Name: Microbacterium humi CC-012309
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7450

Type strain:

Species: Microbacterium humi

Strain Designation: CC-012309, CC-12309

Culture col. no.: CCUG 58052, DSM 21799, CCM 7687, JCM 18706

Strain history: CCM 7687 <-- P. Kämpfer CC-12309.

NCBI tax ID(s): 640635 (species)

SI-ID 402227

DSM 21799

Section

Microbacterium humi CC-012309 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from basidiomycete fungus Agaricus blazei Murill.

Gram-positive
rod-shaped
aerobe
mesophilic
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium humi**
	Full Scientific Name (LPSN)	Microbacterium humi Young et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29488]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29488]	Cell length	2.5 µm

[Ref.: #29488]	Cell width	1.1 µm

[Ref.: #29488]	Cell shape	rod-shaped

[Ref.: #61573]

Incubation period

1-2 days

[Ref.: #29488]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15962]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #15962]

Culture medium growth

[Ref.: #15962]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15962]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15962]	growth	28 °C
[Ref.: #29488]	growth	25-30 °C
[Ref.: #61573]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #15962]	Temperature range	mesophilic
[Ref.: #29488]	Temperature range	mesophilic
[Ref.: #61573]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29488]	Oxygen tolerance	aerobe
[Ref.: #61573]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.984

[Ref.: #15962]	Murein short key	B12
[Ref.: #15962]	Murein types	B2alpha {Gly} [L-Orn] D-Glu-Gly-D-Orn

[Ref.: #67770]

Observation

quinones: MK-11, MK-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29488]	arabinose ChEBI	+	carbon source
[Ref.: #29488]	aspartate ChEBI	+	carbon source
[Ref.: #29488]	esculin ChEBI	+	hydrolysis
[Ref.: #29488]	galactose ChEBI	+	carbon source
[Ref.: #29488]	malate ChEBI	+	carbon source
[Ref.: #29488]	melibiose ChEBI	+	carbon source
[Ref.: #29488]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29488]	pyruvate ChEBI	+	carbon source
[Ref.: #29488]	rhamnose ChEBI	+	carbon source
[Ref.: #29488]	ribose ChEBI	+	carbon source
[Ref.: #29488]	sorbitol ChEBI	+	carbon source
[Ref.: #29488]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29488]		catalase	+	1.11.1.6
[Ref.: #29488]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #15962]	Sample type/isolated from	basidiomycete fungus Agaricus blazei Murill
[Ref.: #15962]	Host species	Agaricus blazei
[Ref.: #15962]	Country	Taiwan
[Ref.: #15962]	Country ISO 3 Code	TWN
[Ref.: #15962]	Continent	Asia

[Ref.: #61573]	Sample type/isolated from	Stalk of the mushroom Agaricus brasiliensi
[Ref.: #61573]	Country	Taiwan
[Ref.: #61573]	Country ISO 3 Code	TWN
[Ref.: #61573]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Stalk of the edible mushroom Agaricus blazei grown in the laboratory
[Ref.: #67770]	Host species	Agaricus blazei
* marker position based on {}

Isolation sources categories

#Host	#Fungi	-
#Host Body-Site	#Plant	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ865215 (>99% sequence identity) for Microbacterium humi subclade from Microbeatlas

Aquatic Samples	18
Soil Samples	63
Animal Samples	24
Plant Samples	6
Total Samples	111

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15962]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15962]	Microbacterium humi strain CC-012309 16S ribosomal RNA gene, partial sequence	FJ865215	1430	ENA	640635 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Microbacterium humi DSM 21799	GCA_900105715	contig	GenBank	640635 tax ID
[Ref.: #66792]	Microbacterium humi strain DSM 21799	640635.3	wgs	PATRIC	640635 tax ID	*
[Ref.: #66792]	Microbacterium humi DSM 21799	2630968996	draft	JGI IMG/M	640635 tax ID	*

[Ref.: #67770]

GC-content

67.3 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microbacterium humi strain DSM 21799 PATRIC: 640635.3
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microbacterium humi strain DSM 21799 PATRIC: 640635.3
[Ref.: #69480]	gram-positive	yes	90.934	yes
[Ref.: #69480]	anaerobic	no	99.282	yes
[Ref.: #69480]	halophile	no	80.798	no
[Ref.: #69480]	spore-forming	no	91.123	no
[Ref.: #69480]	glucose-util	yes	82.704	no
[Ref.: #69480]	thermophile	no	97.657	no
[Ref.: #69480]	flagellated	no	94.475	no
[Ref.: #69480]	aerobic	yes	89.737	yes
[Ref.: #69480]	motile	yes	61.333	no
[Ref.: #69480]	glucose-ferment	no	88.833	no

Availability in culture collections External links

[Ref.: #15962]

Culture collection no.

CCUG 58052, DSM 21799, CCM 7687, JCM 18706

[Ref.: #76898]

SI-ID 402227

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species.	Zhou J, Huang Y, Yang J, Lai XH, Jin D, Lu S, Pu J, Zhang S, Zhu W, Xu M, Huang Y, Liang J, Zheng H, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004858	2021	*
Phylogeny	Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei.	Young CC, Busse HJ, Langer S, Chu JN, Schumann P, Arun AB, Shen FT, Rekha PD, Kampfer P	Int J Syst Evol Microbiol	10.1099/ijs.0.014092-0	2009	*

References

#15962

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21799

#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 )

#29488

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 #25888 (see below)

#61573 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58052

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76898

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-ID402227.1 )

#25888

IJSEM 854 2010 ( DOI 10.1099/ijs.0.014092-0 , PubMed 19661494 )

* These data were automatically processed and therefore are not curated

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Microbacterium humi strain DSM 21799

Microbacterium humi strain DSM 21799

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