Ammonia-oxidizing bacteria (AOB) catalyze the first and rate-limiting step of nitrification. They are essential for nitrogen cycling in engineered and natural environments, yet little is known about their viruses or the consequences of phage infection for host physiology. Here, we report the isolation and characterization of a novel lytic bacteriophage, vB_NeuP-Nir1 (DSM 111086), infecting the model AOB Nitrosomonas europaea. Phage Nir1 ceased ammonia oxidation within hours, and caused complete lysis of host populations even at multiplicities of infection as low as 10-6. Electron microscopy revealed drastic host cell remodeling during infection, including pronounced cell bloating and large-scale disintegration of intracytoplasmic membranes. Integrated transcriptomic and metabolomic analyses showed that loss of these ATP and reducing equivalent generating membrane systems was accompanied by signatures of compromised lipid homeostasis and collapse of autotrophic CO₂ fixation. In parallel, Nir1 infection induced metabolic rewiring of the host, including upregulation of uptake systems for nucleic acids, amino acids, and small organic compounds, increased expression of iron acquisition and putative iron-dependent respiratory components, as well as accumulation of metabolites associated with membrane breakdown and stabilization of viral DNA. Together, these results provide the first detailed mechanistic insight into phage-induced host modulation in a chemolithoautotrophic nitrifier. Our study establishes the Nir1-N. europaea system as a model for investigating virus-host interactions in AOB and lays the foundation for assessing the role of phages in shaping nitrification and nitrogen cycling in engineered and natural ecosystems.

BRENDA (https://www.brenda-enzymes.org/), the most comprehensive enzyme and ligand database for over nearly four decades, has seen major developments since 2021, further solidifying its role as an ELIXIR Core Data Resource and Global Core Biodata Resource in the life sciences. As part of the DSMZ Digital Diversity consortium (https://hub.dsmz.de) since 2023, BRENDA has introduced a prototype knowledge graph accessible via a public SPARQL endpoint, enabling semantic search, data integration, and improved reusability in line with FAIR principles. The database now hosts ∼5.8 million data points on 112 288 enzymes from 15 335 organisms and 173 164 references, alongside 278 840 ligands. Recent updates include the manual annotation of ∼16 000 references, the addition of 615 EC numbers—480 with newly curated data—and revisions to 4422 EC classes. The curated pathway collection has expanded to 195 metabolic maps, now supported by interactive pathway summary pages that organize key information into structured, user-friendly views. BRENDA now also incorporates DSMZCellDive data, visually linking enzyme classes to high-expressing human cell lines. A new gene-centric search interface allows streamlined access to enzyme-specific data using gene symbols or identifiers. These enhancements advance BRENDA’s interoperability and analytical capabilities, reinforcing its integration with major bioinformatics resources such as SILVA, BacDive, and LPSN.

We report on the complete genome sequence of the rhizobacterium Paenibacillus sp. PK1-4R. This might be a new species within the genus Paenibacillus, as evidenced by the taxonomic classification using the TYGS web server. It has a single chromosome (6,961,392 bp) but no plasmid.

Strain DSM 45814T, isolated from forest soil in Canada, was subjected to a polyphasic taxonomic study and genome mining for plant growth-promoting genes. The strain had a 16S rRNA gene sequence similarity of 97.1% with that of Jatrophihabitans telluris N237T and 94.8-96.8% similarity with other validly named Jatrophihabitans species. Average nucleotide identity and digital DNA-DNA hybridization values between DSM 45814T and its closely related Jatrophihabitans strains were below the established prokaryotic species demarcation. In the genome-based phylogeny, strain 45814T was divergent from the Jatrophihabitans cluster and was loosely associated with the family Geodermatophilaceae. The average amino acid identity (AAI) values between DSM 45814T and type (63.5-71.6%) and non-type (63.0-71.6%) strains of Jatrophihabitantaceae, as well as members of Geodermatophilaceae (58.6-59.2%), fell within the defined AAI range of 65-72% and below the recently established cut-off point of 74-76% for genus demarcation. The percentage of conserved proteins (POCP) between strain DSM 45814T and the type strains of Jatrophihabitantaceae and Geodermatophilaceae was below the defined threshold of 50% for genus demarcation, excluding J. telluris, which had a POCP of 55%. Strain DSM 45814T displayed cocci-to-cuboid cells with a flagellum and a G+C content (63.4 mol%) that distinguished it from Jatrophihabitans and Geodermatophilaceae strains, but it had chemotaxonomic features closer to those of Jatrophihabitantaceae than Geodermatophilaceae. The strain appeared to have ecological potential based on a genome mining approach. Based on these results, strain DSM 45814T (=899T=LMG 34134T) represents a novel genus within the family Jatrophihabitantaceae, for which the name Parajatrophihabitans canadensis gen. nov. sp. nov. is proposed.

Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.

Clostridioides difficile infection (CDI), primarily mediated by toxin B (TcdB), is a leading cause of healthcare-associated and community-acquired diarrhea worldwide. Although this genus exhibits substantial genomic diversity, functional studies have focused mainly on a limited set of isolates, leaving other genomospecies understudied in this regard. Here, we characterized five isolates derived from five distinct patients with suspected CDI cases that tested negative for the tcdC PaLoc marker. Integrated genomic, proteomic, and phenotypic analyses confirm that these strains constitute three novel toxin-producing species and their distinct carbon utilization profiles, exoproteomes, and spore protein repertoires suggest niche specialization within the human gut ecosystem. These species harbour monotoxin PaLoc architectures encoding TcdB7 or TcdB11, located on either chromosomal or extrachromosomal elements, which frequently co-occur with binary toxin loci. Functional assays confirmed secretion of active TcdB, cytotoxicity in mammalian cells, and moderate enterotoxicity in a murine ileal loop model, although virulence was attenuated relative to C. difficile R20291 from Clade 2. Collectively, these findings expand the taxonomy of toxigenic Clostridioides, highlight the dynamic evolution of TcdB-mediated pathogenicity, and emphasize the importance of refining diagnostic workflows and surveillance strategies to address emerging diarrheal diseases. The three novel species were designated as Clostridioides cryptodifficilis sp. nov., Clostridioides divergens sp. nov., and Clostridioides subdifficilis sp. nov.

Micromonospora ureilytica DSM 120150, Nocardiopsis akebiae DSM 120151, Streptomyces fildesensis DSM 41987T, Streptomyces hypolithicus DSM 41950T and Streptomyces albidoflavus DSM 120149 are five Antarctic strains. Here, we present the high-quality genome sequences of DSM 120150, DSM 120151, DSM 41987T, DSM 41950T and DSM 120149 with sizes of 7.51 Mbp, 6.90 Mbp, 8.91 Mbp, 6.01 Mbp and 6.85 Mbp, respectively.

A Gram-stain-negative, aerobic, pink-pigmented bacterial strain A03A-229T was isolated from a non-axenic culture of the chromerid alga Vitrella brassicaformis CCMP3155, which originates from the Great Barrier Reef in Australia. Complete genome sequencing revealed the presence of seven circular replicons, representing one chromosome, two chromids and four plasmids. The 142-kb DnaA-like I chromid, which contains the photosynthesis gene cluster (PGC), traces of ubiquinone-11 and the ability to reduce nitrate are diagnostic for A03A-229T. Genomic, physiological, and chemotaxonomic data provided clear evidence that strain A03A-229T (= DSM 112523T = CECT 31310T) represents a new species of the genus Roseobacter, for which the name Roseobacter cerffii sp. nov. is proposed. R. cerffii A03A-229T represents the tenth described species of the genus Roseobacter, but phylogenetic (meta-)genome analyses indicated the presence of at least 27 different species. Reconstruction of the metabolic pathways of the genus Roseobacter revealed a highly conserved metabolism with lineage specific adaptations for the formation of compatible solutes and a surprising abundance of four GAPDH genes. The ability to perform aerobic anoxygenic photosynthesis, which is mediated by the PGC, is responsible for the eponymous pink color of this genus, while it only occurs scattered in the sister genus Sulfitobacter. Our phylogenomic analyses provided clear evidence for a distinct taxonomic status of strain Sulfitobacter sabulilitoris HSMS-29T (= KACC 19870T = NBRC 113549T). Based on its phylogenetic position, low average amino-acid identities (AAI) and a PufC-type PGC, we propose the reclassification of this strain as Billmartinia sabulilitoris gen. nov., comb. nov.

