Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity

Eddy, T. D. et al. Global decline in capacity of coral reefs to provide ecosystem services. One Earth 4, 1278–1285 (2021).
Google Scholar
Rocha, J., Peixe, L., Gomes, N. C. M. & Calado, R. Cnidarians as a source of new marine bioactive compounds—an overview of the last decade and future steps for bioprospecting. Mar. Drugs 9, 1860–1886 (2011).
Google Scholar
Planes, S. et al. The Tara Pacific expedition—a pan-ecosystemic approach of the ‘-omics’ complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol. 17, e3000483 (2019).
Google Scholar
Smith, S. V. Coral-reef area and the contributions of reefs to processes and resources of the world’s oceans. Nature 273, 225–226 (1978).
Google Scholar
Fisher, R. et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr. Biol. 25, 500–505 (2015).
Google Scholar
Knowlton, N. The future of coral reefs. Proc. Natl Acad. Sci. USA 98, 5419–5425 (2001).
Google Scholar
Intergovernmental Panel on Climate Change (IPCC). Global Warming of 1.5 °C: IPCC Special Report on Impacts of Global Warming of 1.5 °C above Pre-industrial Levels in Context of Strengthening Response to Climate Change, Sustainable Development, and Efforts to Eradicate Poverty (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press, Cambridge, 2022).
Rohwer, F., Seguritan, V., Azam, F. & Knowlton, N. Diversity and distribution of coral-associated bacteria. Mar. Ecol. Prog. Ser. 243, 1–10 (2002).
Google Scholar
Galand, P. E. et al. Diversity of the Pacific Ocean coral reef microbiome. Nat. Commun. 14, 3039 (2023).
Google Scholar
Muscatine, L. & Porter, J. W. Reef corals: mutualistic symbioses adapted to nutrient-poor environments. BioScience 27, 454–460 (1977).
Google Scholar
Voolstra, C. R. & Ziegler, M. Adapting with microbial help: microbiome flexibility facilitates rapid responses to environmental change. BioEssays 42, e2000004 (2020).
Google Scholar
Ritchie, K. B. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar. Ecol. Prog. Ser. 322, 1–14 (2006).
Google Scholar
Kobayashi, M. et al. Marine natural products. XXXIV. Trisindoline, a new antibiotic indole trimer, produced by a bacterium of Vibrio sp. separated from the marine sponge Hyrtios altum. Chem. Pharm. Bull. 42, 2449–2451 (1994).
Google Scholar
Bertin, M. J. et al. Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J. Nat. Prod. 78, 493–499 (2015).
Google Scholar
Romero, F. et al. Thiocoraline, a new depsipeptide with antitumor activity produced by a marine Micromonospora. J. Antibiot. 50, 734–737 (1997).
Google Scholar
Blockley, A., Elliott, D. R., Roberts, A. P. & Sweet, M. Symbiotic microbes from marine invertebrates: driving a new era of natural product drug discovery. Diversity 9, 49 (2017).
Google Scholar
Newman, D. J. From large-scale collections to the potential use of genomic techniques for supply of drug candidates. Front. Mar. Sci. 5, 401 (2018).
Google Scholar
Sweet, M. et al. Insights into the cultured bacterial fraction of corals. mSystems 6, e0124920 (2021).
Google Scholar
Pye, C. R., Bertin, M. J., Lokey, R. S., Gerwick, W. H. & Linington, R. G. Retrospective analysis of natural products provides insights for future discovery trends. Proc. Natl Acad. Sci. USA 114, 5601–5606 (2017).
Google Scholar
Blin, K. et al. antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–W87 (2019).
Google Scholar
Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623–1635 (2019).
Google Scholar
Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).
Google Scholar
Loureiro, C. et al. Comparative metagenomic analysis of biosynthetic diversity across sponge microbiomes highlights metabolic novelty, conservation, and diversification. mSystems 7, e00357-22 (2022).
Google Scholar
Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022).
Google Scholar
van de Water, J. A., Tignat-Perrier, R., Allemand, D. & Ferrier-Pagès, C. Coral holobionts and biotechnology: from Blue Economy to coral reef conservation. Curr. Opin. Biotechnol. 74, 110–121 (2022).
Google Scholar
Leopold-Messer, S. et al. Animal-associated marine Acidobacteria with a rich natural-product repertoire. Chem 9, 3696–3713 (2023).
Google Scholar
Voolstra, C. R. et al. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation. NPJ Biodivers. 2, 15 (2023).
Google Scholar
Lombard, F. et al. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci. Data 10, 324 (2023).
