{"id":661197,"date":"2026-06-27T14:01:19","date_gmt":"2026-06-27T14:01:19","guid":{"rendered":"https:\/\/www.newsbeep.com\/uk\/661197\/"},"modified":"2026-06-27T14:01:19","modified_gmt":"2026-06-27T14:01:19","slug":"complex-multicellularity-is-linked-with-expanded-specialized-metabolite-production-in-microorganisms","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/uk\/661197\/","title":{"rendered":"Complex multicellularity is linked with expanded specialized metabolite production in microorganisms"},"content":{"rendered":"

Fischbach, M. A., Walsh, C. T. & Clardy, J. The evolution of gene collectives: how natural selection drives chemical innovation. Proc. Natl Acad. Sci. USA 105, 4601\u20134608 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Clardy, J., Fischbach, M. A. & Currie, C. R. The natural history of antibiotics. Curr. Biol. 19, R437\u2013R441 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Demain, A. L. & Fang, A. The natural functions of secondary metabolites. Adv. Biochem. Eng. Biotechnol. 69, 1\u201339 (2000).<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Traxler, M. F. & Kolter, R. Natural products in soil microbe interactions and evolution. Nat. Prod. Rep. 32, 956\u2013970 (2015).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Demain, A. L. & Sanchez, S. Microbial drug discovery: 80 years of progress. J. Antibiot. 62, 5\u201316 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Knoll, A. H. The multiple origins of complex multicellularity. Annu. Rev. Earth Planet. Sci. 39, 217\u2013239 (2011).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Claessen, D., Rozen, D. E., Kuipers, O. P., S\u00f8gaard-Andersen, L. & van Wezel, G. P. Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies. Nat. Rev. Microbiol. 12, 115\u2013124 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Schirrmeister, B. E., de Vos, J. M., Antonelli, A. & Bagheri, H. C. Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc. Natl Acad. Sci. USA 110, 1791\u20131796 (2013).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Velicer, G. J. & Vos, M. Sociobiology of the myxobacteria. Annu. Rev. Microbiol. 63, 599\u2013623 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Barka, E. A. et al. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol. Mol. Biol. Rev. 80, 1\u201343 (2016).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chandra, G. & Chater, K. F. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol. Rev. 38, 345\u2013379 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gibbs, K. A., Urbanowski, M. L. & Greenberg, E. P. Genetic determinants of self identity and social recognition in bacteria. Science 321, 256\u2013259 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

L\u00f3pez, D., Vlamakis, H. & Kolter, R. Biofilms. Cold Spring Harb. Perspect. Biol. 2, a000398 (2010).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Islam, M. R., Tudryn, G., Bucinell, R., Schadler, L. & Picu, R. C. Morphology and mechanics of fungal mycelium. Sci. Rep. 7, 13070 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Singh, R. K., Tiwari, S. P., Rai, A. K. & Mohapatra, T. M. Cyanobacteria: an emerging source for drug discovery. J. Antibiot. 64, 401\u2013412 (2011).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Krug, D. et al. Discovering the hidden secondary metabolome of Myxococcus xanthus: a study of intraspecific diversity. Appl. Environ. Microbiol. 74, 3058\u20133068 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gavriilidou, A. et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat. Microbiol. 7, 726\u2013735 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Naranjo-Ortiz, M. A. & Gabald\u00f3n, T. Fungal evolution: cellular, genomic and metabolic complexity. Biol. Rev. Camb. Philos. Soc. 95, 1198\u20131232 (2020).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cimermancic, P. et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412\u2013421 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Blin, K. et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51, W46\u2013W50 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Scherlach, K. & Hertweck, C. Mining and unearthing hidden biosynthetic potential. Nat. Commun. 12, 3864 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Udwary, D. W. et al. The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 53, D717\u2013D723 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Terlouw, B. R. et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res. 51, D603\u2013D610 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

van Santen, J. A. et al. The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 50, D1317\u2013D1323 (2022).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Schaible, G. A. et al. Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLoS Biol. 22, e3002638 (2024).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ingham, C. J. & Ben Jacob, E. Swarming and complex pattern formation in Paenibacillus vortex studied by imaging and tracking cells. BMC Microbiol. 8, 36 (2008).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ohno, T. et al. A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037. J. Bacteriol. 178, 5065\u20135070 (1996).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lewin, G. R. et al. Evolution and ecology of Actinobacteria and their bioenergy applications. Annu. Rev. Microbiol. 70, 235\u2013254 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Murphy, C. L. et al. Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation. Appl. Environ. Microbiol. 87, e0170621 (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Traag, B. A. & van Wezel, G. P. The SsgA-like proteins in actinomycetes: small proteins up to a big task. Antonie Van Leeuwenhoek 94, 85\u201397 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Boden, J. S. et al. Evolution of multicellularity genes in Cyanobacteria in the lead up to the great oxidation event. Commun. Biol. 8, 1721 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Whitman, W. B. Bergey\u2019s Manual of Systematics of Archaea and Bacteria (John Wiley & Sons, Limited, 2015).<\/p>\n

