Isolation, Characterization, and Antibacterial Activity of Actinomycetes from Sheep Feces

Iranian Journal of Veterinary Science and Technology

دوره 17، شماره 1 - شماره پیاپی 38، خرداد 2025، صفحه 94-101   

نوع مقاله: Research Article

شناسه دیجیتال (DOI): 10.22067/ijvst.2025.91803.1466

نویسندگان

Talieh Mohammadi؛ Fazel Pourahmad^* ؛ Khalil Saleki

Department of Microbiology, Faculty of Veterinary Sciences, Ilam University, Ilam, Iran

چکیده

Actinomycetes are a vital group of Gram-positive bacteria known for producing a wide range of bioactive secondary metabolites, including important antibiotics. These microorganisms play an essential role in the degradation of organic matter and nutrient cycling, contributing significantly to soil health and fertility. Their capacity to synthesize diverse compounds and the presence of key biosynthetic pathways involving polyketide synthases and non-ribosomal peptide synthetases highlights their potential in antibiotic discovery, particularly against antibiotic-resistant pathogens. This study aimed to isolate and characterize Actinomycetes from fresh sheep feces collected in Ilam Province, Iran, focusing on their antibacterial activity and biosynthetic potential. A total of 86 actinomycete isolates were obtained from fecal samples collected from sheep in 2021. Morphological characterization confirmed all isolates as Gram-positive and filamentous. Molecular identification through PCR amplification of the 16S rRNA gene yielded a product of approximately 640 base pairs for all isolates. Antibacterial screening revealed that 17 isolates exhibited activity against various pathogens, with the highest efficacy observed against Bacillus cereus (62.1%). Molecular analysis also indicated the presence of biosynthetic gene clusters, with 31 isolates (36.05%) bearing non-ribosomal peptide synthetase (NRPS) gene, 15 isolates (17.44%) containing polyketide synthase I (PKS-I), and 16 isolates (18.6%) with polyketide synthase II (PKS-II) genes. This study highlights the significant antibacterial properties and biosynthetic capabilities of actinomycetes from sheep feces, suggesting their potential use in therapeutic, agriculture, and biotechnological applications.

کلیدواژه‌ها

Actinomycetes؛ Polyketide Synthase؛ Non-Ribosomal Peptide Synthetase؛ Antibacterial Activity؛ Sheep Feces

