References
Archie, E. A., & Theis, K. R. (2011). Animal behaviour meets microbial ecology.Animal Behaviour, 82(3), 425–436. https://doi.org/10.1016/j.anbehav.2011.05.029
Beasley, D. E., Koltz, A. M., Lambert, J. E., Fierer, N., & Dunn, R. R. (2015). The Evolution of stomach acidity and its relevance to the human microbiome. PLOS ONE, 10(7), e0134116. https://doi.org/10.1371/journal.pone.0134116
Berlow, M., Kohl, K. D., & Derryberry, E. P. (2020). Evaluation of non-lethal gut microbiome sampling methods in a passerine bird. Ibis, 162(3), 911–923. https://doi.org/10.1111/ibi.12807
Bunker, M. E., Elliot, G., Heyer-Grey, H., Martin, M. O., Arnold, A. E., & Weiss, S. L. (in review). Vertically transmitted microbiome protects eggs from fungal infection and egg failure. BMC Microbiology.
Callahan, B., McMurdie, P., Rosen, M., Han, A., Johnson, A., & Holmes, S. (2016). DADA2: High resolution sample inference from Illumina amplicon data.Nature Methods, 13(7).
Callahan, B., Sankaran, K., Fukuyama, J. A., McMurdie, P., & Holmes, S. (2016). Bioconductor Workflow for Microbiome Data Analysis: From raw reads to community analyses. F1000Research, 5, 1492. https://doi.org/10.12688/f1000research.8986.2
Colston, T. J., & Jackson, C. R. (2016). Microbiome evolution along divergent branches of the vertebrate tree of life: What is known and unknown. Molecular Ecology, 25(16), 3776–3800. https://doi.org/10.1111/mec.13730
Colston, T. J., Noonan, B. P., & Jackson, C. R. (2015). Phylogenetic analysis of bacterial communities in different regions of the gastrointestinal tract of Agkistrodon piscivorus, the cottonmouth snake. PLOS ONE, 10(6), e0128793. https://doi.org/10.1371/journal.pone.0128793
Conroy, C., Papenfuss, T., Parker, J., & Hahn, N. (2009). Use of tricaine methanesulfonate (MS222) for euthanasia of reptiles. Journal of the American Association for Laboratory Animal Science : JAALAS, 48(1), 28–32.
Costello, E. K., Gordon, J. I., Secor, S. M., & Knight, R. (2010). Postprandial remodeling of the gut microbiota in Burmese pythons. The ISME Journal, 4(11), 1375–1385. https://doi.org/10.1038/ismej.2010.71
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome, 6(1), 226. https://doi.org/10.1186/s40168-018-0605-2
Dhar Purkayastha, G., Mangar, P., Saha, A., & Saha, D. (2018). Evaluation of the biocontrol efficacy of a Serratia marcescens strain indigenous to tea rhizosphere for the management of root rot disease in tea. PLoS ONE, 13(2). https://doi.org/10.1371/journal.pone.0191761
Escallón, C., Belden, L. K., & Moore, I. T. (2019). The Cloacal microbiome changes with the breeding season in a wild bird. Integrative Organismal Biology,1(1). https://doi.org/10.1093/iob/oby009
Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report.Bioinformatics, 32(19), 3047–3048. https://doi.org/10.1093/bioinformatics/btw354
Funkhouser, L., & Bordenstein, S. (2013). Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS Biology, 11(8), e1001631. https://doi.org/10.1371/journal.pbio.1001631
Gutiérrez-Román, M. I., Holguín-Meléndez, F., Dunn, M. F., Guillén-Navarro, K., & Huerta-Palacios, G. (2015). Antifungal activity of Serratia marcescens CFFSUR-B2 purified chitinolytic enzymes and prodigiosin against Mycosphaerella fijiensis, causal agent of black Sigatoka in banana (Musa spp.). BioControl, 60(4), 565–572. https://doi.org/10.1007/s10526-015-9655-6
