Hindguts of Kyphosus sydneyanus Harbor Phylogenetically and Genomically Distinct Alistipes Capable of Degrading Algal Polysaccharides and Diazotrophy
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Authors
Facimoto, CT
Clements, KD
White, WL
Handley, KM
Supervisor
Item type
Journal Article
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Publisher
American Society for Microbiology
Abstract
The genus Alistipes (Bacteroidota) is most often associated with human clinical samples and livestock. However, Alistipes are also prevalent in the hindgut of the marine herbivorous fish Kyphosus sydneyanus (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests Alistipes degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to K. sydneyanus-derived Alistipes, we compared 445 high-quality genomes of Alistipes available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the K. sydneyanus gut. Analyses showed that Alistipes from K. sydneyanus are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived Alistipes had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived Alistipes were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by Alistipes from K. sydneyanus was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related Alistipes target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among Alistipes in the fish hindgut that likely contribute to K. sydneyanus digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these Alistipes species.Description
Keywords
Alistipes, CAZyme, cobalamin, fish gut microbiome, macroalgae, nitrogen, 3107 Microbiology, 31 Biological Sciences, 3105 Genetics, Genetics, Nutrition, 14 Life Below Water
Source
Msystems, ISSN: 2379-5077 (Print); 2379-5077 (Online), American Society for Microbiology, 10(1), e0100724-. doi: 10.1128/msystems.01007-24
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Copyright © 2024 Facimoto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.