491–1500

    CAS  Article  PubMed  Google Scholar 

  4. Perez JE, Nirchio M, Alfonsi C, Munoz C (2006) The biology of invasions: the genetic adaptation paradox. Biol Invasions 8:1115–1121

    Article  Google Scholar 

  5. Jayaseelan C, Rahuman AA, Ramkumar R, Perumal P, Rajakumar G, Kirthi AV, Santhoshkumar T, Marimuthu S (2014) Effect of sub-acute exposure to nickel nanoparticles on oxidative stress and histopathological changes in Mozambique tilapia Oreochromis mossambicus. Ecotoxicol Environ Saf 107:220–228

    CAS  Article  PubMed  Google Scholar 

  6. Canonico GC, Arthington A, McCrary JM, Thieme ML (2005) The effects of introduced tilapias on native biodiversity. Aquat Conserv 15:463–483

    Article  Google Scholar 

  7. Lowe S, Browne M, Boudjelas S, De Poorter M (2000) 100 of the world’s worst invasive alien species: a selection from the global invasive species database. Published by The Invasive Species Specialist Group (ISSG) a specialist group of the Species Survival Commission (SSC) of the World Conservation Union (IUCN)

  8. Ringø E, Gatesoue FJ (1998) Lactic acid bacteria in fish: a review. Aquaculture 160:177–203

    Article  Google Scholar 

  9. Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquac Res 41:1553–1573

    Article  Google Scholar 

  10. Ye L, Amberg J, Chapman D, Gaikowski M, Liu WT (2014) Fish gut microbiota analysis differentiates physiology and behaviour of invasive Asian carp and indigenous American fish. ISME 8:541–551

    CAS  Article  Google Scholar 

  11. Wu SG, Tian JY, Gatesoupe FJ, Li WX, Zou H, Yang BJ, Wang GT (2013) Intestinal microbiota of gibel carp (Carassius auratus gibelio) and its origin as revealed by 454 pyrosequencing. World J Microbiol Biotechnol 29:1585–1595

    Article  PubMed  Google Scholar 

  12. Carda-Dieguez M, Mira A, Fouz B (2013) Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets. FEMS Microbiol Ecol 87:451–459

    Article  PubMed  Google Scholar 

  13. Li X, Zhu Y, Yan Q, Tingo E, Yang D (2014) Do the intestinal microbiotas differ between paddlefish (Polydon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? J Appl Microbiol 117:1245–1252

    CAS  Article  PubMed  Google Scholar 

  14. Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH (2014) The intestinal microbiome of fish under starvation. BMC Genom 15:1–11

    Google Scholar 

  15. Franchini P, Fruciano C, Frickey T, Jones JC, Meyer A (2014) The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic–benthic species pairs. PLoS ONE 9:e95027

    Article  PubMed  PubMed Central  Google Scholar 

  16. Giatsis C, Sipkema D, Smidt H, Verreth J, Verdegem M (2014) The colonization dynamics of the gut microbiota in Tilapia larvae. PLoS ONE 9:e103641

    Article  PubMed  PubMed Central  Google Scholar 

  17. Besemer K, Peter H, Logue JB, Langenheder S, Lindstrom ES, Tranvik LJ, Battin TJ (2014) Unravelling assembly of stream biofilm communities. ISME 6:1459–1468

    Article  Google Scholar 

  18. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source platform-independent community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Hammer O, Harper DAT, Ryan PD (2000) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9

    Google Scholar 

  22. Li X, Yan Q, Xie S, Hu W, Yu Y, Hu Z (2013) Gut microbiota contributes to the growth of fast growing transgenic common carp (Cyprinus carpio L). PLoS ONE 8:e64577

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Baldo L, Riera JL, Tooming-Klunderud A, Alba M, Salzburger W (2015) Gut microbiota dynamics during shift in eastern African cichlid fishes. PLoS ONE. doi:10.1371/journalpone0127462

    Google Scholar 

  24. Wu S, Wang G, Angert ER, Wang W, Li W, Zou H (2012) Composition diversity and origin of the bacterial community in grass carp intestine. PLoS ONE 7:e30440

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization manipulation and importance in aquaculture and fisheries. Front Microbiol 5:1–17

    Article  Google Scholar 

  26. Parks D, Beiko R (2013) STAMP: statistical analysis of metagenomic profiles. Encycl Metagenom. doi:10.1007/978-1-4614-6418-1_780-1

    Google Scholar 

  27. Sullam KE, Rubin BER, Dalton CM, Kilham SS, Flecker AS, Russell JA (2015) Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. ISME 9:1508–1522

    Article  Google Scholar 

  28. Smith CCR, Snowberg LK, Caporaso G, Knight R, Bolnick DI (2015) Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota. ISME 9:2515–2526

    CAS  Article  Google Scholar 

  29. Sullam KE, Essinger SD, Lozupone CA, O’Connor MP, Rosen GL, Knight R, Kilham SS, Russell JA (2012) Environmantal and ecological factors that shape the bacterial communities of fish: a meta-analysis. Mol Ecol 21:3363–3378