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مراجع

1.    Chaudhary HS, Soni B, Shrivastava AR, Shrivastava S. Diversity and versatility of actinomycetes and its role in antibiotic production. J Appl Pharm Sci. 2013;3(8):83-94. Doi: 10.7324/JAPS.2013.38.S14.
2.    Lacey HJ, Rutledge PJ. Recently discovered secondary metabolites from Streptomyces species. Molecules. 2022;27(1):1-16. Doi: 10.3390/molecules27030887.
3.    Singh V, Haque S, Singh H, Verma J, Vibha K, Singh R, Jawed A, Tripathi CK. Isolation, screening, and identification of novel isolates of actinomycetes from India for antimicrobial applications. Front Microbiol. 2016;6(7):1921. Doi: 10.3389/fmicb.2016.01921.
4.    Selim MSM, Abdelhamid SA, Mohamed SS. Secondary metabolites and biodiversity of actinomycetes. J Genet Eng Biotechnol. 2021;19(1):72. Doi: 10.1186/s43141-021-00156-9.
5.    Trenozhnikova LP, Baimakhanova GB, Baimakhanova BB, Balgimbayeva AS, Daugaliyeva ST, Faizulina ER, et al. Beyond traditional screening: Unveiling antibiotic potentials of actinomycetes in extreme environments. Heliyon. 2024;10(1):1-16. Doi: 10.1016/j.heliyon.2024.e40371.
6.    Kaale SE, Machangu RS, Lyimo TJ. Molecular characterization and phylogenetic diversity of Actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania. Microbiol Res. 2024;278:127543. Doi: 10.1016/j.micres.2023.127543.
7.    Shrestha B, Nath DK, Maharjan A, Poudel A, Pradhan RN, Aryal S. Isolation and Characterization of Potential Antibiotic‐Producing Actinomycetes from Water and Soil Sediments of Different Regions of Nepal. International J Microbiol. 2021;2021(1):5586165. Doi: 10.1155/2021/5586165.
8.    Behie SW, Bonet B, Zacharia VM, McClung DJ, Traxler MF. Molecules to ecosystems: Actinomycete natural products in situ. Front Microbiol. 2017;7:1-11. Doi: 10.3389/fmicb.2016.02149.
9.    Masand M, Jose PA, Menghani E, Jebakumar SR. Continuing hunt for endophytic actinomycetes as a source of novel biologically active metabolites. World Journal of Microbiol Biotech. 2015;31:1863-75. Doi: 10.1007/s11274-015-1950-y.
10.    Hayashida S, Nanri N, Teramoto Y, Nishimoto T, Ohta K, Miyaguchi M. Identification and characteristics of actinomycetes useful for semicontinuous treatment of domestic animal feces. Appl Environ Microbiol. 1988;54(8):2058-2063. Doi: 10.1128/aem.54.8.2058-2063.1988.
11.    Dentzien-Dias P, Poinar G, Francischini H. A new actinomycete from a Guadalupian vertebrate coprolite from Brazil. Hist Biol. 2017;29(6):770-776. Doi: 10.1080/08912963.2016.1241247.
12.    Lee HW, Ahn JH, Kim M, Weon HY, Song J, Lee SJ, et al. Diversity and antimicrobial activity of actinomycetes from fecal sample of rhinoceros beetle larvae. Korean J Microbiol. 2013;49(2):156-164. Doi: 10.7845/kjm.2013.3041.
13.    Wang X, Zhang Z, Wang X, Bao Q, Wang R, Duan Z. The impact of host genotype, intestinal sites and probiotics supplementation on the gut microbiota composition and diversity in sheep. Biology. 2021;10(1):1-16. Doi: 10.3390/biology10080769.
14.    Ahmad A, Sur S. Biodegradable solid waste management by microorganism: challenge and potential for composting. Int J Recycl Org Waste Agric. 2023;12(1):735-745. Doi: 10.30486/IJROWA.2023.1958655.1465.
15.    Game BC, Deokar CD, Jadhav AC. Characterization of cellulolytic microorganisms associated with naturally decomposing waste material. Int J Curr Microbiol App Sci. 2018;7(1):1710-1719. Doi: 10.20546/ijcmas.2018.704.194.
16.    Sánchez ÓJ, Ospina DA, Montoya S. Compost supplementation with nutrients and microorganisms in composting process. Waste Manag. 2017;69:136-153. Doi: 10.1016/j.wasman.2017.08.012.
17.    Forster SM. The role of microorganisms in aggregate formation and soil stabilization: Types of aggregation. Arid Land Res Manage. 1990;4(1):85-98. Doi: 10.1080/15324989009381236.
