Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastro Hepat. 2012;9(10):577–89.
Article
CAS
Google Scholar
Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Front Microbiol. 2015;6:673.
Article
PubMed
PubMed Central
Google Scholar
Hanning I, Diaz-Sanchez S. The functionality of the gastrointestinal microbiome in non-human animals. Microbiome. 2015;3:51.
Article
PubMed
PubMed Central
Google Scholar
Sabree ZL, Moran NA. Host-specific assemblages typify gut microbial communities of related insect species. Springerplus. 2014;3:138.
Article
PubMed
PubMed Central
CAS
Google Scholar
Colman DR, Toolson EC, Takacs-Vesbach CD. Do diet and taxonomy influence insect gut bacterial communities? Mol Ecol. 2012;21(20):5124–37.
Article
CAS
PubMed
Google Scholar
Dietrich C, Kohler T, Brune A. The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl Environ Microbiol. 2014;80(7):2261–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Anderson KE, Russell JA, Moreau CS, Kautz S, Sullam KE, Hu Y, Basinger U, Mott BM, Buck N, Wheeler DE. Highly similar microbial communities are shared among related and trophically similar ant species. Mol Ecol. 2012;21(9):2282–96.
Article
PubMed
Google Scholar
Kennedy SR, Tsau S, Gillespie R, Krehenwinkel H. Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua. Mol Ecol. 2020;29(5):1001–15.
Article
CAS
PubMed
Google Scholar
Liu H, Guo X, Gooneratne R, Lai R, Zeng C, Zhan F, Wang W. The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels. Sci Rep. 2016;6:24340.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sullam KE, Rubin BE, Dalton CM, Kilham SS, Flecker AS, Russell JA. Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. ISME J. 2015;9(7):1508–22.
Article
PubMed
PubMed Central
Google Scholar
Chang CW, Huang BH, Lin SM, Huang CL, Liao PC. Changes of diet and dominant intestinal microbes in farmland frogs. BMC Microbiol. 2016;16:33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332(6032):970–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, Gonzalez A, Knight R. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol. 2014;23(6):1301–17.
Article
CAS
PubMed
Google Scholar
Bodawatta KH, Sam K, Jonsson KA, Poulsen M. Comparative analyses of the digestive tract microbiota of new Guinean passerine birds. Front Microbiol. 2018;9:1830.
Article
PubMed
PubMed Central
Google Scholar
Hird SM, Sanchez C, Carstens BC, Brumfield RT. Comparative gut microbiota of 59 neotropical bird species. Front Microbiol. 2015;6:1403.
Article
PubMed
PubMed Central
Google Scholar
Capunitan DC, Johnson O, Terrill RS, Hird SM. Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea. Mol Ecol. 2020;29(4):829–47.
Article
CAS
PubMed
Google Scholar
Grond K, Sandercock BK, Jumpponen A, Zeglin LH. The avian gut microbiota: community, physiology and function in wild birds. J Avian Biol. 2018;49(11):e01788.
Waite DW, Taylor MW. Characterizing the avian gut microbiota: membership, driving influences, and potential function. Front Microbiol. 2014;5:223.
Article
PubMed
PubMed Central
Google Scholar
Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun. 2019;10(1):2200.
Article
PubMed
PubMed Central
CAS
Google Scholar
Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, et al. Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats. mBio. 2020;11(1):e02901–19.
Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA, Garber PA. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol. 2015;69(2):434–43.
Article
CAS
PubMed
Google Scholar
Maurice CF, Knowles SCL, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015;9(11):2423–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015;17(1):72–84.
Article
CAS
PubMed
Google Scholar
Ren TT, Boutin S, Humphries MM, Dantzer B, Gorrell JC, Coltman DW, McAdam AG, Wu M. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome. 2017;5:163.
Article
PubMed
PubMed Central
Google Scholar
Hang I, Rinttila T, Zentek J, Kettunen A, Alaja S, Apajalahti J, Harmoinen J, de Vos WM, Spillmann T. Effect of high contents of dietary animal-derived protein or carbohydrates on canine faecal microbiota. BMC Vet Res. 2012;8:90.
Article
CAS
PubMed
PubMed Central
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63.
Article
CAS
PubMed
Google Scholar
Cao J, Hu Y, Liu F, Wang Y, Bi Y, Lv N, Li J, Zhu B, Gao GF. Metagenomic analysis reveals the microbiome and resistome in migratory birds. Microbiome. 2020;8(1):26.
