METABARFOOD project
December 4, 2023
LOW COST: <35$ per sample
FROGS | Qiime2 | DADA2 | USEARCH | |
---|---|---|---|---|
Short | ✅ | ✅ | ✅ | ✅ |
FROGS | Qiime2 | DADA2 | USEARCH | |
---|---|---|---|---|
Long | ✅ | ❎ R1 only | ❎ R1 only | ❎ R1 only |
FROGS | Qiime2 | DADA2 | USEARCH | |
---|---|---|---|---|
Mixed | ✅ | ❎ R1 or only short | ❎ R1 or only short | ❎ R1 and only short |
FROGS | Qiime2 | DADA2 | USEARCH | |
---|---|---|---|---|
Method | Swarm clusters (ASV) | Clustering 97% (OTU) | Denoising (ASV) | Denoising (zOTU) |
Short fragments | ✅ | ✅ | ✅ | ✅ |
Long fragments | ✅ | ❎ R1 only | ❎ R1 only | ❎ R1 only |
Mixed fragments | ✅ | ❎ R1 or only short | ❎ R1 or only short | ❎ R1 and only short |
How to reconcile the advantages of each side?
Note
Interesting challenge in the management of the samples and results
Bread | Cheese | Meat | Wine | |
---|---|---|---|---|
Species | 27 | 25 | 40 | 60 |
Genus | 15 | 16 | 14 | 37 |
Family | 4 | 11 | 8 | 8 |
Conclusion 1
DADA2_FROGS is the best approach on mock communities
Conclusion 2
RPB2 not suitable based on mock communities
Bread | Cheese | Meat | Wine | |
---|---|---|---|---|
Best marker | ITS1 | ITS2 | ITS2 | ITS2 |
Conclusion 3
ITS markers performed better than D1/D2, as they are better represented in public databases and have better specificity to distinguish species
Conclusion 4
No generic recommendation for all fermented food types can be made
Séminaire interne MaIAGE