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Social networks strongly predict the gut microbiota of wild mice

  • 1.

    Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–31.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 2.

    Monachese M, Burton JP, Reid G. Bioremediation and tolerance of humans to heavy metals through microbial processes: a potential role for probiotics?. Appl Environ Microbiol. 2012;78:6397–404.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 3.

    Chevalier C, Stojanovi O, Colin DJ, Suarez-Zamorano N, Tarallo V, Veyrat-Durebex C, et al. Gut microbiota orchestrates energy homeostasis during cold. Cell. 2015;163:1360–74.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 4.

    Kamada N, Kim Y-G, Sham HP, Vallance BA, Puente JL, Martens EC, et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science. 2012;336:1325–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 5.

    Zhang N, He Q-S. Commensal microbiome promotes resistance to local and systemic infections. Chin Med J. 2015;128:2250–5.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 6.

    Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336:1268–73.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 7.

    Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature 2016;535:75–84.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 8.

    Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016;535:65–74.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 9.

    Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci USA. 2012;109:8334–9.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 10.

    De Luca F, Shoenfeld Y. The microbiome in autoimmune diseases. Clin Exp Immuno l. 2019;195:74–85.

    Article 
    CAS 

    Google Scholar 

  • 11.

    Costello EK, Stagaman K, Dethlefsen L, Bohannan BJM, Relman DA. The application of ecological theory toward an understanding of the human microbiome. Science. 2012;336:1255–62.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010;107:11971–5.

    PubMed 
    Article 

    Google Scholar 

  • 13.

    Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133–45.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 14.

    Lane AA, McGuire MK, McGuire MA, Williams JE, Lackey KA, Hagen EH, et al. Household composition and the infant fecal microbiome: the INSPIRE study. Am J Phys Anthropol. 2019;169:526–39.

    PubMed 
    Article 

    Google Scholar 

  • 15.

    Lehtimäki J, Karkman A, Laatikainen T, Paalanen L, von Hertzen L, Haahtela T, et al. Patterns in the skin microbiota differ in children and teenagers between rural and urban environments. Sci Rep. 2017;7:45651.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 16.

    Tamburini S, Shen N, Wu H, medicine JC-N. The microbiome in early life: implications for health outcomes. Nat Med. 2016;22:713–22.

    CAS 
    Article 

    Google Scholar 

  • 17.

    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;1:6ra14.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 18.

    David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559–63.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 19.

    Ottman N, Ruokolainen L, Suomalainen A, Sinkko H, Karisola P, Lehtimäki J, et al. Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model. J Allergy Clin Immunol. 2019;143:1198–206.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 20.

    Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, et al. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc R Soc B Biol Sci. 2019;286:20190431.

    Article 

    Google Scholar 

  • 21.

    Sarkar A, Harty S, Johnson KV-A, Moeller AH, Archie EA, Schell LD, et al. Microbial transmission in animal social networks and the social microbiome. Nat Ecol Evol. 2020;4:1020–35.

    PubMed 
    Article 

    Google Scholar 

  • 22.

    Moeller AH, Suzuki TA, Phifer-Rixey M, Nachman MW. Transmission modes of the mammalian gut microbiota. Science. 2018;362:453–7.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 23.

    Hufeldt MR, Nielsen DS, Vogensen FK, Midtvedt T, Hansen AK. Variation in the gut microbiota of laboratory mice is related to both genetic and environmental factors. Comp Med. 2010;60:336–47.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Hildebrand F, Nguyen TLA, Brinkman B, Yunta R, Cauwe B, Vandenabeele P, et al. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol. 2013;14:R4.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 25.

    Lees H, Swann J, Poucher SM, Nicholson JK, Holmes E, Wilson ID, et al. Age and microenvironment outweigh genetic influence on the Zucker rat microbiome. PloS One. 2014;9:e100916.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 26.

    Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, et al. Social networks predict gut microbiome composition in wild baboons. Elife. 2015;4:e05224.

    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • 27.

    Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, et al. Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. J Anim Ecol. 2018;87:388–99.

    PubMed 
    Article 

    Google Scholar 

  • 28.

    Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA. Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka. Proc Biol Sci. 2017;284:20172274.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. Sci Adv. 2016;2:e1500997.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 30.

    Wikberg EC, Christie D, Sicotte P, Ting N. Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Anim Behav. 2020;163:17–31.

    Article 

    Google Scholar 

  • 31.

    Bennett G, Malone M, Sauther ML, Cuozzo FP, White B, Nelson KE, et al. Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). Am J Primatol. 2016;78:883–92.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 32.

