Name: Secundilactobacillus silagincola IWT5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140409

Type strain:

Species: Secundilactobacillus silagincola

Strain Designation: IWT5

Culture col. no.: DSM 102973, JCM 31144, LMG 30917

Strain history: M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; IWT5.

NCBI tax ID(s): 1714681 (species)

SI-ID 397781

DSM 102973

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Secundilactobacillus*
	Species	**Secundilactobacillus silagincola**
	Full Scientific Name (LPSN)	Secundilactobacillus silagincola (Tohno et al. 2017) Zheng et al. 2020

Synonym

Lactobacillus silagincola

Information on morphological and physiological properties Morphology

[Ref.: #43902]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43902]	Cell length	1.3-3.0 µm

[Ref.: #43902]	Cell width	0.7 µm

[Ref.: #43902]	Cell shape	rod-shaped

[Ref.: #43902]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.837

[Ref.: #43902]	Colony size	0.2-1.0 mm
[Ref.: #43902]	Colony color	white
[Ref.: #43902]	Colony shape	circular
[Ref.: #43902]	Incubation period	3 days
[Ref.: #43902]	Cultivation medium used	de Man, Rogosa and Sharpe (MRS) agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43902]

Culture medium

de Man, Rogosa and Sharpe (MRS) agar

[Ref.: #43902]

Culture medium growth

[Ref.: #43016]

Culture medium

MRS MEDIUM (DSMZ Medium 11)

[Ref.: #43016]

Culture medium growth

[Ref.: #43016]

Culture medium link

Medium recipe at MediaDive

[Ref.: #43016]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43016]	growth	30 °C
[Ref.: #43902]	growth	10-37 °C
[Ref.: #43902]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43016]	Temperature range	mesophilic
[Ref.: #43902]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43902]			growth	4.0-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43902]

Oxygen tolerance

facultative anaerobe

[Ref.: #43902]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43902]		NaCl	no	growth	4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43902]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #43902]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #43902]	amygdalin ChEBI	-	builds acid from
[Ref.: #43902]	arbutin ChEBI	-	builds acid from
[Ref.: #43902]	cellobiose ChEBI	-	builds acid from
[Ref.: #43902]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43902]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43902]	D-fructose ChEBI	-	builds acid from
[Ref.: #43902]	D-fucose ChEBI	-	builds acid from
[Ref.: #43902]	D-galactose ChEBI	+	builds acid from
[Ref.: #43902]	D-glucose ChEBI	+	builds acid from
[Ref.: #43902]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43902]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43902]	D-mannose ChEBI	-	builds acid from
[Ref.: #43902]	D-ribose ChEBI	+	builds acid from
[Ref.: #43902]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43902]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43902]	D-xylose ChEBI	+	builds acid from
[Ref.: #43902]	erythritol ChEBI	-	builds acid from
[Ref.: #43902]	esculin ChEBI	+	hydrolysis
[Ref.: #43902]	esculin ferric citrate	+	builds acid from
[Ref.: #43902]	galactitol ChEBI	-	builds acid from
[Ref.: #43902]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43902]	gluconate ChEBI	+	builds acid from
[Ref.: #43902]	glucose ChEBI	+	builds gas from
[Ref.: #43902]	glycerol ChEBI	-	builds acid from
[Ref.: #43902]	glycogen ChEBI	-	builds acid from
[Ref.: #43902]	inulin ChEBI	-	builds acid from
[Ref.: #43902]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43902]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43902]	L-fucose ChEBI	-	builds acid from
[Ref.: #43902]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43902]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43902]	L-xylose ChEBI	-	builds acid from
[Ref.: #43902]	lactose ChEBI	-	builds acid from
[Ref.: #43902]	maltose ChEBI	+	builds acid from
[Ref.: #43902]	melezitose ChEBI	-	builds acid from
[Ref.: #43902]	melibiose ChEBI	+	builds acid from
[Ref.: #43902]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #43902]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43902]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43902]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43902]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #43902]	raffinose ChEBI	-	builds acid from
[Ref.: #43902]	ribitol ChEBI	-	builds acid from
[Ref.: #43902]	salicin ChEBI	-	builds acid from
[Ref.: #43902]	starch ChEBI	-	builds acid from
[Ref.: #43902]	sucrose ChEBI	-	builds acid from
[Ref.: #43902]	trehalose ChEBI	-	builds acid from
[Ref.: #43902]	turanose ChEBI	-	builds acid from
[Ref.: #43902]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43902]	(R)-lactate ChEBI	yes
[Ref.: #43902]	(S)-lactate ChEBI	yes
[Ref.: #43902]	ammonia ChEBI	yes
[Ref.: #43902]	dextran ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43902]	acid phosphatase	+	3.1.3.2
[Ref.: #43902]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43902]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43902]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43902]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43902]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43902]	beta-galactosidase	+	3.2.1.23
[Ref.: #43902]	beta-glucosidase	+	3.2.1.21
[Ref.: #43902]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43902]	catalase	-	1.11.1.6
[Ref.: #43902]	chymotrypsin	-	3.4.4.5
[Ref.: #43902]	cystine aminopeptidase	-	3.4.11.3
[Ref.: #43902]	esterase (C 4)	+
[Ref.: #43902]	esterase Lipase (C 8)	+
[Ref.: #43902]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #43902]	lipase (C 14)	-
[Ref.: #43902]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43902]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43902]	trypsin	-	3.4.21.4
[Ref.: #43902]	valine aminopeptidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43016]	Sample type/isolated from	total mixed ration silage
[Ref.: #43016]	Geographic location (country and/or sea, region)	Iwate, Hachimantai (141° 2' 6'' E 39° 54' 1'' N)
[Ref.: #43016]	Country	Japan
[Ref.: #43016]	Country ISO 3 Code	JPN
[Ref.: #43016]	Continent	Asia
[Ref.: #43016]	Geographic location	39.9003°/141.0350°

