• 1.

    Carey HV, Assadi-Porter FM. The hibernator microbiome: host-bacterial interactions in an extreme nutritional symbiosis. Annu Rev Nutr. 2017;37:477–500.

    CAS 
    PubMed 

    Google Scholar
     

  • 2.

    Johnson GE. Hibernation of the thirteen-lined ground squirrel, Citellus tridecemlineatus (Mitchell). J Exp Zool. 1928;50(1):15–30.


    Google Scholar
     

  • 3.

    Carey HV, Andrews MT, Martin SL. Mammalian hibernation: cellular and molecular responses to depressed metabolism and low temperature. Physiol Rev. 2003;83:1153–81.

    CAS 
    PubMed 

    Google Scholar
     

  • 4.

    Johnson GE. Hibernation of the thirteen-lined ground squirrel, Citellus tridecemlineatus (Mitchill). III. The rise in respiration, heart beat and temperature in waking from hibernation. Biol Bull. 1929;57(2):107–29.


    Google Scholar
     

  • 5.

    McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, et al. The effects of captivity on the mammalian gut microbiome. Integr Comp Biol. 2017;57(4):690–704.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 6.

    Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, et al. Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell. 2017;171(5):1015–28.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 7.

    Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365(6452):461.


    Google Scholar
     

  • 8.

    Yeung F, Chen YH, Lin JD, Leung JM, McCauley C, Devlin JC, Hansen C, Cronkite A, Stephens Z, Drake-Dunn C, et al. Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host Microbe. 2020;27(5):809–22.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 9.

    Herter CA, Kendall AI. The influence of dietary alterations on the types of intestinal flora. J Biol Chem. 1910;7:203–36.


    Google Scholar
     

  • 10.

    Cannon PR. The effects of diet on the intestinal flora. J Infect Dis. 1921;29(4):369–85.


    Google Scholar
     

  • 11.

    Louis P, Scott KP, Duncan SH, Flint HJ. Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol. 2007;102(5):1197–208.

    CAS 
    PubMed 

    Google Scholar
     

  • 12.

    Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):614.


    Google Scholar
     

  • 13.

    Buddington RK, Sangild PT. Companion animals symposium: development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life. J Anim Sci. 2011;89(5):1506–19.

    CAS 
    PubMed 

    Google Scholar
     

  • 14.

    David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63.

    CAS 

    Google Scholar
     

  • 15.

    Voreades N, Kozil A, Weir TL. Diet and the development of the human intestinal microbiome. Front Microbiol. 2014;5:494.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 16.

    Kalmokoff M, Franklin J, Petronella N, Green J, Brooks SP. Phylum level change in the cecal and fecal gut communities of rats fed diets containing different fermentable substrates supports a role for nitrogen as a factor contributing to community structure. Nutrients. 2015;7(5):3279–99.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 17.

    Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM. Diet-microbiota interactions mediate global epigenetic programming in multiple host tissues. Mol Cell. 2016;64(5):982–92.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 18.

    Backhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 2015;17(5):690–703.

    PubMed 

    Google Scholar
     

  • 19.

    Martinez I, Maldonado-Gomez MX, Gomes-Neto JC, Kittana H, Ding H, Schmaltz R, Joglekar P, Cardona RJ, Marsteller NL, Kembel SW, et al. Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly. Elife. 2018;7:e36521.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 20.

    Uenishi G, Fujita S, Ohashi G, Kato A, Yamauchi S, Matsuzawa T, Ushida K. Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity. Am J Primatol. 2007;69(4):367–76.

    CAS 
    PubMed 

    Google Scholar
     

  • 21.

    Scupham AJ, Patton TG, Bent E, Bayles DO. Comparison of the Cecal microbiota of domestic and wild Turkeys. Microb Ecol. 2008;56:322–31.

    PubMed 

    Google Scholar
     

  • 22.