Article
PubMed
PubMed Central
Google Scholar
Loo WT, Garcia-Loor J, Dudaniec RY, Kleindorfer S, Cavanaugh CM. Host phylogeny, diet, and habitat differentiate the gut microbiomes of Darwin’s finches on Santa Cruz Island. Sci Rep. 2019;9(1):18781.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grond K, Santo Domingo JW, Lanctot RB, Jumpponen A, Bentzen RL, Boldenow ML, Brown SC, Casler B, Cunningham JA, Doll AC, et al. Composition and drivers of gut microbial communities in arctic-breeding shorebirds. Front Microbiol. 2019;10:2258.
Article
PubMed
PubMed Central
Google Scholar
Wang W, Wang F, Li L, Wang A, Sharshov K, Druzyaka A, Lancuo Z, Wang S, Shi Y. Characterization of the gut microbiome of black-necked cranes (Grus nigricollis) in six wintering areas in China. Arch Microbiol. 2020;202:983–93.
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:e231.
Article
Google Scholar
Araújo PM, Viegas I, Rocha AD, Villegas A, Jones JG, Mendonça L, Ramos JA, Masero JA, Alves JA. Understanding how birds rebuild fat stores during migration: insights from an experimental study. Sci Rep-Uk. 2019;9:10065.
Article
CAS
Google Scholar
Pierce BJ, McWilliams SR. Seasonal changes in composition of lipid stores in migratory birds: causes and consequences. Condor. 2005;107(2):269–79.
Article
Google Scholar
Boyle WA, Conway CJ, Bronstein JL. Why do some, but not all, tropical birds migrate? A comparative study of diet breadth and fruit preference. Evol Ecol. 2010;25:219–36.
Article
Google Scholar
Witmer MC. Annual diet of Cedar Waxwings based on U.S. Biological Survey Records (1885-1950) compared to diet of American robins: contrasts in dietary patterns and natural history. Auk. 1996;113(2):414–30.
Article
Google Scholar
Vel’ky M, Kanuch P, Kristin A. Food composition of wintering great tits (Parus major): habitat and seasonal aspects. J Vertebrate Biol. 2011;60(3):228–36.
Google Scholar
Bakour S, Moulaï R. Dietary analysis across breeding seasons of Eleonora's Falcon Falco eleonorae on the western coast of Algeria. Ostrich. 2019;90(1):63–72.
Article
Google Scholar
Westerberg K, Brown R, Eagle G, Votier SC. Intra-population variation in the diet of an avian top predator: generalist and specialist foraging in great black-backed gulls Larus marinus. Bird Stud. 2019;66(3):390–7.
Article
Google Scholar
Ankney CD, Scott DM. Changes in nutrient reserves and diet of breeding Brown-headed cowbirds. Auk. 1980;97(4):684–96.
Google Scholar
Lewis WB, Moore FR, Wang SA. Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico. J Avian Biol. 2016;47(5):659–68.
Article
Google Scholar
Wu Y, Yang Y, Cao L, Yin H, Xu M, Wang Z, Liu Y, Wang X, Deng Y. Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved. Sci Rep. 2018;8(1):13314.
Article
PubMed
PubMed Central
CAS
Google Scholar
Risely A, Waite DW, Ujvari B, Hoye BJ, Klaassen M. Active migration is associated with specific and consistent changes to gut microbiota in Calidris shorebirds. J Anim Ecol. 2018;87(2):428–37.
Article
PubMed
Google Scholar
Dong Y, Xiang X, Zhao G, Song Y, Zhou L. Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales. Peerj. 2019;7:e7045.
Article
PubMed
PubMed Central
Google Scholar
Zhang F, Xiang X, Dong Y, Yan S, Song Y, Zhou L. Significant differences in the gut bacterial communities of hooded crane (Grus monacha) in different seasons at a stopover site on the flyway. Animals. 2020;10(4):701.
Article
PubMed Central
Google Scholar
Liu G, Gong Z, Li Q. Variations in gut bacterial communities between lesser white-fronted geese wintering at Caizi and Shengjin lakes in China. Microbiologyopen. 2020;00:e1037.
CAS
Google Scholar
Juan PAS, Hendershot JN, Daily GC, Fukami T. Land-use change has host-specific influences on avian gut microbiomes. ISME J. 2020;14:318–21.
