Global analysis of the biosynthetic chemical space of marine prokaryotes

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: June 28, 2023

Abstract Background Marine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize metabolites. However, the exact biosynthetic chemical space encoded by marine has yet be systematically evaluated. Results We first investigated metabolic analyzing diversity and novelty gene clusters (BGCs) in 7541 prokaryotic genomes from cultivated single cells, along with 26,363 newly assembled medium-to-high-quality environmental samples. To quantitatively evaluate unexplored prokaryotes, clustering thresholds constructing cluster molecular networks were optimized reach similar level similarity between family (GCF)-encoded (MF) scaffolds using MIBiG database. The global analysis demonstrated that predicted 70,011 BGCs organized into 24,536 mostly new (99.5%) GCFs, while reported natural products only classified 778 MFs at thresholds. number MF is 3.2% GCF-encoded scaffolds, suggesting least 96.8% untapped. was illustrated 88 antimicrobial peptides ribosomally synthesized post-translationally modified peptide BGCs. Furthermore, sea-water-derived Aquimarina strain selected illustrate diverse through untargeted metabolomics genomics approaches, which identified pathways group polyketides two known compounds (didemnilactone B macrolactin A 15-ketone). Conclusions present bioinformatics cheminformatics analyses highlight promising explore provide valuable knowledge targeted discovery biosynthesis products.

Language: Английский

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Light-regulated interactions between Phaeobacter sp. and Ulva ohnoi (Chlorophyta): effects on microbiome dynamics, metabolome composition, and tropodithietic acid production

Environmental and Experimental Botany, Journal Year: 2025, Volume and Issue: unknown, P. 106093 - 106093

Published: Jan. 1, 2025

Language: Английский

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Beyond Restoration: Coral Microbiome Biotechnology

Coral reefs of the world, Journal Year: 2025, Volume and Issue: unknown, P. 215 - 234

Published: Jan. 1, 2025

Language: Английский

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Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Sept. 22, 2022

Abstract Background The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes three octocoral species and seawater. Results Symbionts healthy were affiliated with the taxa Endozoicomonadaceae , Candidatus Thioglobaceae Metamycoplasmataceae unclassified Pseudomonadales Rhodobacteraceae Alphaproteobacteria Ca. Rhabdochlamydiaceae . Phylogenomics inference revealed uncovered here represent two a novel genus unique to temperate octocorals, denoted Gorgonimonas eunicellae leptogorgiae Their capacities thrive under suboxic conditions high gene copy numbers serine-threonine protein kinases, type 3-secretion system, type-4 pili, ankyrin-repeat proteins, suggesting excellent capabilities colonize, aggregate, persist inside host. Contrarily, MAGs obtained seawater frequently lacked symbiosis-related genes. All harbored endo-chitinase chitin-binging protein-encoding genes, indicating they can hydrolyze most abundant polysaccharide in oceans. Other symbionts, including may assimilate smaller chitin oligosaccharides resulting breakdown engage deacetylation, respectively, possibilities for substrate cross-feeding coral microbiome overall turnover. We also observed sharp differences secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria specialize chemical defense guard other which lack such capacity. Conclusion This first study recover dominant those so-far unculturable symbionts. identify thus-far unanticipated, global corals processing chitin, natural oceans major component zoo- phytoplankton feed octocorals. conclude niche partitioning, specialization, adaptation low oxygen among likely contribute plasticity adaptability holobiont changing marine environments. These findings bear implications not only our understanding relationships realm but functioning benthic ecosystems at large.

Language: Английский

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Temperature effects on growth, metabolome, lipidic profile and photosynthetic pigment content of Microglena antarctica (chlorophyceae): A comprehensive analysis

Algal Research, Journal Year: 2024, Volume and Issue: 79, P. 103461 - 103461

Published: March 4, 2024

Antarctic microalgae have evolved a wide range of adaptations to survive at extreme environmental conditions. This study aimed explore the physiological and biochemical processes occurring in Microglena antarctica (Chlorophyceae) response changes temperature. M. cultivated three distinct temperatures (4 °C, 8 °C 16 °C) exhibited variations growth patterns, metabolomes, fatty acid methyl esters (FAMEs) profile photosynthetic pigment concentrations. Our results highlighted decrease confirming cryophilic nature this species. The rates exponential phase were observed progressively with an initial rate (0.29 ± 0.05 d−1) culturing temperature 4 followed by (0.24 0.09 d−1), further reduction (0.16 d−1). An integrative untargeted metabolomics approach combining mass spectral libraries novel in–silico tools was employed improve feature annotation provide additional information on features chemical classes. Significant differences annotated compounds, classes whole metabolomes among 4, °C. Finally, targeted analyses performed evaluate lipid profiles content. Higher percentages polyunsaturated acids (PUFAs) approximately 65.00 % total FAMEs, decreased 60.71 Monounsaturated (MUFAs) significantly increased reaching up 10.96 contrast where content MUFAs around 5.00 %. Additionally, chlorophyll carotenoid 50–100 compared lower temperatures. present work highlights temperature–related responses profile, approaches, physiology, analysis.