Capstick, D. S., Willey, J. M., Buttner, M. J. & Elliot, M. A. SapB and the chaplins: connections between morphogenetic proteins in Streptomyces coelicolor. Mol. Microbiol. 64, 602\u2013613 (2007).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Keijser, B. J. F., van Wezel, G. P., Canters, G. W. & Vijgenboom, E. Developmental regulation of the Streptomyces lividans ram genes: involvement of RamR in regulation of the ramCSAB operon. J. Bacteriol. 184, 4420\u20134429 (2002).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Neuenschwander, S. M., Ghai, R., Pernthaler, J. & Salcher, M. M. Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria. ISME J. 12, 185\u2013198 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Floss, H. G., Yu, T.-W. & Arakawa, K. The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review. J. Antibiot. 64, 35\u201344 (2011).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Surette, M. D., Waglechner, N., Koteva, K. & Wright, G. D. HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics. Mol. Cell 82, 3151\u20133165.e9 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Waglechner, N., McArthur, A. G. & Wright, G. D. Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance. Nat. Microbiol. 4, 1862\u20131871 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

S\u00e9lem-Mojica, N., Aguilar, C., Guti\u00e9rrez-Garc\u00eda, K., Mart\u00ednez-Guerrero, C. E. & Barona-G\u00f3mez, F. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microb. Genom. 5, e000260 (2019).<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Amses, K. R. et al. Diploid-dominant life cycles characterize the early evolution of Fungi. Proc. Natl Acad. Sci. USA 119, e2116841119 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gruninger, R. J. et al. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol. Ecol. 90, 1\u201317 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Swift, C. L. et al. Anaerobic gut fungi are an untapped reservoir of natural products. Proc. Natl Acad. Sci. USA 118, e2019855118 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rokas, A., Mead, M. E., Steenwyk, J. L., Raja, H. A. & Oberlies, N. H. Biosynthetic gene clusters and the evolution of fungal chemodiversity. Nat. Prod. Rep. 37, 868\u2013878 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gluck-Thaler, E. et al. Giant Starship elements mobilize accessory genes in fungal genomes. Mol. Biol. Evol. 39, msac109 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Robey, M. T., Caesar, L. K., Drott, M. T., Keller, N. P. & Kelleher, N. L. An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes. Proc. Natl Acad. Sci. USA 118, e2020230118 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rokas, A., Wisecaver, J. H. & Lind, A. L. The birth, evolution and death of metabolic gene clusters in fungi. Nat. Rev. Microbiol. 16, 731\u2013744 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kiss, E. et al. Comparative genomics reveals the origin of fungal hyphae and multicellularity. Nat. Commun. 10, 4080 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nagy, L. G. Evolution: complex multicellular life with 5,500 genes. Curr. Biol. 27, R609\u2013R612 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Glass, N. L. & Kaneko, I. Fatal attraction: nonself recognition and heterokaryon incompatibility in filamentous fungi. Eukaryot. Cell 2, 1\u20138 (2003).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Saupe, S. J. Molecular genetics of heterokaryon incompatibility in filamentous ascomycetes. Microbiol. Mol. Biol. Rev. 64, 489\u2013502 (2000).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Berbee, M. L. et al. Genomic and fossil windows into the secret lives of the most ancient fungi. Nat. Rev. Microbiol. 18, 717\u2013730 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lutzoni, F. et al. Contemporaneous radiations of fungi and plants linked to symbiosis. Nat. Commun. 9, 5451 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Franco, M. E. E. et al. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytol. 233, 1317\u20131330 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Allen, B. M., Drott, M., Nickles, G. R. & Hoeksema, J. D. Variation in biosynthetic gene clusters among lifestyles across kingdom fungi. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.09.14.613087<\/a> (2024).<\/p>\n

Singh, G., Dal Grande, F., Martin, F. M. & Medema, M. H. Breaking into nature\u2019s secret medicine cabinet: lichens\u2014a biochemical goldmine ready for discovery. New Phytol. 246, 437\u2013449 (2025).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Osbourn, A. E. & Lanzotti, V. Plant-derived Natural Products: Synthesis, Function, and Application (Springer, 2008).<\/p>\n

Del Pup, E. et al. plantiSMASH 2.0: Improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters. J. Mol Biol. https:\/\/doi.org\/10.1016\/j.jmb.2026.169798<\/a> (2026).<\/p>\n

