CITATIONS
Allan, N., Knotts, T. A., Pesapane, R., Ramsey, J. J., Castle, S., &
Clifford, D., et al. (2018). Conservation implications of
shifting gut microbiomes in captive-reared endangered voles intended for
reintroduction into the wild. Microorganisms , 6, 94.
Anand, A., Chattopadhyay, B., & Kandula, S. (2012). Isolation and
characterization of cellulose-degrading and xylanolytic bacteria from
the short-nosed fruit bat Cynopterus sphinx . Acta
Chiropt. , 14, 233-239.
Anderson, M. J. (2014). Permutational multivariate analysis of variance
(PERMANOVA). Wiley Statsref: Stat. Ref. Online , 1-15.
Angelakis, E., & Raoult, D. (2010). The increase ofLactobacillus species in the gut flora of newborn broiler chicks
and ducks is associated with weight gain. PloS one , 5, e10463.
Astudillo‐García, C., Bell, J. J., Webster, N. S., Glasl, B., Jompa, J.,
& Montoya, J. M., et al. (2017). Evaluating the core microbiota
in complex communities: a systematic investigation. Environ.
Microbiol., 19, 1450-1462.
Bates, D., Sarkar, D., Bates, M. D., & Matrix, L. (2007). The lme4
package. R Package Version 2: 74.
Baxter, N. T., Wan, J. J., Schubert, A. M., Jenior, M. L., Myers, P., &
Schloss, P. D. (2015). Intra-and interindividual variations mask
interspecies variation in the microbiota of sympatric Peromyscuspopulations. Appl. Environ. Microb. , 81, 396-404.
Bennett, D. C., Tun, H. M., Kim, J. E., Leung, F. C., & Cheng, K. M.
(2013). Characterization of cecal microbiota of the emu (Dromaius
novaehollandiae ). Vet. Microbiol. , 166, 304-310.
Birrenkott, A. H., Wilde, S. B., Hains, J. J., Fischer, J. R., Murphy,
T. M., & Hope, C. P., et al. (2004). Establishing a food-chain
link between aquatic plant material and avian vacuolar myelinopathy in
mallards (Anas platyrhynchos ). J. Wildlife Dis. , 40,
485-492.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C.
C., & Al-Ghalith, G. A., et al. (2019). Reproducible,
interactive, scalable and extensible microbiome data science using QIIME
2. Nature Biotech. , 37, 852-857.
Brice, K. L., Trivedi, P., Jeffries, T. C., Blyton, M. D., Mitchell, C.,
& Singh, B. K., et al. (2019). The koala (Phascolarctos
cinereus ) faecal microbiome differs with diet in a wild
population. PeerJ , 7 , e6534.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A.
J. A., & Holmes, S. P. (2016). DADA2: high-resolution sample inference
from Illumina amplicon data. Nat. Methods , 13, 581-583.
Cao, J., Hu, Y., Liu, F., Wang, Y., Bi, Y., & Lv, N., et al.(2020). Metagenomic analysis reveals the microbiome and resistome in
migratory birds. Microbiome , 8, 1-18.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman,
F. D., & Costello, et al. (2010). QIIME allows analysis of
high-throughput community sequencing data. Nat. Methods , 7,
335-336.
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley,
J., & Fierer, N., et al. (2012). Ultra-high-throughput microbial
community analysis on the Illumina HiSeq and MiSeq platforms. ISME
J. , 6, 1621-1624.
Capunitan, D. C., Johnson, O., Terrill, R. S., & Hird, S. M. (2020).
Evolutionary signal in the gut microbiomes of 74 bird species from
Equatorial Guinea. Mol. Ecol. , 29, 829-847.
Carey, H. V., & Assadi-Porter, F. M. (2017). The hibernator microbiome:
host-bacterial interactions in an extreme nutritional
symbiosis. Annu. Rev. Nutr. , 37, 477-500.
Caviedes-Vidal, E., McWhorter, T. J., Lavin, S. R., Chediack, J. G.,
Tracy, C. R., & Karasov, W. H. (2007). The digestive adaptation of
flying vertebrates: high intestinal paracellular absorption compensates
for smaller guts. Proc. Nat. Acad. Sci. , 104, 19132-19137.
Cooper, N. W., Ewert, D. N., Hall, K. R., Rockwell, S. M., Currie, D.,
& Wunderle Jr, J. M., et al. (2018). Resighting data reveal weak
connectivity from wintering to breeding grounds in a range-restricted
and endangered long-distance migratory passerine. Avian Conserv.
Ecol. , 13.
