Secundilactobacillus silagincola (DSM 102973, JCM 31144, IWT5)

Name: Secundilactobacillus silagincola (DSM 102973, JCM 31144, IWT5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140409

Type strain

Strain Designation IWT5

Culture col. no. DSM 102973 JCM 31144 IWT5 LMG 30917

NCBI tax ID(s) 1714681

Special Collections DSMZ JCM Literature strains

History <- M. Tohno, National Agriculture and Food Res. Org. (NARO), Japan; IWT5 M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; IWT5.

Links

Secundilactobacillus silagincola IWT5 is a facultative anaerobe, Gram-positive, rod-shaped prokaryote that forms circular colonies and was isolated from total mixed ration silage.

Gram-positive rod-shaped colony-forming facultative anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397781

LMG 30917,JCM 31144,DSM 102973

@ref 20215

Last LPSN update 2025-12-16 10:03:35

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Secundilactobacillus

Species Secundilactobacillus silagincola

Full scientific name Secundilactobacillus silagincola (Tohno et al. 2017) Zheng et al. 2020

Synonyms (1)

Lactobacillus silagincola

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43902	positive	1.3-3.0 µm	0.7 µm	rod-shaped
125438	positive					93.385

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43902	0.2-1.0 mm	white	circular	3 days	de Man, Rogosa and Sharpe (MRS) agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43902	de Man, Rogosa and Sharpe (MRS) agar
43016	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)	Range
43016	positive	growth	30	mesophilic
43902	positive	growth	10-37
43902	positive	optimum	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43902	positive	growth	4.0-7.5	acidophile

Physiology and metabolism

Oxygen tolerance

43902

Oxygen tolerancefacultative anaerobe

Spore formation

43902

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43902	NaCl		growth	4 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43902	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
43902	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
43902	27613 ChEBI	amygdalin	-	builds acid from
43902	18305 ChEBI	arbutin	-	builds acid from
43902	17057 ChEBI	cellobiose	-	builds acid from
43902	17108 ChEBI	D-arabinose	-	builds acid from
43902	18333 ChEBI	D-arabitol	-	builds acid from
43902	15824 ChEBI	D-fructose	-	builds acid from
43902	28847 ChEBI	D-fucose	-	builds acid from
43902	12936 ChEBI	D-galactose	+	builds acid from
43902	17634 ChEBI	D-glucose	+	builds acid from
43902	62318 ChEBI	D-lyxose	-	builds acid from
43902	16899 ChEBI	D-mannitol	-	builds acid from
43902	16024 ChEBI	D-mannose	-	builds acid from
43902	16988 ChEBI	D-ribose	+	builds acid from
43902	17924 ChEBI	D-sorbitol	-	builds acid from
43902	16443 ChEBI	D-tagatose	-	builds acid from
43902	65327 ChEBI	D-xylose	+	builds acid from
43902	17113 ChEBI	erythritol	-	builds acid from
43902	4853 ChEBI	esculin	+	hydrolysis
43902		esculin ferric citrate	+	builds acid from
43902	16813 ChEBI	galactitol	-	builds acid from
43902	28066 ChEBI	gentiobiose	-	builds acid from
43902	24265 ChEBI	gluconate	+	builds acid from
43902	17234 ChEBI	glucose	+	builds gas from
43902	17754 ChEBI	glycerol	-	builds acid from
43902	28087 ChEBI	glycogen	-	builds acid from
43902	15443 ChEBI	inulin	-	builds acid from
43902	30849 ChEBI	L-arabinose	+	builds acid from
43902	18403 ChEBI	L-arabitol	-	builds acid from
43902	18287 ChEBI	L-fucose	-	builds acid from
43902	62345 ChEBI	L-rhamnose	-	builds acid from
43902	17266 ChEBI	L-sorbose	-	builds acid from
43902	65328 ChEBI	L-xylose	-	builds acid from
43902	17716 ChEBI	lactose	-	builds acid from
43902	17306 ChEBI	maltose	+	builds acid from
43902	6731 ChEBI	melezitose	-	builds acid from
43902	28053 ChEBI	melibiose	+	builds acid from
43902	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
43902	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43902	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
43902	17268 ChEBI	myo-inositol	-	builds acid from
43902	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43902	16634 ChEBI	raffinose	-	builds acid from
43902	15963 ChEBI	ribitol	-	builds acid from
43902	17814 ChEBI	salicin	-	builds acid from
43902	28017 ChEBI	starch	-	builds acid from
43902	17992 ChEBI	sucrose	-	builds acid from
43902	27082 ChEBI	trehalose	-	builds acid from
43902	32528 ChEBI	turanose	-	builds acid from
43902	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
43902	16004 ChEBI	(R)-lactate
43902	16651 ChEBI	(S)-lactate
43902	16134 ChEBI	ammonia
43902	52071 ChEBI	dextran

