Microbial Genomics最新文献

{"title":"Association of microbial pathways predicted/inferred using 16S and shotgun metagenome with faecal metabolite abundances.","authors":"Wan-Yu Lin, Yu-Jen Chang, Thiviya Gill, Jianhong Ching, Dovile Anderson, Darren J Creek, Qasim Ayub, Sadequr Rahman, Chun Wie Chong","doi":"10.1099/mgen.0.001855","DOIUrl":"https://doi.org/10.1099/mgen.0.001855","url":null,"abstract":"<p><p>The gut microbiome is an essential metabolic organ influencing host health through metabolite production. While metabolite production levels can be directly measured by gas or liquid chromatography, they are commonly inferred from the abundance of metagenomic functional pathways. To evaluate the accuracy of these inferences, we established a single, manually curated metabolite-pathway/enzyme mapping list as a standardized biological reference. We then compared liquid chromatography-mass spectrometry (LC-MS)-based faecal metabolites with functional pathways/enzymes inferred from four approaches: 16S rRNA gene amplicons, reference-based shotgun, <i>de novo</i> assembly-based contigs and <i>de novo</i> assembly-based metagenome-assembled genomes (MAGs). Our results demonstrate that predictive accuracy is strongly metabolite-specific and method-dependent rather than a uniform characteristic of metagenomic data. While 16S (9.9%), ref-shotgun (14.2%) and <i>de novo</i>-contigs (5.5%) yielded only a small fraction of well-predicted metabolites, the <i>de novo</i>-MAGs approach significantly outperformed other approaches, achieving a 36.9% well-predicted rate for mapped metabolites. Notably, this approach provided the most robust functional-metabolite associations for indicators of gut health. In conclusion, while microbial functional potential does not always mirror metabolic reality, high-quality genomic binning via MAGs offers a significantly more robust framework for selective metabolite prediction.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 10","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149128076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, <i>Zostera marina,</i> include a novel chytrid in the order Lobulomycetales.","authors":"Cassandra L Ettinger, Jonathan A Eisen, Jason E Stajich","doi":"10.1099/mgen.0.001845","DOIUrl":"10.1099/mgen.0.001845","url":null,"abstract":"<p><p>Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, <i>Zostera marina,</i> have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with <i>Z. marina</i> leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Lobulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte alga in the genus <i>Prymnesium</i> (40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent undersequenced and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previous <i>Z. marina</i> amplicon survey results. Annotation of this MAG yielded 5,650 gene models, of which 77% shared homology with current databases. Within these gene models, we predicted 121 carbohydrate-active enzymes (CAZymes) and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes has revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on CAZyme composition classified this MAG's CAZyme profile as most consistent with a symbiotic lifestyle. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13618815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.","authors":"Léa Cavalli, Bradford P Taylor, Beau Schaeffer, Jacquelyn Turcinovic, John H Connor, William P Hanage","doi":"10.1099/mgen.0.001784","DOIUrl":"10.1099/mgen.0.001784","url":null,"abstract":"<p><p>Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant public health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analysed intra-host variation in SARS-CoV-2 genome sequences from Boston University's testing mandate. Focusing on intra-host single nucleotide variants (iSNVs), we inferred transmission events and assessed the selective forces shaping within-host viral evolution. To minimize false-positive iSNVs resulting from systematic biases, we implemented stringent data filtering and developed a heuristic to exclude contamination-derived artefacts arising from batched sequencing. We find that intra-host variation is limited and infrequently transmitted during acute infections, suggesting that shared iSNVs serve as highly specific but insensitive markers of transmission. We also observed incomplete purifying selection shaping within-host diversity, with the loci most affected changing among variants of concern. Finally, we identified a highly recurrent iSNV (G11083T) which may represent a site of positive selection. Our results highlight that within-host variation provides insight into within-host pathogen evolution, in spite of its limited use in genomic epidemiology.