Temporal establishment of the colon microbiota in Angus calves from birth to post-weaning
Bibliographic record
Abstract
During the peri- and early post-partum period, the gastrointestinal tract (GIT) of the calf is colonised by a combination of commensal and pathogenic microbes. Current understanding of the temporal microbial establishment of neonatal colon is, however, limited. This study focused on the ontogeny of colon microbiota establishment in Angus Beef calves from birth through weaning. Colon digesta contents were collected from Aberdeen Angus calves reared on two farms. Calves were euthanized at birth (n=7), day (D) 7 (n=7), D14 (n=6), D21 (n=7), D28 (n=6), and D96 (n=7) of life. Microbial DNA was extracted from colon samples and subjected to 16S rRNA amplicon sequencing. The effect of time on alpha (GLM procedure of SAS; 9.4) and beta (PERMANOVA) diversity of the colon microbiota was assessed with age and farm included as fixed effects. Differential abundance (Maaslin2) analyses were conducted with the same fixed effects. The alpha-diversity of the bacterial community progressed from birth onwards (D0 H’ mean = 0.59 and D96 H’ mean = 5.33) with apparent stabilisation between D14 v D21 (P=0.21). Weaning had a further statistically significant effect on the diversity of the colon microbiota (D28 v D96; P <0.001). Similarly, PERMANOVA analysis indicated stabilised colonisation of the colon microbiota from D14 to D21 (P=0.22), albeit weaning altered the colon microbiota (D28 v D96; P <0.001). This study is amongst the first to describe the ontogeny of colonisation of the colon microbiota, from birth to weaning in beef calves and provides fundamental information to support the establishment of beneficial microbes in the lower GIT of ruminants.
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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) | 0.001 | 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".