Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding
Bibliographic record
Abstract
The aim of this study was to explore the effect of colostrum feeding time on the ileal microbiome of neonatal calves. In this study, 22 male Holstein calves were randomly assigned to different colostrum feeding time treatments: after birth (at 45 min, n = 7); at 6 h after birth (n = 8); and at 12 h after birth (TRT12h; n = 7). At 51 h after birth, calves were killed and ileum digesta was collected for microbiome analysis using shotgun metagenomic sequencing. Bacteria, archaea, eukaryotes, and viruses were identified from the ileum microbiome. For the bacteriome, Firmicutes and Proteobacteria were the predominant phyla, and Escherichia, Streptococcus, Lactobacillus were the 3 most abundant genera. For the archaeal community, Euryarchaeota and Crenarchaeota were the 2 major phyla, and Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the 3 most abundant genera. In total, 116 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified from the ileal microbiome, with "biosynthesis of vancomycin group antibiotics," "biosynthesis of ansamycins," "valine, leucine, and isoleucine biosynthesis," "ribosome," and "d-alanine metabolism" as the top 5 functions. When the ileal microbiomes were compared among the 3 treatments, the relative abundance of Enterococcus was higher in TRT12h calves, suggesting that calves may have a higher abundance of opportunistic pathogens when the feeding of colostrum is delayed for 12 h. Moreover, among all KEGG pathways, the enriched "taurine and hypotaurine metabolism" (KO00430) pathway was identified in the ileal microbiome of TRT12h calves; however, future studies are needed to understand the effect on the host. Additionally, 2 distinct ileal microbial profiles were identified across all samples, indicating that that host factors may play a significant role in driving varied microbiome changes in response to colostrum feeding time. Whether such microbiome shifts affect long-term gut function and calf performance warrants future studies.
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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) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 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) | 0.000 | 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 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".