PSLBI-6 Unveiling the gut mycobiota of pasture- and conventionally raised pigs
Bibliographic record
Abstract
Abstract The gut microbiome has a significant role in mammalian health, in pigs it is influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Although studies of the pig gut microbiome typically focus on bacteria, fungal members are understudied although they may have important roles in pig gut health. The objective of this research was to characterize the mycobiota in gastrointestinal tract of swine raised under two very different production systems, either outdoors on pasture or indoors in a farrow-to-finish operation (conventional). Fecal samples were collected from nursery (n = 7) and growing-finishing (n = 17) pigs as well as from sows (n = 11) on each of these conventional and pasture farms. After DNA extraction, the universal fungal internal transcribed spacer 1 (ITS1) region was PCR amplified and sequenced. A total of 353 fungal species spanning 234 genera and 6 phyla, were identified among all samples. Ascomycetes and Basidiomycetes were found to be the relatively most abundant phyla, comprising 96% of the mycobiota. There were 56 fungal species (relative abundance ≥ 0.10%) identified as differentially abundant in the fecal mycobiota of conventionally vs. pasture-raised pigs. Of these, 11 fungal species were relatively more abundant in the conventional pigs and 45 species were enriched in the pasture pigs. Kazachstania slooffiae, Penicillium polonicum, and Vishniacozyma victoriae were most strongly associated with the pigs raised under a conventional system while Enterocarpus grenotii, Leucosporidium escuderoi, and Sagenomella oligospora were among those species linked with pasture-raised pigs. Furthermore, E. grenotii was not detected in any of the conventionally raised pigs and K. slooffiae was not identified in the pigs raised on pasture. Pasture-raised pigs had significantly greater richness (number of amplicon sequence variants) and diversity (inverse Simpson diversity) in their fecal mycobiota compared with conventionally raised pigs (P < 0.05). Given these differences, it is therefore not surprising that the pigs raised under the two different systems had significantly different fungal community structures (R2 = 0.07, P < 0.001). Overall, the large differences observed between the two groups of pigs are a result of differences in diet, environment, and management system. In addition to their grain-based diet, pasture-raised pigs have access to plants and soil which may enrich their gut mycobiota as observed in the present study.
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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 | 0.000 |
| 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) | 0.001 | 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".