Cite this strain

Bombella apis (DSM 101884, C6)

Name: Bombella apis (DSM 101884, C6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133026

Type strain

Strain Designation C6

Culture col. no. DSM 101884 C6

NCBI tax ID(s) 1785988 1510841

Special Collections DSMZ

History <- V. Corby-Harris, USDA/ARS, Tuscon, Arizona USA; C6

Bombella apis C6 is a mesophilic prokaryote that was isolated from Apis mellifera larvae.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

Culture Collection Numbers

DSM 101884 C6

@ref 20215

Last LPSN update 2026-02-09 11:31:51

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Acetobacteraceae

Genus Bombella

Species Bombella apis

Full scientific name Bombella apis Yun et al. 2017

Synonyms (1)

"Parasaccharibacter apium"

BacDive ID	Other strains from **Bombella apis** (1)	Type strain
140538	B. apis JCM 31623, KCTC 52452, MRM 1 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.7
125438	negative	99.333

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24814	SABOURAND GLUCOSE MEDIUM (DSMZ Medium 1429)		Medium recipe at MediaDive	Name: SABOURAUD GLUCOSE MEDIUM (DSMZ Medium 1429) Composition: SABOURAUD- Glucose-Bouillon 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24814	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		96.9
125438		93.418

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	acetoin degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	valine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	vitamin B1 metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	purine metabolism	65.96	62 of 94
66794	vitamin B6 metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	flavin biosynthesis	60	9 of 15
66794	methionine metabolism	57.69	15 of 26
66794	glutathione metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	d-xylose degradation	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	glycolysis	52.94	9 of 17
66794	non-pathway related	52.63	20 of 38
66794	alanine metabolism	51.72	15 of 29
66794	lipid metabolism	51.61	16 of 31
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycogen biosynthesis	50	2 of 4
66794	tryptophan metabolism	50	19 of 38
66794	suberin monomers biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	pyrimidine metabolism	48.89	22 of 45
66794	histidine metabolism	48.28	14 of 29
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	oxidative phosphorylation	46.15	42 of 91
66794	cholesterol biosynthesis	45.45	5 of 11
66794	lysine metabolism	42.86	18 of 42
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arginine metabolism	37.5	9 of 24
66794	metabolism of disaccharids	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	pantothenate biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	citric acid cycle	28.57	4 of 14
66794	degradation of pentoses	28.57	8 of 28
66794	carotenoid biosynthesis	27.27	6 of 22
66794	polyamine pathway	26.09	6 of 23
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of hexoses	22.22	4 of 18
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
24814	Apis mellifera larvae	Apis mellifera	Tuscon, Arizona	USA	USA	North America

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM291798v1 assembly for Parasaccharibacter apium C6	contig	GCA_002917985	1510841.10	1510841	72.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24814	Parasaccharibacter apium strain C6 16S ribosomal RNA gene, partial sequence	KM014167	1385		1510841

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parasaccharibacter apium C6
NCBI: GCA_002917985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.90	no
125439	motility	BacteriaNetⓘ	yes	76.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	73.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parasaccharibacter apium C6
NCBI: GCA_002917985.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	no
125438	anaerobic	anaerobicⓘ	no	86.37	no
125438	aerobic	aerobicⓘ	yes	67.71	no
125438	spore-forming	spore-formingⓘ	no	93.42	no
125438	thermophilic	thermophileⓘ	no	90.29	yes
125438	flagellated	motile2+ⓘ	yes	54.26	no

Literature

References

#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 )
#24814	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101884
#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 )
#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 .

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