Google Scholar
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Google Scholar
Ruscheweyh, H.-J. et al. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome 10, 212 (2022).
Google Scholar
Sunagawa, S., Woodley, C. M. & Medina, M. Threatened corals provide underexplored microbial habitats. PLoS ONE 5, e9554 (2010).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Novichkov, P. S., Wolf, Y. I., Dubchak, I. & Koonin, E. V. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J. Bacteriol. 191, 65–73 (2009).
Google Scholar
Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).
Google Scholar
Hentschel, U., Piel, J., Degnan, S. M. & Taylor, M. W. Genomic insights into the marine sponge microbiome. Nat. Rev. Microbiol. 10, 641–654 (2012).
Google Scholar
Voolstra, C. R. et al. The coral microbiome in sickness, in health and in a changing world. Nat. Rev. Microbiol. 22, 460–475 (2024).
Google Scholar
Kautsar, S. A., van der Hooft, J. J. J., de Ridder, D. & Medema, M. H. BiG-SLiCE: a highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. GigaScience 10, giaa154 (2021).
Google Scholar
Ghurye, J. S., Cepeda-Espinoza, V. & Pop, M. Metagenomic assembly: overview, challenges and applications. Yale J. Biol. Med. 89, 353–362 (2016).
Google Scholar
Carroll, A. R., Copp, B. R., Davis, R. A., Keyzers, R. A. & Prinsep, M. R. Marine natural products. Nat. Prod. Rep. 39, 1122–1171 (2022).
Google Scholar
Schwarzer, D., Finking, R. & Marahiel, M. A. Nonribosomal peptides: from genes to products. Nat. Prod. Rep. 20, 275–287 (2003).
Google Scholar
MarinLit: a Database of the Marine Natural Products Literature (Royal Society of Chemistry, accessed 12 March 2025); https://marinlit.rsc.org/.
Burkhardt, I., de Rond, T., Chen, P. Y.-T. & Moore, B. S. Ancient plant-like terpene biosynthesis in corals. Nat. Chem. Biol. 18, 664–669 (2022).
Google Scholar
Crits-Christoph, A., Diamond, S., Butterfield, C. N., Thomas, B. C. & Banfield, J. F. Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558, 440–444 (2018).
Google Scholar
Repka, L. M., Chekan, J. R., Nair, S. K. & van der Donk, W. A. Mechanistic understanding of lanthipeptide biosynthetic enzymes. Chem. Rev. 117, 5457–5520 (2017).
Google Scholar
Zhang, Q., Yu, Y., Vélasquez, J. E. & van der Donk, W. A. Evolution of lanthipeptide synthetases. Proc. Natl Acad. Sci. USA 109, 18361–18366 (2012).
Google Scholar
Cavener, D. R. GMC oxidoreductases. A newly defined family of homologous proteins with diverse catalytic activities. J. Mol. Biol. 223, 811–814 (1992).
Google Scholar
Sützl, L., Foley, G., Gillam, E. M. J., Bodén, M. & Haltrich, D. The GMC superfamily of oxidoreductases revisited: Analysis and evolution of fungal GMC oxidoreductases. Biotechnol. Biofuels 12, 118 (2019).
Google Scholar
Pola, S. in Scope of Selective Heterocycles From Organic and Pharmaceutical Perspective Ch. 1 (ed. Varala, R.) (IntechOpen, 2016).
Cox, C. L., Doroghazi, J. R. & Mitchell, D. A. The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics 16, 778 (2015).
Google Scholar
Steinberg, D. A. et al. Protegrin-1: a broad-spectrum, rapidly microbicidal peptide with in vivo activity. Antimicrob. Agents Chemother. 41, 1738–1742 (1997).
Google Scholar
Hoeksema, B. W., Cairns, S. & Samimi-Namin, K. World List of Scleractinia (accessed 20 November 2023); https://www.marinespecies.org/scleractinia.
Limborg, M. T., Winther-Have, C. S., Morueta-Holme, N., Gilbert, M. T. P. & Rasmussen, J. A. The overlooked biodiversity loss. Trends Ecol. Evol. 39, 889–891 (2024).
Google Scholar
Planes, S. & Allemand, D. Insights and achievements from the Tara Pacific expedition. Nat. Commun. 14, 3131 (2023).
Google Scholar
Deshuraud, R. et al. From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites. Preprint at bioRxiv https://doi.org/10.1101/2022.10.21.513203 (2022).
