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.