Additional file 5 of Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Notice bibliographique
Résumé
Supplementary Material 5. Supplementary Figure 5. Influence of species-specific metabolic potential and key taxa presence on cross-feeding activity. A-B. Correlation plots showing the relationship between the average number of unique EC numbers presented in a specie within a sample and (A) the total number of interactions formed by a specie normalized by the number of samples where a specie is present (Pearson) (B) the number of samples where the specie is present (Pearson). Red line is fitted linear regression, and gray area indicates the 95% confidence interval. Each data point represents a species. Only species with at least 10 cross-feeding pairs involving at least 12 metabolites are shown. Selected species (present in at least two samples, above the threshold of 230 total interactions per sample and average number of unique EC per sample > 5) have labels that are color-coded corresponding to the taxonomic family they belong to. C. Effect of E. coli presence across both community categories (HB - High Bacteroides; NB - no Bacteroides) on cross-feeding activity, measured by the cross-feeding coefficient (CFC). Each dot corresponds to a CFC calculated for a single sample. Points and lines are color-coded based on E. coli abundance: red represents communities with high E. coli abundance (>5%), blue represents communities with low E. coli abundance (<5%), and gray represents communities where E. coli is absent. In the NB group, higher E. coli abundance is associated with a notable increase in cross-feeding activity compared to low or absent E. coli, suggesting a significant role for E. coli in enhancing cross-feeding, particularly in the absence of Bacteroides. Conversely, in HB communities, E. coli presence appears to have a more muted effect on cross-feeding, especially in low abundance. D-E. Interaction effects of E. coli and A. butyraticus (D)or L. crispatus (E)on cross-feeding activity, measured by the CFC, across categories. Different colors represent distinct interaction scenarios: E. coli & A. butyraticus (D)/L. crispatus (E) absent (gray), E. coli absent & A. butyraticus (D)/L. crispatus (E) present (cyan), low-abundance E. coli & A. butyraticus (D)/L. crispatus (E) absent (blue), low-abundance E. coli & A. butyraticus (D)/L. crispatus (E) present (orange), high-abundance E. coli & A. butyraticus (D)/L. crispatus (E) absent (red), and high-abundance E. coli & A. butyraticus (D)/L. crispatus (E) present (purple). Each point represents an average CFC for samples within each interaction scenario. NB communities with high E. coli abundance and without A. butyraticus (solid red line, D) show the highest cross-feeding activity. When A. butyraticus is present (dotted lines, D), the interaction patterns change: the cross-feeding coefficient decreases slightly in communities with high E. coli, but it increases in communities with low or no E. coli. This suggests that A. butyraticus may partly compensate for the absence or lower abundance of E. coli, contributing to cross-feeding, particularly in NB communities. The interaction between A. butyraticus and E. coli seems to reveal a potentially competitive relationship where the presence of both may reduce cross-feeding, while the presence of either one alone promotes cross-feeding in different ways. Presence of L. crispatus is associated with increased cross-feeding activity in NB compared to HB communities (E), regardless of E. coli abundance, while absence of L. crispatus doesn’t increase significantly the cross-feeding activity in NB when E. coli levels are low. This points to an impact of antagonistic relationship between L. crispatus and Bacteroides rather than potential competitive relationship between L. crispatus and E. coli.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
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 | 0,010 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,001 |
| Méta-épidémiologie (sens large) | 0,002 | 0,001 |
| Bibliométrie | 0,001 | 0,002 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,003 | 0,002 |
| Science ouverte | 0,003 | 0,001 |
| Intégrité de la recherche | 0,002 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,812 | 0,184 |
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 ».