    Villers LM, Jang SS, Lent CL, Lewin-Koh SC, Norosoarinaivo JA. Survey and comparison of major intestinal flora in captive and wild ring-tailed lemur (Lemur catta) populations. Am J Primatol. 2008;70(2):175–84.

    PubMed 

    Google Scholar
     

  • 23.

    Xenoulis PG, Gray PL, Brightsmith D, Palculict B, Hoppes S, Steiner JM, Tizard I, Suchodolski JS. Molecular characterization of the cloacal microbiota of wild and captive parrots. Vet Microbiol. 2010;146(3–4):320–5.

    CAS 
    PubMed 

    Google Scholar
     

  • 24.

    Dhanasiri AKS, Brunvold L, Brinchmann MF, Korsnes K, Bergh Ø, Kiron V. Changes in the intestinal microbiota of wild Atlantic cod Gadus morhua L. upon captive rearing. Microb Ecol. 2011;61:20–30.

    PubMed 

    Google Scholar
     

  • 25.

    Nakamura N, Amato KR, Garber P, Estrada A, Mackie RI, Gaskins HR. Analysis of the hydrogenotrophic microbiota of wild and captive black howler monkeys (Alouatta pigra) in palenque national park, Mexico. Am J Primatol. 2011;73(9):909–19.

    PubMed 

    Google Scholar
     

  • 26.

    Wienemann T, Schmitt-Wagner D, Meuser K, Segelbacher G, Schink B, Brune A, Berthold P. The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds. Syst Appl Microbiol. 2011;34(7):542–51.

    PubMed 

    Google Scholar
     

  • 27.

    Eigeland K. Bacterial community structure in the hindgut of wild and captive dugongs (Dugong dugon). Aquat Mamm. 2012;38(4):402–11.


    Google Scholar
     

  • 28.

    Nelson TM, Rogers TL, Carlini AR, Brown MV. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol. 2013;15(4):1132–45.

    CAS 
    PubMed 

    Google Scholar
     

  • 29.

    Kohl KD, Dearing MD. Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity. Environ Microbiol Rep. 2014;6(2):191–5.

    PubMed 

    Google Scholar
     

  • 30.

    Kohl KD, Skopec MM, Dearing MD. Captivity results in disparate loss of gut microbial diversity in closely related hosts. Conserv Physiol. 2014;2(1):cou009.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 31.

    Kreisinger J, Cizkova D, Vohanka J, Pialek J. Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing. Mol Ecol. 2014;23(20):5048–60.

    CAS 
    PubMed 

    Google Scholar
     

  • 32.

    Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Tuan BV, Minh VV, et al. Captivity humanizes the primate microbiome. PNAS. 2016;113(37):10376–81.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 33.

    Delport TC, Power ML, Harcourt RG, Webster KN, Tetu SG. Colony location and captivity influence the gut microbial community composition of the Australian Sea Lion (Neophoca cinerea). Appl Environ Microbiol. 2016;82(12):3440–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 34.

    Xie Y, Xia P, Wang H, Yu H, Giesy JP, Zhang Y, Mora MA, Zhang X. Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis). Sci Rep. 2016;6:33350.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 35.

    Borbon-Garcia A, Reyes A, Vives-Florez M, Caballero S. Captivity shapes the gut microbiota of andean bears: insights into health surveillance. Front Microbiol. 2017;8:1316.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 36.

    Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Caviedes-Vidal E, Bordenstein SR. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Mol Ecol. 2017;26(4):1175–89.

    PubMed 

    Google Scholar
     

  • 37.

    Li Y, Hu X, Yang S, Zhou J, Zhang T, Qi L, Sun X, Fan M, Xu S, Cha M, et al. Comparative analysis of the gut microbiota composition between captive and wild forest musk deer. Front Microbiol. 2017;8:1705.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 38.

    Allan N, Knotts TA, Pesapane R, Ramsey JJ, Castle S, Clifford D, Foley J. Conservation implications of shifting gut microbiomes in captive-reared endangered voles intended for reintroduction into the wild. Microorganisms. 2018;6(3):94.

