Biology subjects

Bork, P.

Publications and source records attributed to Bork, P..

At least 19 recordsLinked to original sources

bioRxiv2026

A global genomic survey of prokaryotic carbon fixation reveals an oxygen-tolerant rTCA cycle in the surface ocean

Autotrophic carbon fixation, the conversion of inorganic carbon into biomass, underpins life on Earth. Prokaryotes can carry out this process via at least seven biochemically distinct pathways, yet the phylogenetic and environmental distribution of most remains poorly resolved. Screening approximately 40 billion genes from reference genomes, metagenome-assembled genomes (MAGs) and unbinned metagenomic contigs, we provide a global assessment of the phylogeny and ecophysiology of prokaryotic autotrophs. Most pathway marker genes occurred in unbinned contigs and low-quality MAGs, representing phylogenetically distinct lineages absent from isolate genomes and quality filtered MAGs. Established autotrophs accounted for the large majority of pathway detections in quality filtered MAGs, largely recapitulating known biology from cultivated model organisms. Against this backdrop, the reductive TriCarboxylic Acid (rTCA) cycle, long considered restricted to anoxic environments, was detected in three phylogenetically distinct Campylobacterota lineages from oxygenated surface seawater, suggesting a previously unrecognized and unexpected niche for this pathway. We show that all three MAGs share an enzyme variant, previously described in other oxygen-tolerant lineages, that likely underlies their presence in the oxygenated surface ocean. Read mapping across global ocean metagenomes indicates that the organisms carrying it could be far more widespread than the scarcity of recovered MAGs alone would suggest. Together, these findings illustrate that the current view of global autotrophic carbon fixation is largely shaped by what genome-resolved methods can readily recover, while the true phylogenetic and ecological distribution of autotrophic carbon fixation appears to be much broader.

microbiology↗

bioRxiv2026

Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential

Biological nitrogen fixation sustains productivity across Earths ecosystems, yet the diversity, distribution and ecological drivers of nitrogen-fixing prokaryotes (diazotrophs) remain incompletely resolved. Here we screened approximately 40 billion genes to generate a catalogue of 21,157 diazotroph genomes. Using this catalogue, we quantified diazotroph diversity and abundance across 9,163 metagenomes spanning diverse environments. Diazotrophy was distributed across the prokaryotic tree of life, but both gene diversity and metagenomic abundance were dominated by heterotrophic lineages. Freshwater and sedimentary ecosystems emerged as major reservoirs of nitrogen-fixation potential beyond the environments that have historically anchored the field. Diazotroph-rich assemblages were associated with nitrogen and phosphorus limitation together with carbohydrate-rich metabolic regimes, revealing distinct nutrient and energy niches for cyanobacterial and heterotrophic diazotrophs. Together, this framework unifies disparate views of diazotroph diversity, abundance and ecology, providing a foundation for improved prediction of biological nitrogen fixation across Earths ecosystems.

microbiology↗

bioRxiv2026

The ultrasmall ocean microbiome: a reservoir of microbial diversity and nitrogen fixation.

Marine microbiology has long considered ultrasmall (<0.2 {micro}m) size fractions as virus-dominated, yet emerging evidence suggests potential prokaryotic activity with implications for global biogeochemical cycles. Here, we present the first comprehensive genome-resolved survey of this fraction, built on 4,058 metagenome-assembled genomes (MAGs) representing 1,152 species across Bacteria (90.7%) and Archaea (9.3%), dominated by Pseudomonadota, Bacteroidota, and Nanoarchaeota. Over 490 non-redundant MAGs occurred exclusively in the ultrasmall fraction, with 66.8% representing novel taxa, particularly abundant in Arctic surface waters. Beyond known ultrasmall organisms (e.g., DPANN archaea and Patescibacteria), which show expected genomic and metabolic reduction, functional annotation revealed diverse metabolic potential across nitrogen, sulfur, and carbon cycling. Focusing on nitrogen fixation, we identified 13 non-cyanobacterial diazotroph species with complete nitrogenase operons spanning four bacterial classes. These resolved into two ecotypes: cosmopolitan low-abundance taxa, and Arctic ultrasmall-restricted strains reaching up to 16.7% relative abundance. Two lineages (50-400-T64 and Novosphingobium) showed ultrasmall exclusive bipolar distributions across Arctic and Southern Oceans. Beyond nitrogen fixation, these diazotrophs encoded pathways for denitrification, DNRA, sulfur oxidation, and carbon fixation. Our findings reveal an overlooked reservoir of microbial diversity including diazotrophs in the ultrasmall ocean microbiome, with significant implications for polar nitrogen budgets and global biogeochemical models.