Pesant, S. et al. Tara Pacific samples provenance and environmental context—version 2. Zenodo https://doi.org/10.5281/ZENODO.4068292 (2020).
Belser, C. et al. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Sci. Data 10, 326 (2023).
Google Scholar
Pfeifer, C. R. et al. Quantitative analysis of mouse pancreatic islet architecture by serial block-face SEM. J. Struct. Biol. 189, 44–52 (2015).
Google Scholar
Leblud, J., Moulin, L., Batigny, A., Dubois, P. & Grosjean, P. Artificial coral reef mesocosms for ocean acidification investigations. Biogeosci. Discuss. 11, 15463–15505 (2014).
Google Scholar
Meyer, J. L., Gunasekera, S. P., Scott, R. M., Paul, V. J. & Teplitski, M. Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria. ISME J. 10, 1204–1216 (2016).
Google Scholar
Cai, L. et al. Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont. Sci. Rep. 7, 9320 (2017).
Google Scholar
Sato, Y. et al. Unraveling the microbial processes of black band disease in corals through integrated genomics. Sci. Rep. 7, 40455 (2017).
Google Scholar
Wang, L. et al. Corals and their microbiomes are differentially affected by exposure to elevated nutrients and a natural thermal anomaly. Front. Mar. Sci. 5, 101 (2018).
Google Scholar
Robbins, S. J. et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat. Microbiol. 4, 2090–2100 (2019).
Google Scholar
Yang, S.-H. et al. Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera. Microbiome 7, 3 (2019).
Google Scholar
Lima, L. F. O. et al. Modeling of the coral microbiome: the influence of temperature and microbial network. mBio 11, e02691-19 (2020).
Google Scholar
Messyasz, A. et al. Coral bleaching phenotypes associated with differential abundances of nucleocytoplasmic large DNA viruses. Front. Mar. Sci. 7, 555474 (2020).
Google Scholar
Ngugi, D. K., Ziegler, M., Duarte, C. M. & Voolstra, C. Genomic blueprint of glycine betaine metabolism in coral metaorganisms and their contribution to reef nitrogen budgets. iScience 23, 101120 (2020).
Google Scholar
Vohsen, S. A. et al. Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans. Microbiome 8, 34 (2020).
Google Scholar
Santoro, E. P. et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci. Adv. 7, eabg3088 (2021).
Google Scholar
Keller-Costa, T. et al. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. Microbiome 9, 72 (2021).
Google Scholar
Cárdenas, A. et al. Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility. ISME J. 16, 2406–2420 (2022).
Google Scholar
Palladino, G. et al. Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient. ISME Commun. 2, 65 (2022).
Google Scholar
Agarwal, V. et al. Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat. Chem. Biol. 13, 537–543 (2017).
Google Scholar
Jahn, M. T. et al. A phage protein aids bacterial symbionts in eukaryote immune evasion. Cell Host Microbe 26, 542–550 (2019).
Google Scholar
Busch, K. et al. Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities. Conserv. Genet. 21, 1001–1010 (2020).
Google Scholar
Engelberts, J. P. et al. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J. 14, 1100–1110 (2020).
Google Scholar
Glasl, B. et al. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME J. 14, 1435–1450 (2020).
Google Scholar
Pascelli, C. et al. Viral ecogenomics across the Porifera. Microbiome 8, 144 (2020).
Google Scholar
Storey, M. A. et al. Metagenomic exploration of the marine sponge Mycale hentscheli uncovers multiple polyketide-producing bacterial symbionts. mBio 11, e02997-19 (2020).
Google Scholar
Nguyen, N. A. et al. An obligate peptidyl brominase underlies the discovery of highly distributed biosynthetic gene clusters in marine sponge microbiomes. J. Am. Chem. Soc. 143, 10221–10231 (2021).
Google Scholar
Rusanova, A., Fedorchuk, V., Toshchakov, S., Dubiley, S. & Sutormin, D. An interplay between viruses and bacteria associated with the white sea sponges revealed by metagenomics. Life (Basel) 12, 25 (2021).
Google Scholar
Robbins, S. J. et al. A genomic view of the microbiome of coral reef demosponges. ISME J. 15, 1641–1654 (2021).
Google Scholar
Dharamshi, J. E. et al. Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. ISME J. 16, 2725–2740 (2022).
Google Scholar
Kelly, J. B., Carlson, D. E., Low, J. S. & Thacker, R. W. Novel trends of genome evolution in highly complex tropical sponge microbiomes. Microbiome 10, 164 (2022).
