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Ruminants Nutrition and Feeding

Characteristics of bacterial community and volatile fatty acids in the gastrointestinal tract of Tarim wapiti

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Pages 259-274 | Received 28 Aug 2023, Accepted 10 Jan 2024, Published online: 06 Feb 2024

References

  • Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. 2020. Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool. 17(1):15–31. doi: 10.1186/s12983-020-00379-5.
  • Ahn J, Lkhagva E, Jung S, Kim H, Chung H, Hong S. 2023. 2023. Fecal microbiome does not represent whole gut microbiome. Cell Microbiol. 2023:1–14. doi: 10.1155/2023/6868417.
  • Al-Shaibani MM, Radin Mohamed RMS, Sidik NM, Enshasy HAE, Al-Gheethi A, Noman E, Al-Mekhlafi NA, Zin NM. 2021. Biodiversity of secondary metabolites compounds isolated from Phylum Actinobacteria and Its yherapeutic applications. Molecules. 26(15):4504. doi: 10.3390/molecules26154504.
  • AOAC. 1990. Association of official analytical chemists: official methods of analysis. Rockville (MD): doi: AOAC.
  • Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. 2005. Host-Bacterial Mutualism in the human intestine. Science. 307(5717):1915–1920. doi: 10.1126/science.1104816.
  • Barko PC, McMichael MA, Swanson KS, Williams DA. 2018. The gastrointestinal microbiome: a review. Vet Int Med. 32(1):9–25. doi: 10.1111/jvim.14875.
  • Bergmann GT. 2017. Microbial community composition along the digestive tract in forage- and grain-fed bison. BMC Vet Res. 13(1):253. doi: 10.1186/s12917-017-1161-x.
  • Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 10(1):57–59. doi: 10.1038/nmeth.2276.
  • Contijoch EJ, Yang C, Mogno I, Li Z, Faith JJ. 2019. Gut microbiota density influences host physiology and is shaped by host and microbial factors. Vol. 8. New York (NY): Cold Spring Harbor Laboratory; p. e40553.
  • Doreau M, Ferlay A. 1994. Digestion and utilisation of fatty acids by ruminants. Anim Feed Sci Tech. 45(3–4):379–396. doi: 10.1016/0377-8401(94)90039-6.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity. and speed of chimera detection. Bioinformatics. 27(16):2194–2200. [Database] doi: 10.1093/bioinformatics/btr381.
  • Flint HJ, Bayer EA. 2008. Plant cell wall breakdown by anaerobic microorganisms from the mammalian digestive tract. Ann NY Acad Sci. 1125(1):280–288. doi: 10.1196/annals.1419.022.
  • Gruninger RJ, Sensen CW, McAllister TA, Forster RJ. 2014. Diversity of rumen bacteria in canadian cervids. PLoS One. 9(2):e89682. doi: 10.1371/journal.pone.0089682.
  • Hua C, Tian J, Tian P, Cong R, Luo Y, Geng Y, Tao S, Ni Y, Zhao R. 2017. Feeding a high concentration diet induces unhealthy alterations in the composition and metabolism of ruminal microbiota and host response in a goat model. Front Microbiol. 8:138. doi: 10.3389/fmicb.2017.00138.
  • Ishaq SL, Wright A. 2014. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microb Ecol. 68(2):185–195. doi: 10.1007/s00248-014-0399-0.
  • Jane ME, Van GNO. 1980. Comparison of the action of rumen bacteria on cell walls from Eragrostis tef. The Journal of Agricultural Science. 95(2):313–323.
  • Jiang F, Song P, Wang H, Zhang J, Liu D, Cai Z, Gao H, Chi X, Zhang T. 2022. Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer. Appl Microbiol Biotechnol. 106(3):1325–1339. doi: 10.1007/s00253-022-11775-8.
  • Kim J, Hong SW, Park B, Yoo JG, Oh M. 2019. Characterisation of the bacterial community in the gastrointestinal tracts of elk (Cervus canadensis). Antonie Van Leeuwenhoek. 112(2):225–235. doi: 10.1007/s10482-018-1150-5.
  • Le Van TD, Robinson JA, Ralph J, Greening RC, Smolenski WJ, Leedle JA, Schaefer DM. 1998. Assessment of reductive acetogenesis with indigenous ruminal bacterium populations and Acetitomaculum ruminis. Appl Environ Microbiol. 64(9):3429–3436. doi: 10.1128/AEM.64.9.3429-3436.1998.
  • Leedle JA, Greening RC. 1988. Postprandial changes in methanogenic and acidogenic bacteria in the rumens of steers fed high- or low-forage diets once daily. Appl Environ Microbiol. 54(2):502–506. doi: 10.1128/aem.54.2.502-506.1988.
  • Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Microbial ecology: human gut microbes associated with obesity. Nature. 444(7122):1022–1023. doi: 10.1038/4441022a.
  • Li Y, Hu X, Yang S, Zhou J, Zhang T, Qi L, Sun X, Fan M, Xu S, Cha M, et al. 2017. Comparative analysis of the gut microbiota composition between captive and wild forest musk deer. Front Microbiol. 8:1705. doi: 10.3389/fmicb.2017.01705.
  • Li Z, Wang X, Zhang T, Si H, Nan W, Xu C, Guan L, Wright A-DG, Li G. 2018. The development of microbiota and metabolome in small intestine of sika deer (Cervus nippon) from birth to weaning. Front Microbiol. 9:4. doi: 10.3389/fmicb.2018.00004.
  • Li Z, Zhang Z, Xu C, Zhao J, Liu H, Fan Z, Yang F, Wright ADG, Li G. 2014. Bacteria and methanogens differ along the gastrointestinal tract of Chinese Roe Deer (Capreolus pygargus). PLoS One. 9(12):e114513.
