McKenney EA, Koelle K, Dunn RR, Yoder AD. The ecosystem services of animal microbiomes. Mol Ecol. 2018;27:2164–72.
Google Scholar
Miller ET, Svanbäck R, Bohannan BJM. Microbiomes as metacommunities: understanding host-associated microbes through metacommunity ecology. Trends Ecol Evol. 2018;33:926–35.
Google Scholar
Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe. 2019;25:789–802.
Google Scholar
Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol. 2019;81:1–23.
Sun B, Wang X, Bernstein S, Huffman MA, Xia DP, Gu Z, et al. Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana). Sci Rep. 2016;6:1–8.
Wu Q, Wang X, Ding Y, Hu Y, Nie Y, Wei W, et al. Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas. Proc R Soc B Biol Sci. 2017;284:20170955.
Maurice CF, Knowles SCL, Ladau J, Pollard KS, Fenton A, Pedersen AB, et al. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015;9:2423–34.
Google Scholar
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). Microb Ecol. 2014;69:434–43.
Google Scholar
Orkin JD, Campos FA, Myers MS, Cheves Hernandez SE, Guadamuz A, Melin AD. Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest. ISME J. 2019;13:183–96. 22.
Google Scholar
Springer A, Fichtel C, Al-Ghalith GA, Koch F, Amato KR, Clayton JB, 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;7:5732–45.
Google Scholar
Jagsi R, Jiang J, Momoh AO, Alderman A, Giordano SH, Buchholz TA, et al. Seasonal cycling in the gut microbiome of the Hadza Hunter-Gatherers of Tanzania. Science. 2017;357:802–6.
Hicks AL, Lee KJ, Couto-Rodriguez M, Patel J, Sinha R, Guo C, et al. Gut microbiomes of wild great apes fluctuate seasonally in response to diet. Nat Commun. 2018;9:1786.
Google Scholar
Baniel A, Amato KR, Beehner JC, Bergman TJ, Mercer A, Perlman RF, et al. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas. Microbiome. 2021;9:1–20.
Ren T, Grieneisen LE, Alberts SC, Archie EA, Wu M. Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. Environ Microbiol. 2016;18:1312–25.
Google Scholar
Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One. 2013;8:e57923.
Google Scholar
De Vrieze J, Pinto AJ, Sloan WT, Ijaz UZ. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome. 2018;6:63.
Google Scholar
Kappeler PM, Fichtel C. A 15-year perspective on the social organization and life history of sifaka in Kirindy Forest. In: Long-term field studies of primates. Springer Berlin Heidelberg; 2012. p. 101–21.
Peckre LR, Defolie C, Kappeler PM, Fichtel C. Potential self-medication using millipede secretions in red-fronted lemurs: combining anointment and ingestion for a joint action against gastrointestinal parasites? Primates. 2018;59:483–94.
Google Scholar
Ostner J. Social thermoregulation in redfronted lemurs (Eulemur fulvus rufus). Folia Primatol. 2002;73:175–80.
Amoroso CR, Kappeler PM, Fichtel C, Nunn CL. Water availability impacts habitat use by red-fronted lemurs (Eulemur rufifrons): An experimental and observational study. Int J Primatol. 2020;41:61–80.
Koch F, Ganzhorn JU, Rothman JM, Chapman CA, Fichtel C. Sex and seasonal differences in diet and nutrient intake in Verreaux’s sifakas (Propithecus verreauxi). Am J Primatol. 2017;79:1–10.
Google Scholar
Clough D. Gastro-intestinal parasites of red-fronted lemurs in Kirindy Forest, western Madagascar. J Parasitol. 2010;96:245–51.
Google Scholar
Gogarten JF, Calvignac-Spencer S, Nunn CL, Ulrich M, Saiepour N, Nielsen HV, et al. Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Mol Ecol Resour. 2020;20:204–15.
Google Scholar
Lai GC, Tan TG, Pavelka N. The mammalian mycobiome: A complex system in a dynamic relationship with the host. Wiley Interdiscip Rev Syst Biol Med. 2019;11:e1438.
Google Scholar
Mann AE, Mazel F, Lemay MA, Morien E, Billy V, Kowalewski M, et al. Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME J. 2020;14:609–22.
Google Scholar
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.
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:1–11.
Toju H, Tanabe AS, Yamamoto S, Sato H. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One. 2012;7:e40863.
Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, et al. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol. 2010;60:784–95.
Google Scholar
Gantner S, Andersson AF, Alonso-Sáez L, Bertilsson S. Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. J Microbiol Methods. 2011;84:12–8.
Google Scholar
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.
Google Scholar
Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ Microbiol Rep. 2019;11:487–94.
Google Scholar
Berkelmann D, Schneider D, Hennings N, Meryandini A, Daniel R. Soil bacterial community structures in relation to different oil palm management practices. Sci Data. 2020;7:1–7.
