{"id":{"repo_id":"auckland-ms","oai_identifier":"oai:researchspace.auckland.ac.nz:2292/70116"},"canonical_url":"https://search.dev.ndltd.org/etd/auckland-ms/oai:researchspace.auckland.ac.nz:2292/70116","repository":{"repo_id":"auckland-ms","name":"University of Auckland","base_url":"https://researchspace.auckland.ac.nz/server/oai/request"},"display":{"title":"Community Composition and Function of the Hindgut Microbiome in Seaweed-Eating Marine Fish","abstract":"The gut microbiota of Kyphosus sydneyanus is essential for their nutrition, fermenting dietary macroalgae to short-chain fatty acids (SCFAs) that benefit the host. Microbial communities assist the fish host overcome nutritional limitations (e.g., protein, energy and vitamins). It is unclear which taxonomic groups contribute to the break down of dietary macroalgae along the fish gut and how they help overcome these nutritional constraints. This thesis investigated the role of microbial taxa in the K. sydneyanus gut in algal degradation, nitrogen, amino acid and vitamin metabolism. Analyses used 397 metagenome-assembled genomes (MAGs) and metatranscriptomes from K. sydneyanus collected from waters near Great Barrier and Little Barrier islands, New Zealand. Most bacteria (99%) were unclassified at the species level, and Bacteroidia and Clostridia dominated the gut community. Genes encoding endo-acting carbohydrate-active enzymes (CAZymes) associated with both classes suggest their involvement in initiating glycan depolymerization. Bacteroidia contributed the most to CAZyme-related gene expression in the hindgut, particularly in the biomass-rich hindgut chamber. The enrichment of CAZyme gene clusters (CGCs) within Alistipes underscores its enhanced capacity for utilizing macroalgal polysaccharides including alginate, laminarin and sulfated polysaccharides. Comparative genome analysis of Alistipes from various hosts revealed distinctive genomic attributes of Alistipes from K. sydneyanus, including reduced genome size, lower GC content, and unique metabolic capabilities such as nitrogen fixation and cobalamin biosynthesis. The Alistipes from K. sydneyanus encoded a distinct CAZyme composition for marine polysaccharides, suggesting adaptation of their CAZyme repertoire to the host diet. Analysis of transcriptional activity within the K. sydneyanus hindgut microbiome revealed an increased diversity of processes in the distal gut. Both Bacteroidia and Clostridia expressed genes for nitrogen fixation, but only Clostridia co-expressed genes related to the urea cycle and polyamine biosynthesis, suggesting a role in nitrogen provisioning to the community. Results suggest that the coexistence of Bacteroidia and Clostridia relies on metabolite exchange, particularly cobalamin precursors produced by Clostridia and extracellularly-degraded algal oligosaccharides produced by Bacteroidia. The predicted division of labour between Bacteroidia and Clostridia in algal polysaccharide degradation and cobalamin biosynthesis suggests collaboration in the provisioning of essential resources to the host, including nitrogen, amino acids, SCFAs, and vitamins.","abstract_html":"The gut microbiota of Kyphosus sydneyanus is essential for their nutrition, fermenting dietary macroalgae to short-chain fatty acids (SCFAs) that benefit the host. Microbial communities assist the fish host overcome nutritional limitations (e.g., protein, energy and vitamins). It is unclear which taxonomic groups contribute to the break down of dietary macroalgae along the fish gut and how they help overcome these nutritional constraints. This thesis investigated the role of microbial taxa in the K. sydneyanus gut in algal degradation, nitrogen, amino acid and vitamin metabolism. Analyses used 397 metagenome-assembled genomes (MAGs) and metatranscriptomes from K. sydneyanus collected from waters near Great Barrier and Little Barrier islands, New Zealand. Most bacteria (99%) were unclassified at the species level, and Bacteroidia and Clostridia dominated the gut community. Genes encoding endo-acting carbohydrate-active enzymes (CAZymes) associated with both classes suggest their involvement in initiating glycan depolymerization. Bacteroidia contributed the most to CAZyme-related gene expression in the hindgut, particularly in the biomass-rich hindgut chamber. The enrichment of CAZyme gene clusters (CGCs) within Alistipes underscores its enhanced capacity for utilizing macroalgal polysaccharides including alginate, laminarin