Pseudogemmobacter bohemicus (DSM 103618, cd10, NCCB 100645)

Name: Pseudogemmobacter bohemicus (DSM 103618, cd10, NCCB 100645)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159090

Type strain

Strain Designation cd10, Cd-10

Culture col. no. DSM 103618 cd10 NCCB 100645 Cd-10

NCBI tax ID(s) 2250708

Special Collections DSMZ Literature strains

History <- O. Uhlik, VSCHT; Cd10 <- J. Suman

Links

Pseudogemmobacter bohemicus cd10 is an aerobe, chemoorganotroph, Gram-negative bacterium that was isolated from Heavy metal-contaminated sludge from decantation basin.

Gram-negative rod-shaped aerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406443

NCCB 100645,DSM 103618

@ref 20215

Last LPSN update 2026-02-09 11:38:31

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Pseudogemmobacter

Species Pseudogemmobacter bohemicus

Full scientific name Pseudogemmobacter bohemicus Suman et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
68144	negative	1-2 µm	0.8 µm	rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
68144	creamy white to beige	3 days	half-strength LB medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65913	HALF-CONCENTRATED LB (LURIA BERTANI) MEDIUM (DSMZ Medium 1623)		Medium recipe at MediaDive	Name: HALF-CONCENTRATED LB (Luria-Bertani) MEDIUM (DSMZ Medium 1623; with strain-specific modifications) Composition: NaCl 5.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
65913	positive	growth	28
68144	positive	optimum	28

Culture pH

@ref	Ability	Type	PH
68144	positive	optimum	7-8

Physiology and metabolism

Oxygen tolerance

68144

Oxygen toleranceaerobe

Nutrition type

68144

Typechemoorganotroph

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68144	NaCl	positive	optimum	0 %(w/v)
68144	NaCl	positive	growth	0-1 %(w/v)

Observation

68144

Observationtolerate CdCl 2 in the cultivation medium

Tolerance

@ref	Compound	Concentration
68144	Cd	1.0 g/kg dry matter
68144	Zn	1.0 g/kg dry matter
68144	Pb	1.0 g/kg dry matter

