Pigmentiphaga humi (DSM 107179, CCM 8859, CIP 111626)

Name: Pigmentiphaga humi (DSM 107179, CCM 8859, CIP 111626)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159685

Type strain

Strain Designation IMT-318

Culture col. no. DSM 107179 CCM 8859 CIP 111626 LMG 30658 IMT-318

NCBI tax ID(s) 2478468

Special Collections DSMZ CIP Literature strains

History <- P. Kaempfer, Justus-Liebig-Universität, Giessen, Germany; IMT-318 <- J. McInroy, Department of Entomology and Plant Pathology, Auburn University, Alabama, USA CIP <- 2018, P. Kämpfer, Giessen Univ., Giessen, Germany: strain IMT-318

Links

Pigmentiphaga humi IMT-318 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from soil.

Gram-negative rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406147

LMG 30658,DSM 107179,CIP 111626

@ref 20215

Last LPSN update 2025-12-16 10:08:19

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Pigmentiphaga

Species Pigmentiphaga humi

Full scientific name Pigmentiphaga humi Kämpfer et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
67918	negative	1.6-2.2 µm	0.9-1.1 µm	rod-shaped
125438	negative				97.703
125439	negative				93.3
119984	negative			rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
67918	beige	circular	Reasoner's 2A agar (R2A)

Multimedia

@ref:	66536
multimedia content:	DSM_107179.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_107179.jpg
caption:	DSM 107179 on medium 1 at 28 °C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
66536	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
66536	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
119984	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66536	positive	growth	28	mesophilic
67918	positive	optimum	20-28
67918	positive	growth	15	psychrophilic
67918	negative	growth	30

Culture pH

@ref	Ability	Type	PH
67918	positive	optimum	5.5-6.5
67918	positive	growth	7.0-7.5
67918		growth	5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67918	aerobe
125439	obligate aerobe	95.5

Spore formation

@ref	Spore formation	Confidence
125439		95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67918	NaCl	positive	growth	0.1-1.0 %(w/v)

Observation

@ref	Observation
67918	The polyamine pattern contains the major compounds putrescine and 2-hydroxyputrescine
67918	Ubiquinone Q-8 is the major quinone
67918	The polar lipid profile contains high amounts of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid (APL1)
67918	The peptidoglycan diamino acid is meso-diaminopimelic acid

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
67918	17128 ChEBI	adipate	-	assimilation
67918	16899 ChEBI	D-mannitol	-	assimilation
67918	16024 ChEBI	D-mannose	-	assimilation
67918	17234 ChEBI	glucose	-	fermentation
67918	17234 ChEBI	glucose	-	assimilation
67918	17120 ChEBI	hexanoate	-	assimilation
67918	30849 ChEBI	L-arabinose	-	assimilation
67918	25115 ChEBI	malate	+	assimilation
67918	17632 ChEBI	nitrate	-	reduction
67918	18401 ChEBI	phenylacetate	-	assimilation
67918	32032 ChEBI	potassium gluconate	-	assimilation
67918	53258 ChEBI	sodium citrate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67918	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
67918	acid phosphatase	+	3.1.3.2
67918	alpha-chymotrypsin	+	3.4.21.1
67918	alpha-fucosidase	-	3.2.1.51
67918	alpha-galactosidase	-	3.2.1.22
67918	alpha-mannosidase	-	3.2.1.24
67918	arginine dihydrolase	-	3.5.3.6
67918	beta-galactosidase	-	3.2.1.23
67918	beta-glucosidase	-	3.2.1.21
67918	beta-glucuronidase	-	3.2.1.31
67918	catalase	+	1.11.1.6
67918	cytochrome oxidase	+	1.9.3.1
67918	esterase (C 4)	+
67918	esterase Lipase (C 8)	+
67918	leucine arylamidase	+	3.4.11.1
67918	lipase (C 14)	-
67918	N-acetyl-beta-glucosaminidase	-	3.2.1.52
67918	naphthol-AS-BI-phosphohydrolase	+
67918	trypsin	-	3.4.21.4
67918	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@ref

67918

Fatty acid	Percentage
C16:0	42.7
C18:1 w7c	25.6
C17:0	19.4
C19:0 cyclo w8c	12.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
66536	soil		Alabama, Malvern, field amended with humic acid	USA	USA	North America
67918	soil sampled at a field amended with humic acid	2012	Malvern, Alabama	USA	USA	North America
119984	Environment, Soil		Malvern , Alabama	United States of America	USA	North America	2012-08-31

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
119984	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67918	CIP111626 assembly for Pigmentiphaga humi	contig	GCA_900606115	2478468.3	2832582183	2478468	65.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66536	Pigmentiphaga humi strain IMT-318 16S ribosomal RNA gene, partial sequence	MH667611	1445		2478468

GC content

@ref	GC-content (mol%)	Method
67918	66.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pigmentiphaga humi lm1
NCBI: GCA_900606115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.20	no
125439	motility	BacteriaNetⓘ	yes	79.30	no
125439	gram_stain	BacteriaNetⓘ	negative	93.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pigmentiphaga humi lm1
NCBI: GCA_900606115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.70	yes
125438	anaerobic	anaerobicⓘ	no	93.14	no
125438	aerobic	aerobicⓘ	yes	83.00	no
125438	spore-forming	spore-formingⓘ	no	85.51	no
125438	thermophilic	thermophileⓘ	no	95.98	yes
125438	flagellated	motile2+ⓘ	yes	83.05	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid.	Kampfer P, Busse HJ, Criscuolo A, Bizet C, Clermont D, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.003355	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 )
#66536	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107179
#67918	Peter Kämpfer, Hans-Jürgen Busse, Alexis Criscuolo, Chantal Bizet, Dominique Clermont, John A. McInroy, Stefanie P. Glaeser: Pigmentiphaga humi sp. nov., isolated from soil amended with humic acid. IJSEM 69: 1573 - 1578 2019 ( DOI 10.1099/ijsem.0.003355 )
#119984	Collection of Institut Pasteur ; Curators of the CIP; CIP 111626
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Pigmentiphaga humi (DSM 107179, CCM 8859, CIP 111626)

Name and taxonomic classification