A novel strain, designated Mg75T, was isolated from a vineyard soil sample collected in Mostaganem, Algeria. This Gram-positive, non-motile strain produces a branched, fragmented substrate mycelium with a yellowish-orange colour and a white aerial mycelium on International Streptomyces Project 2 (ISP2), ISP3 and ISP4. Mg75T exhibited growth across a temperature range of 15-40 °C, with an optimal range of 28-30 °C. It thrived at pH levels between 5.0 and 10.0, with an optimum at pH 7.0, and tolerated NaCl concentrations ranging from 0% to 3% (w/v), with an optimal concentration range of 0-1% (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence indicated the highest similarity with Saccharothrix yanglingensis Hhs.015T (98.95%). The G+C content of the genomic DNA of strain Mg75T was 73.4 mol%. Digital DNA-DNA hybridization (dDDH) between strain Mg75T and its neighbouring Saccharothrix species ranged from 23.2% to 39.9%. Average nucleotide identity (ANI) ranged from 82.08% to 90.91%, and average amino acid identity (AAI) ranged from 79.8% to 92.57%, way below the thresholds of 70% for dDDH and 95-96% for ANI and AAI used for species delimitation. Strain Mg75T was found to share a similar chemotaxonomic profile based on genomic chemotaxonomic markers. The phylogenetic and phylogenomic analyses, together with the in silico chemotaxonomic and phenotypic data, indicated that strain Mg75T (=DSM 118769T=CECT 31160T) represented a novel species of the genus Saccharothrix, for which the name Saccharothrix sabaoui sp. nov. is proposed.

The red bibenzoquinone oosporein, a promising biocontrol agent with potential to replace conventional pesticides in insect pest management in crops, was produced by the Basidiomycota Phlebia centrifuga P. Karst isolated from the Black Forest National Park. A submerged system was established, yielding up to 1.60 g L-1 oosporein in the culture supernatant upon supplementation with the key intermediate orsellinic acid, which strongly induced oosporein-specific biosynthetic genes. Using a multiomics approach, genes encoding enzymes for all necessary conversions were predicted, including a type I polyketide synthase, two monooxygenases, and a heme peroxidase. Enzymatic functions were investigated by extensive docking analyses and molecular dynamics simulations, ultimately leading to the prediction of the underlying biosynthetic pathway. In summary, a spore-free, high-yield, scalable production platform for oosporein was established, highlighting the potential of rare, protected fungal species as sources for valuable enzymes and bioactive secondary metabolites for efficient microbial biomanufacturing systems.

The acidobacterial strain JP12T affiliated with the Terriglobales has been isolated from fen soil sampled at Schlöppnerbrunnen II near Bayreuth, Germany. The strain was Gram-stain-negative, non-motile, displayed non-spore-forming rods that divide by binary fission and segregate exopolysaccharide-like structures. JP12T grew at temperatures of 4-40 °C (best between 24 and 30 °C), at pH values of 3.7-6.0 (best between 4.1 and 5.6) and at NaCl concentrations of 0-0.5% (best 0.25%, w/v).MK-8 was identified as the major respiratory quinone. The major fatty acids of the strain JP12T were iso-C15:0, C16:0, iso-C17:1 ω7c, iso-C17:0 and iso-diabolic acid. Phosphatidylglycerol, phosphatidylethanolamine and ornithine-containing lipids were the major polar lipids. Lysophosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol and high-mass intact polar lipids occurred in small amounts. The G+C content of the strain JP12T was 56.4 mol%. 16S rRNA gene sequence similarity values of 96.1-96.7% placed the strain JP12T in the vicinity of the type strains of Occallatibacter savannae A2-1cT, Telmatobacter bradus TPB6017T, Occallatibacter riparius 277T and Terracidiphilus gabretensis S55T, respectively. Based on the phenotypic, phylogenetic and chemotaxonomic data, we propose the new species Occallatibacter bavaricus sp. nov. (type strain JP12T=DSM 110680T=CECT 30267T) within the acidobacterial order Terriglobales. We also propose the reclassification of Terracidiphilus gabretensis as Occallatibacter gabretensis comb. nov.

