in

Dynamics of rumen microbiome in sika deer (Cervus nippon yakushimae) from unique subtropical ecosystem in Yakushima Island, Japan

  • Gruninger, R. J., Ribeiro, G. O., Cameron, A. & McAllister, T. A. Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants. Animal 13, 1843–1854 (2019).

    CAS 

    Google Scholar 

  • Morgavi, D. P., Kelly, W. J., Janssen, P. H. & Attwood, G. T. Rumen microbial (meta)genomics and its application to ruminant production. Animal 7, 184–201 (2013).

    CAS 

    Google Scholar 

  • Bergman, E. N. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol. Rev. 70, 567–590 (1990).

    CAS 

    Google Scholar 

  • Flint, H. J. The rumen microbial ecosystem—Some recent developments. Trends Microbiol. 5, 483–488 (1997).

    CAS 

    Google Scholar 

  • Hobson, P. N. & Stewart, C. S. The Rumen Microbial Ecosystem. (Springer, 2012).

  • Moraïs, S. & Mizrahi, I. The road not taken: The rumen microbiome, functional groups, and community states. Trends Microbiol. 27, 538–549 (2019).

    Google Scholar 

  • Cheng, K. J., Forsberg, C. W., Minato, H. & Costerton, J. W. in Physiological Aspects of Digestion and Metabolism in Ruminants (eds T. Tsuda, Y. Sasaki, & R. Kawashima) 595–624 (Academic Press, 1991).

  • McSweeney, C. S., Palmer, B., McNeill, D. M. & Krause, D. O. Microbial interactions with tannins: Nutritional consequences for ruminants. Anim. Feed Sci. Technol. 91, 83–93 (2001).

    CAS 

    Google Scholar 

  • Skene, I. K. & Brooker, J. D. Characterization of tannin acylhydrolase activity in the ruminal bacterium Selenomonas ruminantium. Anaerobe 1, 321–327 (1995).

    CAS 

    Google Scholar 

  • Khanbabaee, K. & van Ree, T. Tannins: Classification and definition. Nat. Prod. Rep. 18, 641–649 (2001).

    CAS 

    Google Scholar 

  • Makkar, H. P. S. & Becker, K. Isolation of tannins from leaves of some trees and shrubs and their properties. J. Agric. Food Chem. 42, 731–734 (1994).

    CAS 

    Google Scholar 

  • Bhat, T. K., Kannan, A., Singh, B. & Sharma, O. P. Value addition of feed and fodder by alleviating the antinutritional effects of tannins. Agr. Res. 2, 189–206 (2013).

    CAS 

    Google Scholar 

  • Shimada, T. Salivary proteins as a defense against dietary tannins. J. Chem. Ecol. 32, 1149–1163 (2006).

    CAS 

    Google Scholar 

  • Zhu, J., Filippich, L. J. & Alsalami, M. T. Tannic acid intoxication in sheep and mice. Res. Vet. Sci. 53, 280–292 (1992).

    CAS 

    Google Scholar 

  • Kohl, K. D., Stengel, A. & Dearing, M. D. Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets. Environ. Microbiol. 18, 1720–1729 (2016).

    CAS 

    Google Scholar 

  • Kumar, K., Chaudhary, L. C., Agarwal, N. & Kamra, D. N. Isolation and characterization of tannin-degrading bacteria from the rumen of goats fed oak (Quercus semicarpifolia) leaves. Agr. Res. 3, 377–385 (2014).

    Google Scholar 

  • Odenyo, A. A. et al. Characterization of tannin-tolerant bacterial isolates from East African ruminants. Anaerobe 7, 5–15 (2001).

    CAS 

    Google Scholar 

  • Grilli, D. J. et al. Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet. Anaerobe 42, 17–26 (2016).

    Google Scholar 

  • Tong, J. et al. Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows. PLoS ONE 13, e0198225 (2018).

    Google Scholar 

  • Pope, P. B. et al. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE 7, e38571 (2012).

    ADS 
    CAS 

    Google Scholar 

  • Østbye, K., Wilson, R. & Rudi, K. Rumen microbiota for wild boreal cervids living in the same habitat. FEMS Microbiol. Lett. 363, fnw233 (2016).

    Google Scholar 

  • Gruninger, R. J., Sensen, C. W., McAllister, T. A. & Forster, R. J. Diversity of rumen bacteria in Canadian cervids. PLoS ONE 9, e89682 (2014).

    ADS 

    Google Scholar 

  • Henderson, G. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 14567 (2015).

