Metagenomic investigation of the fecal microbiota in Lakor goats of different sexes with a basic diet of field grass
Article Sidebar
Abstract Views: 326
File Views: 70
Main Article Content
Abstract
Abstract. Sangadji I, Kunda RM, Utami P. 2025. Metagenomic investigation of the fecal microbiota in Lakor goats of different sexes with a basic diet of field grass. Biodiversitas 26: 1861-1869. Gut microbiota play a crucial role in the health and productivity of ruminants, including goats. This study investigated the composition and diversity of fecal microbiota in Lakor goats of different sexes fed a basic diet of field grass using a metagenomic approach. A total of 10 samples were collected from male and female goats of 5 samples each, and high-throughput sequencing of the 16S rRNA gene was performed to analyze the microbial community structure. Results revealed significant differences in microbiota composition between sexes, which may be influenced by hormonal differences, feeding behavior, and metabolic needs. This study suggests that sex influences the composition of fecal microbiota in Lakor goats. Moreover, it revealed that sex affects the diversity and composition of the microbiota, with significant differences at the family and species levels. Alpha diversity analysis showed that female goats had higher microbial diversity than male goats, with a Shannon index of 2.03 in females and 1.33 in males, indicating a more complex microbial community in females. The microbial community composition in male goats was dominated by species such as Romboutsia timonensis and Clostridium sp., whereas female goats showed a more balanced microbial distribution, with the dominance of genera such as Pradoshia, Eubacterium, and Lysinibacillus. Phylogenetic analysis showed that female goats have a more stable microbial community, supporting more efficient fiber fermentation and Short-Chain Fatty Acid (SCFA) metabolism. Proximate test results showed differences in feed nutrient content between the wet and dry seasons, with higher crude protein content in the wet season, potentially affecting feed quality and microbiota. Overall, this study highlights the importance of considering sex in microbiota studies to optimize feeding strategies and health management for Lakor goats. These findings suggest that sex-specific dietary interventions and probiotic strategies could improve feed utilization, immune function, and productivity in Lakor goats.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Anderson CL, Fernando SC. 2021. Insights into biosynthetic gene cluster diversity in rumen via genome-resolved metagenomics. Commun Biol 4 (1): 818. DOI: 10.1038/s42003-021-02331-7.
Bolyen E, Rideout JR, Dillon MR et al. 2019. Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nat Biotechnol 37 (8): 852-857. DOI: 10.1038/s41587-019-0209-9.
Cao Y, Feng T, Wu Y et al. 2023. The multi-kingdom microbiome of the goat gastrointestinal tract. Microbiome 11 (1): 219. DOI: 10.1186/s40168-023-01651-6.
Capstaff NM, Miller AJ. 2018. Improving the yields and nutritional qualities of forage crops. Front Plant Sci 9: 535. DOI: 10.3389/fpls.2018.00535.
Cooke AS, Machekano H, Gwiriri LC, Tinsley JHI, Silva GM, Nyamukondiwa C, Safalaoh A, Morgan ER, Lee MRF. 2024. Nutritional feed gap: Seasonal variations in ruminant nutrition and knowledge gaps in relation to food security in Southern Africa. Food Secur 17 (1): 73-100. DOI: 10.1007/s12571-024-01509-1.
Dias e Silva TP, Filho ALA. 2021. Sheep and goat feeding behavior profile in grazing systems. Acta Sci Anim Sci 43 (1): e51265. DOI: 10.4025/actascianimsci.v43i1.51265.
Do TH, Dao TK, Nguyen KHV, Le NG, Nguyen TMP, Le TL, Phung TN, van Straalen NM, Roelofs D, Truong NH. 2018. Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen. Asian-Australas J Anim Sci 31 (5): 738-747. DOI: 10.5713/ajas.17.0174.
Domínguez FF, Crisanto MEV, Castro RLS, Rojas LV, Cuba VMB, Santos GRS, Ramos CAL, Mialhe E. 2022. Metagenomic analysis of the intestinal microbiome in goats fed cactus- and Salicornia-based diets. Open Vet J 12 (1): 61-68. DOI: 10.5455/OVJ.2022.v12.i1.7.
Domínguez-Pino M, Mellado S, Cuesta CM, Grillo-Risco R, García-García F, Pascual M. 2024. Metagenomics reveals sex-based differences in murine fecal microbiota profiles following chronic alcohol consumption. Intl J Mol Sci 25 (23): 12534. DOI: 10.3390/ijms252312534.
Elbir H, Alhumam NA. 2022. Sex differences in the fecal microbiome composition and function of dromedary camels in Saudi Arabia. Animals 12 (23): 3430. DOI: 10.3390/ani12233430.