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13549476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148906313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An integrated genomic framework for <i>Aeromonas</i> genomic species delineation using average nucleotide identity, core-genome phylogeny and digital DNA-DNA hybridisation.","authors":"Alex Chen Lu, Ruochen Wu, Ruiting Lan, Li Zhang","doi":"10.1099/mgen.0.001833","DOIUrl":"10.1099/mgen.0.001833","url":null,"abstract":"<p><p><i>Aeromonas</i> taxonomy has long been complicated by overlapping phenotypic, biochemical and protein profiles. Here, we establish a robust genome-based framework for <i>Aeromonas</i> genomic species delineation. We analysed average nt identity (ANI) across 4,366 available <i>Aeromonas</i> genomes and demonstrated that at a 96% ANI threshold, skANI and fastANI generated too many clusters (65 and 57, respectively) and these clusters were not supported by core-genome phylogeny. We identified 95.4% skANI (equivalent to 95.6% fastANI) as an operational threshold for delineating <i>Aeromonas</i> genomic species. Using the 95.4% skANI threshold, we identified 44 ANI clusters among the 4,366 genomes, of which 43 clusters were genomic species supported by the core-genome phylogeny. Thirty-four of the 43 genomic species corresponded to existing taxonomic species, whilst the remaining 9 are currently not recognised as taxonomic species. All recognised taxonomic species represented in the dataset retained their existing species designation except <i>Aeromonas mytilicola</i>, which was not separated from <i>Aeromonas rivipollensis</i> in both ANI clusters and the core-genome phylogeny. The digital DNA-DNA hybridisation values between the genomic species were below 70%, further supporting genomic species delineation. We further developed AeromonasGStyper, a genomic species typing tool that assigns query genomes based on ANI similarity to medoid genomes. In conclusion, this study establishes a genomic species framework for genome-based classification of <i>Aeromonas</i> and provides a practical approach for future genomic surveillance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13585408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cobalt starvation affects multiple cellular processes in <i>Desulfofundulus kuznetsovii</i> TPOSR during alcohol oxidation.","authors":"Lukas Friedeheim, Sjef Boeren, Irene Sánchez-Andrea, Alfons J M Stams, Diana Z Sousa","doi":"10.1099/mgen.0.001771","DOIUrl":"10.1099/mgen.0.001771","url":null,"abstract":"<p><p>Cobalt influences the methanol metabolism of <i>Desulfofundulus kuznetsovii</i> TPOSR, specifically by modulating the activity of one of its alcohol dehydrogenases (ADH), Adh1. However, the effects of cobalt on the broader proteome of strain TPOSR, as well as the utilization of alcohols besides methanol, remain unexplored. Here, proteomic analyses of strain TPOSR grown with and without cobalt on different alcohol substrates show that cobalt starvation impacts multiple cellular processes, including cobalamin biosynthesis, iron-sulphur cluster assembly and, most prominently, energy metabolism as indicated by altered abundances of hydrogenases and NAD(P)-dependent oxidoreductases. Despite the presence of six ADH-encoding genes in the genome, Adh1 is the dominant ADH during growth not only on methanol but also on several primary alcohols and diols (ethanol, 1-propanol, 1,2-propanediol, 1,3-propanediol, butanol, pentanol and heptanol). Enzymatic assays with purified Adh1 confirm activity with these substrates, except 1,3-propanediol, and show no activity toward secondary alcohols (2-propanol and 2-butanol). Comparative proteomics analyses of other sulphate-reducing microorganisms (SRMs), namely <i>Desulfofundulus australicum</i> and <i>Solidesulfovibrio carbinolicus</i>, further indicate that methanol and ethanol oxidation in SRMs is mediated by a single ADH/AOR pair. Together, these findings highlight the central role of cobalt in alcohol metabolism in strain TPOSR and identify conserved ADH/AOR enzymes as promising candidates for biotechnological applications.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13541210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Psychrobacter</i> sp. XL111, a novel bacterial species from hadal amphipods: genomic insights into environmental adaptation and biotechnological potential.","authors":"Yukun Cui, Yingying Wan, Shuqiang Yan, Yu Xiao, Jiasong Fang, Peipei Wang, Xi Yu","doi":"10.1099/mgen.0.001830","DOIUrl":"10.1099/mgen.0.001830","url":null,"abstract":"<p><p>The hadal zone presents one of the most extreme environments on Earth. While amphipods dominate this realm, the adaptive mechanisms of their resident gut microbiota are not fully understood, which is essential both for understanding the limits of life and for unlocking novel microbial resources. This study investigates <i>Psychrobacter</i> sp. XL111, a novel bacterial species isolated from the gut of hadal amphipods, to elucidate its survival strategies and biotechnological potential. Pan-genome analysis confirms the high genomic plasticity of this genus and highlights the genomic innovations in genes related to environmental adaptation. Genomic analysis revealed specialized adaptations to the deep-sea niche, including expansions in signal transduction systems, pathways for degrading complex organics and the capacity to synthesize stress-resistant compounds. A notable loss of oligosaccharide transporters alongside an enrichment of glycosyltransferases suggests a distinctive evolutionary reconfiguration of carbohydrate metabolism. Functional characterization confirmed that the strain produces an exopolysaccharide with potent radical-scavenging activity, underscoring a key mechanism for mitigating oxidative stress. Our results position hadal micro-organisms as a valuable source of novel enzymes and bioactive molecules for industrial and biomedical applications.