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Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt

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Abstract

Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data’s functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.

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Data availability

The nucleotide sequence dataset generated in this study was deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the accession numbers: Bioproject: PRJNA626022, Biosample 1 (Manzala Lake): SRR11565277, Biosample 2 (Borollus Lake): SRR11565276.

References

  1. Abriouel, H., Lerma, L. L., Casado Muñoz, M. del C., Montoro, B. P., Kabisch, J., Pichner, R., Benomar, N. (2015). The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health. Frontiers in Microbiology, 6https://doi.org/10.3389/fmicb.2015.01197

  2. Adeoye, A. A., Yomla, R., Jaramillo-Torres, A., Rodiles, A., Merrifield, D. L., & Davies, S. J. (2016). Combined effects of exogenous enzymes and probiotic on Nile tilapia (Oreochromis niloticus) growth, intestinal morphology and microbiome. Aquaculture, 463, 61–70. https://doi.org/10.1016/j.aquaculture.2016.05.028

    Article  CAS  Google Scholar 

  3. Al-Harbi, A. H., & Uddin, M. N. (2004). Seasonal variation in the intestinal bacterial flora of hybrid tilapia (Oreochromis niloticus x Oreochromis aureus) cultured in earthen ponds in Saudi Arabia. Aquaculture, 229(1–4), 37–44. https://doi.org/10.1016/S0044-8486(03)00388-0

    Article  Google Scholar 

  4. Badiea, E. A., Sayed, A. A., Maged, M., Fouad, W. M., Said, M. M., & Esmat, A. Y. (2019). A novel thermostable and halophilic thioredoxin reductase from the Red Sea Atlantis II hot brine pool. PLoS ONE, 14(5), e0217565. https://doi.org/10.1371/journal.pone.0217565

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Baroiller, J. F., D’Cotta, H., & Saillant, E. (2009). Environmental effects on fish sex determination and differentiation. Sexual Development, 3, 118–135. https://doi.org/10.1159/000223077

    Article  CAS  PubMed  Google Scholar 

  6. Baumgartner, A., Thurnheer, T., Lüthi-Schaller, H., Gmür, R., & Belibasakis, G. N. (2012). The phylum Synergistetes in gingivitis and necrotizing ulcerative gingivitis. Journal of Medical Microbiology, 61(11), 1600–1609. https://doi.org/10.1099/jmm.0.047456-0

    Article  PubMed  Google Scholar 

  7. Bentzon-Tilia, M., Sonnenschein, E. C., & Gram, L. (2016). Monitoring and managing microbes in aquaculture - Towards a sustainable industry. Microbial Biotechnology, 9(5), 576–584. https://doi.org/10.1111/1751-7915.12392

    Article  PubMed  PubMed Central  Google Scholar 

  8. Booman, M., Forster, I., Vederas, J. C., Groman, D. B., & Jones, S. R. M. (2018). Soybean meal-induced enteritis in Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) but not in pink salmon (O. gorbuscha). Aquaculture, 483, 238–243. https://doi.org/10.1016/j.aquaculture.2017.10.025

    Article  CAS  Google Scholar 

  9. Boutin, S., Bernatchez, L., Audet, C., & Derôme, N. (2013). Network analysis highlights complex interactions between pathogen, host and commensal microbiota. PLoS ONE, 8(12). https://doi.org/10.1371/journal.pone.0084772

  10. Burtseva, O., Kublanovskaya, A., Fedorenko, T., Lobakova, E., & Chekanov, K. (2020). Gut microbiome of the White Sea fish revealed by 16S rRNA metabarcoding. Aquaculture, 533,.

