Name: Polygonibacillus indicireducens In2-9
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133209

Type strain:

Species: Polygonibacillus indicireducens

Strain Designation: In2-9

Culture col. no.: JCM 30831, NCIMB 14982

Strain history: I. Yumoto; Bioprod. Res. Inst., AIST, Japan; In2-9.

NCBI tax ID(s): 1652101 (species)

Special Collections

Section

Polygonibacillus indicireducens In2-9 is a facultative anaerobe, halophilic, spore-forming bacterium that forms circular colonies and was isolated from Polygonum indigo (Polygonum tinctorium; Lour.) fermentation liquor for dyeing obtained from a craft center.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
facultative anaerobe
halophilic
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Polygonibacillus*
	Species	**Polygonibacillus indicireducens**
	Full Scientific Name (LPSN)	Polygonibacillus indicireducens Hirota et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25014]	Gram stain	positive

[Ref.: #25014]	Cell length	1.6-6.4 µm

[Ref.: #25014]	Cell width	0.4-0.8 µm

[Ref.: #25014]	Cell shape	rod-shaped

[Ref.: #25014]	Motility	yes

[Ref.: #25014]	Flagellum arrangement	peritrichous

[Ref.: #25014]	Colony size	1.0-2.5 mm
[Ref.: #25014]	Colony color	creamy white
[Ref.: #25014]	Colony shape	circular
[Ref.: #25014]	Incubation period	2 days
[Ref.: #25014]	Cultivation medium used	PYG agar medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25014]

Culture medium

PYG agar medium

[Ref.: #25014]

Culture medium growth

		Temperature
[Ref.: #25014]	growth	10-45 °C
[Ref.: #25014]	optimum	35-37 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #25014]			optimum	10
[Ref.: #25014]			growth	8.0-12.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25014]

Oxygen tolerance

facultative anaerobe

[Ref.: #25014]	Spore description	ellipsoidal at subterminal to central position in the sporangia, without swollen sporangia
[Ref.: #25014]	Type of spore	endospore
[Ref.: #25014]	Ability of spore formation	yes

[Ref.: #25014]

Halophily / tolerance level

halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25014]		NaCl		growth	0-10.0	%
[Ref.: #25014]		NaCl		optimum	3	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25014]	casein	+	hydrolysis
[Ref.: #25014]	D-fructose ChEBI	+	builds acid from
[Ref.: #25014]	gelatin ChEBI	+	hydrolysis
[Ref.: #25014]	nitrate ChEBI	+	reduction
[Ref.: #25014]	starch ChEBI	+	hydrolysis
[Ref.: #25014]	tween 20 ChEBI	+	hydrolysis
[Ref.: #25014]	tween 40 ChEBI	-	hydrolysis
[Ref.: #25014]	tween 60 ChEBI	-	hydrolysis
[Ref.: #25014]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25014]	xylan ChEBI	-	hydrolysis

	Enzyme	Enzyme activity	EC number
[Ref.: #25014]	acid phosphatase	-	3.1.3.2
[Ref.: #25014]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25014]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25014]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25014]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25014]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25014]	beta-galactosidase	-	3.2.1.23
[Ref.: #25014]	beta-glucosidase	-	3.2.1.21
[Ref.: #25014]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25014]	catalase	+	1.11.1.6
[Ref.: #25014]	cystine arylamidase	-	3.4.11.3
[Ref.: #25014]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25014]	esterase (C 4)	+
[Ref.: #25014]	esterase lipase (C 8)	+
[Ref.: #25014]	leucine arylamidase	+	3.4.11.1
[Ref.: #25014]	lipase (C 14)	-
[Ref.: #25014]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25014]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25014]	trypsin	-	3.4.21.4
[Ref.: #25014]	valine arylamidase	+
	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.: #25014]	Sample type/isolated from	Polygonum indigo (Polygonum tinctorium Lour.) fermentation liquor for dyeing obtained from a craft center
[Ref.: #25014]	Geographic location (country and/or sea, region)	Date City, Hokkaido
[Ref.: #25014]	Country	Japan
[Ref.: #25014]	Country ISO 3 Code	JPN
[Ref.: #25014]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample from a craft centre
[Ref.: #67770]	Geographic location (country and/or sea, region)	Date City, Hokkaido
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Fermented
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Engineered	#Food production	#Beverage

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC054224 (>99% sequence identity) for Polygonibacillus indicireducens subclade from Microbeatlas

Aquatic Samples	110
Soil Samples	108
Animal Samples	37
Plant Samples	47
Total Samples	302

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.: #25014]	Polygonibacillus indicireducens gene for 16S ribosomal RNA, partial sequence, strain: In2-9	LC054224		GenBank ENA

[Ref.: #25014]

GC-content

39.4 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #25014]

Culture collection no.

JCM 30831, NCIMB 14982

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing.	Hirota K, Okamoto T, Matsuyama H, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijsem.0.001405	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 )

#25014

K. O. Hirota, T.,Matsuyama, H.,Yumoto, I.: Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing. IJSEM 66: 4650 - 4656 2016 ( DOI 10.1099/ijsem.0.001405 , PubMed 27503611 )

#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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