Core Microbiome
Identification of microbes that persist within the gut over time will help identify those that are inherently tied to biological processes, termed the community core microbiome. Our analyses identified a group of microbial lineages, including several that likely play a role in digestion and nutrient uptake, as the species-specific community core of Kirtland’s Warblers. Eight ASVs in genus Bacteroides (Phyla Bacteroidetes) were identified as core. Bacteroides are common gut microbes in humans that are frequently associated with food materials breakdown and production of nutrients and energy (Wexler 2007). Though common in birds, the exact function of Bacteroidesis unknown; however, it is thought they play a similar role in food digestion to that in humans (Bennett et al. 2013; Waite and Taylor 2015; Grond et al. 2018). Family Ruminococcaceae(Phyla Firmicutes), contains numerous bacterial species that degrade cellulose (Duncan et al. 2007). Our sampling of Kirtland’s Warblers identified three ASVs from this family that are common throughout the population. Similarly, the Greater Sage-Grouse (Centrocercus urophasianus) has a rich diversity ofRuminococcaceae associated with seasonal variation in foliage consumption (Drovetski et al. 2019). These bacteria may aid in the digestion of the various fruits and berries ingested throughout the year, but which become a primary part of the diet on the wintering grounds.
Defining the core microbiome is a critical step in understanding the consistent components of often dynamic and complex microbial assemblages. These stable components are commonly tied to biological processes within the host and their identification lead to an increased understanding of host-microorganism interactions and dependencies (Tschöp et al. 2009). Identifying core microbes can be confounded by environmental inocula which could inflate the number of ASVs identified as essential core. By resampling the same population we establish a core microbiome that is persistent across multiple environments and time periods. These bacterial lineages will likely play an important role in facilitating biological processes within the birds.
Additionally, through repeated sampling of the same birds at three separate time periods, we have documented the proportion of ASVs that individuals retain over time. Although several previous studies have described the proportion of core ASVs to total ASVs detected within their study, interpretations may vary depending on the number of birds sampled and may therefore not represent the number of core ASVs in each individual (Lewis et al. 2016; Grond et al. 2017). We show that individuals sampled in triplicate retain 18-26 ASVs over time. This represents an average of 25.1% of all lineages detected per individual per sampling point, and we argue it best reflects the proportion of stable, persistent bacteria within an individual. Documenting the species-specific core microbiome of Kirtland’s Warblers as well as persistent lineages across seasons and changing environments provides model data from which we can begin to understand the extent to which birds depend on their gut microbiota.