Cooper, N. W., Ewert, D. N., Wunderle Jr, J. M., Helmer, E. H., &
Marra, P. P. (2019). Revising the wintering distribution and habitat use
of the Kirtland’s Warbler using playback surveys, citizen scientists,
and geolocators. Endanger. Species Res. , 38, 79-89.
Cooper, N. W., & Marra, P. P. (2020). Hidden Long-Distance Movements by
a Migratory Bird. Curr. Biol .
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, 226.
DeCandia, A. L., Brenner, L. J., King, J. L., & vonHoldt, B. M. (2020).
Ear mite infection is associated with altered microbial communities in
genetically depauperate Santa Catalina Island foxes (Urocyon
littoralis catalinae ). Mol. Ecol. , 29, 1463-1475.
Deloria-Sheffield, C. M., Millenbah, K. F., Bocetti, C. I., Sykes Jr, P.
W., & Kepler, C. B. (2001). Kirtland’s Warbler diet as determined
through fecal analysis. Wilson J. Ornithol. , 113, 384-387.
Dewar, M. L., Arnould, J. P., Krause, L., Dann, P., & Smith, S. C.
(2014). Interspecific variations in the faecal microbiota ofProcellariiform seabirds. FEMS Microbiol. Ecol. , 89,
47-55.
Drovetski, S. V., O’Mahoney, M. J., Matterson, K. O., Schmidt, B. K., &
Graves, G. R. (2019). Distinct microbiotas of anatomical gut regions
display idiosyncratic seasonal variation in an avian
folivore. Anim. Microbiome , 1, 1-11.
Duncan, S. H., Louis, P., & Flint, H. J. (2007). Cultivable bacterial
diversity from the human colon. Lett. Appl. Microbiol. , 44,
343-350.
Edenborough, K. M., Mu, A., Mühldorfer, K., Lechner, J., Lander, A., &
Bokelmann, M., et al. (2020). Microbiomes in the insectivorous
bat species Mops condylurus rapidly converge in
captivity. PloS one , 15, e0223629.
Escallón, C., Belden, L. K., & Moore, I. T. (2019). The cloacal
microbiome changes with the breeding season in a wild
bird. Integt. Organismal Biol. , 1, 581-617.
Faust, K., Lahti, L., Gonze, D., De Vos, W. M., & Raes, J. (2015).
Metagenomics meets time series analysis: unraveling microbial community
dynamics. Curr. Opin. Microbiol. , 25, 56-66.
Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala,
D., & Chase, J., et al. (2014). Temporal variability is a
personalized feature of the human microbiome. Genome Biol. , 15,
531.
Fox, A. D., & Walsh, A. (2012). Warming winter effects, fat store
accumulation and timing of spring departure of Greenland White-fronted
Geese Anser albifrons flavirostris from their winter
quarters. Hydrobiologia , 697, 95-102.
García-Amado, M. A., Shin, H., Sanz, V., Lentino, M., Martínez, L. M.,
& Contreras, M et al. (2018). Comparison of gizzard and
intestinal microbiota of wild neotropical birds. PloS one , 13,
e0194857.
García-García, N., Tamames, J., Linz, A. M., Pedrós-Alió, C., &
Puente-Sánchez, F. (2019). Microdiversity ensures the maintenance of
functional microbial communities under changing environmental
conditions. ISME J. , 13, 2969-2983.
Grond, K., Lanctot, R. B., Jumpponen, A., & Sandercock, B. K. (2017).
Recruitment and establishment of the gut microbiome in arctic
shorebirds. FEMS Microbiol. Ecol. , 93, fix142.
Grond, K., Sandercock, B. K., Jumpponen, A., & Zeglin, L. H. (2018).
The avian gut microbiota: community, physiology and function in wild
birds. J. Avian Biol. , 49, e01788.
Grond, K., Perreau, J. M., Loo, W. T., Spring, A. J., Cavanaugh, C. M.,
& Hird, S. M. (2019). Longitudinal microbiome profiling reveals
impermanence of probiotic bacteria in domestic pigeons. PloS
one , 14, e0217804.
Hird, S. M., Carstens, B. C., Cardiff, S. W., Dittmann, D. L., &
Brumfield, R. T. (2014). Sampling locality is more detectable than
taxonomy or ecology in the gut microbiota of the brood-parasitic
Brown-headed Cowbird (Molothrus ater ). PeerJ , 2 ,
e321.
Hird, S. M., Sánchez, C., Carstens, B. C., & Brumfield, R. T. (2015).
Comparative gut microbiota of 59 neotropical bird species. Front.
Microbiol. , 6, 1403.
