Screening and characterization of lactic acid bacteria from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus) as probiotics
Main Article Content
Abstract
Abstract. Anwar K, Putra RA, Karni I, Kurniawan A, Amalyadi R, Unsunnidhal L, Kisworo D, Ali M. 2025. Screening and characterization of lactic acid bacteria from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus) as probiotics. Biodiversitas 26: 2653-2661. Probiotic bacteria have been reported to confer beneficial effects on poultry health and performance. Nevertheless, probiotic strains derived from Indonesian native chickens are not widely available, restricting the application of appropriate probiotic strains as an alternative substitution for antibiotic growth promoters in the poultry industry. In the present study, we aimed to screen, identify, and characterize Lactic Acid Bacteria (LAB) strains from the gastrointestinal tract of a native chicken (Gallus gallus f. domesticus). A native chicken was purchased from an officially approved slaughterhouse. The gastrointestinal tracts, including the small intestine and cecum, were gathered aseptically and used for bacterial isolation. A total of three LAB isolates were obtained and subjected to initial screening according to the morphological, biochemical, and molecular analyses. Two selected isolates (LC12 and LC16) demonstrating Gram-positive, rod-shaped, catalase-negative, and non-motile characteristics were tested under simulated gastrointestinal conditions to reveal potential probiotic characteristics, followed by amplifying and sequencing the 16S rRNA gene. The results demonstrated that two selected isolates had high survival rates, greater than 90% at pH 7.2 and 55% at pH 2.0 after 2-hour and 4-hour incubation, respectively, suggesting adaptability over a wide range of pH conditions. Both isolates indicated tolerance to 0.3% bile salt with a survival rate of more than 70%. Molecular identification using partial-length 16S rRNA sequences showed that the isolates LC12 and LC16 were genetically identified as Lactobacillus johnsonii strain 6-3 with a similarity of 100% for both isolates. The selected LAB isolates are promising probiotic candidates for favorable applications in the poultry industry.
Article Details
Issue
Section

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Adikari AMMU, Priyashantha H, Disanayaka JNK, Jayatileka DV, Kodithuwakku SP, Jayatilake JAMS, Vidanarachchi JK. 2021. Isolation, identification and characterization of Lactobacillus species diversity from Meekiri: Traditional fermented buffalo milk gels in Sri Lanka. Heliyon 7 (10): e08136. DOI: 10.1016/j.heliyon.2021.e08136.
Agustono B, Lokapirnasari WP, Yunita MN, Kinanti RN, Cesa AE, Windria S. 2022. Efficacy of dietary supplementary probiotics as substitutes for antibiotic growth promoters during the starter period on growth performances, carcass traits, and immune organs of male layer chicken. Vet World 15 (2): 324-330. DOI: 10.14202/vetworld.2022.324-330.
Aiba Y, Nakano Y, Koga Y, Takahashi K, Komatsu Y. 2015. A highly acid?resistant novel strain of Lactobacillus johnsonii No. 1088 has antibacterial activity, including that against Helicobacter pylori, and inhibits gastrin?mediated acid production in mice. Microbiologyopen 4 (3): 465-474. DOI: 10.1002/mbo3.252.
Al-Fatah MA. 2020. Probiotic modes of action and its effect on biochemical parameters and growth performance in poultry. Iran J Appl Anim Sci 10 (1): 9-15.
Amelia R, Philip K, Pratama YE, Purwati E. 2021. Characterization and probiotic potential of lactic acid bacteria isolated from dadiah sampled in West Sumatra. Food Sci Technol 41: 746-752. DOI: 10.1590/fst.30020.
Axelsson L. 2004. Lactic Acid Bacteria: Classification and physiology. In: Salminem S, von Wright A, Ouwehand A (eds). Lactic Acid Bacteria Microbiological and Functional Aspects, Third Edition: Revised and Expanded. Marcel Dekker Inc, New York.
Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55 (3): 541-555. DOI: 10.1016/j.mimet.2003.08.009.
Balcázar JL, de Blas I, Ruiz-Zarzuela I, Vendrell D, Gironés O, Muzquiz JL. 2007. Sequencing of variable regions of the 16S rRNA gene for identification of lactic acid bacteria isolated from the intestinal microbiota of healthy salmonids. Comp Immunol Microbiol Infect Dis 30 (2): 111-118. DOI: 10.1016/j.cimid.2006.12.001.