BACKGROUND:Representatives of the phylum Methanobacteriota occur in various anoxic environments, but only members of the genera Methanosphaera and Methanobrevibacter exclusively colonize the digestive tract of animals. Recent phylogenomic analyses revealed that the genus Methanobrevibacter, which harbors the majority of the intestinal species, is severely underclassified and represents a family-level taxon, "Methanobrevibacteraceae", that evolved entirely in the digestive tract of animals. RESULTS:Comparative genome analysis of 158 species of Methanobacteriota, including uncultured representatives in the Genome Taxonomy Database (GTDB), demonstrated that the intestinal lineages are clearly separated from the remaining members of the phylum. They differ from the non-intestinal lineages in genome size, GC content, coding density, an increased number of pseudogenes and adhesin-like proteins, and show numerous adaptations to the copiotrophic gut environment. A decreased biosynthetic potential led to a dependence on other community members and limits the dispersal of intestinal species into other habitats, which is reflected in coevolutionary patterns with their major host groups among arthropods, ungulates, and primates. Certain lineages even engaged in symbiotic associations with intestinal protists, presumably benefiting from the H2 produced by the hydrogenosomes of their anaerobic hosts. CONCLUSIONS:Our results reveal that the transition of free-living Methanobacteriota to a host-associated lifestyle involves the same genomic changes that were previously recognized in gut bacteria and bacterial endosymbionts of protists, reflecting resemblances between the two prokaryotic domains that are caused by evolutionary convergence in similar environments.

Natural products remain vital sources of therapeutics, particularly anti-infectives, and members of the phylum Myxococcota constitute an especially rich reservoir for their discovery. Based on decades of microbiological efforts, we present 154 new Myxococcota genomes and propose a revised taxonomy expanding the number of described families from 11 to 28 and genera from 32 to 90. Comparison with an equivalent set from the prime source Actinomycetota shows that Myxococcota possess a comparable biosynthetic diversity, underscoring their promise for large-scale isolation and sequencing efforts. The vast untapped potential reflected in 2,387 uncharacterized gene cluster families is highlighted by genome mining efforts, yielding four validated compounds exhibiting novel chemistry, including myxolutamids and myxopentacins. We show that many Myxococcota-derived natural products, such as myxolutamid A and two new sorangicin derivatives, are conserved within taxonomic lineages. New described families thus bear high biosynthetic potential underpinning the importance of precise taxonomic classification guiding targeted drug discovery. To facilitate community access and exploration of these data, we provide ABC-Myxo (https://tools.helmholtz-hips.de/abc_myxo/), an interactive web-based atlas of Myxococcota biosynthetic gene clusters.

The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.

Biosolids, widely used as organic fertilizers due to their high nutrient content, are significant reservoirs for antimicrobial-resistant bacteria (ARB) carrying transferable antimicrobial resistance genes (ARGs). This study investigated the transferability of ARG-containing plasmids of bacteria from biosolids originating from 12 German wastewater treatment plants (WWTPs) of varying sizes. Using exogenous plasmid captures with the recipient strain Escherichia coli CV601 gfp+, we collected 103 plasmids from 11 WWTPs. Characterization through DNA-based methods, including real-time PCR and Southern blot hybridization, revealed that the highest proportion of transconjugants harbored IncP (57%) and IncN (20%) plasmids. Complete sequencing of representative plasmids identified IncPβ, IncPε, IncQ2, IncN, and IncU plasmids carrying ARGs linked to mobile genetic elements (MGEs), including class 1 integrons, transposons, and IS elements (e.g., Tn402, IS26, and IS6100). These ARG-MGE complexes were integrated into specific plasmid regions, and similar plasmids were found across WWTPs and diverse geographic locations. The results underscore the role of WWTPs as hotspots for horizontal gene transfer, with biosolids serving as reservoirs for multi-resistant bacteria and resistance plasmids. This highlights the urgent need for improved biosolid management strategies to mitigate the release of ARGs and ARB into agricultural environments. IMPORTANCE This study emphasizes the critical role of wastewater treatment plants (WWTPs) in facilitating the horizontal transfer of ARGs through biosolids. As biosolids are routinely applied to agricultural soils, their load of clinically relevant ARG content and transferability pose risks to animal and human health through plant-associated bacteria or surface water. By identifying conserved ARG-MGE associations across diverse plasmid types and WWTPs, this work highlights the global and persistent nature of resistance dissemination. These findings underscore the urgent need for sustainable management practices to limit the spread of antimicrobial-resistant bacteria (ARB) and associated ARGs in agricultural ecosystems. Ensuring safe biosolid use will contribute to combating antimicrobial resistance gene connectivity from environmental to human- or animal-associated bacteria globally.

