De Palma G, Blennerhassett P, Lu J, et al. Microbiota and host determinants of behavioural phenotype in maternally separated mice. Nat Commun. 2015;6:7735.
Article
CAS
PubMed
Google Scholar
Forsythe P, Kunze W, Bienenstock J. Moody microbes or fecal phrenology: what do we know about the microbiota-gut-brain axis? BMC Med. 2016;14:58.
Article
PubMed
PubMed Central
Google Scholar
Li J, Zhao F, Wang Y, et al. Gut microbiota dysbiosis contributes to the development of hypertension. Microbiome. 2017;5:14.
Article
PubMed
PubMed Central
Google Scholar
Rosshart SP, Vassallo BG, Angeletti D, et al. Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell. 2017;171(5):1015–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sampson TR, Mazmanian SK. Control of brain development, function, and behavior by the microbiome. Cell Host Microbe. 2015;17(5):565–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Serena C, Ceperuelo-Mallafré V, Keiran N, et al. Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota. ISME J. 2018;12(7):1642–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sommer F, Backhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol. 2013;11(4):227–38.
Article
CAS
PubMed
Google Scholar
Strati F, Cavalieri D, Albanese D, et al. New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome. 2017;5:24.
Article
PubMed
PubMed Central
Google Scholar
Thaiss C, Itav S, Rothschild D, et al. Persistent microbiome alterations modulate the rate of post-dieting weight regain. Nature. 2016;540(7634):544–51.
Article
CAS
PubMed
Google Scholar
Thevaranjan N, Puchta A, Schulz C, et al. Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell Host Microbe. 2018;23(4):455–66.
Article
CAS
Google Scholar
Zhao L, Huang Y, Lu L, et al. Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats. Microbiome. 2018;6:107.
Article
PubMed
PubMed Central
Google Scholar
Velagapudi VR, Hezaveh R, Reigstad CS, et al. The gut microbiota modulates host energy and lipid metabolism in mice. J Lipid Res. 2010;51(5):1101–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bredon M, Dittmer J, Noël C, et al. Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Microbiome. 2018;6:162.
Article
PubMed
PubMed Central
Google Scholar
Shabat S, Sasson G, Doron-Faigenboim A, et al. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 2016;10(12):2958–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jami E, Israel A, Kotser A, et al. Exploring the bovine rumen bacterial community from birth to adulthood. ISME J. 2013;7(6):1069–79.
Article
PubMed
PubMed Central
Google Scholar
Zhang W, Liu W, Hou W, et al. Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. ISME J. 2018;12(5):1319–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amato KR, Martinez-Mota R, Righini N, et al. Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia. 2016;180(3):717–33.
Article
PubMed
Google Scholar
Amato KR, Martinez-Mota R, Righini N, et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 2013;7(7):1344–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodrich JK, Waters JL, Poole AC, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hale VL, Tan CL, Niu K, et al. Diet versus phylogeny: a comparison of gut microbiota in captive colobine monkey species. Microb Ecol. 2018;75(2):528.
Article
PubMed
Google Scholar
Lavrinienko A, Mappes T, Tukalenko E, et al. Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. ISME J. 2018;12(11):2801–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Li T, Beasley DE, et al. Diet diversity is associated with beta but not alpha diversity of pika gut microbiota. Front Microbiol. 2016;7:27.
Google Scholar
Trosvik P, de Muinck EJ, Rueness EK, et al. Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate. Microbiome. 2018;6:84.
Article
PubMed
PubMed Central
Google Scholar
Wu Y, Yang Y, Cao L, et al. Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved. Sci Rep. 2018;8:13314.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gogarten JF, Davies TJ, Benjamino J, et al. Factors influencing bacterial microbiome composition in a wild non-human primate community in tai National Park. Cote d'Ivoire Isme Journal. 2018;12(10):2559–74.
CAS
PubMed
Google Scholar
Amato KR, Leigh SR, Kent A, et al. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol. 2015;69(2):434–43.
Article
CAS
PubMed
Google Scholar
Sun B, Wang X, Bernstein S, et al. Marked variation between winter and spring gut microbiota in free-ranging Tibetan macaques (Macaca thibetana). Sci Rep. 2016;6:26035.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu L, Wu Q, Deng C, et al. Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes. Environ Microbiol. 2018;20(5):1711–22.
Article
CAS
PubMed
Google Scholar
Caldwella AJ, While GM, Wapstra E, et al. Plasticity of thermoregulatory behaviour in response to the thermal environment by widespread and alpine reptile species. Anim Behav. 2017;132:217–27.
Article
Google Scholar
Hanya G, Ménard N, Qarro M, et al. Dietary adaptations of temperate primates: comparisons of Japanese and Barbary macaques. Primates. 2011;52(2):187–98.
Article
PubMed
Google Scholar
Huerta-Sánchez E, Jin X, Asan, et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 2014;512(7513):194–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lorenzo F, Huff C, Myllymäki M, et al. A genetic mechanism for Tibetan high-altitude adaptation. Nat Genet. 2014;46(9):951–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miao B, Wang Z, Li Y. Genomic analysis reveals hypoxia adaptation in the tibetan mastiff by introgression of the gray wolf from the Tibetan plateau. Mol Biol Evol. 2017;34(3):734–43.
CAS
PubMed
Google Scholar
Qiu Q, Zhang G, Ma T, et al. The yak genome and adaptation to life at high altitude. Nat Genet. 2012;44(8):946–9.
Article
CAS
PubMed
Google Scholar
Simonson TS, Yang Y, Huff CD, et al. Genetic evidence for high-altitude adaptation in Tibet. Science. 2010;329(5987):72–5.
