Biology subjects

Overmann, J.

Publications and source records attributed to Overmann, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The StrainDiscoveryDatabase: an open framework for standardized microbial strain data

The vast amount of existing data on microbial strains holds immense potential to revolutionize bioindustry through the application of Artificial Intelligence (AI). However, the training of robust predictive AI models requires large-scale, unified, and non-redundant microbial datasets, which is currently severely hindered by the deep fragmentation of the data and the existence of synonymous strain identifiers in different culture collections. To overcome these infrastructural bottlenecks, we have established the StrainDiscoveryDatabase (SDD), a comprehensive, machine-readable dataset encompassing over 6.2 million harmonized data points for 256,889 microbial strains. The SDD does not rely on its own data repository, but rather on existing data that is retrieved on the fly from highly curated databases. Through an automated pipeline phenotypic, genotypic, and contextual data are systematically retrieved via the Application Programming Interfaces (APIs) of the Bacterial Diversity database (BacDive), the Microbial Resource Research Infrastructure Information System (MIRRI-IS) and the catalogue of the DSMZ. In order to reliably resolve synonymous strain identifiers, the StrainInfo database and its identification tools are employed, enabling the accurate deduplication and unification of records from disparate sources. The resulting aggregated, globally unique dataset is provided in a highly standardized JSON format in strict adherence to the FAIR data principles. By bridging isolated database silos and linking distributed knowledge to discrete biological entities, the SDD provides a high-quality, foundational resource designed to accelerate trait-based strain discovery, large-scale comparative analysis, and machine learning applications, thereby supporting the translation of the extensive existing knowledge on microbial traits to bioindustrial applications.

microbiology↗

bioRxiv2026

Ancestral phototrophic Rhizobiaceae evolved in association with algae, then plants

Rhizobiaceae serve as classical models for elucidating mutualistic plant-microbe interactions yet they represent a narrow phylogenetic subgroup of Alphaproteobacteria. Studying additional lineages of Rhizobiaceae, we observed broad associations with oxygenic phototrophs beyond land plants, including early branching clades of submerged plants, multicellular and unicellular algae, as well as cyanobacteria. In particular, bacteria of the genus Hoeflea were often affiliated with cyanobacteria or microbial algae, whereas Peteryoungia spp. colonized roots of submerged plants. While both genera were originally described as nonpigmented heterotrophs, our detailed genomic, biochemical and physiological analyses revealed that most strains actually contained genes for anoxygenic photosynthesis. Under oligotrophic, oxic growth conditions, each characterized representative expressed bacteriochlorophyll a-containing functional photosynthetic complexes. Photosynthesis genes shared the highest homology among phylogenetically closest relatives, displaying topologies congruent to cognate house-keeping gene phylogenies, and maintained highly conserved gene synteny across the chromosomes of different species. Together, this indicated a vertical inheritance and long ancestral history of aerobic anoxygenic photosynthesis in Rhizobiaceae rather than multiple recent horizontal transfers. Subsequent time-scale phylogenetic analysis suggested that the last common ancestor of Rhizobiaceae was an aquatic phototroph, with different lineages of Rhizobiaceae consecutively evolving in association with algae, land plants, then later legumes. While aquatic lineages maintained photosynthetic machinery till today, Rhizobia which developed symbioses with land plants either as mutualistic endosymbiosis within root nodules or as plant pathogens, concomitantly lost photosynthetic capability. Based on our results, multiple biotic interactions with diverse oxygenic phototrophs drove the early evolution of Rhizobiaceae.

evolutionary biology↗

bioRxiv2026

Interspecies transfer of giant virulence-factor-like proteins in a bacterial symbiosis

The transfer of virulence factors into eukaryotic cells is a hallmark of bacterial pathogenesis. We report the expression, interspecies transfer, subcellular localization, and potential functions of three unusually large virulence factor-like proteins that underlie a bipartite mutualistic bacterial symbiosis. These proteins are synthesized by green sulfur bacterial epibionts surrounding a central motile chemoheterotroph in the multicellular phototrophic consortium Chlorochromatium aggregatum. While symbiosis-proteins remain intracellular during axenic epibiont growth, they are transferred to the partner bacterium in the association. An RTX-like protein secreted towards the central bacterium is capable of degrading its alginate capsule, thereby promoting direct cell-to-cell contact. Two gigantic hemagglutinin-like proteins are predicted to fold when binding extracellular Ca2+ to form Type 6-like auto injection needles, explaining their observed transfer into the central bacterium. These functionalities extend far beyond the known pathogenic interactions of bacteria with eukaryotes and provide new perspectives on the evolution of bacterial virulence factors.

microbiology↗

bioRxiv2026

Unveiling the taxonomic diversity and unprecedented biosynthetic treasure of the phylum Myxococcota