18.    Abdelrahman OY, Yagi S, El Siddig M, El Hussein A, Germanier F, De Vrieze M, et al. Evaluating the antagonistic potential of actinomycete strains isolated from Sudan's soils against Phytophthora infestans. Front Microbiol. 2022;13:1-13. Doi: 10.3389/fmicb.2022.827824.
19.    Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing modular polyketide synthases and non-ribosomal peptide synthetases for novel chemical biosynthesis. Front Mol Biosci. 2020;7:1-27. Doi: 10.3389/fmolb.2020.00087.
20.    Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci. 2014;111(25):9259-9264. Doi: 10.1073/pnas.1401734111.
21.    Quadri LE. Assembly of aryl‐capped siderophores by modular peptide synthetases and polyketide synthases. Mol Microbiol. 2000;37(1):1-12. Doi: 10.1046/j.1365-2958.2000.01941.x.
22.    Lee LH, Zainal N, Azman AS, Eng SK, Goh BH, Yin WF, et al. Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia. Sci World J. 2014;2014:1-16. Doi: 10.1155/2014/698178.
23.    Tatar D. Isolation, phylogenetic analysis and antimicrobial activity of halophilic actinomycetes from different saline environments located near Çorum province. Biologia. 2021;76(5):773-780. Doi: 10.2478/s11756-020-00612-w.
24.    Okada BK, Seyedsayamdost MR. Antibiotic dialogues: Induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiol Rev. 2017;41(1):19-33. Doi: 10.1093/femsre/fuw035.
25.    Lima SMA, Pereira PS, da Silva BIM, Ribeiro NE, de Oliveira Borba EF, Tintino CDDM, et al. Antioxidant, antimicrobial and cytotoxic activities of secondary metabolites from Streptomyces sp. isolated of the Amazon-Brazil region. Res Soc Dev. 2021;10(1):e366101018974. Doi: 10.33448/rsd-v10i1.18974.
26.    Shikuku BO, Kiruki S, Kuria E, Mutembei M, Ogolla FO. Characterization of antibiotic-producing actinomycetes isolated from River Tana and Lake Elementaita in Kenya. Asian J Res Biochem. 2023;13(1):26-41. Doi: 10.9734/ajrb/2023/v13i1247.
27.    Bandara N, Tmiuk T. Isolation and identification of actinomycetes with antibacterial activity from soil samples around Kandy, Sri Lanka. Curr Res Pharm Sci. 2023;13(1):118-125. Doi: 10.24092/CRPS.2023.130301.
28.    Setiawati S, Nuryastuti T, Sholikhah EN, Lisdiyanti P, Pratiwi SUT, Sulistiyani TR, et al. The potency of actinomycetes extracts isolated from Pramuka Island, Jakarta, Indonesia as antimicrobial agents. Biodiver J Biol Divers. 2021;22(1):1104-1111. Doi: 10.13057/biodiv/d220304.
29.    Brendecke JW, Axelson RD, Pepper IL. Soil microbial activity as an indicator of soil fertility: long-term effects of municipal sewage sludge on an arid soil. Soil Biol Biochem. 1993;25(6):751-758. Doi: 10.1016/0038-0717(93)90117-T.
30.    Ghosh S, Tripathi SK. Microbial succession and changes in carbon and nitrogen during decomposition of leaf litters of Tephrosia candida (Roxb.) DC. and Oryza sativa L. under shifting cultivation in Mizoram, northeast India. J Appl Nat Sci. 2021;13(1):1032-1040. Doi: 10.31018/jans.v13i3.2855.
31.    Kumar V, Bisht GS, Gusain O. Terrestrial actinomycetes from diverse locations of Uttarakhnad, India: Isolation and screening for their antibacterial activity. Iranian J Microbiol. 2013;5(4):299-308. 
32.    Paul S, Paul S, Tisad ZM. Antimicrobial potentialities of Streptomyces species isolated from mangrove soil samples of Sundarbans. Methodology. 2020;5(1):295-330. 
33.    Rozirwan RO, Muda HI, Ulqodry TZ. Antibacterial potential of Actinomycetes isolated from mangrove sediment in Tanjung Api-Api, South Sumatra, Indonesia. Biodivers J Biol Divers. 2020;21(1):1-14. Doi: 10.13057/biodiv/d211232.
34.    Graça AP, Calisto R, Lage OM. Planctomycetes as novel source of bioactive molecules. Front Microbiol. 2016;7:1-16. Doi: 10.3389/fmicb.2016.01241.
35.    Zhao LY, Shi J, Xu ZY, Sun JL, Yan ZY, Tong ZW, et al. Hybrid type I and II polyketide synthases yield distinct aromatic polyketides. J Am Chem Soc. 2024;146(1):29462-29468. Doi: 10.1021/jacs.4c08803.