Elolimy AA, Arroyo JM, Batistel F, Iakiviak MA, Loor JJ. 2018. Association between residual feed intake and the abundance of ruminal bacteria and biopolymer hydrolyzing enzyme activities during the peripartal period and early lactation in Holstein dairy cows. J Anim Sci Biotechnol 9: 43. DOI: 10.1186/s40104-018-0258-9.
Gharechahi J, Vahidi MF, Bahram M, Han J-L, Ding X-Z, Salekdeh GH. 2021. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. ISME J 15 (4): 1108-1120. DOI: 10.1038/s41396-020-00837-2.
Gomez A, Luckey D, Taneja V. 2015. The gut microbiome in autoimmunity: Sex matters. Clin Immunol 159 (2): 154-162. DOI: 10.1016/j.clim.2015.04.016.
Guerra V, Tiago I, Aires A, Coelho C, Nunes J, Martins LO, Veríssimo A. 2022. The gastrointestinal microbiome of browsing goats (Capra hircus). PLoS One 17 (10): e0276262. DOI: 10.1371/journal.pone.0276262.
Guo X, Sha Y, Lv W, Pu X, Liu X, Luo Y, Hu J, Wang J, Li S, Zhao Z. 2022. Sex differences in rumen fermentation and microbiota of Tibetan goat. Microb Cell Fact 21 (1): 55. DOI: 10.1186/s12934-022-01783-8.
Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas?Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F, Camargo A. 2016. Intestinal microbiota is influenced by gender and body mass index. PLoS One 11 (5): e0154090. DOI: 10.1371/journal.pone.0154090.
He B, Jin S, Cao J, Mi L, Wang J. 2019. Metatranscriptomics analysis of Hu sheep rumen microbiome reveals novel cellulases. Biotechnol Biofuels 12: 153. DOI: 10.1186/s13068-019-1498-4.
Huang Q, Xing J, Tang F, Ren J, Wang C, Xue F. 2024. Recombinant Lactiplantibacillus plantarum modulates gut microbial diversity and function. BMC Microbiol 24: 423. DOI: 10.1186/s12866-024-03570-4.
Jami E, Mizrahi I. 2012. Composition and similarity of the bovine rumen microbiota across individual animals. PLoS One 7 (3): e33306. DOI: 10.1371/journal.pone.0033306.
Kameoka S, Motooka D, Watanabe S, Kubo R, Jung N, Midorikawa Y, Shinozaki NO, Sawai Y, Takeda AK, Nakamura S. 2021. Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets. BMC Genomics 22 (1): 527. DOI: 10.1186/s12864-021-07746-4.
Kaur H, Kaur G, Gupta T, Mittal D, Ali SA. 2023. Integrating omics technologies for a comprehensive understanding of the microbiome and its impact on cattle production. Biology 12 (9): 1200. DOI: 10.3390/biology12091200.
Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. 2023. Evolution of the understanding of rumen methanogen ecophysiology. Front Microbiol 14: 1296008. DOI: 10.3389/fmicb.2023.1296008.
Kunda RM, Volkandari SD, Rumanta M, Kakisina P. 2020. Polymorphism of the Growth Hormone (GH) gene in lakor goats from lakor island, southwest maluku Regency. Buletin Peternakan 44 (4): 194-199. DOI: 10.21059/buletinpeternak.v44i4.58934.
Liu K, Zhang Y, Yu Z, Xu Q, Zheng N, Zhao S, Huang G, Wang J. 2021. Ruminal microbiota-host interaction and its effect on nutrient metabolism. Anim Nutr 7: 49-55. DOI: 10.1016/j.aninu.2020.12.001.
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489 (7415): 220-230. DOI: 10.1038/nature11550.
Ma Z, Zuo T, Frey N, Rangrez AY. 2024. A systematic framework for understanding the microbiome in human health and disease: From basic principles to clinical translation. Signal Transduct Target Ther 9 (1): 237. DOI: 10.1038/s41392-024-01946-6.
Mao S, Zhang M, Liu J, Zhu W. 2015. Characterizing the bacterial microbiota across the gastrointestinal tract of dairy cattle: Membership and potential function. Sci Rep 5: 16116. DOI: 10.1038/srep16116.
Núñez L, Hirigoyen A, Durante M, Arroyo JM, Cazzuli F, Bremm C, Jaurena M. 2022. What factors control the crude protein content variation of a basaltic “campos” native grassland of South America. Agronomy 12 (8): 1756. DOI: 10.3390/agronomy12081756.
