loading page

Genetic adaptation shapes gut microbiome composition in Astyanax mexicanus
  • +4
  • Misty Riddle,
  • Nguyen Nguyen,
  • Maeve Nave,
  • Robert Peuß,
  • Ernesto Maldonado,
  • Nicolas Rohner,
  • Clifford Tabin
Misty Riddle
University of Nevada Reno

Corresponding Author:[email protected]

Author Profile
Nguyen Nguyen
Microbiome Insights
Author Profile
Maeve Nave
University of Nevada Reno
Author Profile
Robert Peuß
University of Munster Institute for Evolution and Biodiversity
Author Profile
Ernesto Maldonado
Institute of Marine Sciences and Limnology of the UNAM
Author Profile
Nicolas Rohner
Stowers Institute for Medical Research
Author Profile
Clifford Tabin
Harvard Medical School
Author Profile


The ecological and genetic changes that underlie evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, Astyanax mexicanus, in their natural environments and under controlled laboratory conditions. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish adaptation shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrate that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.