Hird, S. M., Ganz, H., Eisen, J. A., & Boyce, W. M. (2018). The cloacal
microbiome of five wild duck species varies by species and influenza a
virus infection status. mSphere , 3.
Janssen, P. H. (2006). Identifying the dominant soil bacterial taxa in
libraries of 16S rRNA and 16S rRNA genes. Appl. Environ.
Microb. , 72, 1719-1728.
Jenni, L., & Jenni-Eiermann, S. (1998). Fuel supply and metabolic
constraints in migrating birds. J. Avian Biol. , 521-528.
Kepler, C. B., Irvine, G. W., DeCapita, M. E., & Weinrich, J. (1996).
The conservation management of Kirtland’s Warbler Dendroica
kirtlandii . Bird Conserv. Int. , 6, 11-22.
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., &
Debelius, J., et al. (2018). Best practices for analysing
microbiomes. Nat. Rev. Microbiol. , 16, 410-422.
Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. (2015).
Package “lmerTest”: R package (Version, 2.0).
Lewis, W. B., Moore, F. R., & Wang, S. (2016). Characterization of the
gut microbiota of migratory passerines during stopover along the
northern coast of the Gulf of Mexico. J. Avian Biol. , 47,
659-668.
Lewis, W. B., Moore, F. R., & Wang, S. (2017). Changes in gut
microbiota of migratory passerines during stopover after crossing an
ecological barrier. Auk , 134, 137-145.
Mandal, S., Van Treuren, W., White, R. A., Eggesbø, M., Knight, R., &
Peddada, S. D. (2015). Analysis of composition of microbiomes: a novel
method for studying microbial composition. Microb. Ecol. Health
D. , 26, 27663.
Maurice, C. F., Knowles, S. C., Ladau, J., Pollard, K. S., Fenton, A.,
& Pedersen, A. B., et al. (2015). Marked seasonal variation in
the wild mouse gut microbiota. ISME Journal , 9, 2423-2434.
Pyle, P. (1997). Identification guide to North American birds: a
compendium of information on identifying, ageing, and sexing”
near-passerines” and passerines in the hand . Slate Creek Press,
Bolinas, CA, USA
McMurdie, P. J., & Holmes, S. (2013). phyloseq: an R package for
reproducible interactive analysis and graphics of microbiome census
data. PloS one , 8, e61217.
McMurdie, P. J., & Holmes, S. (2014). Waste not, want not: why
rarefying microbiome data is inadmissible. PLoS Comput Biol , 10,
e1003531.
McWilliams, S. R., & Karasov, W. H. (2005). Birds of two worlds:
the ecology and evolution of migration. Smithsonian Institution Press,
Washington, DC, USA, pp. 67-78.
Oksanen, J., Kindt, R., Legendre, P., O’Hara, B., Stevens, M. H. H., &
Oksanen, M. J., et al. (2007). The vegan package. Community
ecology package , 10, 719.
Pearce, D. S., Hoover, B. A., Jennings, S., Nevitt, G. A., & Docherty,
K. M. (2017). Morphological and genetic factors shape the microbiome of
a seabird species (Oceanodroma leucorhoa ) more than environmental
and social factors. Microbiome , 5, 1-16.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., & Yarza,
P., et al. (2012). The SILVA ribosomal RNA gene database project:
improved data processing and web-based tools. Nucleic Acids
Res. , 41, D590-D596.
Rappole, J. H., & Tipton, A. R. (1991). New harness design for
attachment of radio transmitters to small passerines (Nuevo Diseño de
Arnés para Atar Transmisores a Passeriformes Pequeños). Journal
Field Ornithol. , 335-337.
Rathore, A. S., & Gupta, R. D. (2015). Chitinases from bacteria to
human: properties, applications, and future perspectives. Enzyme
Res. , 2015 .
Ren, T., Boutin, S., Humphries, M. M., Dantzer, B., Gorrell, J. C., &
Coltman, D. W., et al. (2017). Seasonal, spatial, and maternal
effects on gut microbiome in wild red squirrels. Microbiome , 5,
163.
Ren, T., & Wu, M. (2016). PhyloCore: A phylogenetic approach to
identifying core taxa in microbial communities. Gene , 593,
330-333.
Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A.
D., & Gasbarrini, A., et al. (2019). What is the healthy gut
microbiota composition? A changing ecosystem across age, environment,
diet, and diseases. Microorganisms , 7, 14.
Risely, A., Waite, D., Ujvari, B., Klaassen, M., & Hoye, B. (2017). Gut
microbiota of a long‐distance migrant demonstrates resistance against
environmental microbe incursions. Mol. Ecol. , 26, 5842-5854.