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the genomic landscape of <i>Trichophyton indotineae</i> in China and exploring a correlative model for azole resistance prediction.","authors":"Heping Xu, Ying Mao, Yixuan Hu, Jiangshan Huang, Wannan Chen, Lingling Lu","doi":"10.1099/mgen.0.001812","DOIUrl":"10.1099/mgen.0.001812","url":null,"abstract":"<p><p><b>Background.</b> <i>Trichophyton indotineae</i> is an emerging multidrug-resistant dermatophyte that has rapidly spread across continents, posing a serious threat to global public health. Limited genomic data from mainland China hinder a comprehensive understanding of its evolutionary origin, underscoring the urgent need for molecular susceptibility data to guide clinical antifungal therapy. To clarify the evolutionary origin and genome-wide characteristics of three newly identified clinical isolates of <i>T. indotineae</i> from Fujian Province, China, we sequenced these isolates to a mean coverage of 1,300× using the Salus Pro sequencing platform and delineated a comprehensive genomic portrait. Additionally, a linear regression model was constructed between the copy-number variation (CNV) of the <i>CYP51B</i> gene and the minimum inhibitory concentration (MIC) values of four antifungal agents to achieve molecular susceptibility prediction for <i>T. indotineae</i>. Finally, functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were employed to identify virulence-associated genes and pathways. Three <i>T. indotineae</i> isolates recovered in Xiamen, Fujian Province, China, fell into two distinct phylogenetic clades (Group II and Group IV). Notably, genome-wide scanning identified <i>CYP51B</i> CNV and the SQLE p.Phe397Leu mutation as the most prominent genomic determinants associated with azole and terbinafine (TRB) resistance, respectively. Structural modelling provided mechanistic support at the protein level for the functional impact of this mutation, revealing that the SQLE F397 substitution triggers a collapse of the hydrophobic binding pocket, thereby hindering TRB binding. Furthermore, a linear regression model was established to achieve molecular susceptibility prediction, showing a robust correlation between the <i>CYP51B</i> CNV and the MIC values of four azoles (<i>P</i><0.05). Core-gene analysis against the reference genome identified a shared core genome. KEGG pathway analysis revealed the biological pathways where virulence genes are located, including the MAPK signalling pathway and the <i>O</i>-glycan biosynthesis pathway, which suggests potential pathogenic mechanisms. The study delineates the genomic landscape of <i>T. indotineae</i> isolates from China and demonstrates a stepwise elevation in azole MICs. The linear regression model reveals a significant positive correlation between <i>CYP51B</i> CNV and MIC values for four azoles, thereby advancing the CNV-resistance association from a qualitative observation to a quantitative prediction. These insights enhance the global understanding of the pathogen's genomic epidemiology and virulence, establishing a critical foundation for genome-guided surveillance and individualized antifungal therapy.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic diversity and chromatic acclimation in phycoerythrin-containing <i>Microcystis aeruginosa</i>.","authors":"Yuuhiko Tanabe, Haruyo Yamaguchi, Tomoharu Sano","doi":"10.1099/mgen.0.001852","DOIUrl":"10.1099/mgen.0.001852","url":null,"abstract":"<p><p><i>Microcystis aeruginosa</i> is a bloom-forming cyanobacterium widely distributed in eutrophic freshwater systems. Most strains are blue-green due to the presence of the photosynthetic pigments phycocyanin and chlorophyll <i>a</i>. Less commonly, brownish strains have been reported, reflecting the presence of the red pigment phycoerythrin (PE). However, the genomic basis, phylogeny and evolutionary origin of PE pigmentation in <i>M. aeruginosa</i> remain poorly understood. Here, we characterized PE-containing <i>M. aeruginosa</i> strains, including six newly sequenced genomes. All genomes harboured putative PE synthesis and regulatory genes (the <i>cpe</i> cluster). Phylogenomic analysis further revealed that these PE-containing strains are distributed across three distinct phylogenetic groups. In contrast, the genomic organization of the <i>cpe</i> cluster was largely conserved. Spectroscopic analyses further indicated that strains belonging to different phylogenetic