Formivibrio citricus (DSM 6150, ATCC 49791, CreCit1)

Name: Formivibrio citricus (DSM 6150, ATCC 49791, CreCit1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10459

Type strain

Strain Designation CreCit1

Culture col. no. DSM 6150 ATCC 49791 CreCit1

NCBI tax ID(s) 1121905 83765

Special Collections DSMZ

Links

Formivibrio citricus CreCit1 is an anaerobe, mesophilic prokaryote that was isolated from anoxic fresh water mud.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42689

ATCC 49791,DSM 6150

@ref 20215

Last LPSN update 2025-12-16 09:49:20

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Neisseriales

Family Chromobacteriaceae

Genus Formivibrio

Species Formivibrio citricus

Full scientific name Formivibrio citricus Tanaka et al. 1991

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494
125439	negative	98.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2505	FORMIVIBRIO MEDIUM (DSMZ Medium 505)		Medium recipe at MediaDive	Name: FORMIVIBRIO MEDIUM (DSMZ Medium 505) Composition: Trisodium citrate x 2 H2O 2.99103 g/l Na2CO3 1.49551 g/l KH2PO4 1.39581 g/l NH4Cl 0.498505 g/l Na2S x 9 H2O 0.299103 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2505	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

2505

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ubiquinone biosynthesis	100	7 of 7
66794	aspartate and asparagine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	butanoate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	acetate fermentation	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	serine metabolism	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	hydrogen production	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	citric acid cycle	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	lipid metabolism	54.84	17 of 31
66794	leucine metabolism	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	selenocysteine biosynthesis	50	3 of 6
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	starch degradation	50	5 of 10
66794	oxidative phosphorylation	49.45	45 of 91
66794	histidine metabolism	48.28	14 of 29
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	pentose phosphate pathway	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	glutathione metabolism	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	ketogluconate metabolism	37.5	3 of 8
66794	polyamine pathway	34.78	8 of 23
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	degradation of pentoses	28.57	8 of 28
66794	arachidonic acid metabolism	27.78	5 of 18
66794	degradation of hexoses	27.78	5 of 18
66794	carotenoid biosynthesis	27.27	6 of 22
66794	cholesterol biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	degradation of sugar alcohols	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2505	anoxic fresh water mud	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence Y17602 (>99% sequence identity) for Formivibrio citricus subclade from Microbeatlas

Aquatic Samples	4307
Soil Samples	1024
Animal Samples	200
Plant Samples	162
Total Samples	5693

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2505	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2599185172 annotated assembly for Formivibrio citricus DSM 6150	contig	GCA_900115065	83765.7	2599185172	83765	67.11
66792	Formivibrio citricus strain DSM 6150	contig		83765.3		83765	56.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2505	Formivibrio citricus 16S rRNA gene, partial	Y17602	1490		83765

GC content

2505

GC-content (mol%)59.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Formivibrio citricus DSM 6150
NCBI: GCA_900115065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	87.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	79.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Formivibrio citricus strain DSM 6150
PATRIC: 83765.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	61.85	no
125438	aerobic	aerobicⓘ	no	78.55	yes
125438	spore-forming	spore-formingⓘ	no	89.75	no
125438	thermophilic	thermophileⓘ	no	96.40	yes
125438	flagellated	motile2+ⓘ	yes	73.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.	Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf H	Int J Syst Evol Microbiol	10.1099/ijs.0.64771-0	2007
Phylogeny	Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the 'Betaproteobacteria'.	Yang HC, Im WT, An DS, Park WS, Kim IS, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63837-0	2005
Phylogeny	Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan.	Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK, Fu HM	Int J Syst Evol Microbiol	10.1099/ijs.0.02834-0	2004

References

#2505	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6150
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Formivibrio citricus (DSM 6150, ATCC 49791, CreCit1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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