Paw\u0142owicz, T. et al. Biologically active compounds in true slime molds and their prospects for sustainable pest and pathogen control. Int. J. Mol. Sci. 26, 1951 (2025).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Torres, J. P. & Schmidt, E. W. The biosynthetic diversity of the animal world. J. Biol. Chem. 294, 17684\u201317692 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhang, Z. et al. Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation. Sci. Adv. 6, eaay5781 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Oh, D.-C., Poulsen, M., Currie, C. R. & Clardy, J. Dentigerumycin: a bacterial mediator of an ant\u2013fungus symbiosis. Nat. Chem. Biol. 5, 391\u2013393 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kwan, J. C. et al. Genome streamlining and chemical defense in a coral reef symbiosis. Proc. Natl Acad. Sci. USA 109, 20655\u201320660 (2012).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Daskalov, A. Regulated cell death in fungi from a comparative immunology perspective. Cell Death Differ. 33, 244\u2013258 (2026).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jensen, P. R. Natural products and the gene cluster revolution. Trends Microbiol. 24, 968\u2013977 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Haas, H., Eisendle, M. & Turgeon, B. G. Siderophores in fungal physiology and virulence. Annu. Rev. Phytopathol. 46, 149\u2013187 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lee, M. D. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35, 4162\u20134164 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Coleman, G. A. et al. A rooted phylogeny resolves early bacterial evolution. Science 372, eabe0511 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dos Reis, M. Dating microbial evolution with MCMCtree. Methods Mol. Biol. 2569, 3\u201322 (2022).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Louca, S. et al. Bacterial diversification through geological time. Nat. Ecol. Evol. 2, 1458\u20131467 (2018).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dav\u00edn, A. A. et al. A geological timescale for bacterial evolution and oxygen adaptation. Science 388, eadp1853 (2025).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586\u20131591 (2007).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Khabbazian, M., Kriebel, R., Rohe, K. & An\u00e9, C. Fast and accurate detection of evolutionary shifts in Ornstein\u2013Uhlenbeck models. Methods Ecol. Evol. 7, 811\u2013824 (2016).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. https:\/\/doi.org\/10.1093\/nar\/gkab776<\/a> (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dahl, J. L. et al. Identification of major sporulation proteins of Myxococcus xanthus using a proteomic approach. J. Bacteriol. 189, 3187\u20133197 (2007).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Singh, P., Khan, A. & Srivastava, A. in Advances in Cyanobacterial Biology (eds Singh, P. K. et al.) Ch. 16, 235\u2013248 (Academic Press, 2020).<\/p>\n

Xu, Q. et al. Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes. J. Biol. Chem. 284, 25268\u201325279 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Girard, G. et al. A novel taxonomic marker that discriminates between morphologically complex actinomycetes. Open Biol. 3, 130073 (2013).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Woodcroft, B. J. et al. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-025-02738-1<\/a> (2025).<\/p>\n

Kim, D., Gilchrist, C. L. M., Chun, J. & Steinegger, M. UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Res. 51, D777\u2013D784 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Shen, W. & Ren, H. TaxonKit: a practical and efficient NCBI taxonomy toolkit. J. Genet. Genomics 48, 844\u2013850 (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y. O. & Borodovsky, M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18, 1979\u20131990 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gilchrist, C. L. M. & Chooi, Y.-H. Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases. Fungal Biol. Biotechnol. 8, 13 (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Klau, L. J. et al. The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function. J. Biol. Chem. 298, 102480 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233\u2013D238 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yin, Y. et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40, W445\u2013W451 (2012).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256\u2013W259 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Salamzade, R., Kalan, L. & Currie, C. Genome annotations for Salamzade, Kalan and Currie, 2025. Zenodo https:\/\/doi.org\/10.5281\/zenodo.15168076<\/a> (2025).<\/p>\n

Salamzade, R. Kalan-Lab\/Ancestral_BGC_Exansions_Study: v1.0.2 (v1.0.2). Zenodo https:\/\/doi.org\/10.5281\/zenodo.19632677<\/a> (2026).<\/p>\n","protected":false},"excerpt":{"rendered":"Fischbach, M. A., Walsh, C. T. & Clardy, J. The evolution of gene collectives: how natural selection drives…\n","protected":false},"author":2,"featured_media":661198,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[10],"tags":[6154,59,3250,102,7925,6194,33193,116014,33192,218150,33194,34425,56,54,55,181],"class_list":["post-661197","post","type-post","status-publish","format-standard","has-post-thumbnail","category-health","tag-evolutionary-genetics","tag-gb","tag-general","tag-health","tag-infectious-diseases","tag-life-sciences","tag-medical-microbiology","tag-microbial-genetics","tag-microbiology","tag-natural-products","tag-parasitology","tag-phylogenetics","tag-uk","tag-united-kingdom","tag-unitedkingdom","tag-virology"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/661197","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/comments?post=661197"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/661197\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media\/661198"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media?parent=661197"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/categories?post=661197"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/tags?post=661197"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}