  11. Butt, R. L., & Volkoff, H. (2019). Gut microbiota and energy homeostasis in fish. Frontiers in Endocrinology, 10https://doi.org/10.3389/fendo.2019.00009

  12. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335–336. https://doi.org/10.1038/nmeth.f.303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Clements, K. D., Pasch, I. B. Y., Moran, D., & Turner, S. J. (2007). Clostridia dominate 16S rRNA gene libraries prepared from the hindgut of temperate marine herbivorous fishes. Marine Biology, 150(6), 1431–1440. https://doi.org/10.1007/s00227-006-0443-9

    Article  CAS  Google Scholar 

  14. Clements, K. D., Raubenheimer, D., & Choat, J. H. (2009). Nutritional ecology of marine herbivorous fishes: Ten years on. Functional Ecology, 23, 79–92. https://doi.org/10.1111/j.1365-2435.2008.01524.x

    Article  Google Scholar 

  15. Comeau, A. M., Harding, T., Galand, P. E., Vincent, W. F., & Lovejoy, C. (2012). Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Scientific Reports, 2https://doi.org/10.1038/srep00604

  16. Comeau, A. M., Li, W. K. W., Tremblay, J. -É., Carmack, E. C., & Lovejoy, C. (2011). Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum. PLoS ONE, 6(11), e27492. https://doi.org/10.1371/journal.pone.0027492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Copley, S. D. (2009). August). Evolution of efficient pathways for degradation of anthropogenic chemicals. Nature Chemical Biology, 5, 559–566. https://doi.org/10.1038/nchembio.197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Dahle, H., & Birkeland, N. K. (2006). Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. International Journal of Systematic and Evolutionary Microbiology, 56(7), 1539–1545. https://doi.org/10.1099/ijs.0.63894-0

    Article  CAS  PubMed  Google Scholar 

  19. de Albuquerque, F. P., de Oliveira, J. L., Moschini-Carlos, V., & Fraceto, L. F. (2020). An overview of the potential impacts of atrazine in aquatic environments: Perspectives for tailored solutions based on nanotechnology. Science of the Total Environment, 700https://doi.org/10.1016/j.scitotenv.2019.134868

  20. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., … Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72(7), 5069-5072https://doi.org/10.1128/AEM.03006-05

  21. Dong, H. T., Techatanakitarnan, C., Jindakittikul, P., Thaiprayoon, A., Taengphu, S., Charoensapsri, W., & Senapin, S. (2017). Aeromonas jandaei and Aeromonas veronii caused disease and mortality in Nile tilapia, Oreochromis niloticus (L.). Journal of Fish Diseases, 40(10), 1395–1403. https://doi.org/10.1111/jfd.12617

    Article  CAS  PubMed  Google Scholar 

  22. Fadeev, E., Salter, I., Schourup-Kristensen, V., Nöthig, E. M., Metfies, K., Engel, A., Bienhold, C. (2018). Microbial communities in the east and west fram strait during sea ice melting season. Frontiers in Marine Science, 5(NOV). https://doi.org/10.3389/fmars.2018.00429

  23. Fath El-Bab, A., Farag, M., Ramadan, A., & Hassan, A. (2011). Effect of temperature and female weight on reproductive performance of two Nile tilapia (Oreochromis niloticus) populations. Egyptian Journal of Aquatic Biology and Fisheries, 15(2), 179–193. https://doi.org/10.21608/ejabf.2011.2087

    Article  Google Scholar 

  24. Feio, M. J., Zinkevich, V., Beech, I. B., Llobet-Brossa, E., Eaton, P., Schmitt, J., & Guezennec, J. (2004). Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir. International Journal of Systematic and Evolutionary Microbiology, 54(5), 1747–1752. https://doi.org/10.1099/ijs.0.63118-0

    Article  CAS  PubMed  Google Scholar 

  25. Fernández-Pinos, M.-C., Vila-Costa, M., Arrieta, J. M., Morales, L., González-Gaya, B., Piña, B., & Dachs, J. (2017). Dysregulation of photosynthetic genes in oceanic Prochlorococcus populations exposed to organic pollutants. Scientific Reports, 7(1), 8029. https://doi.org/10.1038/s41598-017-08425-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Foysal, M. J., Nguyen, T. T. T., Chaklader, M. R., Siddik, M. A. B., Tay, C.-Y., Fotedar, R., & Gupta, S. K. (2019). Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum. PeerJ, 7(8), e7553. https://doi.org/10.7717/peerj.7553