Article
Google Scholar
Phillips JN, Berlow M, Derryberry EP. The effects of landscape urbanization on the gut microbiome: an exploration into the gut of urban and rural white-crowned sparrows. Front Ecol Evol. 2018;6:148. https://doi.org/10.3389/fevo.2018.00148.
Teyssier A, Rouffaer LO, Saleh Hudin N, Strubbe D, Matthysen E, Lens L, White J. Inside the guts of the city: urban-induced alterations of the gut microbiota in a wild passerine. Sci Total Environ. 2018;612:1276–86.
Article
CAS
PubMed
Google Scholar
Gillingham MAF, Bechet A, Cezilly F, Wilhelm K, Rendon-Martos M, Borghesi F, Nissardi S, Baccetti N, Azafzaf H, Menke S, et al. Offspring microbiomes differ across breeding sites in a panmictic species. Front Microbiol. 2019;10:35.
Article
PubMed
PubMed Central
Google Scholar
Murray MH, Lankau EW, Kidd AD, Welch CN, Ellison T, Adams HC, Lipp EK, Hernandez SM. Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird. PLoS One. 2020;15(3):e0220926.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teyssier A, Matthysen E, Hudin NS, de Neve L, White J, Lens L. Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine. Proc Biol Sci. 2020;287(1920):20192182.
PubMed
PubMed Central
Google Scholar
Davidson G, Wiley N, Cooke AC, Johnson CN, Fouhy F, Reichert MS, Hera I, Crane JMS, Kulahci IG, Ross RP, et al. Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird. Sci Rep. 2020;10:20783.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hicks AL, Lee KJ, Couto-Rodriguez M, Patel J, Sinha R, Guo C, Olson SH, Seimon A, Seimon TA, Ondzie AU, et al. Gut microbiomes of wild great apes fluctuate seasonally in response to diet. Nat Commun. 2018;9(1):1786.
Article
PubMed
PubMed Central
CAS
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–6.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Finke MD. Complete nutrient composition of commercially raised invertebrates used as food for insectivores. Zoo Biol. 2002;21:269–85.
Article
CAS
Google Scholar
Muhammad Anjum F, Nadeem M, Issa Khan M, Hussain S. Nutritional and therapeutic potential of sunflower seeds. Br Food J. 2012;114(4):544–52.
Article
Google Scholar
Barbeau WE, Hilu KW. Protein, calcium, iron, and amino acid content of selected wild and domesticated cultivars of finger millet. Plant Foods Hum Nutr. 1993;43(2):97–104.
Article
CAS
PubMed
Google Scholar
Escarnot E, Jacquemin J, Agneessens R, Paquot M. Comparative study of the content and profiles of macronutrients in spelt and wheat, a review. Biotechnol, Agronomy, Soc Environ. 2012;16(2):243–56.
Google Scholar
Trevelline BK, Sosa J, Hartup BK, Kohl KD. A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc Biol Sci. 2020;287(1923):20192988.
CAS
PubMed
PubMed Central
Google Scholar
Hofstad T. The genus Fusobacterium. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes - A handbook on the biology of bacteria, vol. 2. New York: Springer-Verlag; 2006. p. 1016–27.
Google Scholar
Bennett DC, Tun HM, Kim JE, Leung FC, Cheng KM. Characterization of cecal microbiota of the emu (Dromaius novaehollandiae). Vet Microbiol. 2013;166(1–2):304–10.
Article
PubMed
Google Scholar
Wang W, Zheng SS, Li LX, Yang YS, Liu YB, Wang AZ, Sharshov K, Li Y. Comparative metagenomics of the gut microbiota in wild Greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea). Microbiologyopen. 2019;8(5):e00725.
Article
PubMed
CAS
Google Scholar
Drovetski SV, O'Mahoney M, Ransome EJ, Matterson KO, Lim HC, Chesser RT, Graves GR. Spatial organization of the gastrointestinal microbiota in urban Canada geese. Sci Rep-Uk. 2018;8:3713.
Article
CAS
Google Scholar
Burapan S, Kim M, Han J. Demethylation of polymethoxyflavones by human gut bacterium, Blautia sp MRG-PMF1. J Agr Food Chem. 2017;65(8):1620–9.
Article
CAS
Google Scholar
Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1–24.
Article
CAS
PubMed
Google Scholar
La Reau AJ, Suen G. The Ruminococci: key symbionts of the gut ecosystem. J Microbiol. 2018;56(3):199–208.
