Name: Herminiimonas contaminans DSM 28178
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24261

Type strain:

Species: Herminiimonas contaminans

Culture col. no.: DSM 28178, CCM 7991, CCUG 53591

Strain history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; CCUG 53591 <- CCUG

NCBI tax ID(s): 1111140 (species)

SI-ID 303389

CCUG 53591, CCM 7991, DSM 28178

Section

Herminiimonas contaminans DSM 28178 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminant of biopharmaceutical process.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Herminiimonas*
	Species	**Herminiimonas contaminans**
	Full Scientific Name (LPSN)	Herminiimonas contaminans Kämpfer et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30576]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #30576]	Cell length	1 µm

[Ref.: #30576]	Cell width	0.5 µm

[Ref.: #30576]	Cell shape	rod-shaped

[Ref.: #30576]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.634

[Ref.: #30576]

Pigment production

yes

Multimedia content

[Ref.: #20498]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20498]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #20498]

Culture medium growth

[Ref.: #20498]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20498]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20498]	growth	28 °C
[Ref.: #30576]	growth	04-30 °C
[Ref.: #30576]	optimum	27.5 °C
[Ref.: #59938]	growth	30 °C

[Ref.: #20498]	Temperature range	mesophilic
[Ref.: #30576]	Temperature range	mesophilic
[Ref.: #59938]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30576]	Oxygen tolerance	aerobe
[Ref.: #59938]	Oxygen tolerance	aerobe

[Ref.: #30576]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30576]	acetate ChEBI	+	carbon source
[Ref.: #30576]	lactate ChEBI	+	carbon source
[Ref.: #30576]	malate ChEBI	+	carbon source
[Ref.: #30576]	propionate ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30576]	catalase	+	1.11.1.6
[Ref.: #30576]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30576]	urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #59938]

Fatty acid	Percentage	ECL
C17:0 CYCLO	41.7	16.888
C16:0	20.1	16
C19:0 CYCLO ω8c	10.7	18.9
C16:1 ω7c	9.9	15.819
C10:0 3OH	7.5	11.423
C18:1 ω7c /12t/9t	4.4	17.824
unknown 9.140	1.4	9.14
unknown 18.445	1.1	18.445
Unidentified	0.9	17.751
Unidentified	0.9	16.09
C19:0 ISO	0.5	18.633
Unidentified	0.4	18.962
C14:0	0.4	14
Unidentified	0.3	9.985

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

[Ref.: #20498]	Sample type/isolated from	contaminant of biopharmaceutical process
[Ref.: #20498]	Country	Sweden
[Ref.: #20498]	Country ISO 3 Code	SWE
[Ref.: #20498]	Continent	Europe

[Ref.: #59938]	Sample type/isolated from	Contaminant,biopharmaceuticals
[Ref.: #59938]	Sampling date	2006-10-01
[Ref.: #59938]	Country	Sweden
[Ref.: #59938]	Country ISO 3 Code	SWE
[Ref.: #59938]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Laboratory	#Contaminant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HE610501 (>99% sequence identity) for Herminiimonas from Microbeatlas

Aquatic Samples	491
Soil Samples	780
Animal Samples	395
Plant Samples	819
Total Samples	2485

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

[Ref.: #20498]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20498]	Herminiimonas contaminans partial 16S rRNA gene, type strain CCUG 53591T	HE610501	1442	ENA	1111140 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Herminiimonas contaminans strain Marseille-Q4544	1111140.3	wgs	PATRIC	1111140 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Herminiimonas contaminans strain Marseille-Q4544 PATRIC: 1111140.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Herminiimonas contaminans strain Marseille-Q4544 PATRIC: 1111140.3
[Ref.: #69480]	motile	yes	89.706	no
[Ref.: #69480]	flagellated	yes	72.802	no
[Ref.: #69480]	gram-positive	no	98.206	no
[Ref.: #69480]	anaerobic	no	98.626	no
[Ref.: #69480]	aerobic	yes	88.829	yes
[Ref.: #69480]	halophile	no	95.152	no
[Ref.: #69480]	spore-forming	no	95.128	yes
[Ref.: #69480]	thermophile	no	99.428	yes
[Ref.: #69480]	glucose-util	no	70.802	no
[Ref.: #69480]	glucose-ferment	no	91.19	no

Availability in culture collections External links

[Ref.: #20498]

Culture collection no.

DSM 28178, CCM 7991, CCUG 53591

[Ref.: #88203]

SI-ID 303389

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals.	Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen E	Int J Syst Evol Microbiol	10.1099/ijs.0.039073-0	2012	*
Genetics	Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991(T), a Biopharmaceutical Contaminant.	Kangale LJ, Zgheib R, Ghigo E, Raoult D, Fournier PE	Microbiol Resour Announc	10.1128/MRA.01432-20	2021	*

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 )

#20498

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28178

#30576

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 #26907 (see below)

#59938 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53591

#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 )

#88203

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-ID303389.1 )

#26907

IJSEM 412 2013 ( DOI 10.1099/ijs.0.039073-0 , PubMed 22447701 )

* These data were automatically processed and therefore are not curated

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Herminiimonas contaminans strain Marseille-Q4544

Herminiimonas contaminans strain Marseille-Q4544

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