Google Scholar
Morganti, T. M. et al. Giant sponge grounds of Central Arctic seamounts are associated with extinct seep life. Nat. Commun. 13, 638 (2022).
Google Scholar
Pankey, M. S. et al. Cophylogeny and convergence shape holobiont evolution in sponge–microbe symbioses. Nat. Ecol. Evol. 6, 750–762 (2022).
Google Scholar
Engelberts, J. P. et al. Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta. Environ. Microbiol. 25, 646–660 (2023).
Google Scholar
Thompson, C. C. et al. Genomic taxonomy of vibrios. BMC Evol. Biol. 9, 258 (2009).
Google Scholar
Kimes, N. E. et al. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J. 6, 835–846 (2012).
Google Scholar
Bondarev, V. et al. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ. Microbiol. 15, 2095–2113 (2013).
Google Scholar
Ushijima, B. et al. Vibrio coralliilyticus strain OCN008 is an etiological agent of acute Montipora white syndrome. Appl. Environ. Microbiol. 80, 2102–2109 (2014).
Google Scholar
Asahina, A. Y. & Hadfield, M. G. Draft genome sequence of Pseudoalteromonas luteoviolacea HI1, determined using Roche 454 and PacBio single-molecule real-time hybrid sequencing. Genome Announc. 3, e01590-14 (2015).
Google Scholar
Meyer, J. L. et al. Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata. Stand. Genomic Sci. 10, 75 (2015).
Google Scholar
Ding, J.-Y., Shiu, J.-H., Chen, W.-M., Chiang, Y.-R. & Tang, S.-L. Genomic insight into the host-endosymbiont relationship of Endozoicomonas montiporae CL-33T with its coral host. Front. Microbiol. 7, 251 (2016).
Google Scholar
Franco, T., Califano, G., Gonçalves, A. C., Cúcio, C. & Costa, R. Draft genome sequence of Vibrio sp. strain Evh12, a bacterium retrieved from the gorgonian coral Eunicella verrucosa. Genome Announc. 4, e01729-15 (2016).
Google Scholar
Keller-Costa, T., Silva, R., Lago-Lestón, A. & Costa, R. Genomic insights into Aquimarina sp. strain EL33, a bacterial symbiont of the gorgonian coral Eunicella labiata. Genome Announc. 4, e00855-16 (2016).
Google Scholar
Wan, X., Miller, J. M., Rowley, S. J., Hou, S. & Donachie, S. P. Draft genome sequence of a novel Luteimonas sp. strain from coral mucus, Hawai’i. Genome Announc. 4, e01228-16 (2016).
Google Scholar
Henao, J. et al. Genome sequencing of three bacteria associated to black band disease from a Colombian reef-building coral. Genom. Data 11, 73–74 (2017).
Google Scholar
Braun, D. R. et al. Complete genome sequence of Dietzia sp. strain WMMA184, a marine coral-associated bacterium. Genome Announc. 6, e01582-17 (2018).
Google Scholar
Kumari, P., Badhai, J. & Das, S. K. Draft genome sequence of Marinomonas fungiae strain AN44T (JCM 18476 T), isolated from the coral Fungia echinata from the Andaman Sea. Genome Announc. 6, e00112-18 (2018).
Google Scholar
Raimundo, I., Silva, S. G., Costa, R. & Keller-Costa, T. Bioactive secondary metabolites from octocoral-associated microbes: new chances for blue growth. Mar. Drugs 16, 485 (2018).
Google Scholar
Rodrigues, G. N., Lago-Lestón, A., Costa, R. & Keller-Costa, T. Draft genome sequence of Labrenzia sp. strain EL143, a coral-associated Alphaproteobacterium with versatile symbiotic living capability and strong halogen degradation potential. Genome Announc. 6, e00132-18 (2018).
Google Scholar
Silva, S. G., Lago-Lestón, A., Costa, R. & Keller-Costa, T. Draft genome sequence of Sphingorhabdus sp. strain EL138, a metabolically versatile Alphaproteobacterium isolated from the gorgonian coral Eunicella labiata. Genome Announc. 6, e00142-18 (2018).
Google Scholar
Tandon, K., Chiang, P.-W., Chen, W.-M. & Tang, S.-L. Draft genome sequence of Endozoicomonas acroporae strain Acr-14T, isolated from Acropora coral. Genome Announc. 6, e01576-17 (2018).
Google Scholar
Deb, S., Badhai, J. & Das, S. K. Draft genome sequences of two Vibrio fortis strains isolated from coral (Fungia sp.) from the Andaman Sea. Microbiol. Resour. Announc. 9, e01225-19 (2020).
