Changes in the Composition and Function of the Human Salivary Microbiome After Heart Transplantation: A Pilot Study
Bibliographic record
Abstract
Heidi Joyce,1 Michael R Taylor,1 Andrew Moffat,1 Mia Hong,1 Debra Isaac,2 Nowell Fine,2 Steven C Greenway1– 3 1Department of Pediatrics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; 2Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; 3Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, CanadaCorrespondence: Steven C GreenwaySection of Cardiology, Alberta Children’s Hospital, 28 Oki Drive NW, Calgary, AB, T3B 6A8, CanadaTel +1-403-955-5049Fax +1-403-955-7621Email scgreenw@ucalgary.caIntroduction: Interactions between our commensal microbes and immune system are well recognized but the impact of immunosuppression on this relationship is less well characterized, particularly outside of the gastrointestinal tract. In this pilot case-control study, we examined microbial composition and inferred function in the saliva of patients after heart transplantation.Methods: Saliva samples were collected from 26 healthy adolescent and adult heart transplant patients and 27 healthy non-transplant controls. Bacterial DNA was isolated and the V3 and V4 regions of the 16S rRNA gene were sequenced. Measures of bacterial diversity and inferred function were calculated using the software packages DADA2, Phyloseq, QIIME, PICRUSt and STAMP.Results: Transplant patients were on average 51.6 ± 18.2 years of age and 8.6 ± 5.3 years post-transplant. Both alpha (p = 0.0009) and beta (p = 0.001) diversity differed significantly between the groups, and there were statistically significant changes (p < 0.01) in 101 individual functional pathways.Discussion: We conclude that the effects of chronic immunosuppression on bacterial composition and function in the oropharynx appear relatively subtle with no obvious ill effects on patient health. Full interpretation is limited by our lack of knowledge for many of the bacterial functional pathways.Keywords: microbiome, saliva, transplant, heart, immune suppression
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".