Name: Humibacter soli R1-20
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140819

Type strain:

Species: Humibacter soli

Strain Designation: R1-20

Culture col. no.: KCTC 39614, JCM 31015

Strain history: S. B. Kim; Chungnam Natl. Univ., South Korea; R1-20.

NCBI tax ID(s): 1770544 (species)

Special Collections

Section

Humibacter soli R1-20 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from Soil of a white heron nesting site.

colony-forming
Gram-positive
rod-shaped
aerobe
16S sequence
Bacteria

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 soli**
	Full Scientific Name (LPSN)	Humibacter soli Park et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43609]	Gram stain	positive

[Ref.: #43609]	Cell length	0.8-1.2 µm

[Ref.: #43609]	Cell width	0.4-0.5 µm

[Ref.: #43609]	Cell shape	rod-shaped

[Ref.: #43609]	Motility	no

[Ref.: #43609]	Colony size	1-1.8 mm
[Ref.: #43609]	Colony color	gradually change from white to yellow
[Ref.: #43609]	Colony shape	circular
[Ref.: #43609]	Incubation period	3 days
[Ref.: #43609]	Cultivation medium used	TSA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43609]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #43609]

Culture medium growth

		Temperature
[Ref.: #43609]	growth	20-37 °C
[Ref.: #43609]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43609]			optimum	6
[Ref.: #43609]			growth	5-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43609]

Oxygen tolerance

aerobe

[Ref.: #43609]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43609]		NaCl		growth	0-2	%(w/v)
[Ref.: #43609]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43609]	adipate ChEBI	-	assimilation
[Ref.: #43609]	amygdalin ChEBI	+	builds acid from
[Ref.: #43609]	arbutin ChEBI	+	builds acid from
[Ref.: #43609]	cellobiose ChEBI	+	builds acid from
[Ref.: #43609]	D-fructose ChEBI	+	builds acid from
[Ref.: #43609]	D-galactose ChEBI	+	builds acid from
[Ref.: #43609]	D-glucose ChEBI	-	fermentation
[Ref.: #43609]	D-glucose ChEBI	+	assimilation
[Ref.: #43609]	D-glucose ChEBI	+	builds acid from
[Ref.: #43609]	D-mannitol ChEBI	-	assimilation
[Ref.: #43609]	D-mannose ChEBI	+	assimilation
[Ref.: #43609]	D-mannose ChEBI	+	builds acid from
[Ref.: #43609]	D-ribose ChEBI	+	builds acid from
[Ref.: #43609]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43609]	D-xylose ChEBI	+	builds acid from
[Ref.: #43609]	decanoate ChEBI	-	assimilation
[Ref.: #43609]	esculin ChEBI	+	hydrolysis
[Ref.: #43609]	ferric citrate ChEBI	+	hydrolysis
[Ref.: #43609]	gelatin ChEBI	-	hydrolysis
[Ref.: #43609]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43609]	L-arabinose ChEBI	-	assimilation
[Ref.: #43609]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43609]	L-sorbose ChEBI	+	builds acid from
[Ref.: #43609]	L-xylose ChEBI	+	builds acid from
[Ref.: #43609]	lactose ChEBI	+	builds acid from
[Ref.: #43609]	malate ChEBI	-	assimilation
[Ref.: #43609]	maltose ChEBI	-	assimilation
[Ref.: #43609]	maltose ChEBI	+	builds acid from
[Ref.: #43609]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #43609]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #43609]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43609]	nitrate ChEBI	-	reduction
[Ref.: #43609]	phenylacetate ChEBI	-	assimilation
[Ref.: #43609]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43609]	ribitol ChEBI	+	builds acid from
[Ref.: #43609]	salicin ChEBI	+	builds acid from
[Ref.: #43609]	sodium citrate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43609]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43609]	acid phosphatase	+	3.1.3.2
[Ref.: #43609]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43609]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43609]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43609]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43609]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43609]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43609]	beta-galactosidase	+	3.2.1.23
[Ref.: #43609]	beta-glucosidase	+	3.2.1.21
[Ref.: #43609]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43609]	catalase	-	1.11.1.6
[Ref.: #43609]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43609]	esterase (C 4)	+
[Ref.: #43609]	esterase Lipase (C 8)	+
[Ref.: #43609]	leucine arylamidase	+	3.4.11.1
[Ref.: #43609]	lipase (C 14)	-
[Ref.: #43609]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43609]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43609]	trypsin	-	3.4.21.4
[Ref.: #43609]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43609]

Fatty acid	Percentage
C15:0 iso	15.4
C17:0 iso 3OH	12.5
C15:0 iso 3OH	8.4
C17:1 iso ω9c / C16:0 10-methyl	8.2
C18:1ω7c / C18:1ω6c	7.6
C16:0	5.8
C16:1ω7c / C16:1ω6c	5.6
C15:0 anteiso	4.5
C16:0 iso 3OH	4.2
C19:0cycloω8c	3.1
C16:0 iso	2.2
C15:0 2OH	1.8
iso-C15:1F	1.5
C12:0	1.4
C18:0	1.3
C17:1ω6c	1.3
C16:1 iso H	1.2
C17:0 2OH	1.2
C12:0 3OH	1.2
C17:0	1.1
C17:1 anteiso ω9c	1
C15:1ω6c	1
C14:0 iso	0.8
C10:0 3OH	0.7
C17:1ω8c	0.7
C14:0 iso 3OH	0.6
C17:0 iso	0.5

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

[Ref.: #43609]	Sample type/isolated from	Soil of a white heron nesting site
[Ref.: #43609]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #43609]	Country	Republic of Korea
[Ref.: #43609]	Country ISO 3 Code	KOR
[Ref.: #43609]	Continent	Asia
[Ref.: #43609]	Geographic location	36.3640°/127.3490°

[Ref.: #67770]	Sample type/isolated from	Soil at a white heron nesting site
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Birds	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT318606 (>99% sequence identity) for Humibacter soli subclade from Microbeatlas

Aquatic Samples	13
Soil Samples	21
Animal Samples	1
Plant Samples	120
Total Samples	155

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.: #43609]	Humibacter soli strain R1-20 16S ribosomal RNA gene, partial sequence	KT318606		GenBank ENA

[Ref.: #43609]	GC-content	65.5 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	65.5 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #43609]

Culture collection no.

KCTC 39614, JCM 31015

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Humibacter soli sp. nov., isolated from soil.	Park J, Kim YR, Kim MK, Jo JH, Im WT, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.001081	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 )

#43609

Jisun Park, Yu Ri Kim, Min-Kyeong Kim, Jung Hun Jo, Wan-Taek Im, Seung Bum Kim: Humibacter soli sp. nov., isolated from soil. IJSEM 66: 2509 - 2514 2016 ( DOI 10.1099/ijsem.0.001081 , PubMed 27081846 )

#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 .

* These data were automatically processed and therefore are not curated

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