microbiology↗

bioRxiv2026

Preoperative biliary stenting is associated with functional dysbiosis and impaired bile acid metabolism in pancreatic cancer - Impact of preoperative biliary stenting on gut microbiota

Recent evidence suggests that the gut microbiome plays a role in the development and treatment response of pancreatic ductal adenocarcinoma (PDAC). However, the functional impact of tumor location and preoperative biliary stenting (PBS) on microbial composition and metabolism remains poorly understood. In this prospective study, preoperative stool specimens were collected from patients undergoing surgery for PDAC at Heidelberg University Hospital, Germany, between March 2020 and July 2021. Whole-genome shotgun metagenomic sequencing was performed to characterize microbial composition and functional pathways. A total of 63 preoperative stool samples were analyzed, including 40 patients with pancreatic head tumors (63.5%) and 23 with body/tail tumors (36.5%). Microbial community composition differed significantly according to tumor location (Bray-Curtis, p=0.005), with enrichment of Ruminococcus bromii in body/tail tumors. Among patients with pancreatic head tumors, PBS was associated with reduced alpha diversity (Shannon index, p=0.04), depletion of taxa including members of the Eubacteriales and Clostridiales orders as well as the genera Raoultella and Prevotella, and reduced abundance of selected genes involved in secondary bile acid metabolism. PBS was also associated with a higher rate of major postoperative complications according to Clavien-Dindo >3a (28.6% vs 3.8%; p=0.04). These findings suggest that biliary intervention may induce functional dysbiosis characterized by reduced microbial diversity and impaired bile acid metabolism, potentially disrupting host- microbiome crosstalk and contributing to adverse postoperative outcomes in pancreatic cancer.

microbiology↗

bioRxiv2026

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats

SummaryWe introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories. Data Availabilitymicrontology controlled vocabulary terms and term hierarchies 1, and curated annotations for 305,626 metagenomic samples 2 are available via Zenodo and as supplemental tables S1 and S2. User feedback, suggestions and bug reports are welcome under https://github.com/grp-schmidt/microntology/issues.

bioinformatics↗

bioRxiv2025

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from equator to poles, are a pervasive macroecological pattern, yet their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed layer microbiomes exhibited diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) showed no latitudinal diversity structuring. Taxonomic resolution revealed that the mixed layer LDG was underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibited distinct or contrasting LDGs. Diversity structuring also varied by seasons and regions, governed by temperature and nutrient availability. Together, these findings highlight that within the ocean microbiome, LDGs are not universal, but lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.

microbiology↗

bioRxiv2025

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 73,082 samples from humans (including 58,506 of the gut microbiome), 10,703 animal samples, 5,146 ocean water samples, and 21,802 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status and medication for humans, host species and captivity status for animals, and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.

microbiology↗

bioRxiv2025

The JEDI marker as a universal measure of planetary biodiversity

Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hindering our capacity to document Earths biota and track its change. Here, we propose the Joint, cellular life-Encompassing DIversity (JEDI) marker as a simple, effective and quantitative measure to assess and monitor biodiversity. The JEDI marker is a ribosomal RNA gene fragment that can be amplified from all domains of life using a single pair of PCR primers. We demonstrate the applicability and effectiveness of this approach for assessing biodiversity across ecological and biological scales, from holobionts to diverse ecosystems. In addition, we provide an automated bioinformatic workflow to support the standardised and reproducible analysis of the JEDI marker in future studies. While this approach is not free from trade-offs, we argue that its advantages outweigh its limitations by providing a unique, operational and scalable solution that builds on established infrastructure to integrate the microbial majority into biodiversity assessments and provide fundamental insights into organismal dynamics and associations across domains of life. Thus, the JEDI marker approach addresses the urgent need for a universal and standardised framework to effectively measure and monitor biodiversity at planetary scales in an era of profound global change.

ecology↗

bioRxiv2025

Nuclear rerouting of paracrine Fgf3 in source cells represses target genes to pattern morphogen responses