and sulfated polysaccharides. Comparative genome analysis of Alistipes from various hosts revealed distinctive genomic attributes of Alistipes from K. sydneyanus, including reduced genome size, lower GC content, and unique metabolic capabilities such as nitrogen fixation and cobalamin biosynthesis. The Alistipes from K. sydneyanus encoded a distinct CAZyme composition for marine polysaccharides, suggesting adaptation of their CAZyme repertoire to the host diet. Analysis of transcriptional activity within the K. sydneyanus hindgut microbiome revealed an increased diversity of processes in the distal gut. Both Bacteroidia and Clostridia expressed genes for nitrogen fixation, but only Clostridia co-expressed genes related to the urea cycle and polyamine biosynthesis, suggesting a role in nitrogen provisioning to the community. Results suggest that the coexistence of Bacteroidia and Clostridia relies on metabolite exchange, particularly cobalamin precursors produced by Clostridia and extracellularly-degraded algal oligosaccharides produced by Bacteroidia. The predicted division of labour between Bacteroidia and Clostridia in algal polysaccharide degradation and cobalamin biosynthesis suggests collaboration in the provisioning of essential resources to the host, including nitrogen, amino acids, SCFAs, and vitamins.","abstract_has_math":false,"creators":["Facimoto, Cesar"],"institution":"ResearchSpace@Auckland","degree_name":"PhD","degree_level":"Doctoral","degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":[],"advisors":["Handley, Kim","Clements, Kendall"],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024","date_published":"2024","updated_at":"2026-07-24T01:04:34Z","subjects":[],"languages":[],"rights":["Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated."],"rights_urls":["https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2292/70116","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Handley, Kim","Clements, Kendall"]},{"key":"dc:creator","label":"Author","values":["Facimoto, Cesar"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2024-09-26T21:55:44Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2024-09-26T21:55:44Z"]},{"key":"dc:date.issued","label":"Date","values":["2024"]},{"key":"dc:publisher","label":"Institution","values":["ResearchSpace@Auckland"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["PhD"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["The University of Auckland"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated."]},{"key":"dc:rights.uri","label":"Rights URI","values":["https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/2292/70116"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The gut microbiota of Kyphosus sydneyanus is essential for their nutrition, fermenting dietary macroalgae to short-chain fatty acids (SCFAs) that benefit the host. Microbial communities assist the fish host overcome nutritional limitations (e.g., protein, energy and vitamins). It is unclear which taxonomic groups contribute to the break down of dietary macroalgae along the fish gut and how they help overcome these nutritional constraints. This thesis investigated the role of microbial taxa in the K. sydneyanus gut in algal degradation, nitrogen, amino acid and vitamin metabolism. Analyses used 397 metagenome-assembled genomes (MAGs) and metatranscriptomes from K. sydneyanus collected from waters near Great Barrier and Little Barrier islands, New Zealand. Most bacteria (99%) were unclassified at the species level, and Bacteroidia and Clostridia dominated the gut community. Genes encoding endo-acting carbohydrate-active enzymes (CAZymes) associated with both classes suggest their involvement in initiating glycan depolymerization. Bacteroidia contributed the most to CAZyme-related gene expression in the hindgut, particularly in the biomass-rich hindgut chamber. The enrichment of CAZyme gene clusters (CGCs) within Alistipes underscores its enhanced capacity for utilizing macroalgal polysaccharides including alginate, laminarin and sulfated polysaccharides. Comparative genome analysis of Alistipes from various hosts revealed distinctive genomic attributes of Alistipes from K. sydneyanus, including reduced genome size, lower GC content, and unique metabolic capabilities such as nitrogen fixation and cobalamin biosynthesis. The Alistipes from K. sydneyanus encoded a distinct CAZyme composition for marine polysaccharides, suggesting adaptation of their CAZyme repertoire