Roth, T. L., Switzer, A., Watanabe-Chailland, M., Bik, E. M., Relman, D.
A., & Romick-Rosendale, L. E., et al. (2019). Reduced Gut
Microbiome Diversity and Metabolome Differences in Rhinoceros Species at
Risk for Iron Overload Disorder. Front Microbiol. , 10, 2291.
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T.,
& Zeevi, D., et al. (2018). Environment dominates over host
genetics in shaping human gut microbiota. Nature , 555, 210-215.
Segawa, T., Fukuchi, S., Bodington, D., Tsuchida, S., Mbehang Nguema, P.
P., & Mori, H., et al. (2019). Genomic analyses ofbifidobacterium moukalabense reveal adaptations to
frugivore/folivore feeding behavior. Microorganisms , 7, 99.
Shade, A., & Handelsman, J. (2012). Beyond the Venn diagram: the hunt
for a core microbiome. Environ. Microbiol. , 14, 4-12.
Sivonen, K. (1996). Cyanobacterial toxins and toxin
production. Phycologia , 35, 12-24.
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman,
J. S., &Reid, G., et al. (2017). Seasonal cycling in the gut
microbiome of the Hadza hunter-gatherers of
Tanzania. Science , 357, 802-806.
Sommer, F., Ståhlman, M., Ilkayeva, O., Arnemo, J. M., Kindberg, J.,
&Josefsson, J., et al. (2016). The gut microbiota modulates
energy metabolism in the hibernating brown bear Ursusarctos . Cell Rep. , 14, 1655-1661.
Song, S. J., Sanders, J. G., Delsuc, F., Metcalf, J., Amato, K.,
&Taylor, M. W., et al. (2020). Comparative analyses of
vertebrate gut microbiomes reveal convergence between birds and
bats. MBio , 11.
Taylor, P., Crewe, T., Mackenzie, S., Lepage, D., Aubry, Y., & Crysler,
Z., et al. (2017). The Motus Wildlife Tracking System: a
collaborative research network to enhance the understanding of wildlife
movement. Avian Conserv. Ecol. , 12.
Teyssier, A., Lens, L., Matthysen, E., & White, J. (2018). Dynamics of
gut microbiota diversity during the early development of an avian host:
Evidence from a cross-foster experiment. Front. Microbiol. , 9,
1524.
Topp, E., Mulbry, W. M., Zhu, H., Nour, S. M., & Cuppels, D. (2000).
Characterization of s-triazine herbicide metabolism by aNocardioides sp . isolated from agricultural soils. Appl.
Environ. Microb. , 66, 3134-3141.
Tschöp, M. H., Hugenholtz, P., & Karp, C. L. (2009). Getting to the
core of the gut microbiome. Nature Biotech. , 27, 344-346.
Waite, D. W., & Taylor, M. (2015). Exploring the avian gut microbiota:
current trends and future directions. Front. Microbiol. , 6, 673.
Wexler, H. M. (2007). Bacteroides: the good, the bad, and the
nitty-gritty. Clin. Microbiol. Rev. , 20, 593-621.
White, J., Mirleau, P., Danchin, E., Mulard, H., Hatch, S. A., & Heeb,
P., et al. (2010). Sexually transmitted bacteria affect female
cloacal assemblages in a wild bird. Ecol. Lett. , 13, 1515-1524.
Wu, Y., Yang, Y., Cao, L., Yin, H., Xu, M., & Wang, Z., et al.(2018). Habitat environments impacted the gut microbiome of
long-distance migratory swan geese but central species
conserved. Sci. Rep. , 8 , 1-11.
Wunderle Jr, J. M., Currie, D., Helmer, E. H., Ewert, D. N., White, J.
D., & Ruzycki, T. S., et al. (2010). Kirtland’s Warblers in
anthropogenically disturbed early-successional habitats on Eleuthera,
The Bahamas. Condor , 112, 123-137.
Wunderle Jr, J. M., Lebow, P. K., White, J. D., Currie, D., & Ewert, D.
N. (2014). Sex and age differences in site fidelity, food resource
tracking, and body condition of wintering Kirtland’s Warblers
(Setophaga kirtlandii ) in The Bahamas. Ornithol. Monogr. ,
i-62.
Data accessibility statement: Upon acceptance of this
manuscript, data supporting the results will be archived in NCBI
Sequence Read Archive and Dryad. The data DOI will be included at the
end of the article.
Author Contributions: HRS, NWC, and PPM designed the project
with input from SJH and JMB. HRS and NWC collected samples and wrote the
manuscript. HRS processed samples and analyzed data. All authors
contributed to manuscript revisions.