Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt

Serag, Ahmed M.; Abdel-Sabour, M.S.; El-Hadidi, Mohamed; Maged, Mohamad; Magdy, Mahmoud; Ramadan, Mohamed Fawzy; Refaat, Medhat

doi:10.1007/s12010-021-03750-2

Cited by 5 publications

(2 citation statements)

References 69 publications

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“…The genetic study of Kyphosus gut symbionts has been limited to 16S rRNA ( 15 , 18 ) and metabolomic ( 18 ) investigations until the incorporation of shotgun metagenomics in a few recent studies ( 19 , 20 ). What functional profiling has been done in fish guts often relies on extrapolation from amplicon-based taxonomic distributions ( 21 – 24 ), and no study has yet generated a large collection of metagenome-assembled genomes (MAGs) from an algivorous fish gut. A de novo genomic investigation of Kyphosus symbionts has the potential to reveal degradative capacities that cannot be extrapolated from taxonomic lineage or relatedness to database representatives.…”

Section: Introductionmentioning

confidence: 99%

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Oliver,

Podell,

Wegley Kelly

et al. 2024

mBio

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Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea ) and Verrucomicrobiota (order Kiritimatiellales ) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors. IMPORTANCE Seaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

show abstract

Section: Introductionmentioning

confidence: 99%

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Oliver,

Podell,

Wegley Kelly

et al. 2024

mBio

View full text Add to dashboard Cite

show abstract

“…The genetic study of Kyphosus gut symbionts has been limited to 16S rRNA (15,18) and metabolomic (18) investigations until the incorporation of shotgun metagenomics in a few recent studies (19,20). What functional profiling has been done in fish guts often relies on extrapolation from amplicon-based taxonomic distributions (21)(22)(23)(24), and no study has yet generated a large collection of metagenome-assembled genomes (MAGs) from an algivorous fish gut. A de novo genomic investigation of Kyphosus symbionts has the potential to reveal degradative capacities that cannot be extrapolated from taxonomic lineage or relatedness to database representatives.…”

Section: Introductionmentioning

confidence: 99%

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides inKyphosusfish

Oliver,

Podell,

Kelly

et al. 2023

Preprint

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Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce foundational genomic work on the microbiota that perform this degradation. This study explores the potential ofKyphosusgastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae throughin silicostudy of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) reveals differences in enzymatic capabilities between the major microbial taxa inKyphosusguts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzymes able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from theBacillota(genusVallitalea) andVerrucomicrobiota(order Kiritimatiellales) suggest the potential for microbial transfer between marine sediment andKyphosusdigestive tracts. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level amongKyphosussymbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.ImportanceSeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genusKyphosusfeed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study is the first to build genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identifyKyphosusguts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

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Tilapia lake virus infection disrupts the gut microbiota of red hybrid tilapia (Oreochromis spp.)

Paimeeka,

Tangsongcharoen,

Lertwanakarn

et al. 2024

Aquaculture

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Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt

Cited by 5 publications

References 69 publications

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides inKyphosusfish

Tilapia lake virus infection disrupts the gut microbiota of red hybrid tilapia (Oreochromis spp.)

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