Abstract
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.
Highlights
The gut microbiome, defined as the community of living microorganisms and non-living genetic elements inhabiting the gastrointestinal tract (Berg et al, 2020), plays an important role in an individual’s development, digestion, and immune function
The McNemar’s exact test revealed a significant difference in Salmonella detection probability between culturing vs. 16S rRNA gene sequencing for both culture workflow 1 (Figure 2A, p = 0.002) and workflow 2 (Figure 2B, p = 0.035)
A generalized linear model (GLM) showed no significant relationship between Salmonella culture results and the absolute abundance of Salmonella as measured by unrarefied reads of 16S rRNA data for workflow 2 (p = 0.58) and both workflows combined (p = 0.96)
Summary
The gut microbiome, defined as the community of living microorganisms (e.g., bacteria) and non-living genetic elements (e.g., relic DNA) inhabiting the gastrointestinal tract (Berg et al, 2020), plays an important role in an individual’s development, digestion, and immune function (van der Waaij, 1989; Kohl, 2012). Infection with pathogens is linked to changes in the microbiome, as seen in mallards infected with low-pathogenic avian influenza virus (Ganz et al, 2017), as well as Marek’s disease virus (Perumbakkam et al, 2014) and Salmonella infection in chickens (Videnska et al, 2013). It is unclear whether microbial dysbiosis is a result of or a precursor to pathogen infection: commensal microbiota can promote colonization resistance, but changes in the normal microbial community can decrease colonization resistance allowing for pathogen infection (Sorbara and Pamer, 2019). The relationship between pathogen infection and microbiome composition highlights the need to improve our understanding of the how and when the microbiome is influenced by pathogen infections
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