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.

microbiology↗

bioRxiv2026

Longitudinal Dynamics and Site-Specific Recovery of the Human Respiratory Microbiome Following Smoking Cessation

BackgroundThe human respiratory tract harbours diverse microbial communities crucial for health, but their dynamics during environmental perturbations like smoking remain poorly understood. While smoking is a major risk factor for various diseases, its compartment-specific effects on the respiratory microbiome and potential recovery following cessation have not been fully elucidated. Here, we present a longitudinal, multi-site study of respiratory microbiome dynamics in smokers undergoing cessation, benchmarked against healthy never-smokers. MethodsUsing standardized sampling of the anterior nares, oropharynx, and bronchoalveolar lavage (BAL), combined with 16S rRNA gene amplicon sequencing and rigorous contamination controls, we characterized community composition, diversity, personalization, and microbial interactions across airway compartments. ResultsSmokers exhibited pronounced microbiome alterations: nasal richness increased, while lung richness and core taxa were reduced. Smoking-induced changes were compartment-specific and most pronounced in nose and lung. The degree of individuum-specific differences in community structure was elevated in smokers and correlated with smoking intensity and duration. Short-term cessation (6 weeks) led to minor shifts in taxa abundance but increased similarity between oropharyngeal and lung communities, whereas long-term cessation (1 year) resulted in partial restoration, particularly in lung and nasal microbiomes. Some taxa, including Haemophilus and Prevotella_7, showed persistent alterations, highlighting lasting smoking effects. Network analyses revealed that smoking disrupted microbial co-occurrence and reduced community connectivity, whereas cessation partially restored interaction networks, with dynamics differing between oropharynx and lung, reflecting different underlying ecological assembly processes. Recovery trajectories were highly individualized, with lung microbiomes influenced by deterministic processes and upper airway microbiomes shaped by stochastic factors, explaining site-specific responses and the persistence of personalized microbial signatures. ConclusionThese results provide the first time-resolved, multi-compartment characterization of respiratory microbiome recovery after smoking cessation, revealing that smoking leaves long-lasting, site-specific imprints on airway microbial communities and interactions. Our findings underscore the need for individual and compartment-specific approaches when designing microbiome-based interventions to support respiratory health.

microbiology↗

bioRxiv2025

Metabolites produced by gut bacteria under anoxic conditions drive the suppression of Acinetobacter baumannii

Multidrug-resistant (MDR) bacteria pose a significant global health threat. Among these, Acinetobacter baumannii, particularly carbapenem-resistant A. baumannii, is a leading cause of healthcare-associated infections. Emerging evidence links gut colonization to systemic infections, highlighting opportunities for new control strategies. We demonstrate that A. baumannii can survive under anaerobic conditions ([≤]1%) and shows limited growth under low oxygen conditions ([≥]1%), underscoring its adaptation to niches in the intestine. However, specific carbohydrates, including maltose, provide the gut bacteria Klebsiella oxytoca with a competitive advantage under anoxic conditions, enabling it to actively suppress A. baumannii through its metabolism. Notably, maltose induces this suppressive capacity in other commensals and complex gut microbiomes as well. Force-feeding experiments in Galleria mellonella larvae corroborate that K. oxytoca in combination with maltose significantly reduces A. baumannii recovery in gut environments. These findings suggest that targeted carbohydrate supplementation could enhance probiotic strategies, creating an environment unfavorable to A. baumannii.

microbiology↗

bioRxiv2024

Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets

Predicting prokaryotic phenotypes - observable traits that govern functionality, adaptability, and interactions - holds significant potential for fields such as biotechnology, environmental sciences, and evolutionary biology. This study leverages machine learning to explore the relationship between prokaryotic genotypes and phenotypes. Taking advantage of the highly standardized datasets in the BacDive database, we modeled eight physiological properties based on protein family inventories, discuss the evaluation metrics, and explore the biological implications of our models. The high confidence values of our predictions highlight the importance of data quality and quantity for a reliable inference of bacterial phenotypes. Our approach yielded nearly 55,000 new data points for approximately 20,000 strains which are published openly in the BacDive database, enriching existing phenotypic datasets and paving the way for future research and analysis. The open-source software generated can readily be applied to other datasets, for example the IMG/M system for metagenomics, as well as different applications, like the assessment of the potential of soil bacteria for bioremediation projects.

bioinformatics↗

bioRxiv2024

EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens

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. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualising 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. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/608032v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@88ff78org.highwire.dtl.DTLVardef@3c426eorg.highwire.dtl.DTLVardef@2d8481org.highwire.dtl.DTLVardef@5644bb_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Broad diversity of human gut bacteria accessible via a traceable strain deposition system

Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains have been made publicly available. A major hurdle in making strains publicly available is their deposition to public culture collections. We propose a framework for the bulk-deposition of strains to culture collections, which removes many of the barriers previously identified (www.dsmz.de/bulk-deposit). Using this bulk-deposition system we have created a publicly available collection of human gut isolates. The Human intestinal Bacteria Collection (HiBC) (www.hibc.rwth-aachen.de) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

microbiology↗

bioRxiv2024

Isolation and characterization of the new Streptomyces phages Kamino, Geonosis, Abafar and Scarif infecting a broad range of host species

Streptomyces, a multifaceted genus of soil-dwelling bacteria within the phylum Actinobacteria, features intricate phage-host interactions shaped by its complex life cycle and the synthesis of a diverse array of specialized metabolites. Here, we describe the isolation and characterization of four novel Streptomyces phages infecting a variety of different host species. While phage Kamino, isolated on Streptomyces kasugaensis, is predicted to be temperate and encodes a serine integrase in its genome, phages Geonosis (isolated on S. griseus) and phages Abafar and Scarif, isolated on S. albidoflavus, are virulent phages. Phages Kamino and Geonosis were shown to amplify well in liquid culture leading to a pronounced culture collapse already at low titres. Determination of the host range by testing >40 different Streptomyces species identified phages Kamino, Abafar and Scarif as broad host range phages, with Kamino showing productive infections on 15 different species. Isolated phages were further tested regarding their sensitivity to antiphage molecules. Here, the strongest effects were observed for the DNA-intercalating molecule daunorubicin. Overall, the phages described in this study expand the publicly available portfolio of phages infecting Streptomyces and will be instrumental for advancing the mechanistic understanding of the intricate antiviral strategies employed by these multicellular bacteria.

microbiology↗

bioRxiv2024

Old, deciduous stands support both high biodiversity and carbon storage in German forests

Ecosystems worldwide face threats related to human-driven degradation, climate change, and biodiversity loss. Addressing these challenges requires management strategies that combine biodiversity conservation with climate change mitigation. Here, we aimed to identify local-scale management actions that promote biodiversity at multiple trophic levels while also promoting carbon storage and sequestration. We combined data on the diversity of nine taxonomic groups (plants, birds, moths, Mollusca, soil fungi, active soil bacteria, Cercozoan and Endomyxan soil protists, Oomycotan soil protists, and nematodes), with above- and belowground carbon storage in 150 temperate forest plots in three regions of Germany. These were dominated by European beech, pine, spruce and oak. We investigated the relationships between multiple forest structure and management variables, biodiversity and carbon storage and sequestration in forest plots with different management types. Carbon storage was 32% higher in uneven-aged than even-aged forests and increased with mean tree diameter, while carbon sequestration in trees was 15% higher in even-aged than uneven-aged stands. Mean tree diameter was positively related to overall biodiversity, especially bird species richness and the richness of forest specialist birds. Oak and beech-dominated stands harboured higher biodiversity than stands dominated by conifers (especially Pine). One exception to this was the richness of plant species and forest specialist plants, which were highest in spruce plantations. Surprisingly, deadwood input did not significantly affect the diversity of any taxonomic group in this study. By showing that older forests with a high proportion of uneven-aged broad-leafed trees, or oak-dominated forests, can promote both biodiversity and carbon storage, our results could help inform sustainable local-scale forest management in Central Europe that promotes both biodiversity conservation and carbon storage. These findings can form the basis of further larger-scale studies investigating such relations at larger spatial scales to inform landscape-level recommendations for sustainable multifunctional forest management.

ecology↗

bioRxiv2023

COMPLETE GENOME SEQUENCE OF VIBRIO SYNGNATHI SP. NOV., A FISH PATHOGEN, ISOLATED FROM THE KIEL FJORD

A new Vibrio strain K08M4T was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. Infection experiments revealed that K08M4T is highly virulent for juvenile pipefish. Cells of strain K08M4T are Gram-stain-negative, curved rod-shaped and motile by means of a single polar flagellum. The strain can grow aerobically at 9 to 40{degrees}C, at pH 4 to 10.5 and tolerates up to 12% (w/v) NaCl. The most prevalent (> 10%) cellular fatty acids of K08M4T were C16:1{omega} 7c and C16:0. Whole-genome comparisons revealed that K08M4T represents a separate evolutionary lineage which is distinct from other Vibrio species and falls within the Vibrio Splendidus clade. The genome is 4,886,292 bp in size, consists of two circular chromosomes (3,298,328 bp, 1,587,964 bp), and comprises 4,178 protein-coding genes and 175 RNA genes. In this study, we describe the phenotypic features of the new isolate and present the annotation and analysis of its complete genome sequence. Based on these data, the new isolate represents a new species for which we propose the name Vibrio syngnathi. The type strain is K08M4T (=DSM 109818T). Supplementary materialOne supplementary figure and six supplementary table are available with the online version of the Manuscript.