    Article  PubMed  Google Scholar 

  30. Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanback R (2014) Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol Lett 17:979–987

    Article  PubMed  PubMed Central  Google Scholar 

  31. Cnaani A, Ron M, Seroussi E, Hulata G (2002) Genetic analysis of imminological traits in Tilapia Naga. ICLARM Q 25:40–41

    Google Scholar 

  32. Firmat C, Alibert P, Losseau M, Jean-Francois B, Schliewen UK (2013) Successive invasion-mediated interspecific hybridizations and population structure in the endangered cichlid Oreochromis mossambicus. PLoS ONE 8:e63880

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Tsuchiya C, Sakata T, Sugita H (2007) Novel ecological niche of Cetobacterium somerae an anerobic bacterium in the intestinal tracts of freshwater fish. Lett Appl Microbiol 46:43–48

    PubMed  Google Scholar 

  34. Roeselers G, Mittege EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME 5:1595–1608

    CAS  Article  Google Scholar 

  35. Francis-Floyd R (2011) Mycobacterial infection of fishes. SRAC publication 4706

  36. Noga EJ, Wright JF, Pasarell L (1990) Some unusual features of mycobacteriosis in the cichlid fish Oreochromis mossambicus. J Comp Pathol 102:335–344

    CAS  Article  PubMed  Google Scholar 

  37. Sapountzis P, Zhukova M, Hansen LH, Sorensen SJ, Schiott M, Boomsma JJ (2015) Acromyrmex leaf cutting ants have simple gut microbiota with nitrogen-fixing potential. Appl Environ Microbiol. doi:10.1128/AEM00961-15

    Google Scholar 

  38. Saidi-Mehrabad A, He Z, Tamas I, Sharp CE, Brady AL, Rochman FF, Bodrossy L, Abell GC, Penner T, Dong X, Sensen CW, Dunfield PE (2013) Methanotrophic bacteria in oilsands tailings ponds on northen Alberta. ISME 7:908–921

    CAS  Article  Google Scholar 

  39. Kowalski KP, Bacon C, Bickford W, Braun H, Clay K, Leduc-Lapierre M, Lillard E, McCormick MK, Nelson E, Torres M, White J, Wilcox DA (2015) Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes. Front Microbiol 6:1–14

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by Dr. D.S. Kothari postdoctoral fellowship scheme by University Grant Commission, India to SSG; WNG thanks Departmental Research and Development Grant from Department of Biotechnology (DBT), Government of India and University for Potential Excellence (UPE) phase II program and YSS thanks DBT India for providing funds to carry out this work under the MCC project Grant No. BT/PR10054/NDB/52/94/2007.

Author information

Affiliations

  1. Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India

    Swapnil Sopan Gaikwad & Wasudeo N. Gade

  2. Microbial Culture Collection (MCC), First Floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India

    Swapnil Sopan Gaikwad & Yogesh S. Shouche

Authors
  1. Swapnil Sopan Gaikwad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yogesh S. Shouche
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wasudeo N. Gade
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wasudeo N. Gade.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interests.

Electronic supplementary material

Below is the link to the electronic supplementary material.

12088_2017_641_MOESM1_ESM.png

Supplementary Fig. 1 The distribution of bacterial community between TRgut and TLgut samples. Bacterial abundance in the TRgut sample has a negative difference between proportions (green circles), whereas bacterial abundance in the TLgut sample has a positive difference between proportions (blue circles). Bars on the left represent the proportion of each bacterial phyla abundance in the samples. p values are shown in the right side (PNG 110 kb)

12088_2017_641_MOESM2_ESM.png

Supplementary Fig. 2 The distribution of bacterial community between TRwater and TRgut samples. Bacterial abundance in the TRwater sample has a negative difference between proportions (purple circles), whereas bacterial abundance in the TRgut sample has a positive difference between proportions (green circles). Bars on the left represent the proportion of each bacterial phyla abundance in the samples. p values are shown in the right side (PNG 117 kb)

12088_2017_641_MOESM3_ESM.png

Supplementary Fig. 3 The distribution of bacterial community between TLwater and TLgut samples. Bacterial abundance in the TLgut sample has a positive difference between proportions (blue circles), whereas bacterial abundance in the TLwater sample has a negative difference between proportions (orange circles). Bars on the left represent the proportion of each bacterial phyla abundance in the samples. p values are shown in the right side (PNG 117 kb)

Supplementary material 4 (DOC 54 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Gaikwad, S.S., Shouche, Y.S. & Gade, W.N. Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats. Indian J Microbiol 57, 235–240 (2017). https://doi.org/10.1007/s12088-017-0641-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12088-017-0641-9

Keywords

  • Mossambicus tilapia
  • Gut microbiota
  • Next generation sequencing
  • Invasive species
  • Host microbiota interactions