Gu Z, Zhao X, Li N, Wu C. Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants. Mol Phylogenet Evol. 2007;42:248–55.
CAS
PubMed
Google Scholar
Qiu Q, Wang L, Wang K, Yang Y, Ma T, Wang Z, et al. Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions. Nat Commun. 2015;6:1–7.
CAS
Google Scholar
Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, et al. Draft genome sequence of the Tibetan antelope. Nat Commun. 2013;4:1–7.
CAS
Google Scholar
Dolt KS, Mishra MK, Karar J, Baig MA, Ahmed Z, Pasha MAQ. cDNA cloning, gene organization and variant specific expression of HIF-1α in high altitude yak (Bos grunniens). Gene. 2007;386:73–80.
CAS
PubMed
Google Scholar
Shao B, Long R, Ding Y, Wang J, Ding L, Wang H. Morphological adaptations of yak (Bos grunniens) tongue to the foraging environment of the Qinghai-Tibetan plateau. J Anim Sci. 2010;88:2594–603.
CAS
PubMed
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
Dong QM, Zhao XQ, Ma YS, Xu SX, Li QY. Live-weight gain, apparent digestibility, and economic benefits of yaks fed different diets during winter on the Tibetan plateau. Livest Sci. 2006;101:199–207.
Google Scholar
Zhou JW, Liu H, Zhong CL, Degen AA, Yang G, Zhang Y, et al. Apparent digestibility, rumen fermentation, digestive enzymes and urinary purine derivatives in yaks and Qaidam cattle offered forage-concentrate diets differing in nitrogen concentration. Livest Sci. 2018;208:14–21.
Google Scholar
Zhou JW, Zhong CL, Liu H, Degen AA, Titgemeyer EC, Ding LM, et al. Comparison of nitrogen utilization and urea kinetics between yaks (Bos grunniens) and indigenous cattle (Bos taurus). J Anim Sci. 2017;95:4600–12.
CAS
PubMed
Google Scholar
Ishaq SL, Wright ADG. Insight into the bacterial gut microbiome of the north American moose (Alces alces). BMC Microbiol. 2012;12:212.
CAS
PubMed
PubMed Central
Google Scholar
An D, Dong X, Dong Z. Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. Anaerobe. 2005;11:207–15.
CAS
PubMed
Google Scholar
Huang XD, Tan HY, Long R, Liang JB, Wright ADG. Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China. BMC Microbiol. 2012;12:237.
PubMed
PubMed Central
Google Scholar
Guo W, Li Y, Wang L, Wang J, Xu Q, Yan T, et al. Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology. Anaerobe. 2015;34:74–9.
CAS
PubMed
Google Scholar
Liu C, Wu H, Liu S, Chai S, Meng Q, Zhou Z. Dynamic alterations in yak rumen bacteria community and metabolome characteristics in response to feed type. Front Microbiol. 2019;10:1–19.
PubMed
PubMed Central
Google Scholar
Zhou Z, Fang L, Meng Q, Li S, Chai S, Liu S, et al. Assessment of ruminal bacterial and archaeal community structure in yak (Bos grunniens). Front Microbiol. 2017;8:1–10.
Google Scholar
Xue D, Chen H, Zhao X, Xu S, Hu L, Xu T, et al. Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan plateau. Syst Appl Microbiol. 2017;40:227–36.
PubMed
Google Scholar
Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 2016;26:1873–9.
CAS
PubMed
Google Scholar
Rabee AE, Forster RJ, Elekwachi CO, Kewan KZ, Sabra EA, Shawket SM, et al. Community structure and fibrolytic activities of anaerobic rumen fungi in dromedary camels. J Basic Microbiol. 2019;59:101–10.
CAS
PubMed
Google Scholar
Belanche A, Yáñez-Ruiz DR, Detheridge AP, Griffith GW, Kingston-Smith AH, Newbold CJ. Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications. Environ Microbiol. 2019;21:4360–77.
PubMed
PubMed Central
Google Scholar
Rey M, Enjalbert F, Combes S, Cauquil L, Bouchez O, Monteils V. Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential. J Appl Microbiol. 2014;116:245–57.
CAS
PubMed
Google Scholar
Jami E, Israel A, Kotser A, Mizrahi I. Exploring the bovine rumen bacterial community from birth to adulthood. ISME J. 2013;7:1069–79.
PubMed
PubMed Central
Google Scholar
Dill-Mcfarland KA, Breaker JD, Suen G. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Sci Rep. 2017;7:1–12.
Google Scholar
Liu C, Meng Q, Chen Y, Xu M, Shen M, Gao R, et al. Role of age-related shifts in rumen bacteria and methanogens in methane production in cattle. Front Microbiol. 2017;8:1–14.
Google Scholar
Kumar S, Indugu N, Vecchiarelli B, Pitta DW. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows. Front Microbiol. 2015;6:1–10.
