Diet, Climatic Conditions, and Sex Affect the Mycobiome of Wild Common Marmosets ( <i>Callithrix jacchus</i> )
Bibliographic record
Abstract
Abstract Recent research on the gut mycobiome, or the fungal portion of the gut microbial community, suggests that it interacts with host physiology and impacts host health. However, fundamental questions about how the mycobiome is assembled remain unanswered. It remains unclear whether the fungi detected in the gut are predominantly residents of the gastrointestinal tract or if they are largely transient and pass through. To address this question, we sought to determine whether host factors (e.g., sex) or external environmental factors (e.g., variable climatic conditions and diet) were more strongly correlated with the gut mycobiome of common marmosets ( Callithrix jacchus ), a primate species living in the semi-arid Caatinga biome of northeastern Brazil. A stronger correlation with host factors, would suggest a more resident mycobiome, while a stronger association with external environmental factors suggests a more transient mycobiome. We collected 52 marmoset fecal samples across a 2-year period and DNA metabarcoding was used to assess both the mycobiome and diet of each sample. We used FUNGuild to assign ecological roles to the fungi, which were sorted into resident (e.g. animal pathogens) and transient (e.g. plant pathogens) groups. We found that mycobiome richness and evenness varied by host sex and correlated with the arthropod component of the diet while mycobiome composition varied between wetter and drier periods and correlated with the plant portion of the diet. The fact that external environmental factors were associated with the presence of specific taxa led us to conclude that the mycobiome is largely made up of transient taxa. Importance Other than causing infectious diseases, the function of the mycobiome is poorly understood. There is evidence that the mycobiome can play a positive role, such as training the host’s immune system, and a negative role, such as causing cancer and Alzheimer’s disease. To fully understand these associations, basic questions about which taxa live in the host and which pass through, must be addressed. We used DNA metabarcoding and a tool that can group fungi based on their ecological roles, to determine whether the mycobiome of Caatinga marmosets was more strongly correlated with host sex or host diet and environment. We found that the marmoset mycobiome was more strongly correlated with diet and environment and most fungi passed through the host rather than lived in the host’s gut.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".