Taxonomic variability and functional stability in microbial communities infected by phages
Bibliographic record
Abstract
Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.
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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 | 0.000 |
| Science and technology studies | 0.000 | 0.002 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.011 | 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".