Ma X, Wang Q, Li H, Xu C, Cui N, Zhao X. 16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses. Vet Microbiol. 2017;207:195–204.
CAS
PubMed
Google Scholar
Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107–33.
CAS
PubMed
Google Scholar
Morgavi DP, Kelly WJ, Janssen PH, Attwood GT. Rumen microbial (meta) genomics and its application to ruminant production. Animal. 2013;7(Suppl 1):184–201.
CAS
PubMed
Google Scholar
Lederberg J. Infectious history. Science. 2000;288(5464):287–93.
CAS
PubMed
Google Scholar
Kelly D, Conway S, Aminov R. Commensal gut bacteria: mechanisms of immune modulation. Trends Immunol. 2005;26(6):326–33.
CAS
PubMed
Google Scholar
Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol. 2004;12(3):129–34.
CAS
PubMed
Google Scholar
Xu JGJ. Honor thy symbionts. Proc Natl Acad Sci U S A. 2003;100(18):10452–9.
CAS
PubMed
PubMed Central
Google Scholar
Egert M, de Graaf AA, Smidt H, de Vos WM, Venema K. Beyond diversity: functional microbiomics of the human colon. Trends Microbiol. 2006;14(2):86–91.
CAS
PubMed
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
CAS
PubMed
PubMed Central
Google Scholar
Russell JB, Muck RE, Weimer PJ. Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen. FEMS Microbiol Ecol. 2009;67(2):183–97.
CAS
PubMed
Google Scholar
Sanger FNS, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74(12):5463–7.
CAS
PubMed
PubMed Central
Google Scholar
Cavicchioli RWK. Molecular cloning, expression, and characterization of endoglucanase genes from Fibrobacter succinogenes AR1. Appl Environ Microbiol. 1991;57(2):359–65.
CAS
PubMed
PubMed Central
Google Scholar
Forsberg CW, Forano E, Chesson A. Microbial adherence to the plant cell wall and enzymatic hydrolysis. In: Cronje PB, editor. Ruminant physiology digestion metabolism, growth and reproduction; 2000. p. 79–98.
Google Scholar
Jun HS, Qi M, Ha JK, Forsberg CW. Fibrobacter succinogenes, a dominant fibrolytic ruminal bacterium: transition to the post genomic era*. Asian Aust J Anim Sci. 2007;20(5):802–10.
CAS
Google Scholar
Handelsman JRM, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5(10):R245–9.
CAS
PubMed
Google Scholar
Raes JBP. Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol. 2008;6(9):693–9.
CAS
PubMed
Google Scholar
Karlsson FH, Nookaew I, Petranovic D, Nielsen J. Prospects for systems biology and modeling of the gut microbiome. Trends Biotechnol. 2011;29(6):251–8.
CAS
PubMed
Google Scholar
Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332(6032):970–4.
CAS
PubMed
PubMed Central
Google Scholar
von Mering CHP, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science. 2007;315(5815):1126–30.
Google Scholar
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6(10):776–88.
CAS
PubMed
PubMed Central
Google Scholar
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, et al. Evolution of mammals and their gut microbes. Science. 2008;320(5883):1647–51.
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.
CAS
PubMed
PubMed Central
Google Scholar
Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957–63.
CAS
PubMed
PubMed Central
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(Database issue):D633–42.
CAS
PubMed
Google Scholar
Mills DK, Entry JA, Voss JD, Gillevet PM, Mathee K. An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices. FEMS Microbiol Ecol. 2006;57(3):496–503.
CAS
PubMed
Google Scholar
Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71(12):8228–35.
CAS
PubMed
PubMed Central
Google Scholar
Lopez-Gonzalez JA, Suarez-Estrella F, Vargas-Garcia MC, Lopez MJ, Jurado MM, Moreno J. Dynamics of bacterial microbiota during lignocellulosic waste composting: studies upon its structure, functionality and biodiversity. Bioresour Technol. 2015;175:406–16.
CAS
PubMed
Google Scholar
Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, Wang W, Qiu Q, Huang X, Zhou J, et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 2016;26(14):1873–9.
CAS
PubMed
Google Scholar
Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, et al. Draft genome sequence of the Tibetan antelope. Nat Commun. 2013;4:1858.