    Article  PubMed  PubMed Central  Google Scholar 

  27. Fusco, V., Quero, G. M., Cho, G. S., Kabisch, J., Meske, D., Neve, H., … Franz, C. M. A. P. (2015). The genus Weissella: Taxonomy, ecology and biotechnological potential. Frontiers in Microbiology, 6, 155https://doi.org/10.3389/fmicb.2015.00155

  28. Gerzova, L., Videnska, P., Faldynova, M., Sedlar, K., Provaznik, I., Cizek, A., & Rychlik, I. (2014). Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish. PLoS ONE, 9(8), e103865. https://doi.org/10.1371/journal.pone.0103865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Gilmour, C. C., Elias, D. A., Kucken, A. M., Brown, S. D., Palumbo, A. V., Schadt, C. W., & Wall, J. D. (2011). Sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation. Applied and Environmental Microbiology, 77(12), 3938–3951. https://doi.org/10.1128/AEM.02993-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Giovannoni, S. J. (2017). SAR11 bacteria: The most abundant plankton in the oceans. Annual Review of Marine Science, 9(1), 231–255. https://doi.org/10.1146/annurev-marine-010814-015934

    Article  PubMed  Google Scholar 

  31. Hagi, T., Tanaka, D., Iwamura, Y., & Hoshino, T. (2004). Diversity and seasonal changes in lactic acid bacteria in the intestinal tract of cultured freshwater fish. Aquaculture, 234(1–4), 335–346. https://doi.org/10.1016/j.aquaculture.2004.01.018

    Article  CAS  Google Scholar 

  32. Han, D., Gao, P., Li, R., Tan, P., Xie, J., Zhang, R., & Li, J. (2020). Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing. Journal of Advanced Research, 26, 111–121.

    Article  CAS  Google Scholar 

  33. Harman, M., Vig, D. K., Radolf, J. D., & Wolgemuth, C. W. (2013). Viscous dynamics of lyme disease and syphilis spirochetes reveal flagellar torque and drag. Biophysical Journal, 105(10), 2273–2280. https://doi.org/10.1016/j.bpj.2013.10.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hauser, L. J., Land, M. L., Brown, S. D., Larimer, F., Keller, K. L., Rapp-Giles, B. J., … Wall, J. D. (2011, August). Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20. Journal of Bacteriology, 193, 4268-4269https://doi.org/10.1128/JB.05400-11

  35. Huson, D. H., Albrecht, B., Bağci, C., Bessarab, I., Górska, A., Jolic, D., & Williams, R. B. H. (2018). MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biology Direct, 13(1). https://doi.org/10.1186/s13062-018-0208-7

  36. Iwatsuki, T., Kanazawa, T., Ogasawara, T., Hosotani, K., Tsuchiya, K., Watanabe, S., ... & Dohra, H. (2021). 16S rRNA Gene Amplicon Sequencing of Gut Microbiota in Three Species of Deep-Sea Fish in Suruga Bay, Japan. Microbiology Resource Announcements, 10(1)

  37. Janßen, R., Zabel, J., von Lukas, U., & Labrenz, M. (2019). An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts. Marine Pollution Bulletin, 149,.

  38. Kannika, K., Pisuttharachai, D., Srisapoome, P., Wongtavatchai, J., Kondo, H., Hirono, I., & Areechon, N. (2017). Molecular serotyping, virulence gene profiling and pathogenicity of Streptococcus agalactiae isolated from tilapia farms in Thailand by multiplex PCR. Journal of Applied Microbiology, 122(6), 1497–1507. https://doi.org/10.1111/jam.13447

