380 The Sow Milk Microbiome and Resistome
Bibliographic record
Abstract
Abstract In addition to oligosaccharides, proteins (e.g., immunoglobulins), lipids, vitamins, and other nutrients vital for piglet health, sow’s milk contains bacteria believed to be important in gut health. Therefore, certain sow milk isolates with potentially beneficial properties may be of interest for use as probiotic strains. Furthermore, given the relatively large reservoir of antimicrobial-resistant bacteria carried by commercial pigs even in the absence of direct antimicrobial exposure, it is possible that sow’s milk may also transfer antimicrobial-resistant bacteria to their piglets. The objective of this study was to characterize the bacterial microbiome of sow’s milk using both culturing and shotgun metagenomics. To do this, colostrum (within 24 h of farrowing) and milk samples (n = 42) were collected from 14 sows at d 0, 7, and 21 during the suckling phase. We recovered 323 isolates on four different culture media, and 135 of these were chosen for whole-genome sequencing based on their 16S rRNA gene sequence identity to maximize isolate diversity. The majority (n = 90) of the sequenced isolates belonged to either the Staphylococcus or Streptococcus genera. Twelve isolates (Lactiplantibacillus plantarum, Lactobacillus amylovorus, Ligilactobacillus salivarius, Limosilactobacillus reuteri, and Weissella paramesenteroides) were members of lactic acid-producing bacterial species noted for their beneficial properties in mammals. Several potentially pathogenic bacterial species were also isolated including Clostridium perfringens, Escherichia coli, Klebsiella pneumonia, Streptococcus dysgalactiae, Staphylococcus hyicus, and Streptococcus suis. In addition, seven isolates could not be assigned to a specific species (< 95% average nucleotide identity) and thus may represent potentially novel bacterial species. We also mapped the shotgun metagenomic reads back to the sequenced isolate genomes and found Rothia spp. and L. amylovorus to be relatively most abundant ( > 0.25%). Nearly all of the isolates (n = 130) carried at least one antimicrobial resistance gene and many strains, including S. suis and S. dysgalactiae isolates, encoded genes conferring resistance to more than three antimicrobial classes. The tetracycline resistance genes tet(W), tet(Q), tet(W/N/W), tet(K), and tet(O) were the relatively most abundant antimicrobial resistance genes in the colostrum and milk metagenomes. These results show that sow’s milk may be a source of both beneficial and potentially pathogenic bacteria as well as a significant source of antimicrobial-resistant bacteria.
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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 | 0.001 |
| 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) | 0.004 | 0.001 |
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".