Molecular identification and phylogenetic profiling of keratinolytic bacteria isolated from goose and chicken farms in a cold region of Türkiye

Year 2025, Volume: 9 Issue: 2, 436 - 445, 26.06.2025

Orhan Uluçay , Cem Öziç

https://doi.org/10.31015/2025.2.17

Abstract

The aim of this study was to investigate bacterial diversity in certain goose and poultry farms in Kars, Türkiye a cold climate zone. Feather waste samples rich in organic compounds were collectedfrom multiple farm locations and evaluated for bacterial diversity. A total of 27 bacteria were isolated. 16S rRNA gene sequencing, morphological, physiological, biochemical and molecular techniques were used. Isolates included Escherichia coli, Ralstonia picketti, Pantoea agglomerans, Kosakonia cowanii, Bacillus licheniformis, Bacillus zhangzhouensis, Bacillus pumilus, Exiguobacterium sibiricum, Exiguobacterium artemiae, Macrococcus caseolyticus, Mammaliicoccus vitulinus, Mammaliicoccus sciuri and Rothia nasisuis. Most of the isolates are positive for characteristics such as spore formation, motility and catalase activity. These isolates also showed adaptation to nutrient-rich and varying temperature parameters. Molecular identification results confirmed the results of phylogenetic analyses, showing strong bootstrap support. The identification of resistant bacteria in these keratin-rich regions plays an important role in the control of poultry waste management. These bacteria, which are desirable for biotechnological applications, are also importance in enzyme studies. This study provides valuable information on the functional diversity of microbial communities in goose and poultry farming. It draws attention to the importance of microbial enzymes in the disposal of keratin wastes.

Keywords

16S rRNA , Sequence , Microorganisms , Keratinase , Phylogenetic , Poultry and goose farm microbiota

Ethical Statement

Peer-review Externally peer-reviewed. Conflict of interest The authors declare that they have no competing, actual, potential or perceived conflict of interest. Author contribution The contribution of the authors to the present study is equal. All the authors read and approved the final manuscript. All the authors verify that the Text and Table are original and that they have not been published before

Supporting Institution

This study was supported by the Scientific Research Projects Coordination Unit of Kafkas University (2021-FM-63).