    Article  CAS  PubMed  Google Scholar 

  39. Kayed, A. S., Kandeil, A., Gomaa, M. R., El-Shesheny, R., Mahmoud, S., Hegazi, N., & Ali, M. A. (2019). Surveillance for avian influenza viruses in wild birds at live bird markets, Egypt, 2014–2016. Influenza and Other Respiratory Viruses, 13(4), 407–414. https://doi.org/10.1111/irv.12634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Khalil, M. T. (1990). The physical and chemical environment of Lake Manzala. Egypt. Hydrobiologia, 196, 193–199. https://doi.org/10.1007/BF00006132

    Article  CAS  Google Scholar 

  41. Khalil M.T. (2018) Physical and chemical properties of Egypt’s coastal wetlands; Burullus Wetland as a Case Study. In: Negm A., Bek M., Abdel-Fattah S. (eds) Egyptian coastal lakes and wetlands: Part I. The Handbook of Environmental Chemistry, vol 71. Springer, Cham. https://doi.org/10.1007/698_2017_205

  42. Kim, M., Morrison, M., & Yu, Z. (2011). Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. Journal of Microbiological Methods, 84(1), 81–87. https://doi.org/10.1016/j.mimet.2010.10.020

    Article  CAS  PubMed  Google Scholar 

  43. Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., & Huttenhower, C. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31(9), 814–821. https://doi.org/10.1038/nbt.2676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Larsen, A. M., Mohammed, H. H., & Arias, C. R. (2014). Characterization of the gut microbiota of three commercially valuable warmwater fish species. Journal of Applied Microbiology, 116(6), 1396–1404. https://doi.org/10.1111/jam.12475

    Article  CAS  PubMed  Google Scholar 

  45. Libonatti, C., Agüeria, D., García, C., & Basualdo, M. (2019). Weissella paramesenteroides encapsulation and its application in the use of fish waste. Revista Argentina de Microbiologia, 51(1), 81–83. https://doi.org/10.1016/j.ram.2018.03.001

    Article  PubMed  Google Scholar 

  46. Liu, C., Chang, O. Q., Zhang, D. F., Li, K. B., Wang, F., Lin, M. H., & Bergmann, S. M. (2018). Aeromonas shuberti as a cause of multi-organ necrosis in internal organs of Nile tilapia, Oreochromis niloticus. Journal of Fish Diseases, 41(10), 1529–1538. https://doi.org/10.1111/jfd.12848

    Article  CAS  PubMed  Google Scholar 

  47. Maged, M., El Hosseiny, A., Saadeldin, M. K., Aziz, R. K., & Ramadan, E. (2018). Thermal stability of a mercuric reductase from the Red Sea Atlantis II hot brine environment as analyzed by site-directed mutagenesis. Applied and Environmental Microbiology, 85(3), 1–12. https://doi.org/10.1128/AEM.02387-18

    Article  Google Scholar 

  48. Matsuyama, T., Yasuike, M., Fujiwara, A., Nakamura, Y., Takano, T., Takeuchi, T., Nakayasu, C. (2017). A Spirochaete is suggested as the causative agent of Akoya oyster disease by metagenomic analysis. PLoS ONE, 12(8). https://doi.org/10.1371/journal.pone.0182280

  49. Meenatchi, R., Thinesh, T., Brindangnanam, P., Hassan, S., Kiran, G. S., & Selvin, J. (2020). Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis. Microbiological Research, 233,.

  50. Morris, R. M., Rappé, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., Carlson, C. A., & Giovannoni, S. J. (2002). SAR11 clade dominates ocean surface bacterioplankton communities. Nature, 420(6917), 806–810. https://doi.org/10.1038/nature01240

    Article  CAS  PubMed  Google Scholar 

  51. Ortiz-Estrada, Á. M., Gollas-Galván, T., Martínez-Córdova, L. R., & Martínez-Porchas, M. (2019). Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems. Reviews in Aquaculture, 11(1), 234–245.