    CAS 

    Google Scholar 

  • Reese, A. T. & Kearney, S. M. Incorporating functional trade-offs into studies of the gut microbiota. Curr. Opin. Microbiol. 50, 20–27 (2019).

    CAS 

    Google Scholar 

  • Moeller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997 (2016).

    ADS 

    Google Scholar 

  • Okano, T. & Matsuda, H. Biocultural diversity of Yakushima Island: Mountains, beaches, and sea. J. Mar. Isl. Cult. 2, 69–77 (2013).

    Google Scholar 

  • Agetsuma, N., Agetsuma-Yanagihara, Y. & Takafumi, H. Food habits of Japanese deer in an evergreen forest: Litter-feeding deer. Mamm. Biol. 76, 201–207 (2011).

    Google Scholar 

  • Higashi, Y., Hirota, S. K., Suyama, Y. & Yahara, T. Geographical and seasonal variation of plant taxa detected in faces of Cervus nippon yakushimae based on plant DNA analysis in Yakushima Island. Ecol. Res. 37, 582–597 (2022).

    CAS 

    Google Scholar 

  • Kuroiwa, A. Nutritional ecology of the Yakushika (Cervus nippon yakushimae) population under high density Ph.D. thesis, Kyushu University, (2017).

  • Koda, R., Agetsuma, N., Agetsuma-Yanagihara, Y., Tsujino, R. & Fujita, N. A proposal of the method of deer density estimate without fecal decomposition rate: A case study of fecal accumulation rate technique in Japan. Ecol. Res. 26, 227–231 (2011).

    Google Scholar 

  • Yahara, T. in Deer eats world heritages: Ecology of deer and forets (eds T. Yumoto & H. Matsuda) 168–187 (Bunichi-Sogo-Shuppan, 2006).

  • Onoda, Y. & Yahara, T. in Challenges for Conservation Ecology in Space and Time. (eds T. Miyashita & J. Nishihiro) 126–149 (University of Tokyo Press, 2015).

  • Kagoshima Prefecture Nature Conservation Division. The current status of Yakusika in FY 2020, available at https://www.rinya.maff.go.jp/kyusyu/fukyu/shika/attach/pdf/yakushikaWG_R3_2-23.pdf (2020).

  • Kuroiwa, A., Kuroe, M. & Yahara, T. Effects of density, season, and food intake on sika deer nutrition on Yakushima Island, Japan. Ecol. Res. 32, 369–378 (2017).

    Google Scholar 

  • Hiura, T., Hashidoko, Y., Kobayashi, Y. & Tahara, S. Effective degradation of tannic acid by immobilized rumen microbes of a sika deer (Cervus nippon yesoensis) in winter. Anim. Feed Sci. Technol. 155, 1–8 (2010).

    CAS 

    Google Scholar 

  • Kawarai, S. et al. Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan. Sci. Rep. 12, 6356 (2022).

    ADS 
    CAS 

    Google Scholar 

  • Li, Z. et al. Response of the rumen microbiota of sika deer Cervus nippon fed different concentrations of tannin rich plants. PLoS ONE 10, e0123481 (2015).

    Google Scholar 

  • McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).

    CAS 

    Google Scholar 

  • Kim, M., Morrison, M. & Yu, Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol. Ecol. 76, 49–63 (2011).

    CAS 

    Google Scholar 

  • Weimer, P. J. Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations. Front. Microbiol. 6, 296 (2015).

    Google Scholar 

  • Scott, K. P., Gratz, S. W., Sheridan, P. O., Flint, H. J. & Duncan, S. H. The influence of diet on the gut microbiota. Pharmacol. Res. 69, 52–60 (2013).

    CAS 

    Google Scholar 

  • Tapio, I. et al. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS ONE 12, e0180260 (2017).

    Google Scholar 

  • Ohara, M. in Agriculture in Hokkaido v2 (ed K. Iwama, Ohara, M., Araki, H., Yamada, T., Nakatsuji, H., Kataoka, T., Yamamoto, Y.) 1–18(Faculty of Agriculture, Hokkaido Univ., 2009).

  • Igota, H., Sakuragi, M. & Uno, H. in Sika Deer: Biology and Management of Native and Introduced Populations (eds. Dale R. McCullough, Seiki Takatsuki, & Koichi Kaji) 251–272 (Springer Japan, 2009).

  • Fernando, S. C. et al. Rumen microbial population dynamics during adaptation to a high-grain diet. Appl. Environ. Microbiol. 76, 7482–7490 (2010).

