Hooper LV, Bry L, Falk PG, Gordon JI. Host-microbial symbiosis in the mammalian intestine: exploring an internal ecosystem. BioEssays. 1998;20:336–43.
Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122:107–18.
Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012;149:1578–93.
Heijtz RD, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA. 2011;108:3047–52.
Erny D, de Angelis ALH, Jaitin D, Wieghofer P, Staszewski O, David E, et al. Host microbiota constantly control maturation and function of microglia in the CNS. Nat Neurosci. 2015;18:965–77.
van der Waaij D. The ecology of the human intestine and its consequences for overgrowth by pathogens such as clostridium difficile. Annu Rev Microbiol. 1989;43:69–87.
Dinan TG, Stilling RM, Stanton C, Cryan JF. Collective unconscious: how gut microbes shape human behavior. J Psychiatr Res. 2015;63:1–9.
Hird SM. Evolutionary biology needs wild microbiomes. Front Microbiol. 2017;8:1–10.
Scupham AJ, Patton TG, Bent E, Bayles DO. Comparison of the cecal microbiota of domestic and wild turkeys. Micro Ecol. 2008;56:322–31.
Goodrich JK, Davenport ER, Waters JL, Clark AG, Ley RE. Cross-species comparisons of host genetic associations with the microbiome. Science. 2016;352:532–5.
Hird SM, Carstens BC, Cardiff SW, Dittmann DL, Brumfield RT. Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic brown-headed cowbird (Molothrus ater). PeerJ. 2014;2:1–21.
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci. 2019;107:18933–8.
Musitelli F, Ambrosini R, Rubolini D, Saino N, Franzetti A, Gandolfi I. Cloacal microbiota of barn swallows from Northern Italy. Ethol Ecol Evol. 2018;30:362–72.
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332:970–4.
Hird SM, Sánchez C, Carstens BC, Brumfield RT. Comparative gut microbiota of 59 neotropical bird species. Front Microbiol. 2015;6:1403.
Bili M, Cortesero AM, Mougel C, Gauthier JP, Ermel G, Simon JC, et al. Bacterial community diversity harboured by interacting species. PLoS One. 2016;11:1–23.
Sugio A, Dubreuil G, Giron D, Simon J. Plant – insect interactions under bacterial influence: ecological implications and underlying mechanisms. J Exp Bot. 2015;66:467–78.
Hannula SE, Zhu F, Heinen R, Bezemer TM. Foliar-feeding insects acquire microbiomes from the soil rather than the host plant. Nat Commun. 2019;10:1–9.
White J, Mirleau P, Danchin E, Mulard H, Hatch SA, Heeb P, et al. Sexually transmitted bacteria affect female cloacal assemblages in a wild bird. Ecol Lett. 2010;13:1515–24.
Schlechter RO, Miebach M, Remus-Emsermann MNP. Driving factors of epiphytic bacterial communities: a review. J Adv Res. 2019;19:57–65.
Remus-Emsermann MNP, Lücker S, Müller DB, Potthoff E, Daims H, Vorholt JA. Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization. Environ Microbiol. 2014;16:2329–40.
Remus-Emsermann MNP, Tecon R, Kowalchuk GA, Leveau JHJ. Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere. ISME J. 2012;6:756–65.
Rogers TJ, Leppanen C, Brown V, Fordyce JA, LeBude A, Ranney T, et al. Exploring variation in phyllosphere microbial communities across four hemlock species. Ecosphere. 2018;9:1–11.
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol. 2010;12:2885–93.
Laforest-Lapointe I, Messier C, Kembel SW. Host species identity, site and time drive temperate tree phyllosphere bacterial community structure. Microbiome. 2016;4:1–10.
Kembel SW, Mueller RC. Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities. Botany. 2014;92:303–11.
