137 Longitudinal Heritability of Ocular Microbiota in Preweaned Beef Cattle
Notice bibliographique
Résumé
Abstract The bovine ocular microbiome is of interest because of its potential role in ocular disease, such as infectious bovine keratoconjunctivitis. The ocular bacterial community of 223 pre-weaned beef calves from a single cohort were sampled four times; day 0, day 21, day 41, and day 139 (mean calf ages 65, 86, 99, and 204 days, respectively). The bacterial community was phenotyped using the V4 region of the 16S rRNA gene and were grouped into amplicon sequence variants (ASV) which were taxonomically classified at the phylum and family level. Heritability was estimated for the log transformed relative abundance of each phylum, family, and ASV at each time point using ASReml v. 4.2. The model included calf age at time of sampling, calf sex, pinkeye vaccination treatment group, breed fractions, and retained heterosis as fixed effects. The random effect of animal had a (co)variance structure given by an H matrix comprised of 3,025 animals of which 1,207 were genotyped including all of the sampled animals. Heritability estimates ranged from 0.16 to 0.95 at the ASV level, 0.18 to 0.91 at the family level, and 0.18 to 0.81 at the phylum level. Standard errors were approximately 0.20 on average. The number of features (ASV, family, or phylum) with estimates greater than their standard error changed across time points (Table 1). Overall, time point 1 had the largest number of features with estimates greater than their standard error, followed by time point 4. Time point 3 had a greater number ASV with estimates greater than their standard error than time point 2; however, time point 2 had greater numbers of families and phyla with estimates greater than their standard errors. This trend likely stems from the fact that time points 1 and 4 had the greatest diversity of features while time point 2 had the least diversity. Average Chao1 index diversity estimates of ASV were 144.6, 28.1, 64.7, and 194.6, for time points 1 through 4, respectively. We hypothesize this is due to the perturbation of the ocular microbiome at sampling and the fact that overall diversity in the microbiome recovered by the final sampling, although, species composition differed compared with time point 1. While no ASV, family, or phylum had a heritability estimate greater than its standard error across all time points, certain features had heritabilities greater than their standard errors at multiple time points. The phylum Armatimonadota had heritability estimates greater than their standard error at time points 1, 2, and 4 (0.52, 0.18, and 0.37, respectively). Additionally, an ASV of the Streptococcus genus had estimates of 0.26, 0.45, and 0.26 at time points 1, 2, and 3, respectively. These estimates demonstrate that certain features of the ocular microbiome are influenced by host genetics.
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Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 0,002 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».