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.