    Article  Google Scholar 

  52. Ramadan, E., Maged, M., Hosseiny, A. El, Chambergo, F. S., Setubal, J. C., & Dorry, H. El. (2019). Molecular adaptations of bacterial mercuric reductase to the hypersaline Kebrit Deep in the Red Sea. Applied and Environmental Microbiology, 85(4). https://doi.org/10.1128/AEM.01431-18

  53. Ringø, E., Hoseinifar, S. H., Ghosh, K., Doan, H. Van., Beck, B. R., & Song, S. K. (2018). Lactic acid bacteria in finfish-An update. Frontiers in Microbiology, 9, 1818. https://doi.org/10.3389/fmicb.2018.01818

    Article  PubMed  PubMed Central  Google Scholar 

  54. Romarheim, O. H., Øverland, M., Mydland, L. T., Skrede, A., & Landsverk, T. (2011). Bacteria grown on natural gas prevent soybean meal-induced enteritis in Atlantic Salmon. The Journal of Nutrition, 141(1), 124–130. https://doi.org/10.3945/jn.110.128900

    Article  CAS  PubMed  Google Scholar 

  55. Sabry, M., El-Moein, K. A., Hamza, E., & Kader, F. A. (2016). Occurrence of Clostridium perfringens types A, E, and C in fresh fish and its public health significance. Journal of Food Protection, 79(6), 994–1000. https://doi.org/10.4315/0362-028X.JFP-15-569

    Article  CAS  PubMed  Google Scholar 

  56. Salgado-Flores Id, A., Tveit, A. T., Wright, A.-D., Pope, P. B., & Sundset, M. A. (2019). Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.https://doi.org/10.1371/journal.pone.0213503

  57. Schmalenberger, A., Schwieger, F., & Tebbe, C. C. (2001). Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Applied and Environmental Microbiology, 67(8), 3557–3563. https://doi.org/10.1128/AEM.67.8.3557-3563.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Si, Y., Skidmore, A. K., Wang, T., De Boer, W. F., Debba, P., Toxopeus, A. G., & Prins, H. H. T. (2009). Spatio-temporal dynamics of global H5N1 outbreaks match bird migration patterns. Geospatial Health, 4(1), 65–78. https://doi.org/10.4081/gh.2009.211

    Article  PubMed  Google Scholar 

  59. de Silva, F. C. P., Nicoli, J. R., Zambonino-Infante, J. L., Kaushik, S., & Gatesoupe, F. J. (2011). Influence of the diet on the microbial diversity of faecal and gastrointestinal contents in gilthead sea bream (Sparus aurata) and intestinal contents in goldfish (Carassius auratus). FEMS Microbiology Ecology, 78(2), 285–296. https://doi.org/10.1111/j.1574-6941.2011.01155.x

    Article  CAS  PubMed  Google Scholar 

  60. Soares, J. M., Gomes, J. M., Reis, G. C. L., Hoyos, D. C. M., Custódio, F. B., & Gloria, M. B. A. (2021). Biogenic amines in amazonian fish and their health effects are affected by species and season of capture. Food Control, 107773,. https://doi.org/10.1016/j.foodcont.2020.107773.

  61. Srionnual, S., Yanagida, F., Lin, L. H., Hsiao, K. N., & Chen, Y. S. (2007). Weissellicin 110, a newly discovered bacteriocin from Weissella cibaria 110, isolated from plaa-som, a fermented fish product from Thailand. Applied and Environmental Microbiology, 73(7), 2247–2250. https://doi.org/10.1128/AEM.02484-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Tepaamorndech, S., Nookaew, I., Higdon, S. M., Santiyanont, P., Phromson, M., Chantarasakha, K., ... & Visessanguan, W. (2020). Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp. Fish & Shellfish Immunology, 106, 733–741

  63. Vieira, F. do N., Jatobá, A., Mouriño, J. L. P., Vieira, E. A., Soares, M., Silva, B. C. da, Vinatea, L. A. (2013). In vitro selection of bacteria with potential for use as probiotics in marine shrimp culture. Pesquisa Agropecuária Brasileira, 48(8), 998https://doi.org/10.1590/S0100-204X2013000800027

  64. Whiteley, A. S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., … O’Donnell, A. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. Journal of Microbiological Methods, 91(1), 80–88. https://doi.org/10.1016/j.mimet.2012.07.008

  65. Yin, X., Mu, L., Wu, H., Han, K., Guo, Z., & Ye, J. (2020). Expression and functional analysis of Nile tilapia transferrin receptors (TfRs) in host resistance to pathogenic bacteria and iron ion metabolism. Fish & Shellfish Immunology, 100, 407–417. https://doi.org/10.1016/j.fsi.2020.03.027.