PubMed
PubMed Central
Google Scholar
Hook SESM, Northwood KS, Dijkstra J, France J, Wright AD, McBride BW. Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows. FEMS Microbiol Ecol. 2011;78(2):275–84.
CAS
PubMed
Google Scholar
Huo W, Zhu W, Mao S. Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats. World J Microbiol Biotechnol. 2014;30(2):669–80.
CAS
PubMed
Google Scholar
Hess MSA, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z. EM. R. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463–7.
CAS
PubMed
Google Scholar
Kim M, Morrison M, Yu Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol. 2011;76(1):49–63.
CAS
PubMed
Google Scholar
Li Z, Wright AD, Liu H, Bao K, Zhang T, Wang K, Cui X, Yang F, Zhang Z, Li G. Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets. Microb Ecol. 2015;69(2):307–18.
CAS
PubMed
Google Scholar
Ishaq SL, Wright AD. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microb Ecol. 2014;68(2):185–95.
CAS
PubMed
Google Scholar
Gruninger RJ, Sensen CW, McAllister TA, Forster RJ. Diversity of rumen bacteria in Canadian cervids. PLoS One. 2014;9(2):e89682.
PubMed
PubMed Central
Google Scholar
Nyonyo T, Shinkai T, Mitsumori M. Improved culturability of cellulolytic rumen bacteria and phylogenetic diversity of culturable cellulolytic and xylanolytic bacteria newly isolated from the bovine rumen. FEMS Microbiol Ecol. 2014;88(3):528–37.
CAS
PubMed
Google Scholar
Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, Turroni S, Biagi E, Peano C, Severgnini M, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654.
CAS
PubMed
PubMed Central
Google Scholar
Chaucheyras-Durand F, Ossa F. REVIEW: the rumen microbiome: composition, abundance, diversity, and new investigative tools. Prof Anim Sci. 2014;30(1):1–12.
Google Scholar
Cunha IS, Barreto CC, Costa OYA, Bomfim MA, Castro AP, Kruger RH, Quirino BF. Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe. 2011;17(3):118–24.
PubMed
Google Scholar
Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe. 2000;6(5):273–84.
CAS
Google Scholar
Jami E, Israel A, Kotser A, Mizrahi I. Exploring the bovine rumen bacterial community from birth to adulthood. ISME J. 2013;7(6):1069–79.
PubMed
PubMed Central
Google Scholar
Pitta DW, Pinchak WE, Indugu N, Vecchiarelli B, Sinha R, Fulford JD. Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat. Front Microbiol. 2016;7:689.
CAS
PubMed
PubMed Central
Google Scholar
Long RJ, Ding LM, Shang ZH, Guo XH. The yak grazing system on the Qinghai-Tibetan plateau and its status. Rangel J. 2008;30:241–6.
Google Scholar
Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM, et al. The yak genome and adaptation to life at high altitude. Nat Genet. 2012;44(8):946–9.
CAS
PubMed
Google Scholar
Xue D, Chen H, Zhao X, Xu S, Hu L, Xu T, Jiang L, Zhan W. Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan plateau. Syst Appl Microbiol. 2017;40(4):227–36.
PubMed
Google Scholar
Bohra V, Dafale NA, Purohit HJ. Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach. Arch Microbiol. 2019;201(10):1385–97.
CAS
PubMed
Google Scholar
Sbardellati DL, Fischer A, Cox MS, Li W, Kalscheur KF, Suen G. The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. J Dairy Sci. 2020;103(4):3636–47.
CAS
PubMed
Google Scholar
Wang B, Luo Y, Su R, Yao D, Hou Y, Liu C, Du R, Jin Y. Impact of feeding regimens on the composition of gut microbiota and metabolite profiles of plasma and feces from Mongolian sheep. J Microbiol. 2020;58(6):472–82.
CAS
PubMed
Google Scholar
Cui X, Wang Z, Yan T, Chang S, Wang H, Hou F. Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau. Can J Microbiol. 2019;65(12):859–69.
CAS
PubMed
Google Scholar
Cobellis G, Yu Z, Forte C, Acuti G, Trabalza-Marinucci M. Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations. J Anim Sci Biotechnol. 2016;7:27.
PubMed
PubMed Central
Google Scholar