    CAS 
    PubMed Central 

    Google Scholar
     

  • 39.

    Leung JM, Budischak SA, Chung The H, Hansen C, Bowcutt R, Neill R, Shellman M, Loke P, Graham AL. Rapid environmental effects on gut nematode susceptibility in rewilded mice. PLoS Biol. 2018;16(3):e2004108.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 40.

    Chong R, Grueber CE, Fox S, Wise P, Barrs VR, Hogg CJ, Belov K. Looking like the locals—gut microbiome changes post-release in an endangered species. Anim Microbiome. 2019;1(1):8.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 41.

    Gibson KM, Nguyen BN, Neumann LM, Miller M, Buss P, Daniels S, Ahn MJ, Crandall KA, Pukazhenthi B. Gut microbiome differences between wild and captive black rhinoceros—implications for rhino health. Sci Rep. 2019;9(1):7570.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 42.

    Schmidt E, Mykytczuk N, Schulte-Hostedde AI. Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus). ISME J. 2019;13(5):1293–305.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 43.

    Shinohara A, Nohara M, Kondo Y, Jogahara T, Nagura-Kato GA, Izawa M, Koshimoto C. Comparison of the gut microbiotas of laboratory and wild Asian house shrews (Suncus murinus) based on cloned 16S rRNA sequences. Exp Anim. 2019;68(4):531–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 44.

    Smith T. The effect of gut microbiota on host fitness of animals released from captivity. Groningen: University of Groningen; 2019.


    Google Scholar
     

  • 45.

    Xiao Y, Xiao G, Liu H, Zhao X, Sun C, Tan X, Sun K, Liu S, Feng J. Captivity causes taxonomic and functional convergence of gut microbial communities in bats. PeerJ. 2019;7:e6844.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 46.

    Edenborough KM, Mu A, Muhldorfer K, Lechner J, Lander A, Bokelmann M, Couacy-Hymann E, Radonic A, Kurth A. Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity. PLoS ONE. 2020;15(3):e0223629.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 47.

    Lin JD, Devlin JC, Yeung F, McCauley C, Leung JM, Chen YH, Cronkite A, Hansen C, Drake-Dunn C, Ruggles KV, et al. Rewilding Nod2 and Atg16l1 mutant mice uncovers genetic and environmental contributions to microbial responses and immune cell composition. Cell Host Microbe. 2020;27(5):830–40.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 48.

    Martinez-Mota R, Kohl KD, Orr TJ, Denise Dearing M. Natural diets promote retention of the native gut microbiota in captive rodents. ISME J. 2020;14(1):67–78.

    CAS 
    PubMed 

    Google Scholar
     

  • 49.

    Ni Q, He X, Zeng B, Meng X, Xu H, Li Y, Yang M, Li D, Yao Y, Zhang M, et al. Variation in gut microbiota of captive bengal slow lorises. Curr Microbiol. 2020;77(10):2623–32.

    PubMed 

    Google Scholar
     

  • 50.

    Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative analysis of microbial community structure and function in the gut of wild and captive Amur tiger. Front Microbiol. 2020;11:1665.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 51.

    Oliveira BCM, Murray M, Tseng F, Widmer G. The fecal microbiota of wild and captive raptors. Anim Microbiome. 2020;2(1):15.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 52.

    Prabhu VR, Wasimuddin, Kamalakkannan R, Arjun MS, Nagarajan M. Consequences of domestication on gut microbiome: a comparative study between wild gaur and domestic mithun. Front Microbiol. 2020;11:133.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 53.

    Bowerman KL, Knowles SCL, Bradley JE, Baltrūnaitė L, Lynch MDJ, Jones KM, Hugenholtz P. Effects of laboratory domestication on the rodent gut microbiome. ISME Commun. 2021;1(1):1–14.


    Google Scholar
     

  • 54.