Appel MH. The chewing herbivore gut lumen: Physicochemical conditions and their impact on plant nutrients, allelochemicals, and insect pathogens. In: Bernays EA (ed.). Insect-plant interactions, 1st ed. 1994. CRC Press, Boca Raton, pp 209–23.
Shannon AL, Attwood G, Hopcroft DH, Christeller JT. Characterization of lactic acid bacteria in the larval midgut of the keratinophagous lepidopteran, Hofmannophila pseudospretella. Lett Appl Microbiol. 2001;32:36–41.
Kukal O, Dawson TE, Kukal O, Dawson TE. Temperature and food quality influences feeding behavior, assimilation efficiency and growth rate of arctic woolly-bear caterpillars. Oecologia. 1989;79:526–32.
Vilanova C, Baixeras J, Latorre A, Porcar M. The generalist inside the specialist: gut bacterial communities of two insect species feeding on toxic plants are dominated by Enterococcus sp. Front Microbiol. 2016;7:1–8.
Priya NG, Ojha A, Kajla MK, Raj A, Rajagopal R. Host plant induced variation in gut bacteria of Helicoverpa armigera. PLoS One. 2012;7:1–10.
Jones AG, Mason CJ, Felton GW, Hoover K. Host plant and population source drive diversity of microbial gut communities in two polyphagous insects. Sci Rep. 2019;9:1–11.
Hammer TJ, Janzen DH, Hallwachs W, Jaffe SP, Fierer N. Caterpillars lack a resident gut microbiome. PNAS. 2017;114:9641–6.
Whitaker MRL, Salzman S, Sanders JG, Kaltenpoth M, Pierce NE. Microbial communities of lycaenid butterflies do not correlate with larval diet. Front Microbiol. 2016;7:1–13.
Stanley D, Geier MS, Hughes RJ, Denman SE, Moore RJ. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS One. 2013;8:6–13.
Azcárate-García M, Ruiz-Rodríguez M, Díaz-Lora S, Ruiz-Castellano C, Soler JJ. Experimentally broken faecal sacs affect nest bacterial environment, development and survival of spotless starling nestlings. J Avian Biol. 2019;50:1–10.
Devaynes A, Antunes A, Bedford A, Ashton P. Progression in the bacterial load during the breeding season in nest boxes occupied by the Blue Tit and its potential impact on hatching or fledging success. J Ornithol. 2018;159:1009–17.
Janczyk P, Hall B, Souffrant WB. Microbial community composition of the crop and ceca contents of laying hens fed diets supplemented with Chlorella vulgaris. Poult Sci. 2009;88:2324–32.
Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol. 2015;6:1–12.
Pan D, Yu Z. Intestinal microbiome of poultry and its interaction with host and diet. Gut Microbes. 2014;5:108–19.
Lewis WB, Moore FR, Wang S. Changes in gut microbiota of migratory passerines during stopover after crossing an ecological barrier. Auk. 2017;134:137–45.
Kulkarni S, Heeb P. Social and sexual behaviours aid transmission of bacteria in birds. Behav Process. 2007;74:88–92.
Dawkins R. The extended phenotype. Oxford: Oxford University Press; 1982.
Fisher DN, Haines JA, Boutin S, Dantzer B, Lane JE, Coltman DW, et al. Indirect effects on fitness between individuals that have never met via an extended phenotype. Ecol Lett. 2019;22:697–706.
Mennerat A, Perret P, Lambrechts MM. Local individual preferences for nest materials in a passerine bird. PLoS One. 2009;4:1–6.
Blondel J, Thomas DW, Charmantier A, Perret P, Bourgault P, Lambrechts MM. A thirty-year study of phenotypic and genetic variation of blue tits in mediterranean habitat mosaics. Bioscience. 2006;56:661–73.
Blondel J, Dias PC, Maistre M, Perret P. Habitat heterogeneity and life-history variation of mediterranean blue tits (Parus caeruleus). Auk. 1993;110:511–20.
