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Diet and gut microbiome enterotype are associated at the population level in African buffalo

  • 1.

    Tringe, S. G. & Hugenholtz, P. A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 11, 442–446 (2008).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 2.

    Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 3.

    Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 4.

    Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    Pascoe, E. L., Hauffe, H. C., Marchesi, J. R. & Perkins, S. E. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. ISME J. 11, 2644–2651 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 6.

    Gentile, C. L. & Weir, T. L. The gut microbiota at the intersection of diet and human health. Science 362, 776–780 (2018).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 7.

    Gilbert, J. A. et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94–103 (2016).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 8.

    Thaiss, C. A. et al. Persistent microbiome alterations modulate the rate of post-dieting weight regain. Nature 540, 544–551 (2016).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 9.

    Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 16, 276–289 (2014).

  • 10.

    Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc. Biol. Sci. 286, 20182448 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Nishida, A. H. & Ochman, H. Rates of gut microbiome divergence in mammals. Mol. Ecol. 27, 1884–1897 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    Reese, T. & Dunn, R. Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. mBio 9, e01294–18 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 13.

    Allison, M. J. Biosynthesis of amino acids by ruminal microorganisms. J. Anim. Sci. 29, 797–807 (1969).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Matthews, C. et al. The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency. Gut Microbes 10, 115–132 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 15.

    Cui, K., Qi, M., Wang, S., Diao, Q. & Zhang, N. Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs. Sci. Rep. 9, 16612 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 16.

    Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Moeller, A. H. et al. Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat. Commun. 3, 1179 (2012).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 19.

    Knights, D. et al. Rethinking “Enterotypes. Cell Host Microbe 16, 433–437 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Jeffery, I. B., Claesson, M. J., O’Toole, P. W. & Shanahan, F. Categorization of the gut microbiota: enterotypes or gradients? Nat. Rev. Microbiol. 10, 591–592 (2012).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 21.

    Hicks, A. L. et al. Gut microbiomes of wild great apes fluctuate seasonally in response to diet. Nat. Commun. 9, 1786 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 22.

    Ren, T. et al. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome 5, 163 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 23.

    Kartzinel, T. R., Hsing, J. C., Musili, P. M., Brown, B. R. P. & Pringle, R. M. Covariation of diet and gut microbiome in African megafauna. Proc. Natl Acad. Sci. USA 116, 23588–23593 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Bergmann, G. T., Craine, J. M., Robeson, M. S. 2nd & Fierer, N. Seasonal shifts in diet and gut microbiota of the American Bison (Bison bison). PLoS ONE 10, e0142409 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 25.

    Couch, C. E. et al. Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Sci. Rep. 10, 6582 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Burkepile, D. E. & Parker, J. D. Recent advances in plant-herbivore interactions. F1000Res. 6, 119 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 27.

    Dearing, M. D. & Kohl, K. D. Beyond fermentation: other important services provided to endothermic herbivores by their gut microbiota. Integr. Comp. Biol. 57, 723–731 (2017).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 28.

    Honda, K. & Littman, D. R. The microbiome in infectious disease and inflammation. Annu. Rev. Immunol. 30, 759–795 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Buffie, C. G. & Pamer, E. G. Microbiota-mediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol. 13, 790–801 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Sood, U., Bajaj, A., Kumar, R., Khurana, S. & Kalia, V. C. Infection and microbiome: impact of tuberculosis on human gut microbiome of Indian cohort. Indian J. Microbiol. 58, 123–125 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Seetharam, S. & Glass, A. Respiratory infections and their effect on the paediatric lung microbiome. Curr. Opin. Allergy Clin. Immunol. 32, 82–86 (2019).

    Google Scholar 

  • 32.

    Worthington, R. W. & Bigalke, R. D. A review of the infectious disease of African wild ruminants. Onderstepoort J. Vet. Res. 68, 291–323 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • 33.

    Youngblut, N. D. et al. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat. Commun. 10, 2200 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 34.

    Chase, J. M. & Leibold, M. A. Spatial scale dictates the productivity-biodiversity relationship. Nature 416, 427–430 (2002).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 35.

    Bastille-Rousseau, G. et al. Climate change can alter predator—prey dynamics and population viability of prey. Oecologia 186, 141–150 (2018).

    ADS 
    PubMed 
    Article 

    Google Scholar 

  • 36.

    DuBowy, P. J. Waterfowl communities and seasonal environments: temporal variability in interspecific competition. Ecology 69, 1439–1453 (1988).

    Article 

    Google Scholar 

  • 37.

    Sun, C.-H., Liu, H.-Y., Liu, B., Yuan, B.-D. & Lu, C.-H. Analysis of the gut microbiome of wild and captive Père David’s deer. Front. Microbiol. 10, 2331 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Haworth, S. E., White, K. S., Côté, S. D. & Shafer, A. B. A. Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate. FEMS Microbiol. Ecol. 95, fiz095 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 39.

    Li, J.-G. et al. The gut bacterial community composition of wild cervus albirostris (white-lipped deer) detected by the 16S ribosomal RNA gene sequencing. Curr. Microbiol. 74, 1100–1107 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 40.

    Mao, S., Huo, W. & Zhu, W. Use of pyrosequencing to characterize the microbiota in the ileum of goats fed with increasing proportion of dietary grain. Curr. Microbiol. 67, 341–350 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 41.

