Subtercola lobariae (DSM 103962, CGMCC 1.12976, KCTC 33586)

Name: Subtercola lobariae (DSM 103962, CGMCC 1.12976, KCTC 33586)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133103

Type strain

Strain Designation 9583b

Culture col. no. DSM 103962 CGMCC 1.12976 KCTC 33586 9583b JCM 33410

NCBI tax ID(s) 1588641

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- H.-L. Si, Shandong Univ., Jinan, China; 9583b JCM <-- CGMCC 1.12976 <-- Z.-T. Zhao; Shandong Normal Univ., China; 9583b.

Links

Subtercola lobariae 9583b is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from specimens of the lichen Lobaria retigera collected from Jiaozi Snow Mountain, Yunnan Province.

Gram-positive rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400288

KCTC 33586,DSM 103962

@ref 20215

Last LPSN update 2026-05-29 08:38:01

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Subtercola

Species Subtercola lobariae

Full scientific name Subtercola lobariae Si et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
25307	positive	0.7-1.0 µm	0.5-0.6 µm	rod-shaped
125438						91

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25307	3-5 mm	white	circular	3 days	ISP2

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
25307	ISP2
64131	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
64131	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

Culture temp

@ref	Growth	Type	Temperature (°C)
25307	positive	growth	4-28
25307	positive	optimum	20
64131	positive	growth	20
67770	positive	growth	20

Culture pH

@ref	Ability	Type	PH	PH range
25307	positive	optimum	6
25307	positive	growth	4.0-8.0	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25307	aerobe
125439	obligate aerobe	97.689

Observation

67770

Observationquinones: MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25307	17128 ChEBI	adipate	-	assimilation
25307	17925 ChEBI	alpha-D-glucose	+	respiration
25307	22599 ChEBI	arabinose	+	assimilation
25307	17968 ChEBI	butyrate	-	assimilation
25307	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
25307		casein	-	hydrolysis
25307	17057 ChEBI	cellobiose	+	respiration
25307	16947 ChEBI	citrate	-	assimilation
25307	18333 ChEBI	D-arabitol	-	respiration
25307	12936 ChEBI	D-galactose	+	respiration
25307	8391 ChEBI	D-gluconate	-	respiration
25307	16024 ChEBI	D-mannose	+	respiration
25307	23652 ChEBI	dextrin	+	respiration
25307	16991 ChEBI	dna	-	hydrolysis
25307	4853 ChEBI	esculin	+	hydrolysis
25307	28066 ChEBI	gentiobiose	+	respiration
25307	24265 ChEBI	gluconate	-	assimilation
25307	17234 ChEBI	glucose	+	builds acid from
25307	17234 ChEBI	glucose	+	assimilation
25307	17754 ChEBI	glycerol	+	respiration
25307	25115 ChEBI	malate	-	assimilation
25307	17306 ChEBI	maltose	-	assimilation
25307	29864 ChEBI	mannitol	-	assimilation
25307	37684 ChEBI	mannose	+	assimilation
25307	28053 ChEBI	melibiose	+	respiration
25307	17268 ChEBI	myo-inositol	+	respiration
25307	506227 ChEBI	N-acetylglucosamine	-	assimilation
25307	17632 ChEBI	nitrate	-	reduction
25307	18401 ChEBI	phenylacetate	+	assimilation
25307	17814 ChEBI	salicin	+	respiration
25307	28017 ChEBI	starch	-	hydrolysis
25307	27082 ChEBI	trehalose	-	respiration
25307	53426 ChEBI	tween 80	+/-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite
25307		1 % sodium lactate
25307	161680	aztreonam
25307	16523	d-serine
25307	71321	fusidate
25307	32735	guanidinium chloride
25307	6472	lincomycin
25307	48607	lithium chloride
25307	50694	minocycline
25307	100147	nalidixic acid
25307	75273	niaproof
25307	75248	potassium tellurite
25307	29673	rifamycin sv
25307	75229	sodium bromate
25307	64103	sodium butyrate
25307	75193	tetrazolium violet
25307	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25307	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
25307	acid phosphatase	+	3.1.3.2
25307	alpha-galactosidase	-	3.2.1.22
25307	alpha-glucosidase	+	3.2.1.20
25307	alpha-mannosidase	+	3.2.1.24
25307	arginine dihydrolase	-	3.5.3.6
25307	beta-galactosidase	+	3.2.1.23
25307	beta-glucosidase	+	3.2.1.21
25307	catalase	+	1.11.1.6
25307	cystine arylamidase	+/-	3.4.11.3
25307	cytochrome oxidase	-	1.9.3.1
25307	esterase Lipase (C 8)	+/-
25307	gelatinase	-
25307	leucine arylamidase	+	3.4.11.1
25307	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25307	naphthol-AS-BI-phosphohydrolase	+
25307	trypsin	+	3.4.21.4
25307	urease	-	3.5.1.5
25307	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