Article
CAS
PubMed
Google Scholar
Storz JF, Runck AM, Sabatino SJ, et al. Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proc Natl Acad Sci U S A. 2009;106(34):14450–5.
Article
PubMed
PubMed Central
Google Scholar
Wang J, Shi Y, Elzo MA, et al. Genetic diversity of ATP8 and ATP6 genes is associated with high-altitude adaptation in yak. Mitochondrial DNA Part A. 2018;29(3):385–93.
Article
CAS
Google Scholar
Wang Z, Yonezawa T, Liu B, et al. Domestication relaxed selective constraints on the yak mitochondrial genome. Mol Biol Evol. 2011;28(5):1553–6.
Article
CAS
PubMed
Google Scholar
Zhang M, Pan Y, Dorfman RG, et al. Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig. Sci Rep. 2017;7:7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Z, Xu D, Wang L, et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 2016;26(14):1873–9.
Article
CAS
PubMed
Google Scholar
Li H, Qu J, Li T, et al. Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas. Appl Microbiol Biotechnol. 2018;102(15):6739–51.
Article
CAS
PubMed
Google Scholar
Estrada A, Garber PA, Rylands AB, et al. Impending extinction crisis of the world's primates: why primates matter. Sci Adv. 2017;3(1):e1600946.
Article
PubMed
PubMed Central
Google Scholar
Timmins RJ, Richardson M, Chhangani A, et al. Macaca mulatta. The IUCN Red List of Threatened Species 2008. https://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2008.RLTS.T12554A3356486.en.
Zhao J, Yao Y, Li D, et al. Characterization of the gut microbiota in six geographical populations of chinese rhesus macaques (Macaca mulatta), implying an adaptation to high-altitude environment. Microb Ecol. 2018;76(2):565–77.
Article
PubMed
Google Scholar
Flint HJ, Scott KP, Duncan SH, et al. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306.
Article
PubMed
PubMed Central
Google Scholar
Reese AT, Pereira FC, Schintlmeister A, et al. Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol. 2018;3(12):1441–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smits SA, Leach J, Sonnenburg ED, et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science. 2017;357(6353):802–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barelli C, Albanese D, Donati C, et al. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. Sci Rep. 2015;5:14862.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perofsky AC, Lewis RJ, Meyers LA. Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals. ISME J. 2019;13(1):50–63.
Article
PubMed
Google Scholar
Li L, Zhao X. Comparative analyses of fecal microbiota in Tibetan and Chinese Han living at low or high altitude by barcoded 454 pyrosequencing. Sci Rep. 2015;5:14682.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turnbaugh P, Ley R, Mahowald M, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027–31.
Article
PubMed
Google Scholar
Chevalier C, Stojanović O, Colin DJ, et al. Gut microbiota orchestrates energy homeostasis during cold. Cell. 2015;163(6):1360–74.
Article
CAS
PubMed
Google Scholar
Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489(7415):242–9.
Article
CAS
PubMed
Google Scholar
Springer A, Fichtel C, Ghalith G, et al. Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi). Ecol Evol. 2017;7(15):5732–45.
Article
PubMed
PubMed Central
Google Scholar
White BA, Lamed R, Bayer EA, et al. Biomass utilization by gut microbiomes. Annu Rev Microbiol. 2014;68(1):279–96.
Article
CAS
PubMed
Google Scholar
Hicks AL, Lee KJ, Couto-Rodriguez M, et al. Gut microbiomes of wild great apes fluctuate seasonally in response to diet. Nat Commun. 2018;9:1786.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amato KR, Sanders G, Song J, et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 2019;13(3):576–87.
Article
CAS
PubMed
Google Scholar
Oki K, Toyama M, Banno T, et al. Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type. BMC Microbiol. 2016;16:284.
Article
PubMed
PubMed Central
Google Scholar
Goodrich JK, Davenport ER, Beaumont M, et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe. 2016;19(5):731–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu TW, Park YM, Hannah HD, et al. Physical activity differentially affects the cecal microbiota of ovariectomized female rats selectively bred for high and low aerobic capacity. PLoS One. 2015;10(8):e0136150.
Article
CAS
PubMed
PubMed Central
Google Scholar
Warnecke F, Luginbühl P, Ivanova N, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560–5.
Article
CAS
PubMed
Google Scholar
Schnorr S, Candela M, Rampelli S, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654.
Article
CAS
PubMed
Google Scholar
Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016;164(3):337–40.
Article
CAS
PubMed
Google Scholar
Valdes AM, Walter J, Segal E, et al. Role of the gut microbiota in nutrition and health. Bmj. 2018;361:k2179.
Article
PubMed
PubMed Central
Google Scholar
Olendzenski L, Gogarten JP. Evolution of genes and organisms the tree/web of life in light of horizontal gene transfer. Nat Genet Eng Nat Genome Editing. 2009;1178:137–45.
CAS
Google Scholar
Theis KR, Dheilly NM, Klassen JL, et al. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. Msystems. 2016;1(2):e00028–16.
Article
PubMed
PubMed Central
Google Scholar
Raetz CR, Whitfield C. Lipopolysaccharide endotoxins. Annu Rev Biochem. 2002;71:635–700.
Article
CAS
PubMed
Google Scholar
Caporaso J, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Gevers D, Earl AM, et al. Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21(3):494–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–8.
Article
CAS
PubMed
Google Scholar
Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–6.
Article
CAS
PubMed
Google Scholar
Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33(9):496–503.
Article
CAS
PubMed
Google Scholar
Langille M, Zaneveld J, Caporaso J, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31(9):814–21.
Article
CAS
PubMed
PubMed Central
Google Scholar