Project Number

2021-FM-63

References

• Adil, S., & Magray, S. N. (2012). Impact and manipulation of gut microflora in poultry: a review. J. Anim. Vet. Adv, 11(6), 873-877.
• Akhtar, M. F., Shafiq, M., & Ali, I. (2022). Improving gander reproductive efficacy in the context of globally sustainable goose production. Animals, 12(1), 44.
• Akhter, M., Wal Marzan, L., Akter, Y., & Shimizu, K. (2020). Microbial bioremediation of feather waste for keratinase production: an outstanding solution for leather dehairing in tanneries. Microbiology insights, 13, 1178636120913280.
• Althouse, G. C., & Lu, K. G. (2005). Bacteriospermia in extended porcine semen. Theriogenology, 63(2), 573-584.
• Areche, F. O., Cáceres, C. G. M., Quispe, V. I., Jorge, J. L. C., Llatasi, F. G. C., Ticona, D. C. P., . . . Huaman, C. W. T. (2025). Optimizing protein quality and bioactive peptide production in almond-based dairy alternatives through lactic acid fermentation and enzyme-assisted hydrolysis for cardiovascular health benefits. Journal of Food Science and Technology, 1-20.
• Berinson, B., Bellon, E., Christner, M., Both, A., Aepfelbacher, M., & Rohde, H. (2020). Identification of Kosakonia cowanii as a rare cause of acute cholecystitis: Case report and review of the literature. BMC infectious diseases, 20, 1-4.
• Beveridge, T. J., Lawrence, J. R., & Murray, R. G. E. (2007). Sampling and staining for light microscopy. Methods for general and molecular microbiology, 19-33.
• Charnock, C. (2004). The microbial content of non-sterile pharmaceuticals distributed in Norway. Journal of Hospital Infection, 57(3), 233-240.
• Clarridge Iii, J. E. (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical microbiology reviews, 17(4), 840-862.
• Dafale, N. A., Srivastava, S., & Purohit, H. J. (2020). Zoonosis: an emerging link to antibiotic resistance under “one health approach”. Indian Journal of Microbiology, 60, 139-152.
• de Oliveira Sousa, T., Araújo da Silva, N., de Melo Oliveira, V., da Silva Ramos, A. V., Barbosa Filho, J. P. M., Batista, J. M. d. S., . . . de Paula Ferreira Teixeira, M. (2025). Use of proteases for animal feed supplementation: scientific and technological updates. Preparative Biochemistry & Biotechnology, 1-13.
• Dutkiewicz, J., Mackiewicz, B., Lemieszek, M. K., Golec, M., & Milanowski, J. (2016). Pantoea agglomerans: a mysterious bacterium of evil and good. Part IV. Beneficial effects. Annals of Agricultural and Environmental Medicine, 23(2).
• Felsenstein, J. (1992). Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method. Genetics Research, 60(3), 209-220.
• Galván, F. S., Alonso-Reyes, D. G., & Albarracín, V. H. (2025). From genes to nanotubes: exploring the UV-resistome in the Andean extremophile Exiguobacterium sp. S17. Extremophiles, 29(1), 17.
• Geletu, U. S., Usmael, M. A., & Ibrahim, A. M. (2022). Isolation, identification, and susceptibility profile of E. coli, Salmonella, and S. aureus in dairy farm and their public health implication in Central Ethiopia. Veterinary Medicine International, 2022(1), 1887977.
• Gerlicz, W., Sypka, M., Jodłowska, I., & Białkowska, A. M. (2024). Isolation, Selection, and Identification of Keratinolytic Bacteria for Green Management of Keratin Waste. Molecules, 29(14), 3380.
• Gilbert, M., Xiao, X., & Robinson, T. P. (2017). Intensifying poultry production systems and the emergence of avian influenza in China: a ‘One Health/Ecohealth’epitome. Archives of public health, 75, 1-7.
• Holmström, T. C. N., David, L. A., Pinto, L. B., Makita, M. T., Reis, T. L., Rocha-de-Souza, C. M., . . . Melo, D. A. (2025). Antimicrobial resistance and virulence studies in broiler chicken production: a one health approach. Arquivo Brasileiro de Medicina Veterinária e Zootecnia, 77(2), e13271.
• Josephson, P. R. (2020). Chicken: A history from farmyard to factory: John Wiley & Sons.
• Md Sidek, N. L., Halim, M., Tan, J. S., Abbasiliasi, S., Mustafa, S., & Ariff, A. B. (2018). Stability of bacteriocin‐like inhibitory substance (BLIS) produced by Pediococcus acidilactici kp10 at different extreme conditions. Biomed Research International, 2018(1), 5973484.
• Meena, R. P., & Baranwal, V. K. (2016). Development of multiplex polymerase chain reaction assay for simultaneous detection of clostero-, badna-and mandari-viruses along with huanglongbing bacterium in citrus trees. Journal of Virological Methods, 235, 58-64.
• Mokoena, K. K. (2013). Airborne microbiota and related environmental parameters associated with a typical dairy farm plant.
• Moktip, T., Salaipeth, L., Cope, A. E., Taherzadeh, M. J., Watanabe, T., & Phitsuwan, P. (2025). Current Understanding of Feather Keratin and Keratinase and Their Applications in Biotechnology. Biochemistry Research International, 2025(1), 6619273.
• Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics: Oxford university press.
• Nikunjkumar, B. D. (2012). Molecular identification of bacteria using 16s rDNA sequencing. Gujarat University, Gujarat, India.
• Ningthoujam, D. S., Tamreihao, K., Mukherjee, S., Khunjamayum, R., Devi, L. J., & Asem, R. S. (2018). Keratinaceous wastes and their valorization through keratinolytic microorganisms Keratin: IntechOpen.
• Oztas Gulmus, E., & Gormez, A. (2020). Identification and characterization of novel thermophilic bacteria from hot springs, Erzurum, Turkey. Current Microbiology, 77(6), 979-987.
• Peng, L.-Y., Shi, H.-T., Gong, Z.-X., Yi, P.-F., Tang, B., Shen, H.-Q., & Fu, B.-D. (2021). Protective effects of gut microbiota and gut microbiota-derived acetate on chicken colibacillosis induced by avian pathogenic Escherichia coli. Veterinary Microbiology, 261, 109187.
• Ryan, M. P., & Adley, C. C. (2013). The antibiotic susceptibility of water-based bacteria Ralstonia pickettii and Ralstonia insidiosa. Journal of Medical Microbiology, 62(7), 1025-1031.
• Rychlik, I. (2020). Composition and function of chicken gut microbiota. Animals, 10(1), 103.
• Sambrook, J. (1989). Commonly used techniques in molecular cloning. Molecular cloning.
• Silva-de la Fuente, M. C., Stekolnikov, A. A., Weitzel, T., Beltrami, E., Martínez-Valdebenito, C., Abarca, K., & Acosta-Jamett, G. (2021). Chigger mites (Acariformes: Trombiculidae) of Chiloé Island, Chile, with descriptions of two new species and new data on the genus Herpetacarus. Journal of Medical Entomology, 58(2), 646-657.
• Tadevosyan, M., Margaryan, A., & Panosyan, H. (2025). Assessment of feather degrading activity of thermophilic bacilli isolated from Armenian geothermal springs. Biologia, 1-13.
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38(7), 3022-3027.
• Turenne, C. Y., Snyder, J. W., & Alexander, D. C. (2015). Bacillus and other aerobic endospore‐forming bacteria. Manual of clinical microbiology, 441-461.
• Ulucay, O., Gormez, A., & Ozic, C. (2022a). For biotechnological applications: Purification and characterization of recombinant and nanoconjugated xylanase enzyme from thermophilic Bacillus subtilis. Biocatalysis and Agricultural Biotechnology, 44, 102478.
• Ulucay, O., Gormez, A., & Ozic, C. (2022b). Identification, characterization and hydrolase producing performance of thermophilic bacteria: geothermal hot springs in the Eastern and Southeastern Anatolia Regions of Turkey. Antonie van Leeuwenhoek, 1-18.
• Väisänen, Weber, Bennasar, Rainey, & Busse. (1998). Microbial communities of printing paper machines. Journal of applied microbiology, 84(6), 1069-1084.
• Vikash, V. L., Kamini, N. R., Ponesakki, G., & Anandasadagopan, S. K. (2025). Keratinous bioresources: their generation, microbial degradation, and value enhancement for biotechnological applications. World Journal of Microbiology and Biotechnology, 41(4), 1-26.
• Wang, G., & Jin, X. (2019). Lactic acid bacteria in animal breeding and aquaculture. Lactic Acid Bacteria: Bioengineering and Industrial Applications, 257-283.
• Xu, X., Zhou, W., Xie, C., Zhu, Y., Tang, W., Zhou, X., & Xiao, H. (2022). Airborne bacterial communities in the poultry farm and their relevance with environmental factors and antibiotic resistance genes. Science of the Total Environment, 846, 157420.
• Yu, W., Sun, Z., Wang, M., Li, Z., Zhang, C., Sun, Y., & Wang, S. (2025). The First Infant Bloodstream Infection Caused by Pantoea dispersa in China: A Case Report and Literature Review. Infection and Drug Resistance, 661-667.