Biology subjects

Van Rossum, T.

Publications and source records attributed to Van Rossum, T..

5 recordsLinked to original sources

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↗

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↗

bioRxiv2022

C. difficile is overdiagnosed in adults and a commensal in infants

Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. To investigate the gut microbiome composition in CDI patients, we analysed 534 metagenomes from 10 publicly available CDI study populations. We then tracked C. difficile on a global scale, screening 42,900 metagenomes from 253 public studies. Among the CDI cohorts, we detected C. difficile in only 30% of the stool samples from CDI patients. However, we found that multiple other toxigenic species capable of inducing CDI-like symptomatology were prevalent. In addition, the majority of the investigated studies did not adhere to the recommended guidelines for a correct CDI diagnosis. In the global survey, we found that C. difficile prevalence, abundance and biotic context were age-dependent. C. difficile is a rare taxon associated with reduced diversity in healthy adults, but common and associated with increased diversity in infants. We identified a group of species co-occurring with C. difficile exclusively in healthy infants, enriched in obligate anaerobes and in species typical of the healthy adult gut microbiome. C. difficile in healthy infants was therefore associated with multiple indicators of healthy gut microbiome maturation. Our analysis raises concerns about potential CDI overdiagnosis and suggests that C. difficile is an important commensal in infants and that its asymptomatic carriage in adults depends on microbial context.

microbiology↗

bioRxiv2021

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation

Faecal microbiota transplantation (FMT) is an efficacious therapeutic intervention, but its clinical mode of action and underlying microbiome dynamics remain poorly understood. Here, we analysed the metagenomes associated with 142 FMTs, in a time series-based meta-study across five disease indications. We quantified strain-level dynamics of 1,089 microbial species based on their pangenome, complemented with 47,548 newly constructed metagenome-assembled genomes. Using subsets of procedural-, host- and microbiome-based variables, LASSO-regularised regression models accurately predicted the colonisation and resilience of donor and recipient microbes, as well as turnover of individual species. Linking this to putative ecological mechanisms, we found these sets of variables to be informative of the underlying processes that shape the post-FMT gut microbiome. Recipient factors and complementarity of donor and recipient microbiomes, encompassing entire communities to individual strains, were the main determinants of individual strain population dynamics, and mostly independent of clinical outcomes. Recipient community state and the degree of residual strain depletion provided a neutral baseline for donor strain colonisation success, in addition to inhibitive priority effects between species and conspecific strains, as well as putatively adaptive processes. Our results suggest promising tunable parameters to enhance donor flora colonisation or recipient flora displacement in clinical practice, towards the development of more targeted and personalised therapies.

microbiology↗

bioRxiv2018

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes

Freshwater is an essential resource of increasing value, as clean water sources diminish. Microorganisms in rivers, a major source of renewable freshwater, are significant due to their role in drinking water safety, signalling environmental contamination1, and driving global nutrient cycles2,3. However, a foundational understanding of microbial communities in rivers is lacking4, especially temporally and for viruses5-7. No studies to date have examined the composition of the free-floating river virome over time, and explanations of the underlying causes of spatial and temporal changes in riverine microbial composition, especially for viruses, remain unexplored. Here, we report relationships among riverine microbial communities and their environment across time, space, and superkingdoms (viruses, bacteria, and microeukaryotes), using metagenomics and marker-based microbiome analysis methods. We found that many superkingdom pairs were synchronous and had consistent shifts with sudden environmental change. However, synchrony strength, and relationships with environmental conditions, varied across space and superkingdoms. Variable relationships were observed with seasonal indicators and chemical conditions previously found to be predictive of bacterial community composition4,8-10, emphasizing the complexity of riverine ecosystems and raising questions around the generalisability of single-site and bacteria-only studies. In this first study of riverine viromes over time, DNA viral communities were stably distinct between sites, suggesting the similarity in riverine bacteria across significant geographic distances10-12 does not extend to viruses, and synchrony was surprisingly observed between DNA and RNA viromes. This work provides foundational data for riverine microbial dynamics in the context of environmental and chemical conditions and illustrates how a bacteria-only or single-site approach would lead to an incorrect description of microbial dynamics. We show how more holistic microbial community analysis, including viruses, is necessary to gain a more accurate and deeper understanding of microbial community dynamics.

microbiology↗