    Article  CAS  Google Scholar 

  66. Yu, Z., & Morrison, M. (2004). Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Applied and Environmental Microbiology, 70(8), 4800–4806. https://doi.org/10.1128/AEM.70.8.4800-4806.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Yukgehnaish, K., Kumar, P., Sivachandran, P., Marimuthu, K., Arshad, A., Paray, B. A., & Arockiaraj, J. (2020). Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish. Reviews in Aquaculture. https://doi.org/10.1111/raq.12416.

    Article  Google Scholar 

  68. Zhou, T., Yuan, Z., Tan, S., Jin, Y., Yang, Y., Shi, H., Liu, Z. (2018). A review of molecular responses of catfish to bacterial diseases and abiotic stresses. Frontiers in Physiology, 9(AUG). https://doi.org/10.3389/fphys.2018.01113

  69. Zhou, A., Xie, S., Junaid, M., Sun, D., Tang, H., Chuan, J., ... & Zou, J. (2021). First insight into the environmental microbial communities associated with potentially pathogenic strains in pond cultured tilapia (Oreochromis niloticus) at various growth stages based on 16S, 18S, and ITS2 rRNA gene amplicons sequencing. Aquaculture, 532, 736007

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Acknowledgements

The authors extend their appreciation to the scientific research fund at the Benha University for funding this work through the research support program, Project No. (M5/3/2).

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Authors and Affiliations

  1. Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Benha, Egypt

    Ahmed M. Serag, Mohamed S. Abdel-Sabour & Mohamed H. Refaat

  2. Moshtohor Research Park, Molecular Biology Lab, Benha University, Benha, Egypt

    Ahmed M. Serag & Mohamed H. Refaat

  3. Bioinformatics Group, Center of Informatics Science (CIS), Nile University, Giza, Egypt

    Mohamed El-Hadidi

  4. School of Life and Medical Sciences, University of Hertfordshire, Hosted By Global Academic Foundation (GAF), New Administrative Capital, Egypt

    Mohamad Maged

  5. Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt

    Mahmoud Magdy

  6. Deanship of Scientific Research, Umm Al-Qura University, Makkah, Saudi Arabia

    Mohamed Fawzy Ramadan

  7. Department of Agricultural Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt

    Mohamed Fawzy Ramadan

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  6. Mohamed Fawzy Ramadan
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  7. Mohamed H. Refaat
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Contributions

A. S., M. A., M. E., and M. M. collected and analyzed the samples. A. S., M. A., M. E., M. M., M. M., and M. R. carried out the experimental analyses. M. F. R. and M. R. reviewed and edited the article. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Ahmed M. Serag or Mohamed Fawzy Ramadan.

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Research Highlights

• Manzala and Borollus lakes in the north of Egypt are subject to anthropogenic pollutants and man-made contaminants.

• This pilot study compared the gut microbiome of the Nile tilapia fish from both lakes.

• The presence of pathogenic bacteria in Nile tilapia fish guts from both lakes is alarming.

• The abundance of mercury accumulating bacteria in Lake Borollus may have negative consequences to the fish members and to humans consuming this fish.

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Serag, A., Abdel-Sabour, M., El-Hadidi, M. et al. Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt. Appl Biochem Biotechnol 194, 2168–2182 (2022). https://doi.org/10.1007/s12010-021-03750-2

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  • DOI: https://doi.org/10.1007/s12010-021-03750-2

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