Chen S, Zhou Y, Chen Y, Gu J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Google Scholar
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: A fast and accurate Illumina paired-end read mergeR. Bioinformatics. 2014;30:614–20.
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: A versatile open source tool for metagenomics. PeerJ. 2016;2016:1–22.
Edgar RC UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv. 2016;081257.
Edgar RC UCHIME2: improved chimera prediction for amplicon sequencing. bioRxiv. 2016;074252.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:590–6.
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The protist ribosomal reference database (PR2): A catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013;41:597–604.
Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, et al. The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019;47:D259–64.
Google Scholar
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12:635–45.
Google Scholar
Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–7.
Google Scholar
Team Rc. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020. Available from: https://www.r-project.org.
Team Rs. RStudio: Integrated Development for R. Boston, MA: RStudio; 2019.
Andersen KS, Kirkegaard RH, Albertsen M ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv. 2018;10–1.
Paradis E, Claude J, Strimmer K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90.
Google Scholar
Wickham H, Rstudio. stringr: Simple, consistent wrappers for common string operations. 2019. Available from: https://cran.r-project.org/package=stringr.
Wickham H. Reshaping data with the reshape package. J Stat Softw. 2007;21:1–20.
Dowle M, Srinivasan A, Gorecki J, Chirico M, Stetsenko P, Short T, et al. data.table: Extension of “data.frame”. 2019. Available from: https://cran.r-project.org/package=data.table.
Wickham H, Averick M, Bryan J, Chang W, McGowan L, François R, et al. Welcome to the Tidyverse. J Open Source Softw. 2019;4:1686.
Wickham H ggplot2: Elegant graphics for data analysis. New York: Spinger-Verlag New York; 2016.
Chen L, Reeve J, Zhang L, Huang S, Wang X, Chen J. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ. 2018;2018:1–20.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
Rambaut A. FigTree—tree figure drawing tool. Institute of Evolutionary Biology, University of Edinburg; 2020. Available from: http://tree.bio.ed.ac.uk/software/figtree.
Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26:1463–4.
Google Scholar
Marzano V, Mancinelli L, Bracaglia G, Del Chierico F, Vernocchi P, Di Girolamo F, et al. “Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome.”. PLoS Negl Trop Dis. 2017;11:e0005916.
Google Scholar
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Heal Dis. 2015;26:27663.
Hothorn T, Hornik K exactRankTests: exact distributions for rank and permutation tests. 2019. Available from: https://cran.r-project.org/package=exactRankTests.
Pinheiro J, Bates D, DebRoy S, Sarkar D, Core Team R nlme: Linear and nonlinear mixed effects models. 2020. Available from: https://cran.r-project.org/package=nlme.
van den Boogaart G, Tolosana R compositions: an R package for compositional data analysis. 2020. Available from: http://www.stat.boogaart.de/compositions/.
Wickham H, Francois R, Core Team R, Rstudio, Jylänki J, Jorgensen M readr: Read rectangular text data. 2018. Available from: http://readr.tidyverse.org.
Oksanen J, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community ecology package. 2019. Available from: https://cran.r-project.org/package=vegan.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: An effective distance metric for microbial community comparison. ISME J. 2011;5:169–72.
Google Scholar
Bates D, Mächler M, Bolker BM, Walker SC. Fitting linear mixed-effects models using lme4. J Stat Softw. 2015;67:1–48.
Reitmeier S, Hitch TCA, Treichel N, Fikas N, Hausmann B, Ramer-Tait AE, et al. Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling. ISME COMMUN. 2021;1:31.
Sweeny AR, Lemon H, Ibrahim A, Nussey DH, Free A, McNally L. A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance (preprint). bioRxiv. 2020; https://doi.org/10.1101/2020.11.24.395715.
Barr DJ, Levy R, Scheepers C, Tily HJ. Random effects structure for confirmatory hypothesis testing: Keep it maximal. J Mem Lang. 2013;68:255–78.
Matuschek H, Kliegl R, Vasishth S, Baayen H, Bates D. Balancing type I error and power in linear mixed models. J Mem Lang. 2017;94:305–15.
Fox J, Weisberg S. An R companion to applied regression. 3rd ed. Thousand Oaks, California: Sage Publishing; 2019.
Bolker BM. Ecological models and data in R. New Jersey, USA: Princeton University Press; 2008.
Adams DC, Anthony CD. Using randomization techniques to analyse behavioural data. Anim Behav. 1996;51:733–8.
Baayen RH. Analyzing linguistic data. Cambridge: Cambridge University Press; 2008.
Bartón K MuMIn: Multi-Model Inference. 2020. Available from: https://cran.r-project.org/package=MuMIn.
