Humibacter albus SC-083 | Type strain | DSM 18994, CCUG 54538, LMG 23996, JCM 16029, KACC 20986, NBRC 106151 | BacDiveID:7498

Strain identifier

BacDive ID: 7498

Type strain:

Species: Humibacter albus

Strain Designation: SC-083

Culture col. no.: DSM 18994, CCUG 54538, LMG 23996, JCM 16029, KACC 20986, NBRC 106151

Strain history: LMG 23996 <-- C. M. Manaia SC-083 <-- I. Vaz-Moreira et al..

NCBI tax ID(s): 1121952 (strain), 427754 (species)

SI-ID 294507

LMG 23996, CCUG 54538, DSM 18994, JCM 16029

Special Collections

Section

Humibacter albus SC-083 is an aerobe, Gram-positive, motile bacterium that was isolated from sewage sludge compost.

Gram-positive
motile
rod-shaped
aerobe
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	*Humibacter*
	Species	**Humibacter albus**
	Full Scientific Name (LPSN)	Humibacter albus Vaz-Moreira et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32289]	Gram stain	positive

[Ref.: #32289]	Cell length	1.3 µm

[Ref.: #32289]	Cell width	0.59 µm

[Ref.: #32289]	Cell shape	rod-shaped

[Ref.: #32289]	Motility	yes
[Ref.: #69480]	Motility	no Confidence in %95.5

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7819]			growth	28 °C
[Ref.: #19775]			optimum	28 °C
[Ref.: #32289]			growth	22-36 °C
[Ref.: #32289]			optimum	30 °C
[Ref.: #67770]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32289]			optimum	7
[Ref.: #32289]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32289]		NaCl		growth	<3	%
[Ref.: #32289]		NaCl		optimum	<1	%

Observation

quinones: MK-11, MK-12, MK-10

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32289]		arabinose ChEBI	+	carbon source
[Ref.: #32289]		cellobiose ChEBI	+	carbon source
[Ref.: #68379]		D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]		D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]		D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]		D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32289]		esculin ChEBI	+	hydrolysis
[Ref.: #68379]		esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #32289]		fructose ChEBI	+	carbon source
[Ref.: #32289]		galactose ChEBI	+	carbon source
[Ref.: #68379]		gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #32289]		glucose ChEBI	+	carbon source
[Ref.: #68379]		glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #32289]		L-arabitol ChEBI	+	carbon source
[Ref.: #32289]		lactose ChEBI	+	carbon source
[Ref.: #68379]		lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32289]		maltose ChEBI	+	carbon source
[Ref.: #68379]		maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32289]		mannitol ChEBI	+	carbon source
[Ref.: #32289]		mannose ChEBI	+	carbon source
[Ref.: #32289]		melibiose ChEBI	+	carbon source
[Ref.: #32289]		N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32289]		nitrate ChEBI	+	reduction
[Ref.: #68379]		nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #32289]		rhamnose ChEBI	+	carbon source
[Ref.: #32289]		salicin ChEBI	+	carbon source
[Ref.: #32289]		sucrose ChEBI	+	carbon source
[Ref.: #68379]		sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #32289]		trehalose ChEBI	+	carbon source
[Ref.: #68379]		urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #32289]		xylose ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]		alkaline phosphatase	-	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]		alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]		alpha-fucosidase	+	3.2.1.51	* from API zym
[Ref.: #68382]		alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]		alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]		alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]		beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]		beta-glucosidase	+	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]		beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #32289]		catalase	+	1.11.1.6
[Ref.: #68382]		cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]		esterase (C 4)	-		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]		gelatinase	-		* from API Coryne
[Ref.: #68382]		leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68379]		pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]		pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]		trypsin	-	3.4.21.4	* from API zym
[Ref.: #32289]		urease	+	3.5.1.5
[Ref.: #68379]		urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]		valine arylamidase	+		* from API zym
		Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #19775]	314	-	-	+	-	-	+	+	+	+	+	-	not determinedn.d.	-	-	-	-	-	-	+	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19775]	599	not determinedn.d.	-	-	+	-	+	+	-	-	-	+	-	+	+	-	+	+	+	+	+

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

[Ref.: #7819]	Sample type/isolated from	sewage sludge compost
[Ref.: #7819]	Geographic location (country and/or sea, region)	Porto
[Ref.: #7819]	Country	Portugal
[Ref.: #7819]	Country ISO 3 Code	PRT
[Ref.: #7819]	Continent	Europe

[Ref.: #60222]	Sample type/isolated from	Compost,municipal sewage sludge
[Ref.: #60222]	Sampling date	2005
[Ref.: #60222]	Geographic location (country and/or sea, region)	Porto ?
[Ref.: #60222]	Country	Portugal
[Ref.: #60222]	Country ISO 3 Code	PRT
[Ref.: #60222]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Sewage sludge compost
[Ref.: #67770]	Geographic location (country and/or sea, region)	Porto
[Ref.: #67770]	Country	Portugal
[Ref.: #67770]	Country ISO 3 Code	PRT
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Sewage sludge

What are isolation sources categories?

Global distribution of 16S sequence AM494541 (>99% sequence identity) for Humibacter albus subclade from Microbeatlas

Aquatic Samples	51
Soil Samples	41
Animal Samples	49
Plant Samples	20
Total Samples	161

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

[Ref.: #7819]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19775]	Biosafety level	1	Risk group (German classification)

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.: #7819]	Humibacter albus partial 16S rRNA gene, type strain SC-083T	AM494541	1488	GenBank ENA	1121952 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Humibacter albus DSM 18994	GCA_000421825	contig	GenBank ENA	1121952 tax ID
[Ref.: #66792]	Humibacter albus DSM 18994	1121952.3	wgs	PATRIC	1121952 tax ID	*
[Ref.: #66792]	Humibacter albus DSM 18994	2523533583	draft	JGI IMG/M	1121952 tax ID	*

[Ref.: #7819]	GC-content	67.6 mol%
[Ref.: #32289]	GC-content	68 mol%
[Ref.: #67770]	GC-content	67.4-67.8 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Humibacter albus DSM 18994 PATRIC: 1121952.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	85	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Humibacter albus DSM 18994 PATRIC: 1121952.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	88.999	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.361	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	75.421	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.713	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.466	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	95.5	no

Availability in culture collections External links

Culture collection no.

DSM 18994, CCUG 54538, LMG 23996, JCM 16029, KACC 20986, NBRC 106151

SI-ID 294507

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Humibacter antri sp. nov., an actinobacterium isolated from a natural cave, and emended description of the genus Humibacter.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.050708-0	2013	*
Phylogeny	Humibacter albus gen. nov., sp. nov., isolated from sewage sludge compost.	Vaz-Moreira I, Nobre MF, Ferreira AC, Schumann P, Nunes OC, Manaia CM	Int J Syst Evol Microbiol	10.1099/ijs.0.65266-0	2008	*
Phylogeny	Humibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from activated sludge.	Choi GM, Lee YW, Choe H, Kim SY, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.005442	2022	*

References

#7819

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18994

#19775

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#32289

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 #28529 (see below)

#60222 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54538

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 )

#76944

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-ID294507.1 )

#28529

IJSEM 1014 2008 ( DOI 10.1099/ijs.0.65266-0 , PubMed 18398211 )

* These data were automatically processed and therefore are not curated

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