Pre-imported exchange-flux tables for 56 microbial-community
solutions enumerated by MiSoSoup. Each list element captures a
single alternative optimal community around a focal strain on a
single carbon source, in the flat metabolite /
species / flux long form that
ConsortiumMetabolism() consumes directly.
Format
A named list of 56 data.frames, each with columns:
- species
Character, species identifier. The species flagged as focal appears in the list element name (see naming convention in Details); the remaining species are the support community selected by the MILP solver to keep the focal strain viable.
- metabolite
Character, metabolite identifier following the BiGG namespace (King et al. 2016). Common examples:
ac(acetate),co2(CO2),etoh(ethanol),pyr(pyruvate),ala__L(L-alanine),ala__D(D-alanine). The double-underscore convention encodes stereochemistry (e.g.__L= L-isomer,__D= D-isomer). See https://bigg.ucsd.edu for the full namespace.- flux
Numeric, metabolic flux. Negative values denote consumption (uptake by the species), positive values denote production (secretion).
Details
What MiSoSoup is. MiSoSoup is a Mixed-Integer Linear Programming (MILP) enumerator that, given a community-level metabolic-modelling objective, returns multiple alternative optimal community compositions satisfying that objective. The output ramen consumes is the per-solution exchange-flux table: which species exchange which metabolites, and at what flux, in each viable community.
Focal strain and support community. Each MiSoSoup run is anchored on a focal strain – the species the solver is instructed to keep alive while exploring viable communities around it. The other species in each solution are the support: the MILP picks them so that the focal strain achieves the requested objective. A single focal-strain / substrate combination typically yields many alternative optima with distinct support compositions; these become the separate list elements that share a substrate / strain prefix.
Biological scope. The 56 solutions span three focal
strains (A1R12, A3R04, B3M02) on three
carbon sources: acetate (ac), citrate (cit), and
fructose-6-phosphate (f6p). The growth medium is a
minimal medium with the named substrate as the sole carbon
source (see source paper for the full medium composition).
Naming convention. List element names follow the
pattern {substrate}_{focal-strain}_{solution-id}. For
example, ac_A1R12_1 is alternative optimum 1 for focal
strain A1R12 on acetate. The substrate / strain grouping
can be recovered by splitting the names on underscores.
Caution – alternative optima. Two solutions with the same substrate / strain prefix are alternative optima of the same MILP, not biologically independent communities. Their pairwise FOS overlap is expected to be high by construction; treat such overlaps as solver-consistency diagnostics rather than ecological signal.
Relationship to importMisosoup(). For raw
MiSoSoup YAML output, use importMisosoup(), which
parses the nested format and attaches per-solution biomass and
medium metadata to the resulting CMs. The misosoup24
list is already flattened to the long form that
ConsortiumMetabolism() accepts directly, so
medium composition is implicit rather than stored on each
element.
Metabolite identifiers. BiGG (Biochemically,
Genetically and Genomically structured) knowledge base
identifiers (https://bigg.ucsd.edu; King et al. 2016).
Raw exchange reaction IDs from flux-balance simulators
(e.g. R_EX_ac_e, EX_ac_e) are normalised to bare
metabolite names by importMisosoup() via
normalize_ids = TRUE (default).
References
King ZA et al. (2016) BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1), D515–D522. doi:10.1093/nar/gkv1049
Examples
data("misosoup24")
length(misosoup24)
#> [1] 56
head(names(misosoup24))
#> [1] "ac_A1R12_1" "ac_A1R12_10" "ac_A1R12_11" "ac_A1R12_12" "ac_A1R12_13"
#> [6] "ac_A1R12_14"
head(misosoup24[[1]])
#> # A tibble: 6 × 3
#> metabolite species flux
#> <chr> <chr> <dbl>
#> 1 ac A1R12 0.773
#> 2 ac I2R16 -10.8
#> 3 acald A1R12 -1.12
#> 4 acald I2R16 1.12
#> 5 ala__D A1R12 0.760
#> 6 ala__D I2R16 -0.760