The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the human ectocervical epithelium and submucosa
Bibliographic record
Abstract
The cervicovaginal microbiome is a key biological determinant of human immunodeficiency virus (HIV) susceptibility, but its underlying impact on the ectocervical transcriptional landscape is unclear. Ectocervical tissue samples from Kenyan female sex workers were categorized into pre-defined cervicovaginal microbiome groups based on dominant compositions: Lactobacillus crispatus/acidophilus, Lactobacillus iners, Gardnerella, and 'highly diverse'. The tissue samples (n = 21) were assessed using spatial transcriptomics, revealing three epithelial, one mixed border, and nine submucosal gene clusters. Differential gene expression analysis across the microbiome groups and gene clusters identified 3,771 unique genes. The highly diverse microbiome group associated with the largest differences, mostly located near the epithelial basal membrane, encompassing genes involved in epithelial maintenance, submucosal extracellular matrix structures, and immune function. The L. crispatus/acidophilus-dominated group was identified by genes involved in active immune engagement, supporting mucosal barrier integrity. Weighted gene co-expression analysis confirmed tissue-wide altered gene expression associated with all microbiome groups and with individual bacterial taxa. Despite the assumption that microbiome colonization is restricted to the luminal surface, the transcriptional landscape was affected throughout the mucosa, with the most pronounced effect near both sides of the basal membrane. This broad association with the mucosal barrier integrity could affect susceptibility to HIV acquisition.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".