Lactobacillus apis (CCM 8403, LMG 26964, R4B)

Name: Lactobacillus apis (CCM 8403, LMG 26964, R4B)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134046

Type strain

Strain Designation R4B

Culture col. no. CCM 8403 LMG 26964 R4B

NCBI tax ID(s) 303541

Special Collections Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 379756

LMG 26964,CCM 8403

@ref 20215

Last LPSN update 2025-12-16 10:01:57

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Lactobacillus

Species Lactobacillus apis

Full scientific name Lactobacillus apis Killer et al. 2014

BacDive ID	Other strains from **Lactobacillus apis** (2)	Type strain
130366	L. apis Hma 11 N, Hma11N, DSM 26264
130367	L. apis H1HS25N, DSM 26311

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31131	positive	rod-shaped
125438			93.5
125438	positive		94.618

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31131	anaerobe
125439	obligate aerobe	98.9

Spore formation

@ref	Spore formation	Confidence
31131
125438		91.391

Observation

31131

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31131	17814 ChEBI	salicin	+	carbon source

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	#Stomach

Isolation

31131

Sample typestomach of honeybees

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1463536v1 assembly for Lactobacillus apis CCM 8403	contig	GCA_014635365	303541.15	8112505403	303541	72.62
66792	ASM283705v1 assembly for Lactobacillus apis LMG 26964	contig	GCA_002837055	303541.6	2814123166	303541	55.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31131	Lactobacillus apis strain R4B 16S ribosomal RNA gene, partial sequence	KF386017	1428		303541
124043	Lactobacillus apis strain CCM 8403 16S ribosomal RNA gene, partial sequence.	MT760199	1401		303541

GC content

31131

GC-content (mol%)41.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lactobacillus apis LMG 26964
NCBI: GCA_002837055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	62.60	no
125439	motility	BacteriaNetⓘ	yes	68.60	no
125439	gram_stain	BacteriaNetⓘ	positive	74.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus apis strain CCM 8403
PATRIC: 303541.15

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.62	yes
125438	anaerobic	anaerobicⓘ	no	50.94	no
125438	spore-forming	spore-formingⓘ	no	91.39	yes
125438	aerobic	aerobicⓘ	no	95.40	no
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	no	93.50	yes

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 )
#27460	IJSEM 152 2014 ( DOI 10.1099/ijs.0.053033-0 , PubMed 24096349 )
#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
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Lactobacillus apis (CCM 8403, LMG 26964, R4B)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014635365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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