Comparison of Different DNA Sampling and Extraction Protocols for Bacterial and Archaeal Populations Analysis in Water Buffalo
Bibliographic record
Abstract
Methane (CH4) is a potent greenhouse gas, and ruminants are a significant source of agricultural emissions. It has been hypothesized that the host's genome controls rumen microbial communities, but robust results require numerous samples. The feasibility of a research project will depend on the ease and representativeness of the sampling method, as well as the cost-efficiency of large-scale sequencing. This study aimed to compare different protocols to investigate whether non-invasive samples could serve as a substitute for ruminal digesta. DNA recovery was tested in various matrices (whole rumen content, feces, and buccal swabs) from five cannulated buffalo cows. Three types of buccal swabs were tested, as well as feces in different forms (as-is, pelleted, or in a glycerol solution) and the rumen content. The study compared different protocols for DNA extraction, including WUR protocol, Maxwell®, and Quick Extract™, and two sampling times. Saliva was a challenging matrix to process, obtaining unsatisfactory DNA yield. Feces showed higher yields when pelleted but lower than rumen. The highest amount of DNA was obtained from whole rumen content using all three DNA extraction methods. Quick Extract was the easiest method to perform, while WUR resulted in the highest yield of DNA, swabs excluded. The Maxwell® method gave satisfactory results with all three matrices. However, further metagenomic analysis is required to verify if the species composition is comparable.
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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 | 0.003 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".