Google Scholar
Dill-McFarland KA, Weimer PJ, Breaker JD, Suen G. Diet influences early microbiota development in dairy calves without Long-term impacts on Milk production. Appl Environ Microbiol. 2019;85:1–12.
Google Scholar
Yáñez-Ruiz DR, Abecia L, Newbold CJ. Manipulating rumen microbiome and fermentation through interventions during early life: a review. Front Microbiol. 2015;6:1–12.
Google Scholar
Abecia L, Martínez-Fernandez G, Martín-García AI, Ramos-Morales E, Yáñez-Ruiz DR, Waddams KE, et al. An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by archaea. Archaea. 2014;2014:1–12.
Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, et al. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future. Front Microbiol. 2018;9:1–33.
Google Scholar
Wiener GH, Jianlin H, Ruijun L. Origins, domestication and distribution of yak. The yak. 2nd ed: RAP Publication; 2003.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Google Scholar
Ruggles KV, Wang J, Volkova A, Contreras M, Noya-Alarcon O, Lander O, et al. Changes in the gut microbiota of urban subjects during an immersion in the traditional diet and lifestyle of a rainforest village. mSphere. 2018;3:1–8.
Google Scholar
Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.
CAS
PubMed
PubMed Central
Google Scholar
Dias J, Marcondes MI, Noronha MF, Resende RT, Machado FS, Mantovani HC, et al. Effect of pre-weaning diet on the ruminal archaeal, bacterial, and fungal communities of dairy calves. Front Microbiol. 2017;8:1553.
PubMed
PubMed Central
Google Scholar
Malmuthuge N, Liang G, Guan LL. Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes. Genome Biol. 2019;20:1–6.
CAS
Google Scholar
Yan XT, Yan BY, Ren QM, Dou JJ, Wang WW, Zhang JJ, et al. Effect of slow-release urea on the composition of ruminal bacteria and fungi communities in yak. Anim Feed Sci Technol. 2018;244:18–27.
CAS
Google Scholar
Thoetkiattikul H, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Pattarajinda V, Eurwilaichitr L, et al. Comparative analysis of microbial profiles in cow rumen fed with different dietary fiber by tagged 16S rRNA gene pyrosequencing. Curr Microbiol. 2013;67:130–7.
CAS
PubMed
Google Scholar
Dias J, Marcondes MI, de Souza SM, da Mata e Silva BC, Noronha MF, Resende RT, et al. Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development. Appl Environ Microbiol. 2018;84:e02675–17.
CAS
PubMed
PubMed Central
Google Scholar
Anderson KL, Nagaraja TG, Morrill JL, Avery TB, Galitzer SJ, Boyer JE. Ruminal microbial development in conventionally or early-weaned calves. J Anim Sci. 1987;64:1215–26.
CAS
PubMed
Google Scholar
Wang Z, Elekwachi CO, Jiao J, Wang M, Tang S, Zhou C, et al. Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats. Sci Rep. 2017;7:422.
PubMed
PubMed Central
Google Scholar
Jiao J, Li X, Beauchemin KA, Tan Z, Tang S, Zhou C. Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation. Br J Nutr. 2015;113:888–900.
CAS
PubMed
Google Scholar
Henderson G, Cox F, Ganesh S, Jonker A, Young W, Janssen PH, et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep. 2015;5:14567.
CAS
PubMed
PubMed Central
Google Scholar
Chaucheyras-Durand F, Ameilbonne A, Auffret P, Bernard M, Mialon MM, Dunière L, et al. Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs. Sci Rep. 2019;16:1–6.
Google Scholar
Bird SH, Hegarty RS, Woodgate R. Modes of transmission of rumen protozoa between mature sheep. Anim Prod Sci. 2010;50:414–7.
Google Scholar
Opperman MH, Wood M, Harris PJ. Changes in microbial populations following the application of cattle slurry to soil at two temperatures. Soil Biol Biochem. 1989;21:263–8.
Google Scholar
Canals O, Serrano-Suárez A, Salvadó H, Méndez J, Cervero-Aragó S, De Porras VR, et al. Effect of chlorine and temperature on free-living protozoa in operational man-made water systems (cooling towers and hot sanitary water systems) in Catalonia. Environ Sci Pollut R. 2015;22:6610–8.
CAS
Google Scholar
Leng J, Zhong X, Zhu RJ, Yang SL, Gou X, Mao HM. Assessment of protozoa in Yunnan yellow cattle rumen based on the 18S rRNA sequences. Mol Biol Rep. 2011;38:577–85.
CAS
PubMed
Google Scholar
Shin EC, Cho KM, Lim WJ, Hong SY, An CL, Kim EJ, et al. Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences. J Appl Microbiol. 2004;97:378–83.
CAS
PubMed
Google Scholar
Mao SY, Huo WJ, Zhu WY. Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model. Environ Microbiol. 2016;18:525–41.
CAS
PubMed
Google Scholar
Wright ADG. Rumen protozoa. In: Rumen microbiology: from evolution to revolution; 2015.
