Allochromatium humboldtianum (DSM 21881, KCTC 15448, AX1YC10)

Name: Allochromatium humboldtianum (DSM 21881, KCTC 15448, AX1YC10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131413

Type strain

Strain Designation AX1YC10, AX1YPE

Culture col. no. DSM 21881 KCTC 15448 AX1YC10 AX1YPE

NCBI tax ID(s) 504901

Special Collections DSMZ KCTC

Links

Allochromatium humboldtianum AX1YC10 is an anaerobe, mesophilic, motile prokaryote that was isolated from shallow water, soft marine sediments.

motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407631

KCTC 15448,DSM 21881

@ref 20215

Last LPSN update 2025-12-16 10:01:14

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Chromatiaceae

Genus Allochromatium

Species Allochromatium humboldtianum

Full scientific name Allochromatium humboldtianum Serrano et al. 2015

Morphology

Cell morphology

@ref	Cell shape	Flagellum arrangement	Gram stain	Confidence
67771	rod-shaped	monotrichous, polar
67771			negative
125438			negative	99.494

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22640	PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)		Medium recipe at MediaDive	Name: PFENNIG'S MEDIUM I (DSMZ Medium 28; with strain-specific modifications) Composition: NaCl 30.0 g/l NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l Ammonium chloride 0.349999 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22640	positive	growth	28	mesophilic
67771	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22640	shallow water, soft marine sediments	central coast, Callao Bay (12° 02' S 72° 13' W) at a depth of 47 m	Peru	PER	Middle and South America	-12.051	-77.129 -12.051/-77.129
67771	From marine coastal sediments at 47 m depth in Callao Bay	central coast	Peru	PER	Middle and South America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22640	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1338517v1 assembly for Allochromatium humboldtianum DSM 21881	contig	GCA_013385175	504901.4	2914811602	504901	61.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22640	Allochromatium humboldtianum strain AX1YPE 16S ribosomal RNA gene, partial sequence	EU442182	1451		504901

GC content

@ref	GC-content (mol%)	Method
22640	63.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Allochromatium humboldtianum DSM 21881
NCBI: GCA_013385175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.40	no
125439	motility	BacteriaNetⓘ	yes	53.60	no
125439	gram_stain	BacteriaNetⓘ	negative	85.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	65.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Allochromatium humboldtianum strain DSM 21881
PATRIC: 504901.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.49	yes
125438	anaerobic	anaerobicⓘ	yes	77.76	yes
125438	spore-forming	spore-formingⓘ	no	88.66	no
125438	aerobic	aerobicⓘ	no	80.79	no
125438	thermophilic	thermophileⓘ	no	89.95	yes
125438	flagellated	motile2+ⓘ	yes	83.96	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms.	Hesketh-Best PJ, Bosco-Santos A, Garcia SL, O'Beirne MD, Werne JP, Gilhooly WP, Silveira CB.	Commun Earth Environ	10.1038/s43247-023-00796-4	2023
Phylogeny	Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov.	Imhoff JF, Kyndt JA, Meyer TE.	Microorganisms	10.3390/microorganisms10020295	2022
Phylogeny	Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments.	Serrano W, Schrubbers J, Amann R, Fischer U	Int J Syst Evol Microbiol	10.1099/ijs.0.000364	2015

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 )
#22640	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21881
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Allochromatium humboldtianum (DSM 21881, KCTC 15448, AX1YC10)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013385175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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