Bergey DH, Holt JG. 1994. Bergey’s Manual of Determinative Bacteriology. 9th ed. Williams & Wilkins: Baltimore, Maryland.
Bin Masalam MS, Bahieldin A, Alharbi MG, Al-Masaudi S, Al-Jaouni SK, Harakeh SM, Al-Hindi RR. 2018. Isolation, molecular characterization and probiotic potential of lactic acid bacteria in Saudi raw and fermented milk. Evid Based Complement Alternat Med 2018: 7970463. DOI: 10.1155/2018/7970463.
Chakravorty S, Sarkar S, Gachhui R. 2015. Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family. Mol Biol 49: 668-677. DOI: 10.1134/S0026893315050052.
Chen C, Li J, Zhang H, Xie Y, Xiong L, Liu H, Wang F. 2020. Effects of a probiotic on the growth performance, intestinal flora, and immune function of chicks infected with Salmonella pullorum. Poult Sci 99 (11): 5316-5323. DOI: 10.1016/j.psj.2020.07.017.
Cui Y, Wang M, Zheng Y, Miao K, Qu X. 2021. The carbohydrate metabolism of Lactiplantibacillus plantarum. Intl J Mol Sci 22 (24): 13452. DOI: 10.3390/ijms222413452.
de Mesquita Souza Saraiva M, Lim K, do Monte DFM, Givisiez PEN, Alves LBR, de Freitas Neto OC, Kariuki S, Júnior AB, de Oliveira CJB, Gebreyes WA. 2022. Antimicrobial resistance in the globalized food chain: A one health perspective applied to the poultry industry. Braz J Microbiol 53: 465-486. DOI: 10.1007/s42770-021-00635-8.
Elvan Gezer M, Gravlund Fønss K, Bambace MF, Marietou A, Sandberg Overby S, Sundekilde U, Schwab C. 2024. Investigation on L-rhamnose metabolism of Loigolactobacillus coryniformis subsp. coryniformis DSM 20001 and its propionate-containing fermentates. Appl Environ Microbiol 91: e01613-24. DOI: 10.1128/aem.01613-24.
FAO/WHO. 2001. Evaluation of Health and Nutritional Properties of Probiotics in Food Including Powder Milk with Live Acid Bacteria. Report of a Joint FAO/WHO Expert Consultation, Córdoba, Argentina. http://www.who.int/foodsafety/publications/fs_management/ en/probiotics.pdf?ua=1 [26 January 2025]
Ferrer L, Mindt M, Suarez-Diez M, Jilg T, Zagorš?ak M, Lee JH, Gruden K, Wendisch VF, Cankar K. 2022. Fermentative indole production via bacterial tryptophan synthase alpha subunit and plant indole-3-glycerol phosphate lyase enzymes. J Agric Food Chem 70 (18): 5634-5645. DOI: 10.1021/acs.jafc.2c01042.
Forte C, Manuali E, Abbate Y, Papa P, Vieceli L, Tentellini M, Trabalza-Marinucci M, Moscati L. 2018. Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens. Poult Sci 97 (3): 930-936. DOI: 10.3382/ps/pex396.
Gharbi Y, Fhoula I, Ruas-Madiedo P, Afef N, Boudabous A, Gueimonde M, Ouzari HI. 2019. In-vitro characterization of potentially probiotic Lactobacillus strains isolated from human microbiota: Interaction with pathogenic bacteria and the enteric cell line HT29. Ann Microbiol 69: 61-72. DOI: 10.1007/s13213-018-1396-1.
Hashemitabar SH, Hosseinian SA. 2024. The comparative effects of probiotics on growth, antioxidant indices and intestinal histomorphology of broilers under heat stress condition. Sci Rep 14 (1): 23471. DOI: 10.1038/s41598-024-66301-9.
Heak C, Sukon P, Sornplang P. 2018. Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: A meta-analysis of controlled trials. Asian-Australas J Anim Sci 31 (11): 1781-1794. DOI: 10.5713/ajas.18.0009.
Hossain MT, Sardar D, Afsana S, Datta M, Habib MA. 2024. Comparative analysis between multi-strain probiotics and antibiotic as starter feed supplement of poultry on growth performance, serum metabolites and meat quality. Vet Anim Sci 24: 100346. DOI: 10.1016/j.vas.2024.100346.
