Graham, A. L. et al. Fitness consequences of immune responses: Strengthening the empirical framework for ecoimmunology. Funct. Ecol. 25, 5–17 (2011).
Maynard, C. L., Elson, C. O., Hatton, R. D. & Weaver, C. T. Reciprocal interactions of the intestinal microbiota and immune system. Nature 489, 231–241 (2012).
Baldo, L., Riera, J. L., Tooming-Klunderud, A., Albà, M. M. & Salzburger, W. Gut microbiota dynamics during dietary shift in eastern African cichlid fishes. PLoS ONE 10, 1–23. https://doi.org/10.1371/journal.pone.0127462 (2015).
Shapira, M. Gut microbiotas and host evolution: Scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016).
Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974 (2011).
Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789–799 (2014).
Org, E. et al. Sex differences and hormonal effects on gut microbiota composition in mice. Gut Microbes 7, 313–322 (2016).
Russell, J. B. Factors that alter rumen microbial ecology. Science 292, 1119–1122 (2001).
DuPont, A. W. & DuPont, H. L. The intestinal microbiota and chronic disorders of the gut. Nat. Rev. Gastroenterol. Hepatol. 8, 523–531 (2011).
Walters, A. W. et al. The microbiota influences the Drosophila melanogaster life history strategy. Mol. Ecol. 29, 639–653 (2020).
Moreno, S., Villafuerte, R., Cabezas, S. & Lombardi, L. Wild rabbit restocking for predator conservation in Spain. Biol. Cons. 118, 183–193 (2004).
Webb, N. J. Growth and mortality in juvenile European wild rabbits (Oryctolagus cuniculus). J. Zool. 230, 665–677 (1993).
Villafuerte, R. & Delibes-Mateos, M. The IUCN red list of threatened species: Oryctolagus cuniculus (2019). https://doi.org/10.2305/IUCN.UK.2019-3.RLTS.T41291A45189779.en (2019).
Ferrand, N. Inferring the evolutionary history of the European rabbit (Oryctolagus cuniculus) from molecular markers. In Lagomorph Biology: Evolution, Ecology and Conservation (eds Alves, P. C. et al.) 47–63 (Springer, Berlin, 2008).
Rafati, N. N. et al. A genomic map of clinal variation across the European rabbit hybrid zone. Mol. Ecol. 27, 1457–1478 (2018).
Delibes-Mateos, M., Villafuerte, R., Cooke, B. & Alves, P. C. Oryctolagus cuniculus (Linnaeus, 1758). In Lagomorphs: Pikas, Rabbits and Hares of the World (eds Smith, A. T. et al.) 99–104 (John Hopkins University Press, Baltimore, 2018).
Geraldes, A. et al. Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula. Mol. Ecol. 17, 4489–4499 (2008).
Sneddon, I. A. Latrine use by the European rabbit (Oryctolagus cuniculus). J. Mammal. 72, 769–775 (1991).
Mykytowycz, R. & Dudzinski, M. L. A study on the weight of odoriferous and other glands in relation to the social status and degree of sexual activity in the wild rabbit, Oryctolagus cuniculus (L.). Wildl. Res. 11, 31–47 (1996).
Rouco, C., Villafuerte, R., Castro, F. & Ferreras, P. Effect of artificial warren size on a restocked European wild rabbit population. Anim. Conserv. 14, 117–123 (2011).
Villafuerte, R. & Viñuela, J. Size of rabbits consumed by black kites increased after a rabbit epizootic. Mammal Rev. 29, 261–264 (1999).
Ferrera, I. et al. High-diversity biofilm for the oxidation of sulfide-containing effluents. Appl. Environ. Microbiol. 64, 726–734 (2004).
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516–4522 (2011).
Edgar, R. C. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 10, 996–998 (2013).
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).
Paulson, J. N., Stine, O. C., Bravo, H. C. & Pop, M. Differential abundance analysis for microbial marker-gene surveys. Nat. Methods 10, 1200–1202 (2013).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, New York, 2016).
Oksanen, J. et al. Vegan: Community Ecology Package. R package version 2.3-5 (2016).
Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Tax4fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 31, 2882–2884 (2015).
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Bayer, E. A., Shoham, Y. & Lamed, R. Cellulose-Decomposing Bacteria and Their Enzyme Systems 3rd edn. (Springer, Berlin, 2006).
Foley, W. J. & Cork, S. J. Use of fibrous diets by small herbivores: How far can the rules be ‘bent’?. Trends Ecol. Evol. 7, 159–162 (1992).
Hirakawa, H. Coprophagy in leporids and other mammalian herbivores. Mammal Rev. 31, 61–80 (2001).
Zeng, B. et al. The bacterial communities associated with fecal types and body weight of rex rabbits. Sci. Rep. 5, 9342. https://doi.org/10.1038/srep09342 (2015).
Grimont, F. & Grimont, P. A. D. Proteobacteria: Gamma subclass. In The Prokaryotes Vol. 6 (eds Falkow, S. et al.) 219–244 (Springer, New York, 2006).
