Name: Puia dinghuensis 4GSH07
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141170

Type strain:

Species: Puia dinghuensis

Strain Designation: 4GSH07

Culture col. no.: CGMCC 1.15448, LMG 29214

NCBI tax ID(s): 1792502 (species)

Special Collections

Literature strains

Section

Puia dinghuensis 4GSH07 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from monsoon evergreen broad-leaved forest soil.

colony-forming
Gram-negative
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	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Puia*
	Species	**Puia dinghuensis**
	Full Scientific Name (LPSN)	Puia dinghuensis Lv et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #44090]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %91.771

[Ref.: #44090]	Cell shape	rod-shaped

[Ref.: #44090]	Motility	no

[Ref.: #44090]	Colony size	0.5-1.0 mm
[Ref.: #44090]	Colony color	grey
[Ref.: #44090]	Colony shape	circular
[Ref.: #44090]	Cultivation medium used	GYS

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYS

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

MacConkey

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #44090]			growth	16-33 °C
[Ref.: #44090]			optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #44090]			optimum	4
[Ref.: #44090]			growth	3.0-6.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44090]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44090]		NaCl		growth	0-0.5	%(w/v)
[Ref.: #44090]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44090]	2-dehydro-D-gluconate ChEBI	-	carbon source
[Ref.: #44090]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #44090]	adipate ChEBI	-	carbon source
[Ref.: #44090]	amygdalin ChEBI	+	carbon source
[Ref.: #44090]	arbutin ChEBI	+	carbon source
[Ref.: #44090]	casein	-	hydrolysis
[Ref.: #44090]	cellobiose ChEBI	+	carbon source
[Ref.: #44090]	chitin ChEBI	-	hydrolysis
[Ref.: #44090]	citrate ChEBI	-	carbon source
[Ref.: #44090]	D-arabinose ChEBI	-	carbon source
[Ref.: #44090]	D-arabitol ChEBI	-	carbon source
[Ref.: #44090]	D-fructose ChEBI	+	carbon source
[Ref.: #44090]	D-fucose ChEBI	-	carbon source
[Ref.: #44090]	D-galactose ChEBI	+	carbon source
[Ref.: #44090]	D-lyxose ChEBI	-	carbon source
[Ref.: #44090]	D-ribose ChEBI	-	carbon source
[Ref.: #44090]	D-sorbitol ChEBI	-	carbon source
[Ref.: #44090]	D-tagatose ChEBI	-	carbon source
[Ref.: #44090]	D-xylose ChEBI	+	carbon source
[Ref.: #44090]	decanoate ChEBI	-	carbon source
[Ref.: #44090]	erythritol ChEBI	-	carbon source
[Ref.: #44090]	esculin ChEBI	+	hydrolysis
[Ref.: #44090]	galactitol ChEBI	-	carbon source
[Ref.: #44090]	gelatin ChEBI	-	hydrolysis
[Ref.: #44090]	gentiobiose ChEBI	+	carbon source
[Ref.: #44090]	glucose ChEBI	+	carbon source
[Ref.: #44090]	glycerol ChEBI	-	carbon source
[Ref.: #44090]	glycogen ChEBI	+	carbon source
[Ref.: #44090]	inulin ChEBI	-	carbon source
[Ref.: #44090]	L-arabinose ChEBI	+	carbon source
[Ref.: #44090]	L-arabitol ChEBI	+	carbon source
[Ref.: #44090]	L-arginine ChEBI	-	hydrolysis
[Ref.: #44090]	L-fucose ChEBI	-	carbon source
[Ref.: #44090]	L-rhamnose ChEBI	+	carbon source
[Ref.: #44090]	L-sorbose ChEBI	-	carbon source
[Ref.: #44090]	L-xylose ChEBI	-	carbon source
[Ref.: #44090]	malate ChEBI	-	carbon source
[Ref.: #44090]	maltose ChEBI	+	carbon source
[Ref.: #44090]	mannitol ChEBI	-	carbon source
[Ref.: #44090]	mannose ChEBI	+	carbon source
[Ref.: #44090]	melezitose ChEBI	+	carbon source
[Ref.: #44090]	methyl alpha-D-mannoside ChEBI	+	carbon source
[Ref.: #44090]	methyl beta-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #44090]	myo-inositol ChEBI	-	carbon source
[Ref.: #44090]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #44090]	phenylacetate ChEBI	-	carbon source
[Ref.: #44090]	raffinose ChEBI	+	carbon source
[Ref.: #44090]	ribitol ChEBI	-	carbon source
[Ref.: #44090]	salicin ChEBI	+	carbon source
[Ref.: #44090]	starch ChEBI	-	hydrolysis
[Ref.: #44090]	starch ChEBI	+	carbon source
[Ref.: #44090]	sucrose ChEBI	+	carbon source
[Ref.: #44090]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #44090]	amikacin ChEBI	yes	30	µg (disc)
[Ref.: #44090]	chloramphenicol ChEBI				yes	30	µg (disc)
[Ref.: #44090]	ciprofloxacin ChEBI				yes	5	µg (disc)
[Ref.: #44090]	erythromycin ChEBI				yes	15	µg (disc)
[Ref.: #44090]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #44090]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #44090]	netilmycin ChEBI	yes	30	µg (disc)
[Ref.: #44090]	novobiocin ChEBI				yes	5	µg (disc)
[Ref.: #44090]	penicillin g ChEBI				yes	10	Unit (disc)
[Ref.: #44090]	polymyxin b ChEBI	yes	300	Unit (disc)
[Ref.: #44090]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #44090]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #44090]	tobramycin ChEBI	yes	10	µg (disc)
[Ref.: #44090]	vancomycin ChEBI				yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #44090]	acid phosphatase	+	3.1.3.2
[Ref.: #44090]	alkaline phosphatase	+	3.1.3.1
[Ref.: #44090]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #44090]	alpha-galactosidase	+	3.2.1.22
[Ref.: #44090]	alpha-glucosidase	+	3.2.1.20
[Ref.: #44090]	alpha-mannosidase	-	3.2.1.24
[Ref.: #44090]	beta-D-fucosidase	+	3.2.1.38
[Ref.: #44090]	beta-galactosidase	+	3.2.1.23
[Ref.: #44090]	beta-glucosidase	+	3.2.1.21
[Ref.: #44090]	beta-glucuronidase	-	3.2.1.31
[Ref.: #44090]	catalase	-	1.11.1.6
[Ref.: #44090]	cystine arylamidase	+	3.4.11.3
[Ref.: #44090]	cytochrome oxidase	-	1.9.3.1
[Ref.: #44090]	esterase (C 4)	+
[Ref.: #44090]	esterase Lipase (C 8)	+
[Ref.: #44090]	leucine arylamidase	+	3.4.11.1
[Ref.: #44090]	lipase (C 14)	-
[Ref.: #44090]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #44090]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #44090]	trypsin	-	3.4.21.4
[Ref.: #44090]	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.: #44090]	Sample type/isolated from	monsoon evergreen broad-leaved forest soil
[Ref.: #44090]	Geographic location (country and/or sea, region)	Dinghushan Biosphere Reserve, Guangdong Province
[Ref.: #44090]	Country	China
[Ref.: #44090]	Country ISO 3 Code	CHN
[Ref.: #44090]	Continent	Asia
[Ref.: #44090]	Geographic location	23.1667°/112.5170°
[Ref.: #44090]	Enrichment culture	GYS
[Ref.: #44090]	Enrichment culture duration	14 days
[Ref.: #44090]	Enrichment culture temperature	28 ̊C
[Ref.: #44090]	Isolation/enrichment procedure	5g soil sample was thoroughly suspended in 100ml of 100mM phosphate-buffered saline (pH 7.0), and 100µl of the suspension was spread on GYS plates (pH 4.0) after serial dilution.
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT805281 (>99% sequence identity) for Puia dinghuensis subclade from Microbeatlas