Hird, S. M. (2017). Evolutionary biology needs wild microbiomes. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.00725
Hong, P.-Y., Wheeler, E., Cann, I. K. O., & Mackie, R. I. (2011). Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. The ISME Journal, 5(9), 1461–1470. https://doi.org/10.1038/ismej.2011.33
Jiang, H.-Y., Ma, J.-E., Li, J., Zhang, X.-J., Li, L.-M., He, N., Liu, H.-Y., Luo, S.-Y., Wu, Z.-J., Han, R.-C., & Chen, J.-P. (2017). Diets alter the gut microbiome of crocodile lizards. Frontiers in Microbiology,8, 2073. https://doi.org/10.3389/fmicb.2017.02073
Kalbe, C., Marten, P., & Berg, G. (1996). Strains of the genus Serratia as beneficial rhizobacteria of oilseed rape with antifungal properties.Microbiological Research, 151(4), 433–439. https://doi.org/10.1016/S0944-5013(96)80014-0
Keenan, S. W., Engel, A. S., & Elsey, R. M. (2013). The alligator gut microbiome and implications for archosaur symbioses. Scientific Reports,3(1), 2877. https://doi.org/10.1038/srep02877
Kembel, S. W., Cowan, P. D., Helmus, M. R., Cornwell, W. K., Morlon, H., Ackerly, D. D., Blomberg, S. P., & Webb, C. O. (2010). Picante: R tools for integrating phylogenies and ecology. Bioinformatics, 26(11), 1463–1464. https://doi.org/10.1093/bioinformatics/btq166
Kohl, K. D., Brun, A., Magallanes, M., Brinkerhoff, J., Laspiur, A., Acosta, J. C., Caviedes‐Vidal, E., & Bordenstein, S. R. (2017). Gut microbial ecology of lizards: Insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Molecular Ecology,26(4), 1175–1189. https://doi.org/10.1111/mec.13921
Kreisinger, J., Čížková, D., Kropáčková, L., & Albrecht, T. (2015). Cloacal microbiome structure in a long-distance migratory bird assessed using deep 16sRNA pyrosequencing. PloS One, 10(9), e0137401. https://doi.org/10.1371/journal.pone.0137401
Lee, W. Y. (2015). Avian gut microbiota and behavioral studies. Korean Journal of Ornithology. 22, 1–11.
Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: Evolution of the vertebrate gut microbiota. Nature Reviews Microbiology, 6(10), 776–788. https://doi.org/10.1038/nrmicro1978
Martin, B., Witten, D., & Willis, A. (2020). corncob: Count Regression for Correlated Observations with the Beta-binomial (0.1.0) [R]. https://github.com/bryandmartin/corncob
Martin, M., Gilman, F. R., & Weiss, S. L. (2010). Sex-specific asymmetry within the cloacal microbiota of the striped plateau lizard, Sceloporus virgatus.Symbiosis, 51(1), 97–105. https://doi.org/10.1007/s13199-010-0078-y
McFall-Ngai, M., Hadfield, M. G., Bosch, T. C. G., Carey, H. V., Domazet-Lošo, T., Douglas, A. E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S. F., Hentschel, U., King, N., Kjelleberg, S., Knoll, A. H., Kremer, N., Mazmanian, S. K., Metcalf, J. L., Nealson, K., Pierce, N. E., … Wernegreen, J. J. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), 3229–3236. https://doi.org/10.1073/pnas.1218525110
McMurdie, P., & Holmes, S. (2013). phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE,8(4), e61217. https://doi.org/10.1371/journal.pone.0061217
Moran, N, McCutcheon, J, & Nakanachi, A. (2008). Genomes and evolution of heritable bacterial symbionts. Annual Review Genetics, 42, 165–190.