Lüdecke D. sjPlot: Data Visualization for Statistics in Social Science. 2021. Available from: https://cran.r-project.org/package=sjPlot.
Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
Google Scholar
NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018;46:D8–13.
Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol. 2019;17:95–109. 15.
Google Scholar
Koskinen K, Pausan MR, Perras AK, Beck M, Bang C, Mora M, et al. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. MBio. 2017;8:1–17.
Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2017;2:1–12.
Ley RE. Prevotella in the gut: choose carefully. Nat Rev Gastroenterol Hepatol. 2016;13:69–70.
Google Scholar
Manara S, Asnicar F, Beghini F, Bazzani D, Cumbo F, Zolfo M, et al. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biol. 2019;20:299.
Google Scholar
Umanets A, de Winter I, IJdema F, Ramiro-Garcia J, van Hooft P, Heitkönig IMA, et al. Occupancy strongly influences faecal microbial composition of wild lemurs. FEMS Microbiol Ecol. 2018;94:1–13.
Greene LK, Clayton JB, Rothman RS, Semel BP, Semel MA, Gillespie TR, et al. Local habitat, not phylogenetic relatedness, predicts gut microbiota better within folivorous than frugivorous lemur lineages. Biol Lett. 2019;15:5–11.
Daniel H, Gholami AM, Berry D, Desmarchelier C, Hahne H, Loh G, et al. High-fat diet alters gut microbiota physiology in mice. ISME J. 2014;8:295–308.
Google Scholar
Hiippala K, Kainulainen V, Kalliomäki M, Arkkila P, Satokari R. Mucosal prevalence and interactions with the epithelium indicate commensalism of Sutterella spp. Front Microbiol. 2016;7:1–13.
Heintz-Buschart A, Wilmes P. Human gut microbiome: Function matters. Trends Microbiol. 2018;26:563–74.
Google Scholar
Ricaboni D, Mailhe M, Cadoret F, Vitton V, Fournier PE, Raoult D. ‘Colidextribacter massiliensis’ gen. nov., sp. nov., isolated from human right colon. New Microbes New Infect. 2017;17:27–9.
Google Scholar
Qin P, Zou Y, Dai Y, Luo G, Zhang X, Xiao L. Characterization a novel butyric acid-producing bacterium Collinsella aerofaciens subsp. shenzhenensis subsp. nov. Microorganisms. 2019;7:78.
Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, et al. Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. Int J Syst Evol Microbiol. 2014;64:2642–9.
Google Scholar
Amato KR, Garber PA. Nutrition and foraging strategies of the black howler monkey (Alouatta pigra) in Palenque National Park, Mexico. Am J Primatol. 2014;76:774–87.
Google Scholar
White TCR. The significance of unripe seeds and animal tissues in the protein nutrition of herbivores. Biol Rev. 2011;86:217–24.
Google Scholar
Ortmann S, Bradley BJ, Stolter C, Ganzhorn JU. Estimating the quality and composition of wild animal diets—a critical survey of methods. In: Hohmann G, Robbins M, Boesch C, editors. Feeding ecology in apes and other primates ecological, physical, and behavioral aspects. Cambridge: Cambridge University Press; 2006. p. 395–418.
Hippe H, Hagelstein A, Kramer I, Swiderski J, Stackebrandt E. Phylogenetic analysis of Formivibrio citricus, Propionivibrio dicarboxylicus, Anaerobiospirillum thomasii, Succinirnonas amylolytica and Succinivibrio dextrinosolvens and proposal of Succinivibrionaceae fam. nov. Int J Syst Evol Microbiol. 1999;49:779–82.
Privé F, Kaderbhai NN, Girdwood S, Worgan HJ, Pinloche E, Scollan ND, et al. Identification and characterization of three novel lipases belonging to families II and V from Anaerovibrio lipolyticus 5ST. PLoS One. 2013;8:e69076.
Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R, Bengelsdorf FR. Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens. Int J Syst Evol Microbiol. 2020;70:4269–79.
Google Scholar
Watanabe Y, Nagai F, Morotomi M. Characterization of Phascolarctobacterium succinatutens sp. Nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. Appl Environ Microbiol. 2012;78:511–8.
Google Scholar
Clough D, Heistermann M, Kappeler PM. Host intrinsic determinants and potential consequences of parasite infection in free-ranging red-fronted lemurs (Eulemur fulvus rufus). Am J Phys Anthropol. 2010;142:441–52.
Google Scholar
Sarkar A, Harty S, Johnson KVA, 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.
Google Scholar
van Vliet DM, Lin Y, Bale NJ, Koenen M, Villanueva L, Stams AJM, et al. Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., two marine anaerobes of the Pontiellaceae fam. nov. producing sulfated glycosaminoglycan-like exopolymers. Microorganisms. 2020;8:920. 18.
Google Scholar
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