Gastrointestinal microbiota play a vital role in maintaining organismal health, through facilitating nutrient uptake, detoxification and interactions with the immune system. The gastrointestinal microbiota of birds has been poorly studied, especially in wild species under natural conditions. Studies of avian gut microbiota are outnumbered ten to one by studies of mammals, and are dominated by research on domestic poultry. Unlike domestic poultry, wild birds vary widely in environmental preferences, physiology, and life‐history traits, such as migratory behavior and mating systems. Species characteristics result in a vast diversity in gut microbiota and its composition and function. Avian life‐history characteristics pose selection pressures on the gut microbiota, and ultimately affect host health. Here, we review current knowledge of the gut microbiota of wild birds, including: partitioning of digestive function and microbiota among different gastrointestinal compartments, microbial diversity and function in the context of host diet, energetics and behavior, and the intrinsic and extrinsic factors impacting gut microbiota in free‐living birds. The shared core microbiota of wild bird species is dominated by members of four major phyla: Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. However, microbial communities varies inter‐ and intra‐specifically, and among gastrointestinal tract sections. To conclude, we identify three key research areas that warrant further investigation: 1) expanding the range of avian host taxa investigated, 2) identifying the function of avian gut microbiota in physiology and immunology, and 3) transitioning from observational studies to experimental manipulations to identify key determinants of wild bird gut microbiota composition.

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Gut microbiota play a key role in host health. Mammals acquire gut microbiota during birth, but timing of gut microbial recruitment in birds is unknown. We evaluated whether precocial chicks from three species of arctic-breeding shorebirds acquire gut microbiota before or after hatching, and then documented the rate and compositional dynamics of accumulation of gut microbiota. Contrary to earlier reports of microbial recruitment before hatching in chickens, quantitative PCR and Illumina sequence data indicated negligible microbiota in the guts of shorebird embryos before hatching. Analyses of chick feces indicated an exponential increase in bacterial abundance of guts 0-2 days post-hatch, followed by stabilization. Gut communities were characterized by stochastic recruitment and convergence towards a community dominated by Clostridia and Gammaproteobacteria. We conclude that guts of shorebird chicks are likely void of microbiota prior to hatch, but that stable gut microbiome establishes as early as 3 days of age, probably from environmental inocula.

The ecological consequences of climate change have been recognized in numerous species, with perhaps phenology being the most well‐documented change. Phenological changes may have negative consequences when organisms within different trophic levels respond to environmental changes at different rates, potentially leading to phenological mismatches between predators and their prey. This may be especially apparent in the Arctic, which has been affected more by climate change than other regions, resulting in earlier, warmer, and longer summers. During a 7‐year study near Utqiaġvik (formerly Barrow), Alaska, we estimated phenological mismatch in relation to food availability and chick growth in a community of Arctic‐breeding shorebirds experiencing advancement of environmental conditions (i.e., snowmelt). Our results indicate that Arctic‐breeding shorebirds have experienced increased phenological mismatch with earlier snowmelt conditions. However, the degree of phenological mismatch was not a good predictor of food availability, as weather conditions after snowmelt made invertebrate availability highly unpredictable. As a result, the food available to shorebird chicks that were 2–10 days old was highly variable among years (ranging from 6.2 to 28.8 mg trap−1 day−1 among years in eight species), and was often inadequate for average growth (only 20%–54% of Dunlin and Pectoral Sandpiper broods on average had adequate food across a 4‐year period). Although weather conditions vary among years, shorebirds that nested earlier in relation to snowmelt generally had more food available during brood rearing, and thus, greater chick growth rates. Despite the strong selective pressure to nest early, advancement of nesting is likely limited by the amount of plasticity in the start and progression of migration. Therefore, long‐term climatic changes resulting in earlier snowmelt have the potential to greatly affect shorebird populations, especially if shorebirds are unable to advance nest initiation sufficiently to keep pace with seasonal advancement of their invertebrate prey.

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Gut microbiota can have important effects on host health, but explanatory factors and pathways that determine gut microbial composition can differ among host lineages. In mammals, host phylogeny is one of the main drivers of gut microbiota, a result of vertical transfer of microbiota during birth. In birds, it is less clear what the drivers might be, but both phylogeny and environmental factors may play a role. We investigated host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds. We characterized bacterial communities from 375 fecal samples collected from adults of eight shorebird species captured at a network of nine breeding sites in the Arctic and sub-Arctic ecoregions of North America, by sequencing the V4 region of the bacterial 16S ribosomal RNA gene. Firmicutes (55.4%), Proteobacteria (13.8%), Fusobacteria (10.2%), and Bacteroidetes (8.1%) dominated the gut microbiota of adult shorebirds. Breeding location was the main driver of variation in gut microbiota of breeding shorebirds (R2 = 11.6%), followed by shorebird host species (R2 = 1.8%), and sampling year (R2 = 0.9%), but most variation remained unexplained. Site variation resulted from differences in the core bacterial taxa, whereas rare, low-abundance bacteria drove host species variation. Our study is the first to highlight a greater importance of local environment than phylogeny as a driver of gut microbiota composition in wild, migratory birds under natural conditions.

Birds breeding in cold environments regularly have to interrupt incubation to forage, causing a trade-off between two mutually exclusive behaviours. Earlier studies showed that uniparental Arctic sandpipers overall spend less time incubating their eggs than biparental species, but interspecific differences in size and ecology were potential confounding factors. This study reports on a within-species comparison of breeding schedules and metal egg temperatures in uni- and biparental sanderlings (Calidris alba) in Northeast Greenland in relation to ambient temperature. We recorded incubation schedules with nest temperature loggers in 34 sanderling clutches (13 uniparentals, 21 biparentals). The temperature of a metal egg placed within the clutch of 17 incubating birds (6 uniparentals, 9 biparentals) was measured as an indicator of the heat put into eggs. Recess frequency, recess duration and total recess time were higher in uniparentals than in biparentals and positively correlated with ambient temperatures in uniparentals only. Uniparental sanderlings maintained significantly higher metal egg temperatures during incubation than biparentals (1.4°C difference on average). Our results suggest that uniparental sanderlings compensate for the lower nest attendance, which may prolong the duration of the incubation period and negatively affect the condition of the hatchlings, by maintaining a higher heat flux into the eggs.

dUsing 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in red knot (Calidris canutus; n ‫؍‬ 40), ruddy turnstone (Arenaria interpres; n ‫؍‬ 35), and semipalmated sandpiper (Calidris pusilla; n ‫؍‬ 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of Campylobacter spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of Bacilli (63.5%), Fusobacteria (12.7%), Epsilonproteobacteria (6.5%), and Clostridia (5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as Campylobacter (82.3%) or Helicobacter (17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as C. lari (>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of Campylobacter, such as C. jejuni and C. coli, were not detected in excreta of any of the three bird species. Most Helicobacter-like sequences identified were closely related to H. pametensis (>99% sequence identity) and H. anseris (92% sequence identity). qPCR results showed that the occurrence and abundance of Campylobacter spp. was relatively high compared to those of fecal indicator bacteria, such as Enterococcus spp., E. faecalis, and Catellicoccus marimammalium. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic Campylobacter species.