Nyholm, S. V., & McFall-Ngai, M. (2004). The winnowing: Establishing the squid–vibrio symbiosis. Nature Reviews Microbiology, 2(8), 632–642. https://doi.org/10.1038/nrmicro957
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P. R., O’Hara, R., Simpson, G. L., Solymos, P., Stevens, M. H. H., Szoecs, E., & Wagner, H. (2019). vegan: Community Ecology Package(2.5-6) [Computer software]. https://CRAN.R-project.org/package=vegan
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596. https://doi.org/10.1093/nar/gks1219
R Core Team. (2020).R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/
Reese, A. T., & Dunn, R. R. (2018). Drivers of microbiome biodiversity: A review of general rules, feces, and ignorance. MBio, 9(4). https://doi.org/10.1128/mBio.01294-18
Rose, B. (1981). Factors Affecting Activity in Sceloporus Virgatus. Ecology,62(3), 706–716. https://doi.org/10.2307/1937739
Sarmiento, C., Zalamea, P.-C., Dalling, J. W., Davis, A. S., Stump, S. M., U’Ren, J. M., & Arnold, A. E. (2017). Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proceedings of the National Academy of Sciences,114(43), 11458–11463. https://doi.org/10.1073/pnas.1706324114
Schliep, K., Potts, A. A., Morrison, D. A., & Grimm, G. W. (2016). Intertwining phylogenetic trees and networks [Preprint]. PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.2054v1
Shterzer, N., Rothschild, N., Sbehat, Y., Stern, E., Nazarov, A., & Mills, E. (2020). Large overlap between the intestinal and reproductive tract microbiomes of chickens. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.01508
Stanley, D., Geier, M. S., Chen, H., Hughes, R. J., & Moore, R. J. (2015). Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC Microbiology, 15, 1-11.
Stebbins, R. C. (2003). A Peterson Field Guide to Western Reptiles and AmphibiansR. T. Peterson, Ed.; 3rd edition. Houghton Mifflin Harcourt.
Taylor, M. J., Mannan, R. W., U’Ren, J. M., Garber, N. P., Gallery, R. E., & Arnold, A. E. (2019). Age-related variation in the oral microbiome of urban Cooper’s hawks (Accipiter cooperii). BMC Microbiology,19(1), 47. https://doi.org/10.1186/s12866-019-1413-y
Trevelline, B. K., Fontaine, S. S., Hartup, B. K., & Kohl, K. D. (2019). Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices.Proceedings of the Royal Society B: Biological Sciences,286(1895), 20182448. https://doi.org/10.1098/rspb.2018.2448
Videvall, E., Strandh, M., Engelbrecht, A., Cloete, S., & Cornwallis, C. K. (2018). Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling.Molecular Ecology Resources, 18(3), 424–434. https://doi.org/10.1111/1755-0998.12744
Vinegar, M. (1975). Demography of the striped plateau lizard, Sceloporus virgatus.Ecology, 56(1), 172-182.
Wen, C., Li, Q., Lan, F., Li, X., Li, G., Yan, Y., Wu, G., Yang, N., & Sun, C. (2021). Microbiota continuum along the chicken oviduct and its association with host genetics and egg formation. Poultry Science, 101104. https://doi.org/10.1016/j.psj.2021.101104
White, J., Richard, M., Massot, M., & Meylan, S. (2011). Cloacal bacterial diversity increases with multiple mates: Evidence of sexual transmission in female common lizards. PLOS ONE, 6(7), e22339. https://doi.org/10.1371/journal.pone.0022339
Wickham, H. (2017). ggplot2—Elegant Graphics for Data Analysis (2nd Edition).Journal of Statistical Software, 77.
Williams, T., & Athrey, G. (2020). Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens. Microorganisms, 8(5), 718. https://doi.org/10.3390/microorganisms8050718
Wright, E., S. (2016). Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R.The R Journal, 8(1), 352. https://doi.org/10.32614/RJ-2016-025
Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., Miller, A. D., Westmoreland, S. V., Mansfield, K. G., Vallender, E. J., Miller, G. M., Rowlett, J. K., Gevers, D., Huttenhower, C., & Morgan, X. C. (2015). Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host & Microbe, 17(3), 385–391. https://doi.org/10.1016/j.chom.2015.01.015
Zhang, C., Derrien, M., Levenez, F., Brazeilles, R., Ballal, S., Kim, J., Degivry, M.-C., Quéré, G., Garault, P., van Hylckama Vlieg, J. E. T., Garrett, W. S., Doré, J., & Veiga, P. (2016). Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes.The ISME Journal, 10(9), 2235–2245. https://doi.org/10.1038/ismej.2016.13