Evolution of novel host-microbiota coupling underlies adaptation to nutrient-scarce environments.
- 1School of Life Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
Abstract
Animals colonizing food-limited environments need to overcome growth constraints by adapting to low, inconsistent nutritional inputs. Comparative studies of surface and cave populations of the Mexican tetra fish species Astyanax mexicanus provide a powerful system to explore evolution to food scarcity. In nutrient-scarce caves, evolved traits such as eye loss and increased fat storage have been shown to conserve energy in cavefish1-3 . However, the role of microbiota-mediated metabolism in sustaining growth and survival under food limitation remains poorly understood. Here, we demonstrate that surface and cave populations distinctly modulate their gut microbiota, with cavefish recruiting microbes whose predicted metabolites specifically promote growth under nutrient-limited conditions. Using microbiota data from three distinct dietary regimes and a fasting treatment, integrated topological data analysis4 and sparse modeling identify sugar and fatty acid degradation pathways coupled with growth in cavefish. Notably, the metabolites of these pathways are beneficial only for cavefish growth, and not for surface fish. Fasting in cavefish led to the recruitment of gut microbes capable of metabolizing aromatic compounds inaccessible to the host, whereas it recruited few microbial associates in surface fish. Our findings indicate that cavefish evolved novel host-microbiota coupling to sustain growth and resilience in their nutrient-scarce niche. We anticipate that our findings will broadly inform studies of evolution under extreme nutritional conditions and provide insights into the role of host-microbiota interactions in resilience to food scarcity at varied time scales.
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BibTeX
@misc{iwashita2026evolution,
title = {{Evolution of novel host-microbiota coupling underlies adaptation to nutrient-scarce environments.}},
author = {M. Iwashita and C. Valdez and A. G. Hudson and X. Barragan Gonzalez and J. Kato and E. Doy and A. Tran and L. J. Tuttle Raz and R. D. Prescott and K. J. Coyle and A. Carmona Baez and N. Roberts and R. B. Roberts and F. Nasrin and M. Yoshizawa},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.10.758241},
url = {https://www.biorxiv.org/content/10.64898/2026.10.10.758241v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Evolution of novel host-microbiota coupling underlies adaptation to nutrient-scarce environments.
AU - M. Iwashita
AU - C. Valdez
AU - A. G. Hudson
AU - X. Barragan Gonzalez
AU - J. Kato
AU - E. Doy
AU - A. Tran
AU - L. J. Tuttle Raz
AU - R. D. Prescott
AU - K. J. Coyle
AU - A. Carmona Baez
AU - N. Roberts
AU - R. B. Roberts
AU - F. Nasrin
AU - M. Yoshizawa
PY - 2026
DA - 2026/10/10
PB - bioRxiv
DO - 10.64898/2026.10.10.758241
UR - https://www.biorxiv.org/content/10.64898/2026.10.10.758241v1
AB - Animals colonizing food-limited environments need to overcome growth constraints by adapting to low, inconsistent nutritional inputs. Comparative studies of surface and cave populations of the Mexican tetra fish species Astyanax mexicanus provide a powerful system to explore evolution to food scarcity. In nutrient-scarce caves, evolved traits such as eye loss and increased fat storage have been shown to conserve energy in cavefish1-3 . However, the role of microbiota-mediated metabolism in sustaining growth and survival under food limitation remains poorly understood. Here, we demonstrate that surface and cave populations distinctly modulate their gut microbiota, with cavefish recruiting microbes whose predicted metabolites specifically promote growth under nutrient-limited conditions. Using microbiota data from three distinct dietary regimes and a fasting treatment, integrated topological data analysis4 and sparse modeling identify sugar and fatty acid degradation pathways coupled with growth in cavefish. Notably, the metabolites of these pathways are beneficial only for cavefish growth, and not for surface fish. Fasting in cavefish led to the recruitment of gut microbes capable of metabolizing aromatic compounds inaccessible to the host, whereas it recruited few microbial associates in surface fish. Our findings indicate that cavefish evolved novel host-microbiota coupling to sustain growth and resilience in their nutrient-scarce niche. We anticipate that our findings will broadly inform studies of evolution under extreme nutritional conditions and provide insights into the role of host-microbiota interactions in resilience to food scarcity at varied time scales.
ER -