groups exhibit the same type of chromatic acclimation. Moreover, the phylogenetic relationships inferred for each PE gene were congruent and consistent with the whole-genome phylogeny. Our findings support a single origin of PE genes, with the observed distribution best explained by two independent horizontal transfer events rather than repeated gene loss during intraspecific diversification in <i>M. aeruginosa</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13623022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ribosome-inactivating proteins in bacteria.","authors":"Malak H El-Ramly, Casey C Fowler","doi":"10.1099/mgen.0.001839","DOIUrl":"10.1099/mgen.0.001839","url":null,"abstract":"<p><p>Ribosome-inactivating proteins (RIPs), a group of biological toxins that depurinate a critical residue within the 28S rRNA, exhibit one of the most potent and elegant mechanisms of cellular toxicity. Examples of RIPs include ricin and Shiga toxin, which are amongst the most notorious toxins produced by plants and bacteria, respectively. Here, we discuss RIPs in the Bacteria domain. We review the biology of Shiga toxin and its role as a transformational virulence factor for some of the most virulent <i>Escherichia coli</i> and <i>Shigella</i> pathotypes, as well as recent work identifying an assortment of RIP toxins deployed by <i>Spiroplasma</i> endosymbionts to protect their host from parasitic attack. We further shed light on the expansive but poorly understood arsenal of proteins with the conserved RIP functional domain that can be found in the genomes of diverse bacterial species, including proteins with complex domain architectures thought to occur only in eukaryotic RIP toxins. Based on the impressive arsenal of RIPs found in <i>Streptomyces</i>, as well as the ubiquitous presence of this genus in the niches where many of the other organisms that produce RIPs are found, we speculate that <i>Actinomycetes</i> such as <i>Streptomyces</i> might have been the evolutionary origin of the RIP domain and hypothesize that <i>Streptomyces</i> has played a central role in the spread of RIPs throughout the biosphere.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13592729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into the taxonomy, safety and biotechnological potential of <i>Aphanizomenon flos-aquae</i> and related <i>Nostocales</i>.","authors":"Gabriel D Scoglio, David H Green, Harry O Jackson, Saul Purton","doi":"10.1099/mgen.0.001832","DOIUrl":"10.1099/mgen.0.001832","url":null,"abstract":"<p><p>The <i>Nostocales</i> are filamentous cyanobacteria that include bloom-forming, nitrogen-fixing species with major ecological and biotechnological relevance. Owing to their metabolic diversity, nitrogen-fixing capabilities and nutritional profile, they hold potential for various biotechnological applications including the production of nutraceuticals and biofertilizers. However, the capacity of certain <i>Nostocales</i> species to produce cyanotoxins also raises health concerns. This study provides a comparative bioinformatic analysis of 161 <i>Nostocales</i> genomes from the National Center for Biotechnology Information (NCBI) and three newly sequenced <i>Aphanizomenon flos-aquae</i> (<i>AFA</i>) strains, including Klamath <i>AFA</i>, with a focus on taxonomy, cyanotoxin-associated biosynthetic gene clusters (BGCs), natural competence, restriction-modification systems and vitamin B₁₂ metabolism. Our analysis supports reassessment of several <i>AFA</i>-labelled genomes and refines the boundaries of the core <i>AFA</i> cluster. Cyanotoxin-associated BGCs, specifically for anatoxin-a, saxitoxin, cylindrospermopsin and microcystin/nodularin, were detected in only 7.3% of the genomes. Natural competence genes required for horizontal gene transfer were found in 89.6% of the genomes, although the presence of multiple restriction-modification system-associated proteins in <i>Nostocales</i> species, especially <i>Aphanizomenon, Anabaena, Dolichospermum</i> and <i>Nostoc</i> sp. may limit foreign gene acquisition. Additionally, ~30% of the genomes harbour a shared <i>btu</i> operon arrangement associated with B₁₂ import, observed here across multiple <i>Nostocales</i> genera. B₁₂ content in the <i>AFA</i> strains was measured at ~0.4-0.5 µg g^-1 dry biomass and is likely linked to associated B₁₂-producing bacteria. Fluorescent B₁₂ analogue uptake experiments in NIES 4052 and Klamath <i>AFA</i> support a model for the uptake of exogenous B₁₂ in these strains. Together with the detection of cobalamin-producing commensal bacteria, this suggests that B₁₂ in <i>AFA</i> biomass may be linked to cyanobacterium-bacteria interactions. Overall, this study provides a genomic and experimental framework for evaluating the taxonomy, safety, genetic tractability and nutritional potential of <i>AFA</i> and related <i>Nostocales</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13603067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149030796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}