Google Scholar
Zhou M, Peng YJ, Chen Y, Klinger CM, Oba M, Liu JX, et al. Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle. Microbiome. 2018;6:62.
PubMed
PubMed Central
Google Scholar
Friedman N, Jami E, Mizrahi I. Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages. Environ Microbiol. 2017;19:3365–73.
CAS
PubMed
PubMed Central
Google Scholar
Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014;510:417–21.
CAS
PubMed
PubMed Central
Google Scholar
Long RJ, Zhang DG, Wang X, Hu ZZ, Dong SK. Effect of strategic feed supplementation on productive and reproductive performance in yak cows. Prev Vet Med. 1999;38:195–206.
CAS
PubMed
Google Scholar
Zi XD, Zhong GH, Wen YL, Zhong JC, Liu CL, Ni YA, et al. Growth performance, carcass composition and meat quality of Jiulong-yak (Bos grunniens). Asian-Austr J Anim Sci. 2004;17:410–4.
Google Scholar
Oh J, Byrd AL, Park M, Kong HH, Segre JA. Temporal stability of the human skin microbiome. Cell. 2016;165:854–66.
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Xu Q, Kong F, Yang Y, Wu D, Mishra S, et al. Exploring the goat rumen microbiome from seven days to two years. PLoS One. 2016;11:e0154354.
PubMed
PubMed Central
Google Scholar
Tapio I, Fischer D, Blasco L, Tapio M, Wallace RJ, Bayat AR, et al. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS One. 2017;12:e0180260.
PubMed
PubMed Central
Google Scholar
Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, et al. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One. 2013;8:e47879.
CAS
PubMed
PubMed Central
Google Scholar
Janssen PH, Kirs M. Structure of the archaeal community of the rumen. Appl Environ Microbiol. 2008;74:3619–25.
CAS
PubMed
PubMed Central
Google Scholar
Newbold CJ, De la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The role of ciliate protozoa in the rumen. Front Microbiol. 2015;6:1–14.
Google Scholar
Belanche A, Kingston-Smith AH, Griffith GW, Newbold CJ. A multi-kingdom study reveals the plasticity of the rumen microbiota in response to a shift from non-grazing to grazing diets in sheep. Front Microbiol. 2019;10:122.
PubMed
PubMed Central
Google Scholar
Danielsson R, Dicksved J, Sun L, Gonda H, Müller B, Schnürer A, et al. Methane production in dairy cows correlates with rumen methanogenic and bacterial community structure. Front Microbiol. 2017;8:1–15.
Google Scholar
Li Z, Wright ADG, Si H, Wang X, Qian W, Zhang Z, et al. Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses. Environ Microbiol Rep. 2016;8:1016–23.
CAS
PubMed
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
CAS
PubMed
PubMed Central
Google Scholar
Hakim J, Schram J, Galloway A, Morrow C, Crowley M, Watts S, et al. The Purple Sea urchin Strongylocentrotus purpuratus demonstrates a compartmentalization of gut bacterial microbiota, predictive functional attributes, and taxonomic co-occurrence. Microorganisms. 2019;7:35.
CAS
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
PubMed
PubMed Central
Google Scholar
Gao P, Ma C, Sun Z, Wang L, Huang S, Su X, et al. Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken. Microbiome. 2017;5:91.
PubMed
PubMed Central
Google Scholar
Cernava T, Erlacher A, Soh J, Sensen CW, Grube M, Berg G. Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa mill.). Microbiome. 2019;7:13.
PubMed
PubMed Central
Google Scholar
Pérez-Losada M, Alamri L, Crandall KA, Freishtat RJ. Nasopharyngeal microbiome diversity changes over time in children with asthma. PLoS One. 2017;12:e0170543.
PubMed
PubMed Central
Google Scholar
Manuscript A, Structures T. Fast R functions for robust correlations and hierarchical clustering. NIH Public Access, JStat Softw. 2009;6:247–53.
Google Scholar
Krieger AM, Yekutieli D. Adaptive linear step-up Proceudres that control the false discovery rate. Biometrika. 2006;93:491–507.
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
CAS
PubMed
PubMed Central
Google Scholar
Jiao S, Liu Z, Lin Y, Yang J, Chen W, Wei G. Bacterial communities in oil contaminated soils: biogeography and co-occurrence patterns. Soil Biol Biochem. 2016;98:64–73.
CAS
Google Scholar
Kunz IGZ, Reed KJ, Metcalf JL, Hassel DM, Coleman RJ, Hess TM, et al. Equine fecal microbiota changes associated with anthelmintic administration. J Equine Vet Sci. 2019;77:98–106.
PubMed
Google Scholar
Anderson MJ. PERMANOVA Permutational multivariate analysis of variance. Austral Ecol. 2005;26:32–46.
Google Scholar
Zimmerman DW. Comparative power of student t test and Mann-Whitney U test for unequal sample sizes and variances. J Exp Educ. 1987;55:171–4.
Google Scholar