Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts

Gut microbiomes perform essential services for their hosts, including
helping them to digest food and manage pathogens and parasites. Performing
these services requires a diverse and constantly changing set of metabolic
functions from the bacteria in the microbiome. The metabolic repertoire of
the microbiome is ultimately dependent on the outcomes of the ecological
interactions of its member microbes, as these interactions in part
determine the taxonomic composition of the microbiome. The ecological
processes that underpin the microbiome's ability to handle a variety
of metabolic challenges might involve rapid turnover of the gut microbiome
in response to new metabolic challenges, or it might entail maintaining
sufficient diversity in the microbiome that any new metabolic demands can
be met from an existing set of bacteria. To differentiate between these
scenarios, we examine the gut bacteria and resident eukaryotes of two
generalist-insectivore lizards, while simultaneously identifying the
arthropod prey each lizard was digesting at the time of sampling. We find
that the cohorts of bacteria that occur significantly more or less often
than expected with arthropod diet items or eukaryotes include bacteria
species that are highly similar to each other metabolically. This pattern
in the bacteria microbiome could represent an early step in the taxonomic
shifts in bacteria microbiome that occur when host lineages change their
in diet niche over evolutionary timescales.