25307

Fatty acid	Percentage
C15:0 anteiso	68.8
C14:0 2OH	10.3
C16:0 iso	6.7
C17:0 anteiso	4.2
C17:1ω9c	3.5
C14:0 iso 3OH	2.3
C15:0 iso	1.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Other	#Lichen

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
25307	specimens of the lichen Lobaria retigera collected from Jiaozi Snow Mountain, Yunnan Province	Lobaria retigera	Jiaozi Snow Mountain, Yunnan Province	China	CHN	Asia	25	102 25/102	2012-11
64131	lichen Lobaria retigera		Yunnan Province, Jiaozi Snow Mountain (25.86° N 102.81°E)	China	CHN	Asia	26.86	102.81 26.86/102.81
67770	Lichen (Lobaria retigera) from Jiaozi Snow Mountain	Lobaria retigera	Yunnan Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64131	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	ASM1688114v1 assembly for Subtercola lobariae 9583b	contig	GCA_016881145	1588641.5		1588641	74.31
66792	ASM1464025v1 assembly for Subtercola lobariae CGMCC 1.12976	contig	GCA_014640255	1588641.3	2995264412	1588641	73.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64131	Subtercola lobariae strain 9583b 16S ribosomal RNA gene, partial sequence	KM924549	1460		1588641

GC content

@ref	GC-content (mol%)	Method
64131	66.8	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: ASM1688114v1 assembly for Subtercola lobariae 9583b
NCBI: GCA_016881145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.69	no
125439	gram_stain	BacteriaNetⓘ	positive	81.68	no
125439	motility	BacteriaNetⓘ	no	84.99	no
125439	spore_formation	BacteriaNetⓘ	no	85.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Subtercola lobariae strain CGMCC 1.12976
PATRIC: 1588641.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.04	yes
125438	anaerobic	anaerobicⓘ	no	97.38	yes
125438	spore-forming	spore-formingⓘ	no	83.05	no
125438	aerobic	aerobicⓘ	yes	86.59	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.	Tagirdzhanova G, Saary P, Cameron ES, Allen CCG, Garber AI, Escandon DD, Cook AT, Goyette S, Nogerius VT, Passo A, Mayrhofer H, Holien H, Tonsberg T, Stein LY, Finn RD, Spribille T.	PLoS Biol	10.1371/journal.pbio.3002862	2024
Phylogeny	Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile.	Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JF	Antonie Van Leeuwenhoek	10.1007/s10482-017-0994-4	2017
Phylogeny	Subtercola lobariae sp. nov., an actinobacterium of the family Microbacteriaceae isolated from the lichen Lobaria retigera.	Si HL, Shi FX, Zhang LL, Yue HS, Wang HY, Zhao ZT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001753	2017
Phylogeny	Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana.	Jiang L, Peng Y, Seo J, Jeon D, Jo MG, Lee JH, Jeong JC, Kim CY, Park HC, Lee J	Sci Rep	10.1038/s41598-022-16116-3	2022

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 )
#25307	H. L. S. Si, F. X.,Zhang, L. L.,Yue, H. S.,Wang, H. Y.,Zhao, Z. T.: Subtercola lobariae sp. nov., an actinobacterium of the family Microbacteriaceae isolated from the lichen Lobaria retigera. IJSEM 67: 1516 - 1521 2017 ( DOI 10.1099/ijsem.0.001753 , PubMed 28005519 )
#64131	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103962
#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;
#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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Subtercola lobariae (DSM 103962, CGMCC 1.12976, KCTC 33586)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016881145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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