BioChainDbA Comparative Genomics Resource for Microbial Chain Elongation and Medium Chain Fatty Acids Biosynthesis
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SPECIES · STRAIN AND FUNCTION PROFILE

Clostridium carboxidivorans

Validated caproate producer

Role labels distinguish demonstrated caproate production from community association; validate at strain level before causal interpretation.

1strain profiles
1assemblies
15MCFA marker genes
67%strain metadata coverage

Name, taxonomy and strain identifiers

Curation status: Exact match imported · Genome assembly accession · checked 2026-07-29. Exact strain-level match; curated BacDive fields imported.

Taxonomic record

Scientific name
Clostridium carboxidivorans
Rank
species
NCBI Taxonomy
Not resolved at this level
Database role
Validated caproate producer

P7 Type strain

Full name
Clostridium carboxidivorans Liou et al. 2005
Culture collections
DSM 15243, ATCC BAA-624, KCTC 15178
History
DSMZ <- R. S. Tanner, Department of Botany and Microbiology, University of Oklahoma, Norman, USA; P7 <- R. Laopaiboon; {1999}
BacDive
Strain 2817

Morphology and observable traits

StrainGram stainCell shapeMotilitySpore formationColony morphology
P7positiverod-shapedyesNot curated{"@ref": 43392, "colony size": "2-4 mm", "colony color": "white and opaque", "incubation period": "7-14 days", "medium used": "Acetogen medium"}

Culture and growth conditions

StrainMediumTemperaturepHAtmosphere/result
P7PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)DSMZ Medium 104 · Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water35.00 °C—— · yes
P7Acetogen medium · 35.00 °C—— · yes

Documented condition ranges

ProfilepHTemperatureElectron donorsSubstrates/reactor
BacDive documented cultivation conditions?–?; optimum ?35.00–35.00 °C; optimum ?Not curated—; culture-collection cultivation
Species-level documented cultivation conditions?–?; optimum ?35.00–38.00 °C; optimum ?Not curated—; species-level culture records

Physiology and metabolism

Documented substrates and products

Only approved assertions are shown. Results may be strain- and condition-specific.

RelationshipCompound/source termEvidenceConfidenceCondition
ProductacetateCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
ProductbutanolCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
ProductbutyrateCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
ProductcaproateCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
ProductethanolCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
ProducthexanolCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
SubstrateCOCurator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
SubstrateCO2Curator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded
SubstrateH2Curator assertionExisting mcfaKB curator phenotype summaries0.800Not recorded

Predicted metabolic capabilities

Genome-derived hypotheses requiring review—not demonstrated substrates or products.

CapabilityBasis/statusConfidenceAssembliesLimitation
lactate transport potentialGenomic prediction · Needs review0.450GCA_001038625.1Transporter annotation supports uptake potential but not utilization.

Isolation, environment and safety

StrainIsolation sourceCategory/locationOxygen toleranceBiosafetyGC content
P7Not curated—Not curated1Risk group (German classification)31.000%

Sequence information

Genome assemblies

AccessionSourceLevelSize/GCQualityBioProject
GCA_001038625.1NCBI GenBankComplete Genome5752782 bp / 30.000%99.380% complete; 3.420% contaminationPRJNA285141

Marker and ribosomal sequences

StrainTypeAccessionLengthDescription
P716S rRNAAY170379— bpClostridium carboxidivorans 16S ribosomal RNA gene, partial sequence
P716S rRNAFR7337101499 bpClostridium carboxidivorans partial 16S rRNA gene, type strain DSM15243T
P7GenomeGCA_001038625— bpASM103862v1 assembly for Clostridium carboxidivorans P7
P7GenomeGCA_000175595— bpASM17559v1 assembly for Clostridium carboxidivorans P7
P7GenomeGCA_000163855— bpASM16385v1 assembly for Clostridium carboxidivorans P7

MCFA pathways and genes

Reverse β-oxidation (chain elongation)3 of 5 functions60%60%
Fatty acid biosynthesis (FAS II)2 of 7 functions29%29%
Show 15 annotation-derived MCFA genes
GeneLocusFunctionProteinOrthogroup
crtCcar_014003-hydroxybutyryl-CoA dehydratase (4.2.1.55)AKN29570.1OG0001639
hbdCcar_014053-hydroxybutyryl-CoA dehydrogenase (1.1.1.157)AKN29571.1OG0000229
thlCcar_01410Acetyl-CoA acetyltransferase (2.3.1.9)AKN29572.1OG0000234
crtCcar_014153-hydroxybutyryl-CoA dehydratase (4.2.1.55)AKN29573.1OG0003747
lctPCcar_02265lactate permease [Clostridium carboxidivorans P7]AKN29733.1OG0001228
thlCcar_04220Acetyl-CoA acetyltransferase (2.3.1.9)AKN30073.1OG0000234
lctPCcar_11420lactate permease [Clostridium carboxidivorans P7]AKN31434.1OG0001228
fabZCcar_123453-hydroxyacyl-ACP dehydratase (4.2.1.59)AKN31610.1OG0000119
fabGCcar_173553-oxoacyl-ACP reductase (1.1.1.100)AKN32530.1OG0004652
fabZCcar_183303-hydroxyacyl-ACP dehydratase (4.2.1.59)AKN32700.1OG0001208
fabZCcar_204253-hydroxyacyl-ACP dehydratase (4.2.1.59)AKN33088.1OG0000785
hbdCcar_221003-hydroxybutyryl-CoA dehydrogenase (1.1.1.157)AKN33367.1OG0000229
crtCcar_227803-hydroxybutyryl-CoA dehydratase (4.2.1.55)AKN33499.1OG0001639
hbdCcar_227853-hydroxybutyryl-CoA dehydrogenase (1.1.1.157)AKN33500.1OG0000229
thlCcar_22790Acetyl-CoA acetyltransferase (2.3.1.9)AKN33501.1OG0000234

Curator-approved marker pathway assessments

These summaries use approved candidate predictions only and update after every review decision.

AssemblyPathway ruleApproved markersStatus
No approved-marker pathway assessments.

Profile-HMM marker predictions

Approved candidates and unresolved review calls are genomic hypotheses, not evidence of expression or MCFA production.

MarkerAssembly / proteinConfidence and statusSupportReview history
No active marker predictions for this organism.

Literature and provenance

StudyDOIPublic data
No organism-linked literature indexed yet.

Profile evidence

External databases can change. mcfaKB records source links and separates experimentally reported, curator-entered and predicted information.