Name: Lactobacillus apis R4B
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134046

Type strain:

Species: Lactobacillus apis

Strain Designation: R4B

Culture col. no.: CCM 8403, LMG 26964

NCBI tax ID(s): 303541 (species)

SI-ID 379756

LMG 26964, CCM 8403

Other strains from Lactobacillus apis

L. apis Hma 11 N, Hma11N, DSM 26264
L. apis H1HS25N, DSM 26311

Section

Lactobacillus apis R4B is an anaerobe, Gram-positive, rod-shaped bacterium that was isolated from stomach of honeybees.

Gram-positive
rod-shaped
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Lactobacillus*
	Species	**Lactobacillus apis**
	Full Scientific Name (LPSN)	Lactobacillus apis Killer et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #31131]	Gram stain	positive

[Ref.: #31131]	Cell shape	rod-shaped

[Ref.: #31131]	Motility	no

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31131]

Oxygen tolerance

anaerobe

[Ref.: #31131]

Ability of spore formation

[Ref.: #31131]

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31131]		salicin ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	81.82	18 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	NAD metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	valine metabolism	55.56	5 of 9
[Ref.: #66794]	purine metabolism	55.32	52 of 94
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	threonine metabolism	50	5 of 10
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylalanine metabolism	46.15	6 of 13
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	42.86	12 of 28
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	methionine metabolism	34.62	9 of 26
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	alanine metabolism	31.03	9 of 29
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	citric acid cycle	28.57	4 of 14
[Ref.: #66794]	propanol degradation	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	cysteine metabolism	27.78	5 of 18
[Ref.: #66794]	flavin biosynthesis	26.67	4 of 15
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	histidine metabolism	24.14	7 of 29
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
[Ref.: #66794]	tryptophan metabolism	21.05	8 of 38
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #31131]	Sample type/isolated from	stomach of honeybees
* marker position based on {}

Isolation sources categories

#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF386017 (>99% sequence identity) for Lactobacillus apis subclade from Microbeatlas

Aquatic Samples	68
Soil Samples	42
Animal Samples	6678
Plant Samples	60
Total Samples	6848

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #31131]	Lactobacillus apis strain R4B 16S ribosomal RNA gene, partial sequence	KF386017	1428	GenBank	303541 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lactobacillus apis LMG 26964	GCA_002837055	contig	GenBank	303541 tax ID	*
[Ref.: #66792]	Lactobacillus apis CCM 8403	GCA_014635365	contig	GenBank	303541 tax ID	*
[Ref.: #66792]	Lactobacillus apis strain CCM 8403	303541.15	wgs	PATRIC	303541 tax ID	*
[Ref.: #66792]	Lactobacillus apis strain LMG 26964	303541.6	wgs	PATRIC	303541 tax ID	*
[Ref.: #66792]	Lactobacillus apis LMG 26964	2814123166	draft	JGI IMG/M	303541 tax ID	*

[Ref.: #31131]

GC-content

41.3 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lactobacillus apis strain CCM 8403 PATRIC: 303541.15
[Ref.: #69480]	gram-positive	yes	92.706	yes
[Ref.: #69480]	anaerobic	yes	84.658	no
[Ref.: #69480]	halophile	yes	78.43	no
[Ref.: #69480]	spore-forming	no	97.509	yes
[Ref.: #69480]	glucose-util	yes	90.998	no
[Ref.: #69480]	motile	no	96.132	no
[Ref.: #69480]	flagellated	no	98.828	no
[Ref.: #69480]	aerobic	no	98.248	yes
[Ref.: #69480]	thermophile	no	98.86	no
[Ref.: #69480]	glucose-ferment	yes	88.913	no

Availability in culture collections External links

[Ref.: #31131]

Culture collection no.

CCM 8403, LMG 26964

[Ref.: #91683]

SI-ID 379756

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus bombicola sp. nov., and Weissella bombi sp. nov.	Praet J, Meeus I, Cnockaert M, Houf K, Smagghe G, Vandamme P	Antonie Van Leeuwenhoek	10.1007/s10482-015-0429-z	2015	*
Phylogeny	Lactobacillus apis sp. nov., from the stomach of honeybees (Apis mellifera), having an in vitro inhibitory effect on the causative agents of American and European foulbrood.	Killer J, Dubna S, Sedlacek I, Svec P	Int J Syst Evol Microbiol	10.1099/ijs.0.053033-0	2013	*
Phylogeny	Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread.	Wang C, Huang Y, Li L, Guo J, Wu Z, Deng Y, Dai L, Ma S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002538	2018	*

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 )

#31131

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27460 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#91683

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID379756.1 )

#27460

IJSEM 152 2014 ( DOI 10.1099/ijs.0.053033-0 , PubMed 24096349 )

* These data were automatically processed and therefore are not curated

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Lactobacillus apis strain CCM 8403

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