to the host diet. Analysis of transcriptional activity within the K. sydneyanus hindgut microbiome revealed an increased diversity of processes in the distal gut. Both Bacteroidia and Clostridia expressed genes for nitrogen fixation, but only Clostridia co-expressed genes related to the urea cycle and polyamine biosynthesis, suggesting a role in nitrogen provisioning to the community. Results suggest that the coexistence of Bacteroidia and Clostridia relies on metabolite exchange, particularly cobalamin precursors produced by Clostridia and extracellularly-degraded algal oligosaccharides produced by Bacteroidia. The predicted division of labour between Bacteroidia and Clostridia in algal polysaccharide degradation and cobalamin biosynthesis suggests collaboration in the provisioning of essential resources to the host, including nitrogen, amino acids, SCFAs, and vitamins."]},{"key":"dc:title","label":"Title","values":["Community Composition and Function of the Hindgut Microbiome in Seaweed-Eating Marine Fish"]}]}],"canonical_facts":{"dc:contributor.advisor":["Handley, Kim","Clements, Kendall"],"dc:creator":["Facimoto, Cesar"],"dc:date.accessioned":["2024-09-26T21:55:44Z"],"dc:date.available":["2024-09-26T21:55:44Z"],"dc:date.issued":["2024"],"dc:description.abstract":["The gut microbiota of Kyphosus sydneyanus is essential for their nutrition, fermenting dietary macroalgae to short-chain fatty acids (SCFAs) that benefit the host. Microbial communities assist the fish host overcome nutritional limitations (e.g., protein, energy and vitamins). It is unclear which taxonomic groups contribute to the break down of dietary macroalgae along the fish gut and how they help overcome these nutritional constraints. This thesis investigated the role of microbial taxa in the K. sydneyanus gut in algal degradation, nitrogen, amino acid and vitamin metabolism. Analyses used 397 metagenome-assembled genomes (MAGs) and metatranscriptomes from K. sydneyanus collected from waters near Great Barrier and Little Barrier islands, New Zealand. Most bacteria (99%) were unclassified at the species level, and Bacteroidia and Clostridia dominated the gut community. Genes encoding endo-acting carbohydrate-active enzymes (CAZymes) associated with both classes suggest their involvement in initiating glycan depolymerization. Bacteroidia contributed the most to CAZyme-related gene expression in the hindgut, particularly in the biomass-rich hindgut chamber. The enrichment of CAZyme gene clusters (CGCs) within Alistipes underscores its enhanced capacity for utilizing macroalgal polysaccharides including alginate, laminarin and sulfated polysaccharides. Comparative genome analysis of Alistipes from various hosts revealed distinctive genomic attributes of Alistipes from K. sydneyanus, including reduced genome size, lower GC content, and unique metabolic capabilities such as nitrogen fixation and cobalamin biosynthesis. The Alistipes from K. sydneyanus encoded a distinct CAZyme composition for marine polysaccharides, suggesting adaptation of their CAZyme repertoire to the host diet. Analysis of transcriptional activity within the K. sydneyanus hindgut microbiome revealed an increased diversity of processes in the distal gut. Both Bacteroidia and Clostridia expressed genes for nitrogen fixation, but only Clostridia co-expressed genes related to the urea cycle and polyamine biosynthesis, suggesting a role in nitrogen provisioning to the community. Results suggest that the coexistence of Bacteroidia and Clostridia relies on metabolite exchange, particularly cobalamin precursors produced by Clostridia and extracellularly-degraded algal oligosaccharides produced by Bacteroidia. The predicted division of labour between Bacteroidia and Clostridia in algal polysaccharide degradation and cobalamin biosynthesis suggests collaboration in the provisioning of essential resources to the host, including nitrogen, amino acids, SCFAs, and vitamins."],"dc:identifier.uri":["https://hdl.handle.net/2292/70116"],"dc:publisher":["ResearchSpace@Auckland"],"dc:rights":["Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated."],"dc:rights.uri":["https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm"],"dc:title":["Community Composition and Function of the Hindgut Microbiome in Seaweed-Eating Marine Fish"],"dc:type":["Thesis"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["PhD"],"thesis:institution_name":["The University of Auckland"]},"updated_at":"2026-07-24T01:04:34Z"}