    ADS 
    CAS 

    Google Scholar 

  • Hu, X. et al. High-throughput analysis reveals seasonal variation of the gut microbiota composition within forest musk deer (Moschus berezovskii). Front. Microbiol. 9, (2018).

  • Artzi, L., Morag, E., Shamshoum, M. & Bayer, E. A. Cellulosomal expansion: Functionality and incorporation into the complex. Biotechnol. Biofuels 9, 61 (2016).

    Google Scholar 

  • Biddle, A., Stewart, L., Blanchard, J. & Leschine, S. Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities. Diversity 5, (2013).

  • Eisenhauer, N., Scheu, S. & Jousset, A. Bacterial diversity stabilizes community productivity. PLoS ONE 7, e34517 (2012).

    ADS 
    CAS 

    Google Scholar 

  • Miller, A. W., Oakeson, K. F., Dale, C. & Dearing, M. D. Effect of dietary oxalate on the gut microbiota of the mammalian herbivore Neotoma albigula. Appl. Environ. Microbiol. 82, 2669–2675 (2016).

    ADS 
    CAS 

    Google Scholar 

  • Adams, J. M., Rehill, B., Zhang, Y. & Gower, J. A test of the latitudinal defense hypothesis: Herbivory, tannins and total phenolics in four North American tree species. Ecol. Res. 24, 697–704 (2009).

    CAS 

    Google Scholar 

  • Nabeshima, E., Murakami, M. & Hiura, T. Effects of herbivory and light conditions on induced defense in Quercus crispula. J. Plant Res. 114, 403–409 (2001).

    Google Scholar 

  • Yang, C.-M., Yang, M.-M., Hsu, J.-M. & Jane, W.-N. Herbivorous insect causes deficiency of pigment–protein complexes in an oval-pointed cecidomyiid gall of Machilus thunbergii leaf. Bot. Bull. Acad. Sin. 44, 315–321 (2003).

    Google Scholar 

  • Agetsuma, N., Agetsuma-Yanagihara, Y., Takafumi, H. & Nakaji, T. Plant constituents affecting food selection by sika deer. J. Wildl. Manag. 83, 669–678 (2019).

    Google Scholar 

  • Couch, C. E. et al. Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nat. Commun. 12, 2267 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Goel, G., Puniya, A. K. & Singh, K. Tannic acid resistance in ruminal streptococcal isolates. J. Basic Microbiol. 45, 243–245 (2005).

    CAS 

    Google Scholar 

  • Jiménez, N. et al. Genetic and biochemical approaches towards unravelling the degradation of gallotannins by Streptococcus gallolyticus. Microb. Cell Fact. 13, 154 (2014).

    Google Scholar 

  • Nelson, K. E., Thonney, M. L., Woolston, T. K., Zinder, S. H. & Pell, A. N. Phenotypic and phylogenetic characterization of ruminal tannin-tolerant bacteria. Appl. Environ. Microbiol. 64, 3824–3830 (1998).

    ADS 
    CAS 

    Google Scholar 

  • Selwal, M. K. et al. Optimization of cultural conditions for tannase production by Pseudomonas aeruginosa IIIB 8914 under submerged fermentation. World J. Microbiol. Biotechnol. 26, 599–605 (2010).

    CAS 

    Google Scholar 

  • Kohl, K. D., Weiss, R. B., Cox, J., Dale, C. & Denise Dearing, M. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol. Lett. 17, 1238–1246 (2014).

    Google Scholar 

  • Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Method 7, 335–336 (2010).

    CAS 

    Google Scholar 

  • Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).

    CAS 

    Google Scholar 

  • Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2009).

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    ADS 

    Google Scholar 

  • R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2020).

  • Osawa, R. Formation of a clear zone on tannin-treated brain heart infusion agar by a Streptococcus sp. isolated from feces of koalas. Appl. Environ. Microbiol. 56, 829–831 (1990).

    ADS 
    CAS 

    Google Scholar 

  • Hamamura, N., Olson, S. H., Ward, D. M. & Inskeep, W. P. Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park. Appl. Environ. Microbiol. 71, 5943–5950 (2005).

    ADS 
    CAS 

    Google Scholar 

  • Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2012).

    ADS 

    Google Scholar 

  • Chen, I.-M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2020)

  • Suzuki, M. T., Taylor, L. T. & Delong, E. F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5 ’-nuclease assays. Appl. Environ. Microbiol. 66, 4605–4614 (2000).

    ADS 
    CAS 

    Google Scholar 


  • Source: Ecology - nature.com

    Energy, war, and the crisis in Ukraine

    A signal-like role for floral humidity in a nocturnal pollination system