<i>Malassezia</i> in environmental studies is derived from human inputs
Bibliographic record
Abstract
ABSTRACT The fungus Malassezia is the most prevalent member of the human skin mycobiota, known for its lipid dependence and inability to synthesize long-chain fatty acids. Malassezia exhibits remarkable niche breadth, inhabiting soils, dust, as well as various marine environments from polar regions to deep-sea vents. The consistent presence of Malassezia in marine habitats, including those associated with marine animals, suggests that the fungus is able to grow and play a fundamental role in marine ecosystems. In this study, we explored metagenomic sequences from the Sequence Read Archive database to investigate the presence, distribution, and origins of Malassezia species within marine ecosystems, with the goal of assembling Malassezia genomes. Using various search methods, we found that up to 10% of the shotgun and amplicon data sets analyzed contained Malassezia sequences. However, the relative abundance of Malassezia in each data set was low, and there was a strong correlation between human and Malassezia sequences in marine environments, consistent with contamination. From the most Malassezia -rich data sets, we attempted to generate metagenome-assembled genomes. However, Malassezia contigs together showed low genome completeness levels, with a maximum of 2.2% in a sample. Phylogenetic analysis identified the contigs as closely related to human-associated Malassezia globosa and Malassezia restricta , along with Malassezia sympodialis and Malassezia pachydermatis , which were the most prevalent species across all studied environments. Our data suggest that many observations of Malassezia in the environment are derived from human sources and that widespread contamination confounds the exploration of Malassezia diversity and ecological role in the marine environment. IMPORTANCE Malassezia is the singular fungus most associated with humans. It colonizes mammalian skin and requires host-derived fatty acids to grow. Widespread sequencing of environmental DNA surprisingly showed that Malassezia is also ubiquitous outside of mammalian hosts. Malassezia is frequently found in marine habitats where it is associated with corals, deep sea vents, diatoms, and more. Given its widespread presence, we reasoned that public metagenomic data could be used to assemble a genome sequence of an uncultured marine Malassezia . However, we found that Malassezia was ubiquitous but never abundant in marine samples and that the few metagenomes we could assemble were consistent with recent human introduction. We also found that the presence of human DNA in sequencing data sets is strongly correlated with the presence of Malassezia DNA, and while not ruling out the growth and survival of Malassezia in marine habitats, they suggest widespread contamination of public data with Malassezia .
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".