Rifaximin (RFX) has recently been suggested as an alternative treatment option for Clostridioides difficile infection. This study reports the survey on RFX susceptibility within a C. difficile test cohort that represents the five clinically relevant phylogenetic clades. Agar dilution assays were conducted to determine the minimum inhibitory concentrations (MICs) of RFX for 129 clinical C. difficile isolates from Germany (86), Indonesia (29), and Ghana (14). Genome sequence data were obtained for 50 representative isolates, including all those with a minimum inhibitory concentration MIC[RFX] of ≥ 32.0 µg/mL, to identify the underlying rpoB gene resistance alleles, determine the multilocus sequence typing (MLST) sequence types (STs), and infer phylogenetic relatedness. 10.1

Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, F & eacute;lix d'H & eacute;relle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ. Graphical Abstract

Over the past few decades, the Brucella genus has seen a significant increase in novel strains that deviate from classical Brucella spp. due to their atypical phenotypes. B. inopinata, an atypical Brucella species first isolated from a patient, was recently found in a White’s tree frog, raising the question of whether amphibians are reservoirs for these emerging human pathogens. Unfortunately, monitoring atypical Brucella remains challenging because misidentification with Ochrobactrum spp. and Brucella melitensis is common when using routine microbiological tests. In our study, we describe a Brucella strain isolated from White’s tree frogs (Litoria caerulea) that were initially examined for chytridiomycosis after they had developed dermal abnormalities. Classical microbiological and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses and a species-specific polymerase chain reaction confirmed that isolate CVUAS_1139.3 is an atypical Brucella strain. This non-fastidious, fast growing, flagellated, and motile bacterium is not susceptible to lysis by the Brucella phages used for typing. Further characterization using the differential metabolic phenotyping approach, revealed that Brucella sp. CVUAS_1139.3 could be differentiated from classical Brucella spp., as well as from Ochrobactrum anthropi and O. intermedium, based on its metabolic activity. The substrate utilization patterns may be suitable for a simple and cost-effective diagnostic assay. Phylogenetic analysis positioned Brucella sp. CVUAS_1139.3 distant from the classical Brucella spp. within the novel, non-core Brucella clade. Within this clade, Brucella sp. CVUAS_1139.3 shares a close phylogenetic relationship with B. inopinata strains and various African bullfrog isolates, and it is most closely related to a recently identified human isolate from Australia. Antimicrobial resistance testing revealed that it is susceptible to antibiotics widely applied in standard treatment regimens. In human THP-1 macrophage-like cells, the replication rate of the novel Brucella frog isolate was comparable to that of B. inopinata. In summary, the amphibian-derived strain Brucella sp. CVUAS_1139.3 clusters phylogenetically with and is phenotypically alike to previously reported isolates from amphibian hosts and human brucellosis patients within the novel, non-core clade. Our report and other studies suggest that exotic frogs are potential reservoirs for human pathogenic Brucella spp., which might pose an underestimated zoonotic hazard for exposed individuals.

This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently >1.1 million bacterial isolates, more recently including Streptococcus spp. and Mycobacterium tuberculosis, in addition to Salmonella,Escherichia/Shigella,Clostridioides,Vibrio,Helicobacter,YersiniaandMoraxella. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualizing bacterial genomic population structures, based on pre-computed hierarchical clusters. Access to data and analysis tools is provided through an enhanced graphical user interface and a new application programming interface (RESTful API). EnteroBase is now being developed and operated by an international consortium, to accelerate the development of the platform and ensure the longevity of the resources built. EnteroBase can be accessed at https://enterobase.warwick.ac.uk as well as https://enterobase.dsmz.de.