Article
PubMed
CAS
Google Scholar
Montagne L, Piel C, Lalles JP. Effect of diet on mucin kinetics and composition: nutrition and health implications. Nutr Rev. 2004;62(3):105–14.
Article
CAS
PubMed
Google Scholar
Amaretti A, Gozzoli C, Simone M, Raimondi S, Righini L, Perez-Brocal V, Garcia-Lopez R, Moya A, Rossi M. Profiling of protein degraders in cultures of human gut microbiota. Front Microbiol. 2019;10:2614.
Article
PubMed
PubMed Central
Google Scholar
Leblanc DJ. Enterococcus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes - A handbook on the biology of bacteria, vol. 4. 3rd ed. New York: Springer-Verlag; 2006. p. 175–204.
Google Scholar
Holzapfel WH, Franz CMAP, Ludwig W, Back W, LMT D. The genera Pediococcus and Tetragenococcus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes - A handbook on the biology of bacteria, vol. 4. 3rd ed. New York: Springer-Verlag; 2006. p. 229–66.
Google Scholar
Teuber M, Geis A. The genus Lactococcus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes - A handbook on the biology of bacteria, vol. 4. 3rd ed. New York: Springer-Verlag; 2006. p. 205–28.
Google Scholar
Kwon GT, Yuk HG, Lee SJ, Chung YH, Jang HS, Yoo JS, Cho KH, Kong H, Shin D. Mealworm larvae (Tenebrio molitor L.) exuviae as a novel prebiotic material for BALB/c mouse gut microbiota. Food Sci Biotechnol. 2020;29(4):531–7.
Article
CAS
PubMed
Google Scholar
Kropackova L, Pechmanova H, Vinkler M, Svobodova J, Velova H, Tesicky M, Martin JF, Kreisinger J. Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major). PLoS One. 2017;12(6):e0179945.
Article
PubMed
PubMed Central
CAS
Google Scholar
Drovetski SV, O’Mahoney MJV, Matterson KO, Schmidt BK, Grant BR. Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore. BMC Anim Microbiome. 2019;1:2.
Article
Google Scholar
Przemieniecki SW, Kosewska A, Ciesielski S, Kosewska O. Changes in the gut microbiome and enzymatic profile of Tenebrio molitor larvae biodegrading cellulose, polyethylene and polystyrene waste. Environ Pollut. 2020;256:113265.
Article
CAS
PubMed
Google Scholar
Bodawatta KH, Puzejova K, Sam K, Poulsen M, Jonsson KA. Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of great tits (Parus major). BMC Anim Microbiome. 2020;2:9.
Article
Google Scholar
Moya A, Ferrer M. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol. 2016;24(5):402–13.
Article
CAS
PubMed
Google Scholar
Trosvik P, de Muinck EJ. Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa. Microbiome. 2015;3:44.
Article
PubMed
PubMed Central
Google Scholar
Isaksson C, Anderson S. Carotenoid diet and nestling provisioning in urban and rural great tits Parus major. J Avian Biol. 2007;38(5):564–72.
Article
Google Scholar
Lambertucci SA, Trejo A, Di Martino S, Sánchez-Zapata JA, Donázar JA, Hiraldo F. Spatial and temporal patterns in the diet of the Andean condor: ecological replacement of native fauna by exotic species. Anim Conserv. 2009;12(4):338–45.
Article
Google Scholar
Griffiths R, Double MC, Orr K, Dawson RJG. A DNA test to sex most birds. Mol Ecol. 1998;7(8):1071–5.
Article
CAS
PubMed
Google Scholar
Lezalova-Pialkova R. Molecular evidence for extra-pair paternity and intraspecific brood parasitism in the black-headed Gull. J Ornithol. 2011;152(2):291–5.
Article
Google Scholar
R: A language and environment for statistical computing. [https://www.R-project.org/]. Accessed 15 Jan 2020.
RStudio: Integrated Development for R [http://www.rstudio.com/]. Accessed 15 Jan 2020.
vegan: Community Ecology Package. R package version 2.5–4 [https://CRAN.R-project.org/package=vegan]. Accessed 15 Jan 2020
pairwiseAdonis: Pairwise multilevel comparison using adonis [https://github.com/pmartinezarbizu/pairwiseAdonis]. Accessed 15 Jan 2020.
McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.