36.    Eom JS, Lee SY, Choi HS. Bacillus subtilis HJ18‐4 from traditional fermented soybean food inhibits Bacillus cereus growth and toxin‐related genes. J Food Sci. 2014;79(11):2279-2287. Doi: 10.1111/1750-3841.12569.
37.    Fei P, Xu Y, Zhao S, Gong S, Guo L. Olive oil polyphenol extract inhibits vegetative cells of Bacillus cereus isolated from raw milk. J Dairy Sci. 2019;102(5):3894-3902. Doi: 10.1111/1750-3841.12569.
38.    Tian Y, Lu S, Zhou S, Li Z, Guan S, Chen H, et al. Screening of neutralizing antibodies against FaeG protein of Enterotoxigenic Escherichia coli. Vet Sci. 2024;11(1):1-14. Doi: 10.3390/vetsci11090419.
39.    Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, et al. Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli. J Bacteriol. 2024;206(1):12-24. Doi: 10.1128/jb.00112-24.
40.    Kellogg JJ, Todd DA, Egan JM, Raja HA, Oberlies NH, Kvalheim OM, et al. Biochemometrics for natural products research: comparison of data analysis approaches and application to identification of bioactive compounds. J Nat Prod. 2016;79(2):376-386. Doi: 10.1021/acs.jnatprod.5b01014.
41.    Quitério EG, Grosso C, Ferraz R, Delerue-Matos C, Soares C. A critical comparison of the advanced extraction techniques applied to obtain health-promoting compounds from seaweeds. Mar Drugs. 2022;20(1):1-40. Doi: 10.3390/md20110677.
42.    Bergmann S, Funk AN, Scherlach K, Schroeckh V, Shelest E, Horn U, et al. Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl Environ Microbiol. 2010;76(24):8143-8149. Doi: 10.1128/AEM.00683-10.
43.    Wasil Z, Pahirulzaman KA, Butts C, Simpson TJ, Lazarus CM, Cox RJ. One pathway, many compounds: heterologous expression of a fungal biosynthetic pathway reveals its intrinsic potential for diversity. Chem Sci. 2013;4(10):3845-3856. Doi: 10.1039/C3SC51785C.
44.    Aisy ND, Wardani ARD, Paradhipta DHV, Agus A, Noviadi CT. Chemical composition and fermentation characteristics of different proportions of fermented poultry manure and sheep feces as unconventional feed. J Ilmu-Ilmu Peternakan. 2024;34(1):51-59. Doi: 10.21776/ub.jiip.2024.034.01.06.
45.    Wang J, Fan H, Han Y, Zhao J, Zhou Z. Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis. Asian-Australas J Anim Sci. 2017;30(1):100-110. Doi: 10.5713/ajas.16.0166.
46.    Choi JJ, McCarthy MW. Cefiderocol: a novel siderophore cephalosporin. Expert Opin Investig Drugs. 2018;27(2):193-197. doi.org/10.1080/13543784.2018.1426745.
47.    Rajchakit U, Sarojini V. Recent developments in antimicrobial-peptide-conjugated gold nanoparticles. Bioconjugate Chem. 2017;28(11):2673-2686. Doi: 10.1021/acs.bioconjchem.7b00368.
48.    Waller AS, Clements JM. Novel approaches to antimicrobial therapy: peptide deformylase. Curr Opin Drug Discov Dev. 2002;5(6):785-792. 
49.    Peng X, Yu KQ, Deng GH, Jiang YX, Wang Y, Zhang GX, et al. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags. J Microbiol Methods. 2013;95(3):455-462. Doi: 10.1016/j.mimet.2013.07.015.
50.    Stach JE, Maldonado LA, Ward AC, Goodfellow M, Bull AT. New primers for the class Actinobacteria: Application to marine and terrestrial environments. Environ Microbiol. 2003;5(10):828-841. Doi: 10.1046/j.1462-2920.2003.00483.x.
51.    Ayuso-Sacido A, Genilloud O. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: Detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol. 2005;49(1):10-24. Doi: 10.1007/s00248-004-0249-6.
52.    Metsä-Ketelä M, Salo V, Halo L, Hautala A, Hakala J, Mäntsälä P, et al. An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol Lett. 1999;180(1):1-6. Doi: 10.1111/j.1574-6968.1999.tb08776.x.
53.    Hajizadeh M, Pourahmad F, Nemati M. Isolation and screening of antibacterial activity of Actinomycetota from the medicinal plant, Anthemis pseudocotula Boiss. Arch Razi Inst. 2023;78(1):1638-1646. Doi: 10.22092/ARI.2023.78.5.1638.