[Ref.: #43902]	Sample type/isolated from	TMR silage, Zennoh Feed Mills of the Tohoku District, Miyagi, Japan, stored in Hachimantai, Iwate, Japan
[Ref.: #43902]	Geographic location (country and/or sea, region)	Hachimantai, Iwate
[Ref.: #43902]	Country	Japan
[Ref.: #43902]	Country ISO 3 Code	JPN
[Ref.: #43902]	Continent	Asia
[Ref.: #43902]	Geographic location	39.9003°/141.0350°
[Ref.: #43902]	Enrichment culture	de Man, Rogosa and Sharpe (MRS) agar
[Ref.: #43902]	Enrichment culture duration	3 days
[Ref.: #43902]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Silage
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #43016]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43016]	Lactobacillus silagincola gene for 16S ribosomal RNA, partial sequence, strain: IWT5	LC085283	1488	ENA	1714681 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Secundilactobacillus silagincola IWT5	GCA_002583405	scaffold	GenBank	1714681 tax ID

[Ref.: #43016]	GC-content	43.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	43.1 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Secundilactobacillus silagincola IWT5 NCBI: GCA_002583405.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Secundilactobacillus silagincola IWT5 NCBI: GCA_002583405.1
[Ref.: #69480]	flagellated	no	96.835	yes
[Ref.: #69480]	gram-positive	yes	96.483	no
[Ref.: #69480]	anaerobic	no	89.668	yes
[Ref.: #69480]	aerobic	no	94.012	no
[Ref.: #69480]	halophile	yes	89.097	no
[Ref.: #69480]	spore-forming	no	93.188	no
[Ref.: #69480]	glucose-util	yes	85.716	no
[Ref.: #69480]	thermophile	no	99.54	yes
[Ref.: #69480]	motile	no	94.122	no
[Ref.: #69480]	glucose-ferment	yes	85.303	no

Availability in culture collections External links

[Ref.: #43016]

Culture collection no.

DSM 102973, JCM 31144, LMG 30917

[Ref.: #96685]

SI-ID 397781

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96685

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID397781.1 )

* These data were automatically processed and therefore are not curated

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