    Lau, S. K. P. et al. Differential microbial communities of omnivorous and herbivorous cattle in Southern China. Comput. Struct. Biotechnol. J. 16, 54–60 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 42.

    Turner, W. C., Jolles, A. E. & Owen-Smith, N. Alternating sexual segregation during the mating season by male African buffalo (Syncerus caffer). J. Zool. 267, 291 (2005).

    Article 

    Google Scholar 

  • 43.

    Moeller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 44.

    Gondaira, S. et al. Immunosuppression in cows following intramammary infusion of Mycoplasma bovis. Infect. Immun. https://doi.org/10.1128/IAI.00521-19 (2019).

  • 45.

    Jones, C. Bovine Herpesvirus 1 counteracts immune responses and immune-surveillance to enhance pathogenesis and virus transmission. Front. Immunol. 10, 1008 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 46.

    Kapil, S., Walz, P., Wilkerson, M. & Minocha, H. Immunity and immunosuppression. Bovine viral diarrhea virus: diagnosis, management and control (2005).

  • 47.

    Hijmans, R. J. & van Etten, J. raster: Geographic data analysis and modeling. R package version 2, (2016).

  • 48.

    Pebesma, E. & Bivand, R. S. S classes and methods for spatial data: the sp package. R. N. 5, 9–13 (2005).

    Google Scholar 

  • 49.

    Bivand, R., Keitt, T., Rowlingson, B. & Pebesma, E. rgdal: Bindings for the geospatial data abstraction library. R package version 1, (2016).

  • 50.

    Bivand, R. & Lewin-Koh, N. maptools: Tools for Reading and Handling Spatial Objects. R package version 0.9-2. (2013).

  • 51.

    Bivand, R. & Rundel, C. rgeos: interface to geometry engine. Open source (GEOS). R package ver. 0.3-8. (2013).

  • 52.

    Kock, M., Meltzer, D. & Burroughs, R. Chemical and Physical Restraint of Wild Animals: A Training and Field Manual for African Species (IWCS, 2006).

  • 53.

    Beechler, B. R., Jolles, A. E. & Ezenwa, V. O. Evaluation of hematologic values in free-ranging African buffalo (Syncerus caffer). J. Wildl. Dis. 45, 57–66 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 54.

    Couch, C. E. et al. Serum biochemistry panels in African buffalo: Defining reference intervals and assessing variability across season, age and sex. PLoS ONE 12, e0176830 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 55.

    Glidden, C. K. et al. Detection of pathogen exposure in African buffalo using non-specific markers of inflammation. Front. Immunol. 8, 1944 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 56.

    Ezenwa, V. O., Jolles, A. E. & O’Brien, M. P. A reliable body condition scoring technique for estimating condition in African buffalo. Afr. J. Ecol. 47, 476–481 (2009).

    Article 

    Google Scholar 

  • 57.

    Ezenwa, V. O. Interactions among host diet, nutritional status and gastrointestinal parasite infection in wild bovids. Int. J. Parasitol. 34, 535–542 (2004).

    PubMed 
    Article 

    Google Scholar 

  • 58.

    Christianson, D. & Creel, S. Fecal chlorophyll describes the link between primary production and consumption in a terrestrial herbivore. Ecol. Appl. 19, 1323–1335 (2009).

    PubMed 
    Article 

    Google Scholar 

  • 59.

    Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 60.

    Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 27 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 61.

    R Core Team. R: A Language and Environment for Statistical Computing (R Core Team, 2020).

  • 62.

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

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 63.

    Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–44 (2015).

    Article 

    Google Scholar 

  • 64.

    Reynolds, A. P., Richards, G., de la Iglesia, B. & Rayward-Smith, V. J. Clustering rules: a comparison of partitioning and hierarchical clustering algorithms. J. Math. Model. Algorithms 5, 475–504 (2006).

    MathSciNet 
    MATH 
    Article 

    Google Scholar 

  • 65.

    Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. & Hornik, K. cluster: Cluster Analysis Basics and Extensions. (2019).

  • 66.

    Caliński, T. & Harabasz, J. A dendrite method for cluster analysis. Commun. Stat. Simul. Comput. 3, 1–27 (1974).

    MathSciNet 
    MATH 
    Article 

    Google Scholar 

  • 67.

    Stoffel, M. A., Nakagawa, S. & Schielzeth, H. rptR: repeatability estimation and variance decomposition by generalized linear mixed‐effects models. Methods Ecol. Evol. 8, 1639–1644 (2017).

    Article 

    Google Scholar 

  • 68.

    Oksanen, J. et al. The vegan package. Community Ecol. package 10, 631–637 (2007).

    Google Scholar 

  • 69.

    Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 70.

    Foster, Z. S. L., Sharpton, T. J. & Grünwald, N. J. Metacoder: an R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput. Biol. 13, e1005404 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 71.

    Flannery, J. E. et al. Gut feelings begin in childhood: the gut metagenome correlates with early environment, caregiving, and behavior. MBio 11, e02780–19 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 72.

    Sharpton, T. et al. Development of inflammatory bowel disease is linked to a longitudinal restructuring of the gut metagenome in mice. mSystems 2, e00036-17 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 73.

    Zhang, Y. Likelihood-based and Bayesian methods for Tweedie compound Poisson linear mixed models. Stat. Comput. 23, 743–757 (2013).

    MathSciNet 
    CAS 
    MATH 
    Article 

    Google Scholar 


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