Stecher, B. et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc. Natl. Acad. Sci. USA 109, 1269–1274 (2012).
Gagen, E. J., Padmanabha, J., Denman, S. E. & McSweeney, C. S. Hydrogenotrophic culture enrichment reveals rumen Lachnospiraceae and Ruminococcaceae acetogens and hydrogen-responsive Bacteroidetes from pasture-fed cattle. FEMS Microbiol. Lett. 362, 1–8 (2015).
Meehan, C. J. & Beiko, R. G. A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria. Genome Biol. Evol. 6, 703–713 (2014).
Barcenilla, A. et al. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66, 1654–1661 (2000).
Flint, H. J. Polysaccharide breakdown by anaerobic microorganisms inhabiting the mammalian gut. Adv. Appl. Microbiol. 56, 89–120 (2004).
Stalder, G. L. et al. Gut microbiota of the European hare (Lepus europaeus). Sci. Rep. 9, 2738. https://doi.org/10.1038/s41598-019-39638-9 (2019).
Gillilland, M. G. et al. Ecological succession of bacterial communities during conventionalization of germ-free mice. Appl. Environ. Microbiol. 78, 2359–2366 (2012).
Lupp, C. Host-Mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 119–129 (2007).
Lawley, T. D. & Walker, A. W. Intestinal colonization resistance. Immunology 138, 1–11 (2013).
Punzalan, C. & Qamar, A. Probiotics for the treatment of liver disease. In The Microbiota in Gastrointestinal Pathophysiology: Implications for Human Health, Prebiotics, Probiotics, and Dysbiosis (eds Floch, M. H. et al.) 373–381 (Academic Press, New York, 2017).
Lopez-Siles, M. et al. Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease. Appl. Environ. Microbiol. 81, 7582–7592 (2015).
Li, H. et al. Pika population density is associated with the composition and diversity of gut microbiota. Front. Microbiol. 7, 758 (2016).
Amato, K. R. Co-evolution in context: The importance of studying gut microbiomes in wild animals. Microbiome Sci. Med. 1, 10–29 (2013).
Thompson, H. V. & King, C. M. The European Rabbit: History and Biology of a Successful Colonizer (Oxford Science Publications, Oxford, 1984).
Martins, H., Milne, J. A. & Rego, F. Seasonal and spatial variation in the diet of the wild rabbit (Oryctolagus cuniculus L.) in Portugal. J. Zool. 258, 395–404 (2002).
Cubas, J. et al. Endemic plant species are more palatable to introduced herbivores than non-endemics. Proc. R. Soc. B 286, 20190136. https://doi.org/10.1098/rspb.2019.0136 (2019).
Khalifa, A. Y., Alsyeeh, A. M., Almalki, M. A. & Saleh, F. A. Characterization of the plant growth promoting bacterium, Enterobacter cloacae msr1, isolated from roots of non-nodulating Medicago sativa. Saudi J. Biol. Sci. 23, 79–86 (2016).
Polizeli, M. L. T. M. et al. Xylanases from fungi: properties and industrial applications. Appl. Microbiol. Biotechnol. 67, 577–591 (2005).
Fisher, E. H. & Stein, E. A. α-Amylases. In The Enzyme 2nd edn (eds Boyer, P. D. et al.) 313–143 (Academic Press Inc, New York, 1960).
Bletz, M. C. et al. Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions. Nat. Commun. 7, 13699. https://doi.org/10.1038/ncomms13699 (2016).
Martínez-Mota, R. et al. Natural diets promote retention of the native gut microbiota in captive rodents. ISME J. 14, 67–78 (2020).
Van Leeuwen, P. et al. Effects of captivity, diet, and relocation on the gut bacterial communities of white-footed mice. Ecol. Evol. 10, 4677–4690 (2020).
Grieneisen, L. E., Livermore, J., Alberts, S., Tung, J. & Archie, E. A. Group living and male dispersal to predict core gut microbiome in wild baboons. Integr. Comp. Biol. 57, 770–785 (2017).
Cowan, D. P. Aspects of the social organization of the European wild rabbit (Oryctolagus cuniculus). Ethology 75, 197–210 (1987).
Marsh, M. K., Hutchings, M. R., McLeod, S. R. & White, P. C. Spatial and temporal heterogeneities in the contact behavior of rabbits. Behav. Ecol. Sociobiol. 65, 183–195 (2011).
Moller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997. https://doi.org/10.1126/sciadv.1500997 (2016).
Carro, F., Ortega, M. & Soriguer, R. C. Is restocking a useful tool for increasing rabbit densities?. Glob. Ecol. Conserv. 17, e00560. https://doi.org/10.1016/j.gecco.2019.e00560 (2019).
Rouco, C., Ferreras, P., Castro, F. & Villafuerte, R. A longer confinement period favors European wild rabbit (Oryctolagus cuniculus) survival during soft releases in low-cover habitats. Eur. J. Wildl. Res. 56, 215–219 (2010).
Source: Ecology - nature.com