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68144	16808 ChEBI	2-dehydro-D-gluconate	-	carbon source
68144	58143 ChEBI	5-dehydro-D-gluconate	-	carbon source
68144	27613 ChEBI	amygdalin	+	carbon source
68144	18305 ChEBI	arbutin	+	carbon source
68144	17057 ChEBI	cellobiose	+	carbon source
68144	17108 ChEBI	D-arabinose	-	carbon source
68144	18333 ChEBI	D-arabitol	+	carbon source
68144	15824 ChEBI	D-fructose	+	carbon source
68144	28847 ChEBI	D-fucose	-	carbon source
68144	12936 ChEBI	D-galactose	+	carbon source
68144	17634 ChEBI	D-glucose	+	carbon source
68144	62318 ChEBI	D-lyxose	+	carbon source
68144	16899 ChEBI	D-mannitol	+	carbon source
68144	16024 ChEBI	D-mannose	+	carbon source
68144	16988 ChEBI	D-ribose	-	carbon source
68144	17924 ChEBI	D-sorbitol	+	carbon source
68144	16443 ChEBI	D-tagatose	-	carbon source
68144	65327 ChEBI	D-xylose	+	carbon source
68144	17113 ChEBI	erythritol	+	carbon source
68144	4853 ChEBI	esculin	-	hydrolysis
68144	4853 ChEBI	esculin	-	carbon source
68144	16813 ChEBI	galactitol	-	carbon source
68144	5291 ChEBI	gelatin	-	hydrolysis
68144	24265 ChEBI	gluconate	-	carbon source
68144	17754 ChEBI	glycerol	+	carbon source
68144	28087 ChEBI	glycogen	-	carbon source
68144	15443 ChEBI	inulin	+	carbon source
68144	30849 ChEBI	L-arabinose	-	carbon source
68144	18403 ChEBI	L-arabitol	+	carbon source
68144	18287 ChEBI	L-fucose	-	carbon source
68144	62345 ChEBI	L-rhamnose	-	carbon source
68144	65328 ChEBI	L-xylose	-	carbon source
68144	17716 ChEBI	lactose	-	carbon source
68144	17306 ChEBI	maltose	+	carbon source
68144	28053 ChEBI	melibiose	-	carbon source
68144	43943 ChEBI	methyl alpha-D-mannoside	-	carbon source
68144	74863 ChEBI	methyl beta-D-xylopyranoside	-	carbon source
68144	37657 ChEBI	methyl D-glucoside	+	carbon source
68144	17268 ChEBI	myo-inositol	-	carbon source
68144	506227 ChEBI	N-acetyl-D-glucosamine	-	carbon source
68144	16634 ChEBI	raffinose	+	carbon source
68144	15963 ChEBI	ribitol	+	carbon source
68144	17814 ChEBI	salicin	+	carbon source
68144		skimmed milk	-	hydrolysis
68144	27922 ChEBI	sorbose	-	carbon source
68144	28017 ChEBI	starch	-	hydrolysis
68144	17992 ChEBI	sucrose	+	carbon source
68144	27082 ChEBI	trehalose	+	carbon source
68144	32528 ChEBI	turanose	+	carbon source
68144	17151 ChEBI	xylitol	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68144	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68144	6-phospho-beta-galactosidase	-	3.2.1.85
68144	alanine arylamidase	+	3.4.11.2
68144	alkaline phosphatase	+	3.1.3.1
68144	alpha-arabinosidase	-
68144	alpha-chymotrypsin	+	3.4.21.1
68144	alpha-fucosidase	-	3.2.1.51
68144	alpha-galactosidase	-	3.2.1.22
68144	alpha-glucosidase	+	3.2.1.20
68144	alpha-mannosidase	-	3.2.1.24
68144	arginine arylamidase	+
68144	arginine dihydrolase	-	3.5.3.6
68144	beta-galactosidase	-	3.2.1.23
68144	beta-glucosidase	-	3.2.1.21
68144	beta-glucuronidase	-	3.2.1.31
68144	catalase	+	1.11.1.6
68144	cystine arylamidase	+	3.4.11.3
68144	cytochrome oxidase	+	1.9.3.1
68144	esterase (C 4)	+
68144	esterase Lipase (C 8)	+
68144	glutamate decarboxylase	-	4.1.1.15
68144	glycin arylamidase	+
68144	histidine arylamidase	+
68144	leucine arylamidase	+	3.4.11.1
68144	leucyl glycin arylamidase	+	3.4.11.1
68144	lipase (C 14)	+
68144	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68144	nitrate reductase	+	1.7.99.4
68144	proline-arylamidase	+	3.4.11.5
68144	serine arylamidase	+
68144	trypsin	+	3.4.21.4
68144	tyrosine arylamidase	+
68144	urease	-	3.5.1.5
68144	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

68144

Fatty acid	Percentage
C18:1 w7c	50.3
C18:0	26.3
C16:0	19.9
C16:1 w7c	2.9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Heavy metal
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature
65913	Heavy metal-contaminated sludge from decantation basin		Central Bohemia, Pribram	Czech Republic	CZE	Europe
68144	heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory	03.06.2013	Príbram, Bohemia	Czech Republic	CZE	Europe	solid basic mineral medium	28

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68144	ASM329002v1 assembly for Pseudogemmobacter bohemicus Cd-10	scaffold	GCA_003290025	2250708.3	2886545291	2250708	59.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68144	Pseudogemmobacter bohemicus strain Cd-10 16S ribosomal RNA gene, complete sequence	MF164150.2	1471		2250708

GC content

@ref	GC-content (mol%)	Method
68144	63.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudogemmobacter bohemicus Cd-10
NCBI: GCA_003290025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	79.50	no
125439	motility	BacteriaNetⓘ	yes	66.10	no
125439	gram_stain	BacteriaNetⓘ	negative	84.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	63.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge.	Suman J, Zubrova A, Rojikova K, Pechar R, Svec P, Cajthaml T, Ulbrich P, Ridl J, Strnad H, Uhlik O	Int J Syst Evol Microbiol	10.1099/ijsem.0.003493	2019

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 )
#65913	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103618
#68144	Jachym Suman, Andrea Zubrova, Katerina Rojikova, Radko Pechar, Pavel Svec, Tomas Cajthaml, Pavel Ulbrich, Jakub Ridl, Hynek Strnad and Ondrej Uhlik: Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge. IJSEM 69: 2401 - 2407 2019 ( DOI 10.1099/ijsem.0.003493 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pseudogemmobacter bohemicus (DSM 103618, cd10, NCCB 100645)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Halophily

Observation

Tolerance

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003290025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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