    Theis KR, Schmidt TM, Holekamp KE. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Sci Rep. 2012;2:615.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Leclaire S, Nielsen JF, Drea CM. Bacterial communities in meerkat anal scent secretions vary with host sex, age, and group membership. Behav Ecol. 2014;25:996–1004.

    Article 

    Google Scholar 

  • 34.

    Antwis RE, Lea JMD, Unwin B, Shultz S. Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies. Microbiome. 2018;6:207.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013;2:e00458.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 36.

    Grieneisen LE, Livermore J, Alberts S, Tung J, Archie EA. Group living and male dispersal predict the core gut microbiome in wild baboons. Integr Comp Biol. 2017;57:770–85.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 37.

    Dill-McFarland KA, Tang Z-Z, Kemis JH, Kerby RL, Chen G, Palloni A, et al. Close social relationships correlate with human gut microbiota composition. Sci Rep. 2019;9:703.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 38.

    Wilson EO. Elementary concepts in sociobiology. In: Wilson EO, editors. Sociobiology: The New Synthesis. 25th ed. Cambridge, Massachutes, USA: Harvard University Press; 2000. p. 8.

    Google Scholar 

  • 39.

    Godsall B. Mechanisms of space use in the wood mouse, Apodemus sylvaticus. Doctoral Thesis, London: Imperial College; 2015.

  • 40.

    Wolton RJ. The ranging and nesting behaviour of Wood mice, Apodemus sylvaticus (Rodentia: Muridae), as revealed by radio-tracking. J Zool. 2009;206:203–22.

    Article 

    Google Scholar 

  • 41.

    Stopka P, Macdonald DW. The market effect in the Wood mouse, Apodemus sylvaticus: selling information on reproductive status. Ethology. 2001;105:969–82.

  • 42.

    Walton JB, Andrews JF. Torpor induced by food deprivation in the Wood mouse Apodemus sylvaticus. J Zool. 2009;194:260–3.

    Article 

    Google Scholar 

  • 43.

    Wolton RJ. A possible role for faeces in range-marking by the Wood mouse, Apodemus sylvaticus. J Zool. 2009;206:286–91.

    Article 

    Google Scholar 

  • 44.

    Wolton RJ. Individual recognition by olfaction in the Wood Mouse, Apodemus sylvaticus. Behaviour. 1984;88:191–9.

    Article 

    Google Scholar 

  • 45.

    Godsall B, Coulson T, Malo AF. From physiology to space use: energy reserves and androgenization explain home-range size variation in a woodland rodent. J Anim Ecol. 2014;83:126–35.

    PubMed 
    Article 

    Google Scholar 

  • 46.

    Wang J, Santure AW. Parentage and sibship inference from multilocus genotype data under polygamy. Genetics. 2009;181:1579–94.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Farine DR. Animal social network inference and permutations for ecologists in R using asnipe. Methods Ecol Evol. 2013;4:1187–94.

    Article 

    Google Scholar 

  • 48.

    Csardi G, Nepusz T. The igraph software package for complex network research. Inter J Complex Syst. 2006;1695:1–9.

    Google Scholar 

  • 49.

    Firth JA, Sheldon BC. Social carry-over effects underpin trans-seasonally linked structure in a wild bird population. Ecol Lett. 2016;19:1324–32.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 50.

    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 
    Article 

    Google Scholar 

  • 51.

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

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 52.

    McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. Methods for normalizing microbiome data: an ecological perspective. Methods. Ecol Evol. 2019;10:389–400.

    Google Scholar 

  • 53.

    Hsieh TC, Ma KH, Chao A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods. Ecol Evol. 2016;7:1451–6.

    Google Scholar 

  • 54.

    Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MH, Oksanen MJ, et al. The vegan package. Community Ecol Package. 2007;10:719.

    Google Scholar 

  • 55.

    Bürkner PC. brms: an R package for Bayesian multilevel models using stan. J Stat Softw. 2017;80:1–28.

    Article 

    Google Scholar 

  • 56.

    Bürkner PC. Advanced Bayesian multilevel modeling with the R package brms. R J. 2018;10:395–411.

    Article 

    Google Scholar 

  • 57.

    Hadfield JD. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J Stat Softw. 2010;33:1–22.

    Article 

    Google Scholar 

  • 58.

    Dekker D, Krackhardt D, Snijders TA. Sensitivity of MRQAP tests to collinearity and autocorrelation conditions. Psychometrika. 2007;72:563–81.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 59.