Aquatic Samples	22
Soil Samples	1103
Animal Samples	18
Plant Samples	140
Total Samples	1283

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.: #44090]	Puia dinghuensis strain 4GSH07 16S ribosomal RNA gene, partial sequence	KT805281		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Puia dinghuensis CGMCC 1.15448	GCA_014642875	scaffold	GenBank ENA	1792502 tax ID	*
[Ref.: #66792]	Puia dinghuensis strain CGMCC 1.15448	1792502.3	wgs	PATRIC	1792502 tax ID	*

[Ref.: #44090]

GC-content

50.3 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: Puia dinghuensis CGMCC 1.15448 NCBI: GCA_014642875.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Puia dinghuensis CGMCC 1.15448 NCBI: GCA_014642875.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	91.771	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.637	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.786	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.115	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.173	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	85.375	no

Availability in culture collections External links

[Ref.: #44090]

Culture collection no.

CGMCC 1.15448, LMG 29214

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Puia dinghuensis gen. nov., sp. nov., isolated from monsoon evergreen broad-leaved forest soil.	Lv YY, Gao ZH, Xia F, Chen MH, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002346	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 )

#44090

Ying-ying Lv, Zeng-hong Gao, Fan Xia, Mei-hong Chen and Li-hong Qiu: Puia dinghuensis gen. nov., sp. nov., isolated from monsoon evergreen broad-leaved forest soil. IJSEM 67: 4639 - 4645 2017 ( DOI 10.1099/ijsem.0.002346 , PubMed 28984557 )

#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) .

#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 )

* These data were automatically processed and therefore are not curated

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Puia dinghuensis CGMCC 1.15448

Puia dinghuensis CGMCC 1.15448

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