Johnson A, Miller EA, Weber B, Figueroa CF, Aguayo JM, Johny AK, Noll S, Brannon J, Kozlowicz B, Johnson TJ. 2023. Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry. Poult Sci 102 (9): 102858. DOI: 10.1016/j.psj.2023.102858.
Jomehzadeh N, Javaherizadeh H, Amin M, Saki M, Al-Ouqaili MTS, Hamidi H, Seyedmahmoudi M, Gorjian Z. 2020. Isolation and identification of potential probiotic Lactobacillus species from feces of infants in southwest Iran. Intl J Infect Dis 96: 524-530. DOI: 10.1016/j.ijid.2020.05.034.
Kalia S, K Bharti V, Gogoi D, Giri A, Kumar B. 2017. Studies on the growth performance of different broiler strains at high altitude and evaluation of probiotic effect on their survivability. Sci Rep 7: 46074. DOI: 10.1038/srep46074.
Kassa G, Alemayehu D, Andualem B. 2024. Isolation, identification, and molecular characterization of probiotic bacteria from locally selected Ethiopian free range chickens gastrointestinal tract. Poult Sci 103 (2): 103311. DOI: 10.1016/j.psj.2023.103311.
Khurajog B, Disastra Y, Lawwyne LD, Sirichokchatchawan W, Niyomtham W, Yindee J, Hampson DJ, Prapasarakul N. 2023. Selection and evaluation of lactic acid bacteria from chicken feces in Thailand as potential probiotics. PeerJ 11: e16637. DOI: 10.7717/peerj.16637.
Lin WH, Hwang CF, Chen LW, Tsen HY. 2006. Viable counts, characteristic evaluation for commercial lactic acid bacteria products. Food Microbiol 23 (1): 74-81. DOI: 10.1016/j.fm.2005.01.013.
Maria Cardinal K, Kipper M, Andretta I, Machado Leal Ribeiro A. 2019. Withdrawal of antibiotic growth promoters from broiler diets: Performance indexes and economic impact. Poult Sci 98 (12): 6659-6667. DOI: 10.3382/ps/pez536.
Mishra BK, Das S, Nandy SK, Patel M, Hati S. 2023. Genomic and probiotic attributes of Lactobacillus strains from rice-based fermented foods of North Eastern India. J Food Sci Technol 60 (2): 504-516. DOI: 10.1007/s13197-022-05633-8.
Mokoena MP. 2017. Lactic acid bacteria and their bacteriocins: Classification, biosynthesis and applications against uropathogens: A mini-review. Molecules 22: 1255. DOI: 10.3390/molecules22081255.
Mulaw G, Sisay Tessema T, Muleta D, Tesfaye A. 2019. In vitro evaluation of probiotic properties of lactic acid bacteria isolated from some traditionally fermented Ethiopian food products. Intl J Microbiol 2019: 7179514. DOI: 10.1155/2019/7179514.
Nath S, Roy M, Sikidar J, Deb B, Sharma I, Guha A. 2021. Characterization and in-vitro screening of probiotic potential of novel Weissella confusa strain GCC_19R1 isolated from fermented sour rice. Curr Res Biotechnol 3: 99-108. DOI: 10.1016/j.crbiot.2021.04.001.
Nemska V, Logar P, Rasheva T, Sholeva Z, Georgieva N, Danova S. 2019. Functional characteristics of lactobacilli from traditional Bulgarian fermented milk products. Turk J Biol 43: 148-153. DOI: 10.3906/biy-1808-34.
Ngouénam RJ, Nofal G, Patra S, Njapndounke B, Kouam EMF, Kaktcham PM, Ngoufack FZ. 2024. Characterization of lactic acid bacteria isolated from rotting oranges and use of agropastoral processing by?products as carbon and nitrogen sources alternative for lactic acid production. Biomed Res Intl 2024: 4264229. DOI: 10.1155/2024/4264229.
Niu H, Zhou X, Gong P, Jiao Y, Zhang J, Wu Y, Lyu L, Liang C, Chen S, Han X, Zhang L. 2022. Effect of Lactobacillus rhamnosus MN?431 producing indole derivatives on complementary feeding?induced diarrhea rat pups through the enhancement of the intestinal barrier function. Mol Nutr Food Res 66 (2): 2100619. DOI: 10.1002/mnfr.202100619.
Noohi N, Ebrahimipour G, Rohani M, Talebi M, Pourshafie MR. 2016. Evaluation of potential probiotic characteristics and antibacterial effects of strains of Pediococcus species isolated from broiler chickens. Br Poult Sci 57 (3): 317-323. DOI: 10.1080/00071668.2016.1169247.
