Metabolic specialization in the gut microbiome of aquatic mammalian herbivores

Sirenians, such as manatees, are the only extant mammals fully adapted to aquatic herbivory. Through specialized hindgut fermentation, they play a role in modulating nutrient fluxes and carbon cycling across tropical coastal and riverine ecosystems. However, our understanding of their gut microbiome and its metabolic potential remains elusive. Here we present an ultradeep genomic atlas of the gut microbiome from 47 freshwater and marine manatees spanning distinct developmental stages, comprising 1,215 non-redundant prokaryotic metagenome-assembled genomes and their associated virome. The manatee microbiome encodes a multilayered enzymatic repertoire for plant cell wall deconstruction, including free enzymes, cellulosomes and CAZyme-enriched outer membrane vesicles, alongside diverse pathways for aromatic catabolism. Combining biochemical and structural approaches, we characterize a previously unrecognized enzymatic pathway involving epilactase, which enables a specific Bacillota species to exploit a carbohydrate inaccessible to most microbial life, defining a specialized biochemical strategy for nutrient niche partitioning. Together, these findings uncover the microbial and metabolic basis of aquatic mammalian herbivory.

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Publication Details

Journal
Nature Microbiology
Published
2026-11-02
DOI
https://doi.org/10.1038/s41564-026-02520-2
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
0.00

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article

Metabolic specialization in the gut microbiome of aquatic mammalian herbivores

Vítor Luz Carvalho, Giulio Mendes Braatz, Joaquim Martins, Maxuel O. Andrade et al.
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Nature Microbiology
Gut microbiota and health
article

Metabolic specialization in the gut microbiome of aquatic mammalian herbivores

Vítor Luz Carvalho, Giulio Mendes Braatz, Joaquim Martins, Maxuel O. Andrade, Renan Yuji Miyamoto, Rodrigo Silva Araujo Streit, Gabriela Félix Persinoti, Priscila Oliveira de Giuseppe, Luana Galvão Morão, Heloísa Ciol, Lúcia Daniela Wolf, Nicolas Terrapon, Paula M. R. Higasi, Cláudio Benício Cardoso-Silva, M.A.B. Morais, Leandro Nascimento Lemos, Daniela Magalhães Drummond de Mello, Mario Tyago Murakami, Bernard Henrissat, Octávio Augusto Costa Almeida, Vincent Lombard, Damaris Batistão Martim, Marcele Pandeló Martins, CARLOS H.M. OLIVEIRA, Clelton A. Santos, Fabiane Stoffel, Gustavo Henrique Martins, G.D. Noske, Monyque Karoline de Paula Silva, Evandro A. Araújo, Vera M. F. da Silva, Jorge Porto, Aline R. Souza, Felipe A. C. Gonçalves, Giovana M. Oliveira, Douglas A. A. Paixão
article en

Abstract

Sirenians, such as manatees, are the only extant mammals fully adapted to aquatic herbivory. Through specialized hindgut fermentation, they play a role in modulating nutrient fluxes and carbon cycling across tropical coastal and riverine ecosystems. However, our understanding of their gut microbiome and its metabolic potential remains elusive. Here we present an ultradeep genomic atlas of the gut microbiome from 47 freshwater and marine manatees spanning distinct developmental stages, comprising 1,215 non-redundant prokaryotic metagenome-assembled genomes and their associated virome. The manatee microbiome encodes a multilayered enzymatic repertoire for plant cell wall deconstruction, including free enzymes, cellulosomes and CAZyme-enriched outer membrane vesicles, alongside diverse pathways for aromatic catabolism. Combining biochemical and structural approaches, we characterize a previously unrecognized enzymatic pathway involving epilactase, which enables a specific Bacillota species to exploit a carbohydrate inaccessible to most microbial life, defining a specialized biochemical strategy for nutrient niche partitioning. Together, these findings uncover the microbial and metabolic basis of aquatic mammalian herbivory.

Nature Microbiology
Centre National de la Recherche Scientifique (FR), Universidade de São Paulo (BR), Universidade Estadual de Campinas (UNICAMP) (BR), Instituto Nacional de Pesquisas da Amazônia (BR), Aix-Marseille Université (FR), Brazilian Synchrotron Light Laboratory (BR), Architecture et Fonction des Macromolécules Biologiques (FR), Brazilian Center for Research in Energy and Materials (BR), Technical University of Denmark (DK)
Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Novo Nordisk Fonden
Openalex Percentile: Top 25%
Gut microbiota and health
DOIOpen Access PDFOpenAlex
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