    Liu C, Hu J, Wu Y, Irwin DM, Chen W, Zhang Z, Yu L. Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins. J Genet Genom. 2021;48(9):825–35.


    Google Scholar
     

  • 55.

    Sawaswong V, Praianantathavorn K, Chanchaem P, Khamwut A, Kemthong T, Hamada Y, Malaivijitnond S, Payungporn S. Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand. Sci Rep. 2021;11(1):14280.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 56.

    Carey HV, Walters WA, Knight R. Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle. Am J Physiol Regul Integr Comp Physiol. 2013;304(1):R33-42.

    CAS 
    PubMed 

    Google Scholar
     

  • 57.

    Dill-McFarland KA, Neil KL, Zeng A, Sprenger RJ, Kurtz CC, Suen G, Carey HV. Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol Ecol. 2014;23(18):4658–69.

    CAS 
    PubMed 

    Google Scholar
     

  • 58.

    Stevenson TJ, Buck CL, Duddleston KN. Temporal dynamics of the cecal gut microbiota of juvenile arctic ground squirrels: a strong litter effect across the first active season. Appl Environ Microbiol. 2014;80(14):4260–8.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 59.

    Stevenson TJ, Duddleston KN, Buck CL. Effects of season and host physiological state on the diversity, density, and activity of the arctic ground squirrel cecal microbiota. Appl Environ Microbiol. 2014;80(18):5611–22.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 60.

    Sonoyama K, Fujiwara R, Takemura N, Ogasawara T, Watanabe J, Ito H, Morita T. Response of gut microbiota to fasting and hibernation in Syrian hamsters. Appl Environ Microbiol. 2009;75(20):6451–6.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 61.

    Luo D, Ziebell S, An L. An informative approach on differential abundance analysis for time-course metagenomic sequencing data. Bioinformatics. 2017;33(9):1286–92.

    CAS 
    PubMed 

    Google Scholar
     

  • 62.

    Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS ONE. 2014;9(4):e94249.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 63.

    Sinclair L, Osman OA, Bertilsson S, Eiler A. Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform. PLoS ONE. 2015;10(2):e0116955.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 64.

    Good IJ. The population frequencies of species and the estimation of population parameters. Biometrika. 1953;40(3/4):237–64.


    Google Scholar
     

  • 65.

    La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS ONE. 2012;7(12):e52078.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 66.

    Xia Y, Sun J, Ding-Geng C. Power and sample size calculations for microbiome data. In: Chen J, Ding-Geng C, editors. Statistical analysis of microbiome data with R. Singapore: Springer; 2018.


    Google Scholar
     

  • 67.

    Song H, Kim J, Guk JH, Kim WH, Nam H, Suh JG, Seong JK, Cho S. Metagenomic analysis of the gut microbiota of wild mice, a newly identified reservoir of Campylobacter. Front Cell Infect Microbiol. 2020;10:596149.

    CAS 
    PubMed 

    Google Scholar
     

  • 68.

    Derrien M, van Passel MWJ, van de Bovenkamp JHB, Schipper RG, de Vos WM, Dekker J. Mucin-bacterial interactions in the human oral cavity and digestive tract. Gut Microbes. 2010;1(4):254–68.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 69.

    Ju T, Kong JY, Stothard P, Willing BP. Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota. ISME J. 2019;13(6):1520–34.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 70.

    Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife. 2013;2:e01102.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 71.

    Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P. Photosynthesis is not a universal feature of the phylum Cyanobacteria. PeerJ. 2014. https://doi.org/10.7287/peerj.preprints.204v2.

    Article 

    Google Scholar
     

  • 72.

    Utami YD, Kuwahara H, Murakami T, Morikawa T, Sugaya K, Kihara K, Yuki M, Lo N, Deevong P, Hasin S, et al. Phylogenetic diversity and single-cell genome analysis of “Melainabacteria”, a non-photosynthetic cyanobacterial group, in the termite gut. Microbes Environ. 2018;33(1):50–7.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 73.

    Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 74.

    Kaoutari AE, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11(7):497–504.

    PubMed 

    Google Scholar
     

  • 75.

    Pengelley ET, Fisher KC. Rhythmical arousal from hibernation in the golden-mantled ground squirrel, Citellus lateralis tescorum. Can J Zool. 1961;39:105–20.


    Google Scholar
     

  • 76.

    Yuen KK, Dixon WJ. The approximate behaviour and performance of the two-sample trimmed t. Biometrika. 1973;60(2):369.


    Google Scholar
     

  • 77.

    Yuen KK. The two-sample trimmed t for unequal population variances. Biometrika. 1974;61(1):165.


    Google Scholar
     

  • 78.

    Skarlupka JH, Kamenetsky ME, Jewell KA, Suen G. The ruminal bacterial community in lactating dairy cows has limited variation on a day-to-day basis. J Anim Sci Biotechnol. 2019;10:66.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 79.

    Streubel DP, Fitzgerald JP. Spermophilus tridecemlineatus. Mamm Species. 1978;103:1–5.


    Google Scholar
     

  • 80.

    Stevenson DM, Weimer PJ. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol. 2007;75(1):165–74.

    CAS 
    PubMed 

    Google Scholar
     

  • 81.

    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS. 2011;108(1):4516–22.

    CAS 
    PubMed 

    Google Scholar
     

  • 82.

    Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79(17):5112–20.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 83.

    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 84.

    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35(21):7188–96.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 85.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590-596.

    CAS 

    Google Scholar
     

  • 86.

    Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glockner FO. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014;42(Database issue):D643-648.

    CAS 
    PubMed 

    Google Scholar
     

  • 87.

    Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, et al. 25 Years of serving the community with ribosomal RNA gene reference databases and tools. J Biotechnol. 2017;261:169–76.

    PubMed 

    Google Scholar
     

  • 88.

    R Development Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2020.


    Google Scholar
     

  • 89.

    McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8(4):e61217.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 90.

    Revell LJ. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3(2):217–23.


    Google Scholar
     

  • 91.

    Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2009.


    Google Scholar
     

  • 92.

    Auguie B. gridExtra: miscellaneous functions for “Grid” graphics, 2.3 ed. 2017.

  • 93.

    Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2019;35(3):526–8.

    CAS 
    PubMed 

    Google Scholar
     

  • 94.

    Wickham H, François R, Henry L, Müller K. dplyr: a grammar of data manipulation, 0.8.0.1 edn. 2019.

  • 95.

    Dinno A: dunn.test: Dunn’s test of multiple comparisons using rank sums, 1.3.5 ed. 2017.

  • 96.

    Torchiano M. effsize: efficient effect size computation. R package version 0.8.1 ed. 2020.

  • 97.

    Robinson A. equivalence: provides tests and graphics for assessing tests of equivalence, 0.7.2 ed. 2016.

  • 98.

    Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26(11):1463–4.

    CAS 
    PubMed 

    Google Scholar
     

  • 99.

    Champely S. pwr: basic functions for power analysis. R package version 1.3–0 edn. 2020.

  • 100.

    Wickham H, tidyr: tidy messy data, 1.1.2 ed. 2020.

  • 101.

    Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, et al. vegan: community ecology package, 2.4–6 ed. 2018.

  • 102.

    Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27(379–423):623–56.


    Google Scholar
     

  • 103.

    Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, et al. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol Rev Camb Philos Soc. 2017;92(2):698–715.

    PubMed 

    Google Scholar
     

  • 104.

    Anderson MJ, Walsh DCI. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogenous dispersions: what null hypothesis are you testing? Ecol Monogr. 2013;83(4):557–74.


    Google Scholar
     

  • Rights and permissions

    Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

    Disclaimer:

    This article is autogenerated using RSS feeds and has not been created or edited by OA JF.

    Click here for Source link (https://www.biomedcentral.com/)