Aeromicrobium choanae (9H-4, ZIM B1021, LMG 29165)

Name: Aeromicrobium choanae (9H-4, ZIM B1021, LMG 29165)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133328

Type strain

Strain Designation 9H-4

Culture col. no. 9H-4 ZIM B1021 LMG 29165 CCM 8650 JCM 32379

NCBI tax ID(s) 1736691

Special Collections JCM Literature strains

History CCM 8650 <-- J. Tr?ek; Univ. of Maribor, Slovenia; 9H-4.

Links

Aeromicrobium choanae 9H-4 is an obligate aerobe, Gram-positive, coccus-shaped prokaryote that forms circular colonies and was isolated from choana of a garden warbler .

Gram-positive coccus-shaped colony-forming obligate aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 272207

LMG 29165

@ref 20215

Last LPSN update 2025-12-16 10:01:45

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Aeromicrobium

Species Aeromicrobium choanae

Full scientific name Aeromicrobium choanae Ber et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
25167	positive	1.5 µm	coccus-shaped
125439	positive			94.7
125438				95.5
125438	positive			92.773

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25167	1.8-2.0 mm	dark yellow	circular	4 days	LB agar media

Culture and growth conditions

Culture medium

@ref	Name	Growth
25167	LB agar media

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
25167	positive	growth	8.0-39.0
25167	positive	optimum	29.0-31.0	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
25167	positive	optimum	7
25167	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25167	obligate aerobe
125439	obligate aerobe	98.7

Spore formation

25167

Spore formationno

Halophily

@ref	Salt	Tested relation	Concentration
25167	NaCl	maximum	5 %(w/v)

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25167		casein	+	hydrolysis
25167	16947 ChEBI	citrate	+	carbon source
25167	15824 ChEBI	D-fructose	+	carbon source
25167	17634 ChEBI	D-glucose	+	carbon source
25167	16024 ChEBI	D-mannose	+	carbon source
25167	17754 ChEBI	glycerol	+	carbon source
25167	17306 ChEBI	maltose	+	carbon source
25167	29864 ChEBI	mannitol	+	carbon source
25167	17632 ChEBI	nitrate	+	reduction
25167	17992 ChEBI	sucrose	+	carbon source
25167	27897 ChEBI	tryptophan	-	energy source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25167	16136 ChEBI	hydrogen sulfide
25167	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25167	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25167	acid phosphatase	+	3.1.3.2
25167	alkaline phosphatase	+	3.1.3.1
25167	alpha-chymotrypsin	-	3.4.21.1
25167	alpha-fucosidase	-	3.2.1.51
25167	alpha-galactosidase	-	3.2.1.22
25167	alpha-glucosidase	+	3.2.1.20
25167	alpha-mannosidase	-	3.2.1.24
25167	arginine dihydrolase	-	3.5.3.6
25167	beta-galactosidase	+	3.2.1.23
25167	beta-glucosidase	+	3.2.1.21
25167	beta-glucuronidase	-	3.2.1.31
25167	catalase	+	1.11.1.6
25167	cystine arylamidase	-	3.4.11.3
25167	cytochrome oxidase	-	1.9.3.1
25167	esterase (C 4)	+
25167	esterase Lipase (C 8)	+
25167	leucine arylamidase	+	3.4.11.1
25167	lipase (C 14)	+
25167	lysine decarboxylase	-	4.1.1.18
25167	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25167	naphthol-AS-BI-phosphohydrolase	+
25167	trypsin	+	3.4.21.4
25167	tryptophan deaminase	-	4.1.99.1
25167	urease	-	3.5.1.5
25167	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	enterobactin biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	phenylalanine metabolism	92.31	12 of 13
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pentose phosphate pathway	81.82	9 of 11
66794	lipoate biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	leucine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	vitamin E metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	purine metabolism	71.28	67 of 94
66794	glycolysis	70.59	12 of 17
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	non-pathway related	65.79	25 of 38
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	isoleucine metabolism	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	oxidative phosphorylation	61.54	56 of 91
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	tryptophan metabolism	60.53	23 of 38
66794	Entner Doudoroff pathway	60	6 of 10
66794	glutathione metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	urea cycle	53.85	7 of 13
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	histidine metabolism	48.28	14 of 29
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	cholesterol biosynthesis	45.45	5 of 11
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	aspartate and asparagine metabolism	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	tyrosine metabolism	42.86	6 of 14
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	starch degradation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22
66794	lipid A biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	-
#Host Body-Site	#Oral cavity and airways	#Airways

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature	Host species
25167	choana of a garden warbler (Sylvia borin)	bird was caught at the municipality of Pragersko in Slovenska Bistrica (Slovenia) in the frame of a bird ringing scheme coordinated by EURING (www.euring.org/)	Slovenia	SVN	Europe	nutrient agar (NA; Sigma-Aldrich)	30
67770	Choana of a garden warbler (Sylvia borin) caught at the municipality of Pragersko	Slovenska Bistrica	Slovenia	SVN	Europe			Sylvia borin

Taxonmaps

69479

Global distribution of 16S sequence LN887956 (>99% sequence identity) for Aeromicrobium from Microbeatlas

Aquatic Samples	1247
Soil Samples	1179
Animal Samples	1447
Plant Samples	147
Total Samples	4020

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2708742384 annotated assembly for Aeromicrobium choanae 9H-4	chromosome	GCA_900167475	2708742384	1736691	87.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25167	Aeromicrobium sp. 9H-4 partial 16S rRNA gene, strain 9H-4	LN887956	1488		1736691

GC content

@ref	GC-content (mol%)	Method
25167	70.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aeromicrobium choanae 9H-4
IMG: 2708742384

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.30	no
125439	motility	BacteriaNetⓘ	yes	50.40	no
125439	gram_stain	BacteriaNetⓘ	positive	94.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aeromicrobium choanae 9H-4
NCBI: GCA_900167475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.77	no
125438	anaerobic	anaerobicⓘ	no	96.98	no
125438	aerobic	aerobicⓘ	yes	87.11	yes
125438	spore-forming	spore-formingⓘ	no	67.90	yes
125438	thermophilic	thermophileⓘ	no	98.08	yes
125438	flagellated	motile2+ⓘ	no	95.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Taxonomic descriptions of Aeromicrobium duanguangcaii sp. nov., Aeromicrobium wangtongii sp. nov. and Aeromicrobium senzhongii sp. nov.	Ye L, Zhang G, Yang J, Yang C, Liu Y, Pu J, Huang Y, Zhang S, Jin D, Lu S, Liu L, Xu J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006118	2023
Genetics	Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant.	Lopez Marin MA, Suman J, Jani K, Ulbrich P, Cajthaml T, Filipova A, Pajer P, Neumann-Schaal M, Strejcek M, Uhlik O.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005678	2023
Phylogeny	Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler.	Ber P, Trappen SV, Vandamme P, Trcek J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001632	2017

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 )
#25167	P. T. Ber, S. V.,Vandamme, P.,Trcek, J.: Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler. IJSEM 67: 357 - 361 2017 ( DOI 10.1099/ijsem.0.001632 , PubMed 27902232 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Aeromicrobium choanae (9H-4, ZIM B1021, LMG 29165)

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

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900167475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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