Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

Pekarsky, Sasha; Corl, Ammon; Turjeman, Sondra; Kamath, Pauline L.; Getz, Wayne M.; Bowie, Rauri C. K.; Markin, Yuri; Nathan, Ran

doi:10.1111/mec.16079

Cited by 21 publications

(20 citation statements)

References 149 publications

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“…This sort of pattern has been observed in barn owls (Tyto alba), where owls that traveled greater distances from their nests had more diverse microbiota (Corl et al, 2020). However, migration does not necessarily lead to changes in the microbiota as microbial diversity did not vary between fecal samples collected from common cranes (Grus grus) before and after migration (Pekarsky et al, 2021). Dietary, physiological, or subspecies differences might also explain differences in Salmonella prevalence between migrants and resident barn swallows.…”

Section: Discussionmentioning

confidence: 59%

High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows

et al. 2021

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Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pathogenesis. Little is known about the effects of potential pathogens, such as Salmonella, on the microbiome in wildlife, which are known to play an important role in disease transmission to humans. Culturing techniques have traditionally been used to detect pathogens, but recent studies have utilized high throughput sequencing of the 16S rRNA gene to characterize host-associated microbial communities (i.e., the microbiome) and to detect specific bacteria. Building upon this work, we evaluated the utility of high throughput 16S rRNA gene sequencing for potential bacterial pathogen detection in barn swallows (Hirundo rustica) and used these data to explore relationships between potential pathogens and microbiota. To accomplish this, we first compared the detection of Salmonella spp. in swallows using 16S rRNA data with standard culture techniques. Second, we examined the prevalence of Salmonella using 16S rRNA data and examined the relationship between Salmonella-presence or -absence and individual host factors. Lastly, we evaluated host-associated bacterial diversity and community composition in Salmonella-present vs. -absent birds. Out of 108 samples, we detected Salmonella in six (5.6%) samples based on culture, 25 (23.1%) samples with unrarefied 16S rRNA gene sequencing data, and three (2.8%) samples with both techniques. We found that sex, migratory status, and weight were correlated with Salmonella presence in swallows. In addition, bacterial community composition and diversity differed between birds based on Salmonella status. This study highlights the value of 16S rRNA gene sequencing data for monitoring pathogens in wild birds and investigating the ecology of host microbe-pathogen relationships, data which are important for prediction and mitigation of disease spillover into domestic animals and humans.

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Section: Discussionmentioning

confidence: 59%

High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows

et al. 2021

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“…Of the prevalent genera (a subset of ASVs shared by >10% of birds), 60% were shared across the sampling methods, suggesting a core microbiota can be successfully identified using either method. This is impressive given the high intra-individual diversity previously reported for common cranes (Pekarsky et al, 2021). Similarly, most of the differentially abundant genera were lowabundance taxa, again suggesting that either method can be used to identify many of the most common core microbial taxa.…”

Section: Discussionmentioning

confidence: 61%

“…We obtained samples for this project as part of a wider study of common crane movement, foraging, and microbiome (Pekarsky et al, 2021). During the pre-migration period (early fall), cranes stage in western Russia (Ryazan area; 54°56′N, 41°02E) for several weeks before the onset of migration (Johnsgard, 1983; Leito et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

“…Sample extraction and processing for 16S rRNA metabarcoding is described in Pekarsky et al (2021). Briefly, we PCR-amplified the V4 region of the 16S rRNA in triplicate for sequencing on an Illumina MiSeq.…”

Section: Methodsmentioning

confidence: 99%

“…Briefly, we PCR-amplified the V4 region of the 16S rRNA in triplicate for sequencing on an Illumina MiSeq. Data was processed in R v.4.1.1 to identify amplicon sequence variants (ASVs) as described in Pekarsky et al (2021). In total, 64 samples were sequenced for this study.…”

Section: Methodsmentioning

confidence: 99%

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Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals

Turjeman

Pekarsky

Corl

et al. 2022

Preprint

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In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in microbial composition (alpha and beta diversity), which were not accounted for by noninvasive samples' exposure to soil contaminants, as manually assessed by comparing differentially abundant taxa. They could result from trapped birds' exposure to sedatives. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, stressing or sedation may unravel how trapping affects wildlife microbiota.

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Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota

Liu

et al. 2022

Appl Microbiol Biotechnol

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Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

Cited by 21 publications

References 149 publications

High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows

High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows

Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota

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