Publications

Background: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability. Results: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity. Conclusions: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.

DOI:

10.1186/s40793-026-00887-7External link

University Bibliography Jena:

fsu_mods_00036459External link

DOI:

10.1126/sciadv.aeb8246External link

University Bibliography Jena:

fsu_mods_00036700External link

Motivation: Oxford Nanopore sequencing enables long-read analysis for diverse applications, but artefacts introduced by Nanopore barcoding are poorly characterized and can compromise demultiplexing accuracy and downstream analyses. Results: Using a rapid barcoding experiment on 66 diagnostic samples, we found that only 83% of reads followed the expected single-barcode configuration, while 17% showed complex barcode attachments. We observed similar patterns in public datasets, and also in native barcoding datasets where only 30%–70% of the reads had barcodes on both ends. Widely used demultiplexers, including Dorado, fail to resolve these cases, leaving ∼10% of our rapid barcoding reads partially trimmed and contaminated with adapter fragments. We developed Barbell, a pattern-aware demultiplexer that is designed to detect complex barcode configurations. Barbell reduced contaminated reads from >400 000 (Dorado/Flexiplex) to 166 (99.96% reduction), minimized barcode bleeding, and supports custom experimental designs such as dual-end barcodes and shorter barcodes (e.g. Illumina barcodes). We further show that such contamination is widespread in public databases, with Nanopore sequences detected in hundreds of NCBI entries, some of which are responsible for artificial taxonomic connections. Availability and implementation: Barbell is open source and available at https://github.com/rickbeeloo/barbell.

DOI:

10.1093/bioinformatics/btag349External link

University Bibliography Jena:

fsu_mods_00037506External link

DOI:

10.7554/eLife.105029.3External link

University Bibliography Jena:

fsu_mods_00037136External link

Polycystic ovary syndrome (PCOS) is commonly associated with obesity and metabolic disturbances. Although gut and vaginal microbiome changes have been linked to PCOS, the independent role of body mass index in these alterations remains unclear. This study aimed to compare gut and vaginal microbiomes in women with PCOS and healthy controls, emphasizing the impact of body mass index. Seventy-five women were enrolled, including 55 with PCOS and 20 healthy controls. Participants were stratified into normal-weight (<25) and overweight (≥25) groups. Vaginal and anorectal swabs were analyzed using full-length 16S rRNA nanopore sequencing. Microbial diversity and composition were assessed with alpha diversity indices, principal component analysis, analysis of composition of microbes, PERMANOVA, and vaginal community state type classification. Without body mass index stratification, women with PCOS showed differences in several vaginal taxa compared with healthy controls. Within the PCOS cohort, overweight women exhibited higher vaginal alpha diversity, reduced Lactobacillus dominance, and enrichment of anaerobic taxa compared with normal-weight women with PCOS. Differences in vaginal microbial composition were also observed between healthy and PCOS women with normal body mass index. In contrast, gut microbiome alterations were limited and less consistent across analytical approaches. Vaginal community state type analysis revealed predominance of class IV communities in both healthy women and women with PCOS. These findings suggest that higher body mass index is associated with vaginal microbiome alterations in women with PCOS, although PCOS-related factors independent of body weight may also contribute to the observed microbial differences.

DOI:

10.1530/RAF-26-0051External link

University Bibliography Jena:

fsu_mods_00037572External link

Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.

DOI:

10.1093/femsre/fuaf067External link

University Bibliography Jena:

fsu_mods_00034306External link

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

DOI:

10.1093/nar/gkaf1224External link

University Bibliography Jena:

fsu_mods_00030017External link

Background: Temperate phages play a central role in the evolution and pathogenicity of Staphylococcus aureus. Sa3int phages provide highly human-specific virulence factors that promote immune evasion and survival within the host. The reversible excision of these phages which occurs without phage production and bacterial lysis allows the simultaneous expression of phage virulence genes and the hlb gene where they usually integrate. However, the regulatory mechanisms that control phage assembly and the cross-talk with host factors remain poorly understood. Methods and results: We analyzed the regulatory mechanism controlling late gene transcription of Sa3int phage Φ13. We identified a functional promoter, P ₂₃, located upstream of the late phage genes that control DNA processing and packaging, capsid assembly, bacterial lysis and immune evasion. SAOUHSC_02200, the gene located upstream of P ₂₃ , encodes for a late transcriptional regulator (Ltr). Mutating the P ₂₃ TATA-box or the ltr gene abolished P ₂₃ activity and formation of mature intact phage particles, thus confirming the role of Ltr in regulating P ₂₃ activity. Four direct repeats upstream of the P ₂₃ transcriptional start site were identified as potential Ltr binding sites. RT-qPCR analysis confirmed that Ltr-dependent P ₂₃ activation is essential for the expression of late genes and the subsequent Φ13 propagation. Furthermore, comparative analysis of P ₂₃ activity and ltr expression in different host strain backgrounds revealed strain-specific differences that appear to depend on the alternative sigma factor SigB and its downstream effector SpoVG. Conclusions: Ltr controls the expression of late phage genes, thereby regulating phage assembly and lysis. This process is modulated by SpoVG activity.

DOI:

10.1186/s12985-026-03167-5External link

University Bibliography Jena:

fsu_mods_00035967External link

Bacteriophages (phages) are well known to be one of the major driving forces in bacterial evolution. This also applies to virulent microorganisms, such as the major human pathogen Vibrio cholerae, whose pathogenic potential and epidemic proliferation largely depends on the interaction with environmental phages. Specifically, integration of the CTXϕ phage genome into the first chromosome of V. cholerae also introduced the ctxAB genes, encoding the primary toxin responsible for the severe acute diarrheal disease, cholera. Whereas the mechanisms underlying CTXϕ-associated horizontal gene transfer and transcriptional control of the ctxAB genes have been intensively studied over the past years, posttranscriptional regulation affecting the CTXϕ life cycle has not been documented. Here, we report the identification and characterization of the CisR small RNA (sRNA) that is produced from the 3’UTR (untranslated region) of the prtV gene and inhibits the expression of the CTXϕ-encoded cep mRNA. CisR-mediated repression of cep involves Hfq-assisted base-pairing of the two transcripts and results in reduced CTXϕ production under stress conditions. We further demonstrate that transcription of prtV-cisR requires both the master quorum-sensing regulator HapR and CRP (cAMP receptor protein), a global regulator of carbon metabolism. Taken together, our work provides evidence that V. cholerae employs sRNA-mediated posttranscriptional gene regulation to coordinate CTXϕ activation with both cell density and nutrient availability.

DOI:

10.1073/pnas.2535142123External link

University Bibliography Jena:

fsu_mods_00036851External link

DOI:

10.1038/s41579-024-01107-0External link

University Bibliography Jena:

fsu_mods_00017943External link

This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.

DOI:

10.1099/jgv.0.002111External link

University Bibliography Jena:

fsu_mods_00028013External link

DOI:

10.1128/mmbr.00022-25External link

University Bibliography Jena:

fsu_mods_00027918External link