Fine Scale Transitions of the Microbiota and Metabolome Along the Gastrointestinal Tract of Herbivorous Fishes

Wesley Sparagon, Emily Gentry, Jeremiah Minich, Lisa Vollbrecht, Lieve Laurens, Eric Allen, Neil Sims, Pieter Dorrestein, Linda Kelly, Craig Nelson

Research output: Contribution to journalArticlepeer-review

10 Scopus Citations


Background: Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus. Results: Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions: The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Original languageAmerican English
Article number33
Number of pages21
JournalAnimal Microbiome
Issue number1
StatePublished - 2022

Bibliographical note

Publisher Copyright:
© 2022, The Author(s).

NREL Publication Number

  • NREL/JA-2700-82761


  • Fish gastrointestinal tract microbiota metabolome transitions


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