Apibacter mensalis (DSM 100903, LMG 28357, R-53146)

Name: Apibacter mensalis (DSM 100903, LMG 28357, R-53146)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132969

Type strain

Strain Designation R-53146

Culture col. no. DSM 100903 LMG 28357 R-53146

NCBI tax ID(s) 1586267

Special Collections DSMZ Literature strains

History DSMZ <- P. Vandamme, Lab. Microbiology, Ghent Univ., Belgium; R-53146

Links

Apibacter mensalis R-53146 is an anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from gut of a Bombus lapidarius bumblebee.

Gram-negative rod-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405846

LMG 28357,DSM 100903

@ref 20215

Last LPSN update 2026-05-29 08:37:59

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Weeksellaceae

Genus Apibacter

Species Apibacter mensalis

Full scientific name Apibacter mensalis Praet et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43992	negative	3.0-5.0 µm	1 µm	rod-shaped
125439	negative				98.427
125438	negative				96.425

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43992	1 mm	colourless	circular	2 days	All culture agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43992	All culture agar
43992	Columbia blood agar
24757	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
43992	Basal medium
43992	MacConkey agar

Culture temp

@ref	Growth	Type	Temperature (°C)
24757	positive	growth	37
43992	positive	optimum	37
43992	negative	growth	20
43992	negative	growth	28
43992	negative	growth	45

Culture pH

@ref	Ability	Type	PH
43992	positive	optimum	7
43992		growth	9

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43992	anaerobe
43992	microaerotolerant
125439	facultative anaerobe	93.359

Spore formation

@ref	Spore formation	Confidence
125439		99.327
125438		93.225

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43992	17128 ChEBI	adipate	-	assimilation
43992		casein	-	hydrolysis
43992	17634 ChEBI	D-glucose	-	assimilation
43992	16899 ChEBI	D-mannitol	-	assimilation
43992	16024 ChEBI	D-mannose	-	assimilation
43992	27689 ChEBI	decanoate	-	assimilation
43992	4853 ChEBI	esculin	+	hydrolysis
43992	5291 ChEBI	gelatin	-	hydrolysis
43992	17234 ChEBI	glucose	+	fermentation
43992	30849 ChEBI	L-arabinose	-	assimilation
43992	25115 ChEBI	malate	-	assimilation
43992	17306 ChEBI	maltose	-	assimilation
43992	506227 ChEBI	N-acetylglucosamine	-	assimilation
43992	17632 ChEBI	nitrate	+	reduction
43992	18401 ChEBI	phenylacetate	-	assimilation
43992	32032 ChEBI	potassium gluconate	-	assimilation
43992	53258 ChEBI	sodium citrate	-	assimilation
43992	28017 ChEBI	starch	-	hydrolysis

Enzymes

@ref	Value	Activity	Ec
43992	acid phosphatase	+	3.1.3.2
43992	alkaline phosphatase	+	3.1.3.1
43992	alpha-chymotrypsin	-	3.4.21.1
43992	alpha-fucosidase	-	3.2.1.51
43992	alpha-galactosidase	-	3.2.1.22
43992	alpha-glucosidase	-	3.2.1.20
43992	alpha-mannosidase	-	3.2.1.24
43992	amylase	-
43992	arginine dihydrolase	-	3.5.3.6
43992	beta-galactosidase	-	3.2.1.23
43992	beta-glucosidase	+	3.2.1.21
43992	beta-glucuronidase	-	3.2.1.31
43992	catalase	+	1.11.1.6
43992	cystine arylamidase	+	3.4.11.3
43992	cytochrome oxidase	+	1.9.3.1
43992	DNase	-
43992	esterase (C 4)	+
43992	esterase Lipase (C 8)	+
43992	gelatinase	-
43992	leucine arylamidase	+	3.4.11.1
43992	lipase (C 14)	-
43992	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43992	naphthol-AS-BI-phosphohydrolase	+
43992	trypsin	+	3.4.21.4
43992	tryptophanase	-	4.1.99.1
43992	urease	-	3.5.1.5
43992	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	lipoate biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	vitamin B6 metabolism	72.73	8 of 11
66794	NAD metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	pentose phosphate pathway	63.64	7 of 11
66794	purine metabolism	62.77	59 of 94
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	non-pathway related	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	citric acid cycle	57.14	8 of 14
66794	heme metabolism	57.14	8 of 14
66794	glutamate and glutamine metabolism	57.14	16 of 28
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	oxidative phosphorylation	54.95	50 of 91
66794	proline metabolism	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	lipid metabolism	51.61	16 of 31
66794	pantothenate biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	vitamin B1 metabolism	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	tryptophan metabolism	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	lysine metabolism	40.48	17 of 42
66794	Entner Doudoroff pathway	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	methylglyoxal degradation	40	2 of 5
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	degradation of sugar alcohols	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	polyamine pathway	26.09	6 of 23
66794	biotin biosynthesis	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Fatty acid profile

Metadata FA analysis

@ref

43992

Fatty acid	Percentage
C17:0 iso 3OH	24.25
C15:0 iso	16.92
C16:0	14.7

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Host species
24757	gut of a Bombus lapidarius bumblebee		Ghent	Belgium	BEL	Europe				Bombus lapidarius
43992	gut samples of Bombus lapidarius bumblebees caught in Ghent, Belgium	2013-08	Ghent	Belgium	BEL	Europe	All culture agar	5 days	37

Taxonmaps

69479

Global distribution of 16S sequence LN713847 (>99% sequence identity) for Apibacter mensalis subclade from Microbeatlas

Aquatic Samples	28
Soil Samples	6
Animal Samples	422
Plant Samples	16
Total Samples	472

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24757	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2615840617 annotated assembly for Apibacter mensalis R-53146	scaffold	GCA_900018365	1586267.6	2615840617	1586267	69.34
66792	ASM141868v1 assembly for Apibacter mensalis R-53146	scaffold	GCA_001418685	1586267.5		1586267	68.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24757	Bacteroidetes bacterium LMG 28357 partial 16S rRNA gene, strain LMG 28357	LN713847	1489		1586267

GC content

@ref	GC-content (mol%)	Method
43992	30.4	genome sequence analysis
24757	30.4	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2615840617 annotated assembly for Apibacter mensalis R-53146
NCBI: GCA_900018365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.36	no
125439	gram_stain	BacteriaNetⓘ	negative	98.43	no
125439	motility	BacteriaNetⓘ	no	81.36	no
125439	spore_formation	BacteriaNetⓘ	no	99.33	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Apibacter mensalis R-53146
NCBI: GCA_900018365.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.43	no
125438	anaerobic	anaerobicⓘ	no	81.23	no
125438	aerobic	aerobicⓘ	no	72.74	yes
125438	spore-forming	spore-formingⓘ	no	93.23	no
125438	thermophilic	thermophileⓘ	no	94.85	yes
125438	flagellated	motile2+ⓘ	no	88.60	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Apibacter raozihei sp. nov. isolated from bat feces of Hipposideros and Taphozous spp.	Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Liang H, Zhou P, Shi Z, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003801	2020
Phylogeny	Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota.	Praet J, Aerts M, Brandt E, Meeus I, Smagghe G, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijsem.0.000921	2016

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 )
#24757	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100903
#43992	Jessy Praet, Maarten Aerts, Evie De Brandt, Ivan Meeus, Guy Smagghe, Peter Vandamme: Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota. IJSEM 66: 1645 - 1651 2016 ( DOI 10.1099/ijsem.0.000921 , PubMed 26813786 )
#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 )

Content

About us

Apibacter mensalis (DSM 100903, LMG 28357, R-53146)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900018365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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