Language: Английский

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Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: May 24, 2024

Abstract Background Microbial secondary metabolites play a crucial role in the intricate interactions within natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming promising source of therapeutic agents due to their structural diversity functional versatility. However, biosynthetic capacity ecological functions remain largely underexplored. Results Here, we aim explore profile RiPPs potential roles between microbes viruses ocean, which encompasses vast unique biomes that rich remains chemically We first developed TrRiPP identify from ocean metagenomes, deep learning method detects RiPP precursors hallmark gene-independent manner overcome limitations classic methods processing highly fragmented metagenomic data. Applying this metagenomes global microbiome, uncover diverse array previously uncharacterized putative families with great novelty diversity. Through correlation analysis based on metatranscriptomic data, observed high prevalence antiphage defense-related phage-related protein were co-expressed families. Based association phage infection, constructed an Ocean Virus Database (OVD) established RiPP-involving host-phage interaction network through host prediction co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, families, viral phages. These findings highlight involved prokaryote-phage coevolution, providing insights into microbiome. Conclusions This study provides systematic investigation microbiome at scale, shedding light essential integration approaches, connectivity. serves as valuable example exploring bacterial particularly associations unexplored microbial interactions.

Language: Английский

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Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities

Annals of Microbiology, Journal Year: 2024, Volume and Issue: 74(1)

Published: Aug. 10, 2024

Abstract Background High-throughput sequencing of the full-length 16S rRNA gene has improved taxonomic classification prokaryotes found in natural environments. However, shorter regions from same gene, like V4-V5 region, can provide more cost-effective high throughput. It is unclear which approach best describes prokaryotic communities underexplored In this study, we hypothesize that high-throughput combined with adequate databases improves description environments comparison a short region gene. Results To test our hypothesis, compared profiles seawater samples Arctic Ocean using: and combination either Genome Taxonomy Database (GTDB) or Silva taxonomy database. Our results show all combinations strategies present similar at higher levels. lower levels, namely family, genus, most notably species level, led to proportions Amplicon Sequence Variants (ASVs) assigned formally valid taxa. Hence, was obtained by GTDB combination, some cases allowed for identification intraspecific diversity ASVs. Conclusions We conclude coupling microbiome profiling ranks. The improvements reported here context scientists discuss microbial community dynamics within solid framework still underrepresented sequences public databases.

Language: Английский

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An artificial selection procedure enriches for known and suspected chitin degraders from the prokaryotic rare biosphere of multiple marine biotopes

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

Background Biological chitin degradation is a major process in the ocean, governed primarily by action of microorganisms. It now known that structure and taxonomic profile chitin-degrading microbial communities change across marine biotopes, but efforts to harness turnover potential within these laboratory have seldom been attempted. In this study, we characterized prokaryotic associated with sponge Sarcotragus spinosulus, octocoral Eunicella labiata, their surrounding sediment seawater applied an artificial selection procedure enrich bacterial consortia capable degrading from abovementioned biotopes. Throughout procedure, was monitored, composition four successive enrichment cultures each biotope were followed. Results The naturally occurring two host species distinct other specific taxa animal even though they co-inhabiting same geographic area. We found members rare biosphere recruited all while dominant symbionts likely play role sponges octocorals remained “unculturable” under conditions used study. Well-known degraders such as Vibrio, Pseudoalteromonas Aquimarina, well not or yet poorly for role(s) Aureivirga, Halodesulfovibrio, Motilimonas, Muricauda, Psychromonas, Poseidonibacter, Reichenbachiella, Thalassotalea, among others, enriched using our approach. Distinct biotope, highlighting feasibility approach fostering discovery novel microorganisms enzymes involved pathways relevance biotechnology. Conclusion possessing moderate high efficiencies at unveiled. They composed mix degraders, utilizers many Psychromonas, Motilimonas, Reichenbachiella, Halodesulfovibrio. latter are key players whose study could lead enzyme variants able degrade its derivatives.

Language: Английский

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Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens

Marine Drugs, Journal Year: 2022, Volume and Issue: 21(1), P. 34 - 34

Published: Dec. 30, 2022

Marine microbiomes are prolific sources of bioactive natural products potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-far unclassified lineages identify isolates with potentially rich secondary metabolism antimicrobial activities. Seventy representative had their genomes mined for metabolite biosynthetic gene clusters (SM-BGCs) were screened activities against four pathogenic five Candida strains. In total, 466 SM-BGCs identified, peptide- polyketide synthase-related being frequently detected. Only 38 similarities greater than 70% encoding known compounds, highlighting the novelty encoded by these genomes. Cross-streak assays showed that 33 70 genome-sequenced active at least one species, while 44 activity bacterial pathogen. Taxon-specific differences in among suggested distinct molecules involved antagonism versus pathogens. The here reported constitute a valuable resource understudied displaying biosynthesis novel metabolites, holding promise future sustainable production drug leads.

Language: Английский

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Bile acids as putative social signals in Mozambique tilapia (Oreochromis mossambicus)

Physiology & Behavior, Journal Year: 2023, Volume and Issue: 272, P. 114378 - 114378

Published: Oct. 17, 2023

Chemical cues provide potential mates with information about reproductive status and resource-holding potential. In the Mozambique tilapia (Oreochromis mossambicus), males can distinguish female through chemical cues, accessibility of to females depends on their position in hierarchy, determined part by cues. Here, we hypothesized that faecal are attractive conspecifics once released into water. C18 solid-phase extracts faeces from dominant pre-ovulatory evoked stronger olfactory epithelium electrical responses (EOG) than, respectively, subordinate post-spawning females. Mass spectrometry reverse-phase high-performance liquid chromatography fractions these highest EOG, identified amino acids bile acids. Faeces contain significantly higher concentrations cholic acid (CA) taurocholic (TCH) than both males. A pool had no effect aggression or attraction However, were attracted scent faeces, as well CA TCH, when applied separately. This was accompanied increased digging behaviour compared odour TCH exert action separate receptor mechanisms. These findings consistent a role for - therein communication this species, acting an attractant

Language: Английский

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