Analysis of the fungal, archaeal and bacteriophage diversity in the human distal gut
Bibliographic record
Abstract
The composition and role of bacteria in the human gut has been studied intensely and is a burgeoning field of scientific research. However, there is a relative lack of research on other microorganisms which compose our gut flora such as bacteriophage, archaea and fungi. The aim of our study was to begin to fill this gap. The archaeal, fungal and bacteriophage diversity in the gut was analyzed using a PCR-DGGE fingerprinting method on fecal samples from 3 healthy donors. These samples were inoculated into chemostats and the microbes were grown in continuous culture to model the interactions of our flora in vitro. Norepinephrine was also added to the chemostats to test the microbial community’s reaction to stress. Here we report that, relative to bacteria, fungal and archaeal diversity in the gut is low. The archaeal populations seemed stable over time varied depending on the individual. Fungal populations were more variable over time and changes in the community structure were observed after the addition of norepinephrine. DNA sequence analysis confirmed the presence of fungal species that are not yet cultured, yet are residents of the gut. Species of Podophage can also be detected as residents of the gut based on sequence analysis. It is clear that there is a core set of archaeal and fungal species living as residents in the gut. Bacteriophage are also present but their ecological role and effect on the microbial community in the gut is unknown.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".