O’Flaherty S, Briner Crawley A, Theriot CM, Barrangou R. 2018. The Lactobacillus bile salt hydrolase repertoire reveals niche-specific adaptation. mSphere 3: e00140-18. DOI: 10.1128/mSphere.00140-18.
Papadimitriou K, Alegría Á, Bron PA, de Angelis M, Gobbetti M, Kleerebezem M, Lemos JA, Linares DM, Ross P, Stanton C, Turroni F, van Sinderen D, Varmanen P, Ventura M, Zúñiga M, Tsakalidou E, Kok J. 2016. Stress physiology of lactic acid bacteria. Microbiol Mol Biol Rev 80 (3): 837-890. DOI: 10.1128/MMBR.00076-15.
Penha Filho RA, Díaz SJ, Fernando FS, Chang YF, Andreatti Filho RL, Berchieri Junior A. 2015. Immunomodulatory activity and control of Salmonella Enteritidis colonization in the intestinal tract of chickens by Lactobacillus based probiotic. Vet Immunol Immunopathol 167 (1-2): 64-69. DOI: 10.1016/j.vetimm.2015.06.006.
Risna YK, Harimurti S, Wihandoyo, Widodo W. 2020. Screening for probiotic of lactic acid bacteria isolated from the digestive tract of a native Aceh duck (Anas platyrhynchos). Biodiversitas 21 (7): 3001-3007. DOI: 10.13057/biodiv/d210717.
Saint-Cyr MJ, Haddad N, Taminiau B, Poezevara T, Quesne S, Amelot M, Daube G, Chemaly M, Dousset X, Guyard-Nicodème M. 2017. Use of the potential probiotic strain Lactobacillus salivarius SMXD51 to control Campylobacter jejuni in broilers. Intl J Food Microbiol 247: 9-17. DOI: 10.1016/j.ijfoodmicro.2016.07.003.
Saryono, Ismawati, Pratiwi NW, Devi S, Sipayung MY, Suraya N. 2023. Isolation and identification of lactic acid bacteria from traditional food sarobuong of Kuantan Singingi District, Riau, Indonesia. Biodiversitas 24 (4): 2201-2206. DOI: 10.13057/biodiv/d240432.
Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71 (3): 1501-1506. DOI: 10.1128/AEM.71.3.1501-1506.2005.
Šiki? Poga?ar M, Langerholc T, Mi?eti?-Turk D, Možina SS, Klan?nik A. 2020. Effect of Lactobacillus spp. on adhesion, invasion, and translocation of Campylobacter jejuni in chicken and pig small-intestinal epithelial cell lines. BMC Vet Res 16 (1): 34. DOI: 10.1186/s12917-020-2238-5.
Sirisopapong M, Shimosato T, Okrathok S, Khempaka S. 2023. Assessment of lactic acid bacteria isolated from the chicken digestive tract for potential use as poultry probiotics. Anim Biosci 36 (8): 1209-1220. DOI: 10.5713/ab.22.0455.
Sorescu I, Dumitru M, Ciurescu G. 2021. Lactobacillus spp. strains isolation, identification, preservation and quantitative determinations from gut content of 45-day-old chickens broilers. Braz J Poult Sci 23 (1): eRBCA-2020. DOI: 10.1590/1806-9061-2020-1378.
Sumarsih S, Sulistiyanto B, Sutrisno CI, Rahayu ES. 2013. Characteristic of Lactobacillus isolated from Pengging duck’s intestines as probiotics. Intl J Poult Sci 13 (1): 47-51. DOI: 10.3923/ijps.2014.47.51.
Sutami, Purwanto, Rosariastuti R. 2021. A salt tolerant Sphingosinicella microcystinivorans A3 isolated from soil contaminated with mercury in traditional gold mining of Jendi Village, Wonogiri District, Indonesia. Biodiversitas 22: 3785-3791. DOI: 10.13057/biodiv/d220923.
Takenaka S, Kawashima T, Arita M. 2021. A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria. FEMS Microbiol Lett 368 (17): fnab117. DOI: 10.1093/femsle/fnab117.
