Shared microbial taxa between wild and laboratory-rearedA. mexicanus
We next asked if any of the microbes present in the natural habitat have
been maintained in the laboratory-reared fish by identifying ASVs that
are present in both sample types. We found that 53% of the microbes in
the wild surface fish were present in the lab surface fish (72/135
amplicon sequencing variant (ASVs)). In comparison, 33% of the microbes
in the wild Pachón cavefish were present in the lab Pachón cavefish
(28/86 ASVs, Figure 3C ). Microbes that are shared between
individuals of the same species that have been raised in different
habitats have been referred to as the “core microbiome”. It is
hypothesized that these microbes are essential for normal function of
the host and that host-driven mechanisms may exist to ensure they are
represented . By this definition, Pachón cavefish had fewer core
microbes compared to surface fish (28 versus 72 ASVs) and most of the
core microbes were also present in the surface fish core microbiome (19
out of the 28 ASVs). In other words, many of the same microbes are
essential for host function in surface fish and cavefish, but cavefish
may require fewer. The core microbes are mostly from the phylum
Firmicutes (Figure S4 ). Firmicutes are one of the dominant taxa
in fish microbiomes and are important for carbohydrate metabolism . We
only identified one microbe that was part of the Pachón core and never
found in surface fish, Aeromonas asv.13 (Figure 3C“1a”, Figure S4 ). Aeromonas are gram negative bacteria
associated with infections in fish and humans suggesting that some
“core microbes” reflect a difference in predisposition to infection
rather than difference in maintenance of microbes that are essential to
the host. In summary, A. mexicanus in the laboratory have a
microbiome that is distinct and more diverse compared to their wild
counterparts. In addition, more microbes are shared between lab and wild
surface fish compared to lab and wild cavefish.