Table 2 Overview of experimental data
From: Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
Reference | Data sets | NB species | Medium | Culture condition | For monoculture growth rate | For coculture | |||
|---|---|---|---|---|---|---|---|---|---|
Monoculture | Coculture | Ratio | |||||||
Venturelli et al. [2] | Human 1 | 12 | ABB | Serial dilution | Provided through Lotka Volterra model parameterization | Calculated from OD (visually  extracted) | OD (visually extracted) | OD multiplied with relative abundances from 16S rRNA gene sequencing  | Calculated from monoculture OD and coculture OD-multiplied 16S data |
Interaction coefficient and sign from generalised Lotka Volterra model | |||||||||
Wang et al. [34] | Human 2 | 2 | YCAG | Batch | log 16S rRNA gene copy number per ml culture | Calculated from OD | ddPCR (log 16S rRNA gene copy number per ml, visually extracted) | ddPCR (log 16S rRNA gene copy number per ml, visually extracted) | Calculated from mono and coculture 16S gene copy number |
Das et al. [32] | Human 3 | 2 | YCGMS | Batch | Calculated from qPCR (log 16S rRNA gene copy number per ml culture, visually extracted) | log 16S rRNA gene copy number per ml (visually extracted) | log 16S rRNA gene copy number per ml (visually extracted) | Calculated from mono and coculture 16S gene copy number | |
Cheng et al. [30] | Human 4 | 2 | YCFA | Batch | Calculated from OD (visually extracted) | OD (visually extracted) | OD | No ratio possible | |
D'hoe et al. [31] | Human5-6 | 2_2 | mMCB | Batch | Calculated from qPCR (TaqMan)  | qPCR (TaqMan) | qPCR (TaqMan) | Caclulated from mono and coculture TaqMan qPCR data | |
Das et al. [32] | Human 7 | 2 | YCGD | Batch | Calculated from qPCR (log 16S rRNA gene copy number per ml culture, visually extracted) | log 16S rRNA gene copy number per ml (visually extracted) | log 16S rRNA gene copy number per ml (visually  extracted) | Calculated from mono and coculture 16S gene copy number | |
Weiss et al. [33] | Mouse1 | 8  | AF | Batch | Provided (OD) | qPCR (16S) | qPCR (16S) | Calculated from mono and coculture 16S gene copy number | |