Tarique M, Abdalla A, Masad R, Al-Sbiei A, Kizhakkayil J, Osaili T, Olaimat A, Liu S-Q, Fernandez-Cabezudo M, Al-Ramadi B, Ayyash M. 2022. Potential probiotics and postbiotic characteristics including immunomodulatory effects of lactic acid bacteria isolated from traditional yogurt-like products. LWT 159: 113207. DOI: 10.1016/j.lwt.2022.113207.
Tomczyk G, Niczyporuk JS, Kozdru? W, Sawicka-Durkalec A, Bocian ?, Barabasz M, Michalski M. 2024. Probiotic supplementation as an alternative to antibiotics in broiler chickens. J Vet Res 68 (1): 147-154. DOI: 10.2478/jvetres-2024-0009.
Trip H, Mulder NL, Lolkema JS. 2012. Improved acid stress survival of Lactococcus lactis expressing the histidine decarboxylation pathway of Streptococcus thermophilus CHCC1524. J Biol Chem 287 (14): 11195-11204. DOI: 10.1074/jbc.M111.330704.
Wallinder IB, Neujahr HY. 1971. Cell wall and peptidoglycan from Lactobacillus fermenti. J Bacteriol 105 (3): 918-926. DOI: 10.1128/jb.105.3.918-926.1971.
Wang K, Wang Y, Gu L, Yu J, Liu Q, Zhang R, Liang G, Chen H, Gu F, Liu H, Jiao X, Zhang Y. 2024. Characterization of probiotic properties and whole-genome analysis of Lactobacillus johnsonii N5 and N7 isolated from swine. Microorganisms 12 (4): 672. DOI: 10.3390/microorganisms12040672.
Wang Y, Sun J, Zhong H, Li N, Xu H, Zhu Q, Liu Y. 2017. Effect of probiotics on the meat flavour and gut microbiota of chicken. Sci Rep 7 (1): 6400. DOI: 10.1038/s41598-017-06677-z.
Wang Y, Wu J, Lv M, Shao Z, Hungwe M, Wang J, Bai X, Xie J, Wang Y, Geng W. 2021. Metabolism characteristics of lactic acid bacteria and the expanding applications in food industry. Front Bioeng Biotechnol 9: 612285. DOI: 10.3389/fbioe.2021.612285.
Ward TL, Weber BP, Mendoza KM, Danzeisen JL, Llop K, Lang K, Clayton JB, Grace E, Brannon J, Radovic I, Beauclaire M, Heisel TJ, Knights D, Cardona C, Kogut M, Johnson C, Noll SL, Arsenault R, Reed KM, Johnson TJ. 2019. Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression. mBio 10: e02171-19 DOI: 10.1128/mBio.02171-19.
Watanabe M, Igarashi K, Kato S, Kamagata Y, Kitagawa W. 2023. Self-cloning of the catalase gene in environmental isolates improves their colony-forming abilities on agar media. Microbes Environ 38 (2): ME23006. DOI: 10.1264/jsme2.ME23006.
Wu Z, Yang K, Zhang A, Chang W, Zheng A, Chen Z, Cai H, Liu G. 2021. Effects of Lactobacillus acidophilus on the growth performance, immune response, and intestinal barrier function of broiler chickens challenged with Escherichia coli O157. Poult Sci 100 (9): 101323. DOI: 10.1016/j.psj.2021.101323.
Yadav R, Puniya AK, Shukla P. 2016. Probiotic properties of Lactobacillus plantarum RYPR1 from an indigenous fermented beverage raabadi. Front Microbiol 7: 1683. DOI: 10.3389/fmicb.2016.01683.
Yan W, Sun C, Yuan J, Yang N. 2017. Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency. Sci Rep 7 (1): 45308. DOI: 10.1038/srep45308.
Yulianto B, Lokapirnasari WP. 2018. Isolation and identification of lactic acid bacteria from the digestive tract of kampung chicken (Gallus gallus domesticus). Philipp J Vet Med 55: 67-72.
Zhang Z, Zhao L, Wu J, Pan Y, Zhao G, Li Z, Zhang L. 2023. The effects of Lactobacillus johnsonii on diseases and its potential applications. Microorganisms 11 (10): 2580. DOI: 10.3390/microorganisms11102580.
Zommara M, El-Ghaish S, Haertle T, Chobert JM, Ghanimah M. 2023. Probiotic and technological characterization of selected Lactobacillus strains isolated from different Egyptian cheeses. BMC Microbiol 23 (1): 160. DOI: 10.1186/s12866-023-02890-1.