Org E, Mehrabian M, Parks BW, Shipkova P, Liu X, Drake TA, Lusis AJ. 2016. Sex differences and hormonal effects on the gastrointestinal microbiota composition in mice. Gut Microbes 7 (4): 313-322. DOI: 10.1080/19490976.2016.1203502.
Pereira GF, Neto JVE, dos Santos Difante G, da Silva Lagos Cortes Assis LC, de Oliveira Lima P, da Silva Santos R. 2021. Production and quality of tropical grasses at different regrowth intervals in the Brazilian semiarid. Acta Sci Anim Sci 43 (1): e52842. DOI: 10.4025/actascianimsci.v43i1.52842.
Qi X, Yun C, Pang Y, Qiao J. 2021. The impact of the gut microbiota on the reproductive and metabolic endocrine system. Gut Microbes 13 (1): 1-21. DOI: 10.1080/19490976.2021.1894070.
Rumanta M, Kunda RM, Volkandari SD, Indriawati I, Kakisina P. 2020. Genetic characterization and phylogenetic study of Lakor goat from Southwest Maluku Regency based on mitochondrial COI gene. Vet World 13 (6): 1209-1220. DOI: 10.14202/vetworld.2020.1209-1220.
Santos-Marcos JA, Mora-Ortiz M, Tena-Sempere M, López-Miranda J, Camargo A. 2023. Interactions between the gut microbiota and sex hormones and their relationship with sexual dimorphism in metabolic diseases. Biol Sex Differ 14 (1): 4. DOI: 10.1186/s13293-023-00490-2.
Shabana II, Albakri NN, Bouqellah NA. 2020. Metagenomic analysis of the fecal microbiota of sheep and goats of the same ages. J Taibah Univ Sci 15 (1): 1-9. DOI: 10.1080/16583655.2020.1864930.
Shin N-R, Whon TW, Bae J-W. 2015. Proteobacteria: Microbial signature of dysbiosis in gut microbiota. Trends Biotechnol 33 (9): 496-503. DOI: 10.1016/j.tibtech.2015.06.011.
Tardiolo G, La Fauci D, Riggio V, Daghio M, Di Salvo E, Zumbo A, Sutera AM. 2025. Gut microbiota of ruminants and monogastric livestock: An overview. Animals 15: 758. DOI: 10.3390/ani15050758.
Tatipikalawan JM. 2022. Keberlanjutan pengembangan peternakan kerbau Moa di Pulau Moa Provinsi Maluku. [Dissertation]. Universitas Gadjah Mada, Yogyakarta. [Indonesian]
Wang H, Zheng H, Browne F, Roehe R, Dewhurst RJ, Engel F, Hemmje M, Lu X, Walsh P. 2017. Integrated metagenomic analysis of the rumen microbiome of cattle revealed the key biological mechanisms associated with methane traits. Methods 124: 108-119. DOI: 10.1016/j.ymeth.2017.05.029.
Wassan JT, Wang H, Zheng HJ. 2023. Recent advances in phylogenetic analysis for studying the rumen microbiome. Curr Bioinform 19 (3): 250-263. DOI: 10.2174/1574893618666230605120615.
Widodo S, Shiddieqy MI, Wahyono T, Widiawati Y, Muttaqin Z. 2023. Analysis of the correlation between the nutrient content, digestibility, and gas production of forages in Indonesia. Adv Anim Vet Sci 11 (11): 1770-1778. DOI: 10.17582/journal.aavs/2023/11.11.1770.1778.
Xu Q, Qiao Q, Gao Y, Hou J, Hu M, Du Y, Zhao K, Li X. 2021. Gut microbiota and their role in the health and metabolic diseases of dairy cow. Front Nutr 8: 701511. DOI: 10.3389/fnut.2021.701511.
Yellavila SB, Agbenorhevi JK, Asibuo JY, Sampson GO. 2015. Proximate composition, mineral content, and functional properties of five lima bean accessions. J Food Secur 3 (3): 69-74. DOI: 10.12691/jfs-3-3-1.
Yuan X, Chen R, Zhang Y, Lin X, Yang X. 2020. Sexual dimorphism of gut microbiota at different pubertal status. Microb Cell Fact 19 (1): 152. DOI: 10.1186/s12934-020-01412-2.
Zeng Y, Mou H, He Y, Zhang D, Pan X, Zhou L, Shen Y, Guangxin E. 2024. Effects of key rumen bacteria and microbial metabolites on fatty acid deposition in goat muscle. Animals 14 (22): 3225. DOI: 10.3390/ani14223225.
Zhi W, Tang K, Yang J, Yang T, Chen R, Huang J, Tan HS, Zhao J, Sheng Z. 2022. Gut microbiota of Hainan black goat. Animals 12 (22): 3129. DOI: 10.3390/ani12223129.