  • Magoč T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27(21):2957–2963. doi: 10.1093/bioinformatics/btr507.
  • Mao S, Zhang M, Liu J, Zhu W. 2015. Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function. Sci Rep-Uk. 5(1):16116.
  • Matsui H, Ogata K, Tajima K, Nakamura M, Nagamine T, Aminov RI, Benno Y. 2000. Phenotypic characterization of polysaccharidases produced by four prevotella type strains. Curr Microbiol. 41(1):45–49. doi: 10.1007/s002840010089.
  • Minich D, Madden C, Evans MV, Ballash GA, Barr DJ, Poulsen KP, Dennis PM, Hale VL. 2021. Alterations in fecal microbiota linked to environment and sex in red deer (Cervus elaphus. Sci Rep. 11(1):13218. doi: 10.1038/s41598-021-89896-9.
  • Pérez-Barbería FJ. 2017. Scaling methane emissions in ruminants and global estimates in wild populations. Sci Total Environ. 579:1572–1580. doi: 10.1016/j.scitotenv.2016.11.175.
  • Pi Y, Gao K, Zhu W. 2017. Animal host - advances in gut microbiota-metabolism axis research. Acta Microbiol Sin. 57(2):161–169.
  • Qian W, Li Z, Ao W, Zhao G, Li G, Wu J. 2017. Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries). Can J Microbiol. 63(5):375–383. doi: 10.1139/cjm-2016-0596.
  • Qian W. 2017. Study on adaptation mechanism of high fiber roughage by Tarim Wapiti (Cervus elaphus yarkandensis) [dissertation]. Lanzhou: Gansu Agricultural University
  • Ragsdale SW. 2008. Enzymology of the wood-ljungdahl pathway of acetogenesis. Ann NY Acad Sci. 1125(1):129–136. doi: 10.1196/annals.1419.015.
  • Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CV. 2016. Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii. Int J Syst Evol Micr. 66(3):1268–1274. doi: 10.1099/ijsem.0.000874.
  • Shabat SK, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg MM, White BA, Shterzer N, Mizrahi I. 2016. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 10(12):2958–2972. doi: 10.1038/ismej.2016.62.
  • Stanley D, Hughes RJ, Moore RJ. 2014. Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Appl Microbiol Biotechnol. 98(10):4301–4310. doi: 10.1007/s00253-014-5646-2.
  • Su S, Zhao Y, Liu Z, Liu G, Du M, Wu J, Bai D, Li B, Bou G, Zhang X, et al. 2020. Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments of Mongolian horses. Microbiologyopen. 9(6):1085–1101. doi: 10.1002/mbo3.1020.
  • Sun Y, Yu Y, Guo J, Zhong L, Zhang M. 2023. Alterations in fecal microbiota linked to environment and sex in red deer (Cervus elaphus). Animals. 13(5):929. doi: 10.3390/ani13050929.
  • Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. 2015. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Mi. 5:3.
  • Wang J, Fan H, Han Y, Zhao J, Zhou Z. 2016. Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyrosequencing analysis. Asian-Australas J Anim Sci. 30(1):100–110. doi: 10.5713/ajas.16.0166.
  • Wang Y, Guo H, Gao X, Wang J. 2021. The intratumor microbiota signatures associate with subtype, tumor stage, and survival status of esophageal varcinoma. Front Oncol. 11:754788.
  • Wang RX, Lee JS, Campbell EL, Colgan SP. 2022. Microbiota-derived butyrate dynamically regulates intestinal homeostasis through regulation of actin-associated protein synaptopodin. Proc Natl Acad Sci USA. 117(21):11648–11657. doi: 10.1073/pnas.1917597117.
  • Wang K, Zhang H, Hu L, Zhang G, Lu H, Luo H, Zhao S, Zhu H, Wang Y. 2022. Characterization of the microbial communities along the gastrointestinal tract in crossbred cattle. Animals. 12(7):825. doi: 10.3390/ani12070825.
  • Wilson R. 2019. Association between diet and rumen microbiota in wild roe deer. Fems Microbiol Lett. 20:366.
  • Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, Wang X, Yang C, Li Q, Yan X, et al. 2021. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome. 9(1):137. doi: 10.1186/s40168-021-01078-x.
  • Yildirim E, Ilina L, Laptev G, Filippova V, Brazhnik E, Dunyashev T, Dubrovin A, Novikova N, Tiurina D, Tarlavin N, et al. 2021. The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets. PeerJ. 9:e12389. doi: 10.7717/peerj.12389.
  • Zhang L, Jiang X, Li A, Waqas M, Gao X, Li K, Xie G, Zhang J, Mehmood K, Zhao S, et al. 2019. Characterization of the microbial community structure in intestinal segments of yak (Bos grunniens). Anaerobe. 61:102115. doi: 10.1016/j.anaerobe.2019.102115.
  • Zhang H, Shao M, Huang H, Wang S, Ma L, Wang H, Hu L, Wei K, Zhu R. 2018. The dynamic distribution of small-tail han sheep microbiota across different intestinal segments. Front Microbiol. 9:32. doi: 10.3389/fmicb.2018.00032.
  • Zhen J, Ren Y, Zhang H, Yuan X, Wang L, Shen H, Liu P, Chen Y. 2022. Effect of different dietary regimes on the gut microbiota and fecal metabolites of père David’s deer. Animals. 12(5):584. doi: 10.3390/ani12050584.
  • Zhu Y, Wang Z, Hu R, Wang X, Li F, Zhang X, Zou H, Peng Q, Xue B, Wang L. 2021. Comparative study of the bacterial communities throughout the gastrointestinal tract in two beef cattle breeds. Appl Microbiol Biotechnol. 105(1):313–325. doi: 10.1007/s00253-020-11019-7.