Morphogen gradients direct tissue patterning by inducing dose-dependent transcriptional responses, yet ligand-producing cells often respond differently from their neighbors. Using the zebrafish lateral line organogenesis model, we uncover a cell-autonomous role for the paracrine ligand Fgf3. Transcriptomic profiling and quantitative single-molecule imaging identify target genes, including the chemokine scavenger cxcr7b, whose expression decreases both when FGF receptor signaling is inhibited and when Fgf3 is overexpressed. High-resolution live imaging reveals nuclear accumulation of Fgf3 in producing cells, whereas neighbors receive only extracellular ligand, a feature also observed in other embryonic tissues. Mosaic gain- of-function and nanobody-mediated degradation demonstrate that the nuclear pool of Fgf3 autonomously represses specific targets without impairing canonical receptor signaling. Structure-guided comparative assays indicate nuclear targeting as a latent property of several paracrine FGFs. Dual secreted-nuclear functionality of FGF ligands may represent an intrinsic symmetry-breaking mechanism during organogenesis.

developmental biology↗

bioRxiv2025

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focused on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to other habitats, exemplifying human impact on the planetary microbiome.

microbiology↗

bioRxiv2025

A census of hidden and discoverable microbial diversity beyond genome-centric approaches

Cataloguing Earths biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing census of microbial life is hampered by disparate sampling of Earths habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons, and incomplete recovery of metagenome-assembled genomes (MAGs). Here, we quantified discoverable bacterial and archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 metagenomes. Clustering 502M sequences of 130 marker genes, we detected 705k bacterial and 27k archaeal species-level clades, the vast majority of which was hidden among unbinned contigs. At deeper taxonomic levels, we estimate that 10 archaeal and 145 bacterial novel phyla and around 80k novel genera are discoverable in current data. We identified soils and aquatic environments as novel lineage recovery hotspots, yet predict that discovery will remain in full swing across habitats as more data accrues. Finally, we show that prokaryotic diversity follows power laws, confirming century-old hypotheses on clade size patterns and suggesting that novel lineages arise within common (and fractal) evolutionary patterns, comparable to those among eukaryotic clades and viruses, along the full depth and breadth of the Tree of Life.

microbiology↗

bioRxiv2025

In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex

Cryo-electron tomography has emerged as powerful technology for in-cell structural biology, and in combination with breakthroughs in protein structure prediction, offers a unique opportunity for illuminating functions of previously uncharacterized macromolecular complexes. Here, we used the genome-reduced bacterium Mycoplasma pneumoniae as a minimal cell model, and determined in-cell maps of an unknown complex located at the cell surface. By combining proteomics, structure prediction, and bioinformatics, we identified the complex to include the conserved Sec-translocon and an extracellular dome-like structure largely formed by three uncharacterized proteins (Mdps). The Mdps show structural homology to a periplasmic ATP-independent foldase, PrsA, with Mdp444 retaining key catalytic residues. Our study provides the first sub-nanometer resolution maps of the complete bacterial Sec-translocation machinery, depicting several conformational states that allow us to suggest a model for translocation initiation, and revealing its coordination with a novel, extracellular, protein-folding system.

molecular biology↗

bioRxiv2024

Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes

BackgroundEnterotypes describe human fecal microbiomes grouped by similarity into clusters of microbial community composition, often associated with disease, medications, diet, and lifestyle. Numbers and determinants of enterotypes have been derived by diverse frameworks and applied to cohorts that often lack diversity or inter-cohort comparability. ResultsTo overcome these limitations, we selected 16,772 fecal metagenomes collected from 38 countries to revisit the enterotypes using state-of-the-art fuzzy clustering and found robust clustering regardless of underlying taxonomy, consistent with previous findings. Quantifying the strength of enterotype classifications enriched the enterotype landscape, also reflecting some continuity of microbial compositions. As the classification strength was associated with the patients health status, we established an "Enterotype Dysbiosis Score" (EDS) as a latent covariate for various diseases. ConclusionThis global study confirms the enterotypes, reveals a dysbiosis signal within the enterotype landscape, and enables robust classification of metagenomes with an online "Enterotyper" tool, allowing reproducible analysis in future studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/607711v3_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1611a2org.highwire.dtl.DTLVardef@dfbb57org.highwire.dtl.DTLVardef@848ac0org.highwire.dtl.DTLVardef@1b15808_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria

Nitroxoline is a bacteriostatic quinoline antibiotic, considered a metal chelator inhibiting the activity of RNA-polymerase1. Its clinical indications are limited to uncomplicated urinary tract infections (UTIs), with a clinical susceptibility breakpoint only available for Escherichia coli2. By testing > 1,000 clinical isolates, here we demonstrate a much broader activity spectrum and species-specific bactericidal activity, including multidrug-resistant Gram-negative bacteria for which therapeutic options are limited due to resistance. By combining systematic genetic and proteomic approaches with direct measurement of intracellular metals, we dissect nitroxoline perturbation of metal homeostasis and unveil additional effects on bacterial physiology. We show that nitroxoline affects outer membrane integrity, synergizing with large-scaffold antibiotics and resensitizing colistin-resistant Enterobacteriaceae in vitro and in vivo. We further characterise resistance mechanisms across E. coli, Acinetobacter baumannii and Klebsiella pneumoniae, recapitulating known E. coli resistance determinants and uncovering novel and conserved mechanisms across species, demonstrating their common effect on nitroxoline efflux.

microbiology↗

bioRxiv2024

Emergent survival and extinction of species within gut bacterial communities

Synthetic communities can help uncover metabolic forces shaping microbial ecosystems. Yet, in case of the gut microbiota, culturing in undefined media has prevented detection of metabolic dependencies. Here we show, using chemically defined media, how species survival is jointly determined by supplied resources and community metabolism. We used 63 representative gut bacterial strains and varied inoculum compositions to assemble stable communities in 14 defined media. Over 95% of the species showed markedly improved or diminished performance relative to monoculture in at least one condition, including 153 cases (21%) of emergent survival, i.e., species incapable of surviving on their own but thriving in a community, and 252 (35%) community-driven extinctions. Through single species additions and exclusions, metabolomic analysis, and ecological modelling, we demonstrate how inter-species dependencies - especially in poor media - are mediated by biotic nutrient supply. Our results highlight communal metabolic dividend as a key biotic force promoting emergent survival and diversity.

microbiology↗

bioRxiv2024

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

The microbiota in individual habitats differ both in relative composition and absolute abundance. While sequencing approaches determine only the relative abundances of taxa and genes, experimental techniques for absolute abundance determination are rarely applied to large-scale microbiome studies. Here, we developed a machine learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applied to large-scale datasets (n = 34,539), we demonstrate that microbial load is the major determinant of gut microbiome variation and associated with numerous host factors. We found that for several diseases, the altered microbial load, not the disease itself, was the main driver of the gut microbiome changes. Adjusting for this effect substantially reduced the significance of more than half of the disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.

microbiology↗

bioRxiv2024

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics

By acquiring or evolving resistance to one antibiotic, bacteria can become resistant to a second one, due to shared underlying mechanisms. This is called cross-resistance (XR) and further limits therapeutic choices. The opposite scenario, in which initial resistance leads to sensitivity to a second antibiotic, is termed collateral sensitivity (CS) and can inform cycling or combinatorial treatments. Despite their clinical relevance, our current knowledge of such interactions is limited, mostly due to experimental constraints in their assessment and lack of understanding of the underlying mechanisms. To fill this gap, we used published chemical genetic data on the impact of all Escherichia coli non-essential genes on resistance/sensitivity to 40 antibiotics, and devised a metric that robustly discriminates between known XR and CS antibiotic interactions. This metric, based on chemical genetic profile (dis)similarity between two drugs, allowed us to infer 404 XR and 267 CS interactions, thereby expanding the number of known interactions by more than 3-fold - including reclassifying 116 previously reported interactions. We benchmarked our results by validating 55 out of 59 inferred interactions via experimental evolution. By identifying mutants driving XR and CS interactions in chemical genetics, we recapitulated known and uncovered previously unknown mechanisms, and demonstrated that a given drug pair can exhibit both interactions depending on the resistance mechanism. Finally, we applied CS drug pairs in combination to reduce antibiotic resistance development in vitro. Altogether, our approach provides a systematic framework to map XR/CS interactions and their mechanisms, paving the way for the development of rationally-designed antibiotic combination treatments.

systems biology↗

bioRxiv2023

A catalogue of small proteins from the global microbiome

Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we constructed a global microbial smORFs catalogue (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We found that archaea harbor more small proteins proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.

bioinformatics↗