microbiology↗

bioRxiv2023

Touching the (almost) untouchable: a minimally-invasive workflow for microbiological and biomolecular analyses of cultural heritage objects

Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon -from the prevalent focus on the cultural objects conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts on heritage objects in a global context of a changing climate. Standard microbiology and molecular biology methods were developed for other materials, specimens, disciplines and contexts. Although they could in principle be applied to cultural heritage research, certain characteristics common to several heritage objects - such as uniqueness, fragility, high value and restricted access, demand tailored approaches. In addition, samples from heritage objects often yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology that addresses these material limitations and operational hurdles along all procedural steps are needed. Here were propose a step-by-step standardized laboratory and bioinformatic workflow to analyse the microbiome of cultural heritage objects. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining modularity and flexibility to adapt and/or upscale the proposed workflow to heritage artefacts of a more robust nature or larger dimensions. We hope this review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.

microbiology↗

bioRxiv2023

Microbial fingerprints reveal interaction between museum objects, curators and visitors

Microbiomes populate the border between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To answer this question, museum objects varying in material and size from two museums, the Museum fur Naturkunde and the Pergamonmuseum in Berlin, Germany, which forms part of UNESCO World Heritage since 1999, were defined. In total 126 samples of natural and cultural heritage objects were taken with sterile nylon flocked swabs and subsequently subjected to 16S rRNA amplicon sequencing. By comparing the microbial composition of touched and untouched mollusc and fossil natural heritage objects we derived a robust microbial touch signature characterized by increased abundance of microbes known to be present in human skin. Application of this touch signature to cultural heritage objects from the Pergamonmuseum revealed areas of differential exposure to human contact on the Ishtar gate and Samal gate lions. Moreover, we were able to distinguish museum objects and personal office items touched by two different individuals with high sensitivity. Our results demonstrate that the microbial composition of museum objects gives insight into the degree of exposure to human contact, which is an important parameter for conservation and heritage science, and possibly provenance research.

microbiology↗

bioRxiv2023

Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various agricultural crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in USA, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

microbiology↗

bioRxiv2022

Bursts in biosynthetic gene cluster transcription are accompanied by surges of natural compound production in the myxobacterium Sorangium sp.

We have investigated the time course of genome-wide transcription in the myxobacterium Sorangium sp. So ce836 in relation to its production of natural compounds. Time-resolved RNA sequencing revealed that core biosynthesis genes from 48 biosynthetic gene clusters (BGCs; 92% of all BGCs encoded in the genome) were actively transcribed at specific time points in a batch culture. The majority (80%) of polyketide synthase and non-ribosomal peptide synthetase genes displayed distinct peaks of transcription during exponential bacterial growth. Strikingly, these bursts in BGC transcriptional activity were associated with surges in the production of known natural compounds, indicating that their biosynthesis was critially regulated at the transcriptional level. In contrast, BGC read counts from single time points had limited predictive value about biosynthetic activity, since transcription levels varied >100-fold among BGCs with detected natural products. Taken together, our time-course data provide unique insights into the dynamics of natural compound biosynthesis and its regulation in a wild-type myxobacterium, challenging the commonly cited notion of preferential BGC expression under nutrient-limited conditions. The close association observed between BGC transcription and compound production warrants additional efforts to develop genetic engineering tools for myxobacterial producer strains, to boost compound yields by manipulating transcriptional activity.

genomics↗

bioRxiv2022

Evolution of resilience against heat stress in a red-tide dinoflagellate

"Red tides" are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. Increasingly frequent, HABs are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters. Here, we present the de novo assembled genome (~4.75 Gbp), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we studied the molecular mechanisms that underpin response to temperature stress, which is relevant to current ocean warming trends. We discovered a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. Our multi-omics analyses uncover the molecular response to heat stress in an important HAB species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation.

genomics↗

bioRxiv2022

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. In this work, we expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes the study of strain-level diversity, small-sized bacteria, and the isolation and characterization of the first cultured members of one novel family, 10 novel genera, and 39 novel species. We demonstrate the value of this collection by performing two studies. First, metagenome-educated design allowed establishing custom synthetic communities (SYNs) that reflect different susceptibilities to DSS-induced colitis. Second, nine phylogenetically and functionally diverse species were used to amend the Oligo-Mouse Microbiota (OMM)12 model [Brugiroux et al. 2016 Nat Microbiol]. These strains compensated for differences observed between gnotobiotic OMM12 and specific pathogen-free (SPF) mice at multiple levels, including body composition and immune cell populations (e.g., T-cell subtypes) in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available to the community for use in future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.

microbiology↗