Google Scholar
Almeida, J. F. et al. Marine sponge and octocoral-associated bacteria show versatile secondary metabolite biosynthesis potential and antimicrobial activities against human pathogens. Mar. Drugs 21, 34 (2022).
Google Scholar
Li, J. et al. Cultured bacteria provide insight into the functional potential of the coral-associated microbiome. mSystems 7, e00327-22 (2022).
Google Scholar
Shi, S.-B., Cui, L.-Q., Zeng, Q., Long, L.-J. & Tian, X.-P. Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea. Int. J. Syst. Evol. Microbiol. 72, 005342 (2022).
Google Scholar
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Google Scholar
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).
Google Scholar
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).
Google Scholar
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
Google Scholar
Olm, M. R. et al. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 5, e00731-19 (2020).
Google Scholar
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
Google Scholar
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119 (2010).
Google Scholar
Laslett, D. & Canback, B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32, 11–16 (2004).
Google Scholar
Milanese, A. et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nat. Commun. 10, 1014 (2019).
Google Scholar
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
Google Scholar
Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083 (2019).
Google Scholar
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Google Scholar
Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Google Scholar
Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624 (2016).
Google Scholar
Kautsar, S. A. et al. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 48, D454–D458 (2020).
Google Scholar
Gavriilidou, A. et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat. Microbiol. 8, 726–735 (2022).
Google Scholar
Navarro-Muñoz, J. C. et al. A computational framework to explore large-scale biosynthetic diversity. Nat. Chem. Biol. 16, 60–68 (2020).
Google Scholar
Kautsar, S. A., Blin, K., Shaw, S., Weber, T. & Medema, M. H. BiG-FAM: the biosynthetic gene cluster families database. Nucleic Acids Res. 49, D490–D497 (2021).
Google Scholar
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Google Scholar
Ruscheweyh, H.-J. et al. Tara Pacific 16S rRNA data analysis release. Zenodo https://doi.org/10.5281/ZENODO.4073268 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
Lohans, C. T. & Vederas, J. C. Structural characterization of thioether-bridged bacteriocins. J. Antibiot. 67, 23–30 (2014).
Google Scholar
Bösch, N. M. et al. Landornamides: antiviral ornithine-containing ribosomal peptides discovered through genome mining. Angew. Chem. Int. Ed. 59, 11763–11768 (2020).
Google Scholar
Fuchs, S. W. et al. Entianin, a novel subtilin-like lantibiotic from Bacillus subtilis subsp. spizizenii DSM 15029 T with high antimicrobial activity. Appl. Environ. Microbiol. 77, 1698–1707 (2011).
Google Scholar
Bhushan, R. & Brückner, H. Marfey’s reagent for chiral amino acid analysis: a review. Amino Acids 27, 231–247 (2004).
Google Scholar
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: An R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
Google Scholar
Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R. & Pfister, H. UpSet: visualization of intersecting sets. IEEE Trans. Vis. Comput. Graph. 20, 1983–1992 (2014).
Google Scholar
Krassowski, M. krassowski/complex-upset: v1.3.5. Zenodo https://doi.org/10.5281/zenodo.3700590 (2020).
Wickham, H. in ggplot2: Elegant Graphics for Data Analysis (ed. Wickham, H.) 189–201 (Springer, 2016).
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
Google Scholar
Cheng, J., Karambelkar, B. & Xie Y. leaflet: create interactive web maps with the JavaScript ‘leafletʼ library. https://doi.org/10.32614/CRAN.package.leaflet (v.2.1.2, 2023).
Wiederkehr, F. et al. Unusual enzymology and peptide natural products from novel Acidobacteriota spp. associated with reef-building corals. Zenodo https://doi.org/10.5281/ZENODO.14050210 (2024).
Paoli, L., Wiederkehr, F., Ruscheweyh, H.-J. & Sunagawa, S. Coral microbiomes as reservoirs of novel genomic and biosynthetic diversity. Zenodo https://doi.org/10.5281/ZENODO.10182966 (2025).
Paoli, L. & Wiederkehr, F. SushiLab/reef-microbiomics-paper: initial release for archiving at zenodo. Zenodo https://doi.org/10.5281/zenodo.10201847 (2023).
Tara Pacific Consortium. Tara Pacific expedition participants. Zenodo https://doi.org/10.5281/zenodo.3777759 (2020).
Apprill, A., Weber, L. G. & Santoro, A. E. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems 1, e00143-16 (2016).
Google Scholar




