Gut microbiota of a long‐distance migrant demonstrates resistance against environmental microbe incursions

Abstract

Migratory animals encounter suites of novel microbes as they move between disparate sites during their migrations, and are frequently implicated in the global spread of pathogens. Although wild animals have been shown to source a proportion of their gut microbiota from their environment, the susceptibility of migrants to enteric infections may be dependent upon the capacity of their gut microbiota to resist incorporating encountered microbes. To evaluate migrants' susceptibility to microbial invasion, we determined the extent of microbial sourcing from the foraging environment and examined how this influenced gut microbiota dynamics over time and space in a migratory shorebird, the Red-necked stint Calidris ruficollis. Contrary to previous studies on wild, nonmigratory hosts, we found that stint on their nonbreeding grounds obtained very little of their microbiota from their environment, with most individuals sourcing only 0.1% of gut microbes from foraging sediment. This microbial resistance was reflected at the population level by only weak compositional differences between stint flocks occupying ecologically distinct sites, and by our finding that stint that had recently migrated 10,000 km did not differ in diversity or taxonomy from those that had inhabited the same site for a full year. However, recent migrants had much greater abundances of the genus Corynebacterium, suggesting a potential microbial response to either migration or exposure to a novel environment. We conclude that the gut microbiota of stint is largely resistant to invasion from ingested microbes and that this may have implications for their susceptibility to enteric infections during migration.

Spatiotemporal successions of shrimp gut microbial colonization: high consistency despite distinct species pool

“…S1), revealing that shrimp selects a subset of bacteria (i.e., Gammaproteobacteria and Verrucomicrobia species), while barriers against others (Supporting Information Fig. Consistent with this pattern, there are only weak dissimilarities in gut microbiota between stint flocks residing in separate sites with disparate sediment bacterial communities (Risely et al, 2017). Second, we found similar gut microbiotas between shrimp farming distant locations where bacterioplankton communities were distinct at each life stage (Fig.…”

“…That is, gut microbiotas within shrimp are more similar to one another, despite being in independent ponds, than they are to their own rearing water. Consistent with this pattern, there are only weak dissimilarities in gut microbiota between stint flocks residing in separate sites with disparate sediment bacterial communities (Risely et al, 2017). At last, shrimp life stage is the predominant factor in governing the variation in bacterial communities (Table 1).…”

“…High colonization resistance in shrimp may afford an explanation for why shrimp farming spatially distant locations differed only weakly in their gut microbiotas (Fig. Similarly, SourceTracker revealed that migratory stint sources only 0.2%-0.4% gut microbes from foraging sediment, a pattern observed at two distant locations (Risely et al, 2017). By the same logic, the application of probiotics with water/food generally fails to colonize into shrimp intestine Liu et al, 2018).…”

“…Consequently, there is an inverse relationship with the relative abundances of taxa that are shared between host symbionts and the environment (Walke et al, 2014). Similarly, SourceTracker revealed that migratory stint sources only 0.2%-0.4% gut microbes from foraging sediment, a pattern observed at two distant locations (Risely et al, 2017). The large proportion of 'unknown' source could be colonized into the gut from other environmental sources that we did not investigate, such as vertical transmission, sedimentary biofilm, food or shrimp care staff.…”

Assessing 16S marker gene survey data analysis methods using mixtures of human stool sample DNA extracts

“…For example, a study exploring the microbial ecology of the Red-necked stint Calidris ruficollis, a migratory shorebird, used a hard filter to validate their study conclusions are not biases by false positive features. The study authors compared results with and without prevalence filter ensuring that the study conclusions were not biased by using the arbitrary filter or including the low abundant features [28].…”