Visser ME, Van Noordwijk AJ, Tinbergen JM, Lessells CM. Warmer springs lead to mistimed reproduction in great tits (Parus major). Proc R Soc B Biol Sci. 1998;265:1867–70.
Stenning M. The Blue Tit, 1st ed. (T. & A. D. Poyser, London, UK. 2018) pp 69–109.
Blondel J, Aronson J, Bodiou J-Y, Boeuf G. The mediterranean region: biological diversity in space and time, 2nd ed. 2010. Oxford University Press, Oxford.
Charmantier A, Doutrelant C, Dubuc-messier G, Fargevieille A, Szulkin M. Mediterranean blue tits as a case study of local adaptation. Evol Appl. 2016;9:135–52.
Dubuc-Messier G, Réale D, Perret P, Charmantier A. Environmental heterogeneity and population differences in blue tits personality traits. Behav Ecol. 2017;28:448–59.
Bańbura J, Blondel J, de Wilde-Lambrechts H, Galan M-J, Maistre M. Nestling diet variation in an insular mediterranean population of blue tits Parus caeruleus: effects of years, territories and individuals. Oecologia. 1994;100:413–20.
Alda F, Rey I, Doadrio I. An improved method of extracting degraded DNA samples from birds and other species. Ardeola. 2007;54:331–4.
Oehm J, Juen A, Nagiller K, Neuhauser S, Traugott M. Molecular scatology: how to improve prey DNA detection success in avian faeces? Mol Ecol Resour. 2011;11:620–8.
Eriksson P, Mourkas E, González-Acuna D, Olsen B, Ellström P. Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species. Infect Ecol Epidemiol. 2017;7:1–9.
Chelius MK, Triplett EW. The diversity of archaea and bacteria in association with the roots of Zea mays L. Micro Ecol. 2001;41:252–63.
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.
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:D590–6.
Davis NM, Proctor D, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2017;6:1–8.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:1–11.
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community ecology package. R package version 2.5-7. 2020.
Vorholt JA. Microbial life in the phyllosphere. Nat Rev Microbiol. 2012;10:828–40.
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38.
Müller T, Ruppel S. Progress in cultivation-independent phyllosphere microbiology. FEMS Microbiol Ecol. 2014;87:2–17.
Chaturvedi S, Rego A, Lucas LK, Gompert Z. Sources of variation in the gut microbial community of Lycaeides melissa caterpillars. Sci Rep. 2017;7:1–13.
Videvall E, Strandh M, Engelbrecht A, Cloete S, Cornwallis CK. Measuring the gut microbiome in birds: comparison of faecal and cloacal sampling. Mol Ecol Resour. 2017;18:424–34.
Lewis WB, Moore FR, Wang S. Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico. J Avian Biol. 2016;47:659–68.
Sun CH, Liu H-Y, Zhang Y, Lu C-H. Comparative analysis of the gut microbiota of hornbill and toucan in captivity. Microbiologyopen. 2019;8:1–7.
Teyssier A, Lens L, Matthysen E, White J. Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment. Front Microbiol. 2018;9:1–12.
Ambrosini R, Corti M, Franzetti A, Caprioli M, Rubolini D, Motta VM, et al. Cloacal microbiomes and ecology of individual barn swallows. FEMS Microbiol Ecol. 2019;95:1–13.
Minard G, Tikhonov G, Ovaskainen O, Saastamoinen M. The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant. Environ Microbiol. 2019;21:4253–69.
Godoy-Vitorino F, Leal SJ, Díaz WA, Rosales J, Goldfarb KC, García-Amado MA, et al. Differences in crop bacterial community structure between hoatzins from different geographical locations. Res Microbiol. 2012;163:211–20.
Lucas FS, Heeb P. Environmental factors shape cloacal bacterial assemblages in great tit Parus major and blue tit P. caeruleus nestlings. J Avian Biol. 2005;36:510–6.
Source: Ecology - nature.com