Enzymes

@ref	Value	Activity	Ec
43902	acid phosphatase	+	3.1.3.2
43902	alkaline phosphatase	+	3.1.3.1
43902	alpha-fucosidase	-	3.2.1.51
43902	alpha-galactosidase	+	3.2.1.22
43902	alpha-glucosidase	+	3.2.1.20
43902	alpha-mannosidase	-	3.2.1.24
43902	beta-galactosidase	+	3.2.1.23
43902	beta-glucosidase	+	3.2.1.21
43902	beta-glucuronidase	-	3.2.1.31
43902	catalase	-	1.11.1.6
43902	chymotrypsin	-	3.4.4.5
43902	cystine aminopeptidase	-	3.4.11.3
43902	esterase (C 4)	+
43902	esterase Lipase (C 8)	+
43902	leucine aminopeptidase	+	3.4.1.1
43902	lipase (C 14)	-
43902	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43902	naphthol-AS-BI-phosphohydrolase	-
43902	trypsin	-	3.4.21.4
43902	valine aminopeptidase	+

Fatty acid profile

Metadata FA analysis

@ref

43902

Fatty acid	Percentage
C16:0	33.7
C18:1ω9c	16.5
unknown 18.846 / C19:1ω6c / C19:0&omeg	14.8
C18:1ω6c / C18:1ω7c	9.6
C16:1ω6c / C16:1ω7c	7.6
C14:0	7.6
C19:0ω8c cyclo	3
C19:0 iso	2
10-methyl C19:0	1.2
C17:0 cyclo	1
C18:0	0.9
iso-C19:1 I	0.9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Engineered	#Food production	#Food
#Environmental	#Microbial community	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
43016	total mixed ration silage	Iwate, Hachimantai (141° 2' 6'' E 39° 54' 1'' N)	Japan	JPN	Asia	39.9003	141.035 39.9003/141.035
43902	TMR silage, Zennoh Feed Mills of the Tohoku District, Miyagi, Japan, stored in Hachimantai, Iwate, Japan	Hachimantai, Iwate	Japan	JPN	Asia	39.9003	141.035 39.9003/141.035	de Man, Rogosa and Sharpe (MRS) agar	3 days	30
67770	Silage		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC085283 (>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
43016	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM258340v1 assembly for Secundilactobacillus silagincola IWT5	scaffold	GCA_002583405	1714681.3	2956991292	1714681	58.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43016	Lactobacillus silagincola gene for 16S ribosomal RNA, partial sequence, strain: IWT5	LC085283	1488		1714681

GC content

@ref	GC-content (mol%)	Method
43016	43.2	high performance liquid chromatography (HPLC)
67770	43.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Secundilactobacillus silagincola IWT5
NCBI: GCA_002583405.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.39	no
125438	anaerobic	anaerobicⓘ	no	86.04	yes
125438	aerobic	aerobicⓘ	no	92.01	yes
125438	spore-forming	spore-formingⓘ	no	77.58	yes
125438	thermophilic	thermophileⓘ	no	95.99	yes
125438	flagellated	motile2+ⓘ	no	88.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage.	Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M, Arita M, Ohkuma M, Kobayashi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.002196	2017

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 )
#43016	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102973
#43902	Masanori Tohno, Yasuhiro Tanizawa, Tomohiro Irisawa, Takaharu Masuda, Mitsuo Sakamoto, Masanori Arita, Moriya Ohkuma, Hisami Kobayashi: Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage. IJSEM 67: 3639 - 3644 2017 ( DOI 10.1099/ijsem.0.002196 , PubMed 28879844 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )
#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 silagincola (DSM 102973, JCM 31144, IWT5)

Name and taxonomic classification