    Ormerod KL, Wood DLA, Lachner N, Gellatly SL, Daly JN, Parsons JD, et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome. 2016;4:36.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 60.

    Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological functions of agricultural soil bacteria and microeukaryotes in chitin degradation: a case study. Front Microbiol. 2019;10:1293.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 61.

    Huang X, Liu L, Zhao J, Zhang J, Cai Z. The families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae are the dominant bacterial groups during reductive soil disinfestation with incorporated plant residues. Appl Soil Ecol. 2019; 135:65–72.

  • 62.

    Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, et al. Cospeciation of gut microbiota with hominids. Science. 2016;353:380–2.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 63.

    Tew TE, Macdonald DW. Dynamics of space use and male vigour amongst wood mice, Apodemus sylvaticus, in the cereal ecosystem. Behav Ecol Sociobiol. 1994;34:337–45.

    Article 

    Google Scholar 

  • 64.

    Erazo D, Pedersen AB, Gallagher K, Fenton A. Who acquires infection from whom? Estimating herpesvirus transmission rates between wild rodent host groups. 2020, https://www.biorxiv.org/content/10.1101/2020.09.18.302489v1.

  • 65.

    Taylor SE, Klein LC, Lewis BP, Gruenewald TL, Gurung RAR, Updegraff JA. Biobehavioral responses to stress in females: tend-and-befriend, not fight-or-flight. Psychol Rev. 2000;107:411–29.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 66.

    Amato KR, Van Belle S, Di Fiore A, Estrada A, Stumpf R, White B, et al. Patterns in gut microbiota similarity associated with degree of sociality among sex classes of a neotropical primate. Micro Ecol. 2017;74:250–8.

    Article 

    Google Scholar 

  • 67.

    Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, et al. Transmission of human-associated microbiota along family and social networks. Nat Microbiol. 2019;4:964–71.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 68.

    Johnson KV-A. Gut microbiome composition and diversity are related to human personality traits. Hum Microbiome J. 2020;15:100069.

    Article 

    Google Scholar 

  • 69.

    Levin II, Zonana DM, Fosdick BK, Song SJ, Knight R, Safran RJ. Stress response, gut microbial diversity and sexual signals correlate with social interactions. Biol Lett. 2016;12:20160352.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 70.

    Mouquet N, Loreau M. Community patterns in source‐sink metacommunities. Am Nat. 2003;162:544–57.

    PubMed 
    Article 

    Google Scholar 

  • 71.

    Altizer S, Nunn CL, Thrall PH, Gittleman JL, Antonovics J, Cunningham AA, et al. Social organization and parasite risk in mammals: Integrating theory and empirical studies. Annu Rev Ecol Evol Syst. 2003;34:517–47.

    Article 

    Google Scholar 

  • 72.

    Loehle C. Social barriers to pathogen transmission in wild animal populations. Ecology. 1995;76:326–35.

    Article 

    Google Scholar 

  • 73.

    Moeller A, Dufva R, Allander K. Parasites and the evolution of host social behavior. Adv Study Behav. 1993;22:65–102.

    Article 

    Google Scholar 

  • 74.

    Reese AT, Dunn RR. Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. MBio. 2018;9:4.

    Article 

    Google Scholar 

  • 75.

    Shade A. Diversity is the question, not the answer. ISME J. 2017;11:1–6.

    PubMed 
    Article 

    Google Scholar 

  • 76.

    Pallen MJ. The human microbiome and host-pathogen interactions. In: Metagenomics of the human body. New York, NY: Springer; 2011; p 43–61.

  • 77.

    Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, et al. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Micro Ecol. 2014;69:434–43.

    Article 
    CAS 

    Google Scholar 

  • 78.

    Barribeau SM, Villinger J, Waldman B. Ecological immunogenetics of life-history traits in a model amphibian. Biol Lett. 2012;8:405–7.

    PubMed 
    Article 

    Google Scholar 

  • 79.

    Feng T, Elson CO. Adaptive immunity in the host-microbiota dialog. Mucosal Immunol. 2011;4:15–21.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 80.

    Amato KR. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution. Am J Phys Anthropol. 2016;159:196–215.

    Article 

    Google Scholar 

  • 81.

    Knowles SCL, Eccles RM, Baltrūnaitė L. Species identity dominates over environment in shaping the microbiota of small mammals. Ecol Lett. 2019;22:826–37.

    CAS 
    PubMed 
    Article 

    Google Scholar 


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