Secundilactobacillus silagei (DSM 27022, JCM 19001, KCTC 21050)

Name: Secundilactobacillus silagei (DSM 27022, JCM 19001, KCTC 21050)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24138

Type strain

Strain Designation IWT126

Culture col. no. DSM 27022 JCM 19001 KCTC 21050 IWT126

NCBI tax ID(s) 1302250 1293415

Special Collections DSMZ JCM KCTC

History DSMZ <- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; IWT126 JCM <-- M. Tohno IWT126. KCTC <- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, IWT126

Links

Secundilactobacillus silagei IWT126 is a microaerophile, rod-shaped bacterium that was isolated from orchardgrass silage.

rod-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 391583

KCTC 21050,JCM 19001,DSM 27022,LMG 28405

@ref 20215

Last LPSN update 2026-05-29 08:30:33

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Secundilactobacillus

Species Secundilactobacillus silagei

Full scientific name Secundilactobacillus silagei (Tohno et al. 2013) Zheng et al. 2020

Synonyms (1)

Lactobacillus silagei

Morphology

Cell morphology

@ref	Cell shape	Gram stain	Confidence
67771	rod-shaped
67771		positive
125438		positive	92.079

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20998	MRS MEDIUM (DSMZ Medium 11)		Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
20998	positive	growth	30
67770	positive	growth	30
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
20998	microaerophile
67771	anaerobe
125439	facultative anaerobe	93.18

Spore formation

67771

Spore formationno

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	+	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
20998	-	-	-	-	+	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
20998	orchardgrass (Dactylis glomerata L.) silage	Dactylis glomerata	Iwate, Hachimantai	Japan	JPN	Asia
67770	Orchardgrass silage		Hachimantai, Iwate	Japan	JPN	Asia
67771	From orchardgrass, `Dactylis glomerata` L., silage	Dactylis glomerata	Hachimantai, Iwate	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC589213 (>99% sequence identity) for Secundilactobacillus from Microbeatlas

Aquatic Samples	237
Soil Samples	155
Animal Samples	1277
Plant Samples	156
Total Samples	1825

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20998	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	ASM435459v1 assembly for Secundilactobacillus silagei JCM 19001 DSM 27022	contig	GCA_004354595	1302250.7		1302250	71.73
67770	ASM221794v1 assembly for Secundilactobacillus silagei JCM 19001 IWT126	scaffold	GCA_002217945	1302250.4	8004797970	1302250	61.66
66792	ASM131322v1 assembly for Secundilactobacillus silagei JCM 19001	contig	GCA_001313225	1302250.3	2734481937	1302250	37.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20998	Lactobacillus silagei gene for 16S ribosomal RNA, partial sequence	AB786910	1488		1302250
67770	Secundilactobacillus silagei JCM 19001 gene for 16S rRNA, partial sequence	LC589213	1502		1302250

GC content

@ref	GC-content (mol%)	Method
20998	45.6	high performance liquid chromatography (HPLC)
67771	44.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM435459v1 assembly for Secundilactobacillus silagei JCM 19001 DSM 27022
NCBI: GCA_004354595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	59.23	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.18	no
125439	motility	BacteriaNetⓘ	no	74.13	no
125439	spore_formation	BacteriaNetⓘ	no	72.44	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus silagei JCM 19001
PATRIC: 1302250.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.08	no
125438	anaerobic	anaerobicⓘ	no	78.46	no
125438	spore-forming	spore-formingⓘ	no	84.27	yes
125438	aerobic	aerobicⓘ	no	92.70	no
125438	thermophilic	thermophileⓘ	no	94.99	yes
125438	flagellated	motile2+ⓘ	no	89.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus silagei sp. nov., isolated from orchardgrass silage.	Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima K	Int J Syst Evol Microbiol	10.1099/ijs.0.053124-0	2013
Phylogeny	Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili.	Zhang Z, Wang Y, Dong Y, Xiang F, Zhang Y, Zhang H, Sun Y, Guo Z	Syst Appl Microbiol	10.1016/j.syapm.2022.126344	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 )
#20998	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27022
#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;
#68371	Automatically annotated from API 50CH acid .
#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 .
#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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Secundilactobacillus silagei (DSM 27022, JCM 19001, KCTC 21050)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004354595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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