Mycobacterium sediminis (DSM 45643, KCTC 19999, YIM M13028)

Name: Mycobacterium sediminis (DSM 45643, KCTC 19999, YIM M13028)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24236

Type strain

Culture col. no. DSM 45643 KCTC 19999 YIM M13028 JCM 17899

NCBI tax ID(s) 1286180

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- S.-K. Tang, YIM; YIM M13028 <- D.-F. Zhang JCM <-- S.-K. Tang YIM M13028. KCTC <- S-K Tang, Yunnan Inst., China

Links

Mycobacterium sediminis DSM 45643 is an aerobe, Gram-positive, ovoid-shaped bacterium that was isolated from marine sediment.

Gram-positive ovoid-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407834

KCTC 19999,DSM 45643

@ref 20215

Last LPSN update 2026-05-29 08:30:35

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium sediminis

Full scientific name Mycobacterium sediminis Zhang et al. 2013

Synonyms (1)

Mycolicibacterium sediminis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31044	positive	ovoid-shaped
67771	positive
125439	positive		92.981
125438	positive		91.225

Pigmentation

31044

Productionyes

Multimedia

@ref:	20671
multimedia content:	DSM_45643.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45643.jpg
caption:	Medium 645 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20671	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
20671	MIDDLEBROOK MEDIUM (DSMZ Medium 645)		Medium recipe at MediaDive	Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
20671	positive	growth	28
31044	positive	growth	05-37
31044	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH
31044	positive	optimum	7
31044	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	97.614

Spore formation

31044

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31044	NaCl	positive	growth	0-4 %
31044	NaCl	positive	optimum	1 %

Enzymes

@ref	Value	Activity	Ec
31044	catalase	+	1.11.1.6
31044	urease	+	3.5.1.5

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
20671	marine sediment	Yunnan, South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 m	China	CHN	Asia	19.5044	111.004 19.5044/111.004
67770	Sediment sample from the South China Sea at a depth of 42 m
67771	From marine sediment	Southe China Sea	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC010490 (>99% sequence identity) for Mycolicibacterium from Microbeatlas

Aquatic Samples	648
Soil Samples	1808
Animal Samples	1323
Plant Samples	680
Total Samples	4459

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20671	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	ASM1073173v1 assembly for Mycolicibacterium sediminis JCM 17899	complete	GCA_010731735	1286180.8	2888243993	1286180	98.49
66792	ASM2582298v1 assembly for Mycolicibacterium sediminis DSM 45643	scaffold	GCA_025822985	1286180.10	8115505212	1286180	74.68
124043	ASM3954087v1 assembly for Mycolicibacterium sediminis JCM 17899	scaffold	GCA_039540875			1286180	71.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20671	Mycobacterium sediminis strain YIM M13028 16S ribosomal RNA gene, partial sequence	KC010490	1515		1286180
67770	Mycolicibacterium sediminis strain YIM M13028 16S-23S ribosomal RNA intergenic spacer, complete sequence	KC010492	490		1286180

GC content

@ref	GC-content (mol%)	Method
20671	64.1	high performance liquid chromatography (HPLC)
31044	64.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1073173v1 assembly for Mycolicibacterium sediminis JCM 17899
BV-BRC: 1286180.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.61	no
125439	gram_stain	BacteriaNetⓘ	positive	92.98	no
125439	spore_formation	BacteriaNetⓘ	no	72.44	no
125439	motility	BacteriaNetⓘ	no	82.02	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium sediminis JCM 17899
NCBI: GCA_010731735.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.23	yes
125438	anaerobic	anaerobicⓘ	no	98.47	no
125438	aerobic	aerobicⓘ	yes	88.89	yes
125438	spore-forming	spore-formingⓘ	no	60.57	yes
125438	thermophilic	thermophileⓘ	no	96.67	yes
125438	flagellated	motile2+ⓘ	no	88.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.	Gupta RS, Lo B, Son J.	Front Microbiol	10.3389/fmicb.2018.00067	2018
Phylogeny	Microbiological features and clinical relevance of new species of the genus Mycobacterium.	Tortoli E.	Clin Microbiol Rev	10.1128/cmr.00035-14	2014
Genetics	Draft genome sequences of five Mycobacterium strains, isolated from Alnus glutinosa root nodules.	Thompson RM, Fox EM, Montero-Calasanz MdC.	Microbiol Resour Announc	10.1128/mra.01132-23	2024
Phylogeny	Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.	Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.050567-0	2013

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 )
#20671	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45643
#27374	IJSEM 4081 2013 ( DOI 10.1099/ijs.0.050567-0 , PubMed 23728378 )
#31044	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 #27374
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Mycobacterium sediminis (DSM 45643, KCTC 19999, YIM M13028)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010731735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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