AllerGen’s 8th research conference
Bibliographic record
Abstract
Background: Asthma is the most prevalent chronic disease among children and affects 235 million people worldwide [1].Although the incidence of asthma in South America is among the highest worldwide, underlying causes and disease phenotypes are poorly defined and may differ to developed countries.Recent evidence in mice [2] and human [3] has identified a 'critical window' early in life where the effects of gut microbial changes (dysbiosis) are most influential in immune development and experimental asthma.Given the differences in gut microbiota between North and South American populations, we aimed to validate our previous work in a microbially-different human population.Methods: We compared the gut microbiota of 97 infants from the coastal community Las Esmeraldas, Ecuador at 3 months of age by 16S sequencing (V4 region) Illumina MiSeq.Subjects were grouped into atopic-wheezers (n = 27) and controls (n = 70) based on a skin prick test and wheezing history at 1 year of age.An exact logistic regression model was developed to evaluate the risk associated with the AW group according to specific clinical and epidemiological metadata.Metagenomes were predicted from 16S rRNA OTU data using PIC-RUSt, and categorized by function using KEGG Orthology.The concentration of fecal short chain fatty acids (SCFA) was determined by gas chromatography.Results: Atopy and wheezing at 1 year of age was significantly associated with asthma diagnosis at 5 years (OR 17.8), birth by C-section (OR 3.1), potable water at home (OR 2.7) and in utero exposure to antibiotics (OR 2.9).This phenotype was also significantly associated with eosinophil concentration at 2 and 5 years (p < 0.05), number of episodes of respiratory infections (p < 0.01), maternal load with Trichuris trichiura during pregnancy (p < 0.05), and inversely associated with the number of diarrheal episodes by 1 year of age (p < 0.05).Similar to what we had previously found in Canadian babies, atopic-wheezing Ecuadorian babies also exhibit gut microbial dysbiosis at 3 months of age.However, the microbial alterations were different and more pronounced in Ecuadorian babies.Predicted metagenomic analysis showed significant differences in genes involved in carbohydrate and taurine metabolism.Fecal acetate was significantly reduced in atopic wheezers.Ongoing experiments will determine if differences in eukaryome are also associated with asthma risk in this population. Conclusions:This study further supports the importance of the microbiota during the first 100 days of life, although the characteristics of the microbial dysbiosis and epidemiological associations depend on geographical location.Reduced fecal acetate as a common feature in both populations suggests that different microbial alterations may have similar metabolic outcomes.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.006 | 0.002 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.391 | 0.240 |
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".