Biology subjects

Schmidt, T. S. B.

Publications and source records attributed to Schmidt, T. S. B..

7 recordsLinked to original sources

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↗

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 MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems

Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet--from the deep subsurface to the mountain tops--covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable SSU rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a long tail of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), both known and newly described species and communities can readily be placed into ecological context, taking full advantage of earlier work.

bioinformatics↗

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↗

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↗

bioRxiv2023

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Multi-omics analyses are increasingly employed in microbiome studies to obtain a holistic view of molecular changes occurring within microbial communities exposed to different conditions. However, it is not always clear to what extent each omics data type contributes to our understanding of the community dynamics and whether they are concordant with each other. Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods complement each other in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.

microbiology↗

bioRxiv2018

Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

The smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts that selection, dispersal and drift are main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.\n\nSIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmental selection, dispersal and random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

ecology↗