Archive BacDiveID:10.13145/bacdive650.20250331.9.3

Strain identifier

BacDive ID: 650

Type strain:

Species: Heyndrickxia coagulans

Strain Designation: M-39

Strain history: IAM 12320 <-- O. Nakayama M-39 ("Bacillus racemilacticus").

NCBI tax ID(s): 1398 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 1042

BacDive-ID: 650

DSM-Number: 2314

keywords: genome sequence, Bacteria, spore-forming, thermophilic, lactate production

description: Heyndrickxia coagulans M-39 is a spore-forming, thermophilic bacterium that produces lactate and was isolated from rhizosphere.

NCBI tax id

NCBI tax id: 1398
Matching level: species

strain history

@ref	history
1042	<- NCIB <- O. Nakayama, M-39 (Bacillus racemilacticus)
67770	IAM 12320 <-- O. Nakayama M-39 ("Bacillus racemilacticus").

doi: 10.13145/bacdive650.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Heyndrickxia
species: Heyndrickxia coagulans
full scientific name: Heyndrickxia coagulans (Hammer 1915) Narsing Rao et al. 2023
synonyms
@ref synonym
20215 Bacillus coagulans
20215 Weizmannia coagulans

@ref	synonym
20215	Bacillus coagulans
20215	Weizmannia coagulans

@ref: 1042

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Heyndrickxia

species: Heyndrickxia coagulans

full scientific name: Heyndrickxia coagulans (Hammer 1915) Narsing-Rao et al. 2023

strain designation: M-39

type strain: no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
1042	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	yes	https://mediadive.dsmz.de/medium/220	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
1042	NUTRIENT AGAR (DSMZ Medium 1)	yes	https://mediadive.dsmz.de/medium/1	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@ref	growth	type	temperature
1042	positive	growth	55
67770	positive	growth	30

Physiology and metabolism

spore formation

@ref: 125438
spore formation: yes
confidence: 91.58

compound production

@ref	compound
1042	L(+) lactic acid
1042	DL lactic acid

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
1042	rhizosphere
67770	Soil	Kofu, Yamanashi Pref.	Japan	JPN	Asia

isolation source categories

Cat1: #Host Body-Site
Cat2: #Plant
Cat3: #Rhizosphere

Safety information

risk assessment

@ref: 1042
pathogenicity human: yes, in single cases
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Heyndrickxia coagulans DSM 2314	GCA_006716385	complete	ncbi	1398
66792	Bacillus coagulans strain DSM 2314	1398.125	complete	patric	1398

GC content

@ref: 1042
GC-content: 45.3

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	75.485	no
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	89.219	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	61.439	no
125438	spore-forming	spore-forming	Ability to form endo- or exospores	yes	91.58	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	80.238	no
125438	motile2+	flagellated	Ability to perform flagellated movement	yes	76.989	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	yes	73.4
125439	BacteriaNet	motility	Ability to perform movement	yes	57.6
125439	BacteriaNet	gram_stain	Reaction to gram-staining	variable	86.6
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	anaerobe	67.2

External links

@ref: 1042

culture collection no.: DSM 2314, ATCC 23498, NCIB 10276, JCM 20478, IAM 12320, NCIMB 10276

straininfo link

@ref: 70325
straininfo: 92159

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Metabolism	18247027	Lactic acid production from lime-treated wheat straw by Bacillus coagulans: neutralization of acid by fed-batch addition of alkaline substrate.	Maas RH, Bakker RR, Jansen ML, Visser D, de Jong E, Eggink G, Weusthuis RA	Appl Microbiol Biotechnol	10.1007/s00253-008-1361-1	2008	Bacillus/enzymology/metabolism, Biodegradation, Environmental, Biomass, Bioreactors, Calcium Compounds/chemistry, Calcium Hydroxide/chemistry, Fermentation, Hydrogen-Ion Concentration, Hydrolysis, Industrial Microbiology, Lactic Acid/chemistry/metabolism, Oxides/chemistry, Triticum/chemistry/*metabolism, Waste Products/analysis	Biotechnology
Metabolism	27464829	Precultivation of Bacillus coagulans DSM2314 in the presence of furfural decreases inhibitory effects of lignocellulosic by-products during L(+)-lactic acid fermentation.	van der Pol E, Springer J, Vriesendorp B, Weusthuis R, Eggink G	Appl Microbiol Biotechnol	10.1007/s00253-016-7725-z	2016	Adaptation, Physiological, Bacillus coagulans/drug effects/metabolism/physiology, Biosynthetic Pathways/genetics, Cell Wall/metabolism, Culture Media/chemistry, Drug Tolerance, Fermentation, Furaldehyde/metabolism/toxicity, Gene Expression Profiling, Lactic Acid/metabolism, Lignin/*metabolism	Cultivation
Biotechnology	27872661	Production of l(+)-lactic acid from acid pretreated sugarcane bagasse using Bacillus coagulans DSM2314 in a simultaneous saccharification and fermentation strategy.	van der Pol EC, Eggink G, Weusthuis RA	Biotechnol Biofuels	10.1186/s13068-016-0646-3	2016
Biotechnology	34799761	Revisiting the production of L( +)-lactic acid from vine shoots: bioconversion improvements by employing thermotolerant bacteria.	Garita-Cambronero J, Hijosa-Valsero M, Paniagua-Garcia AI, Diez-Antolinez R	Appl Microbiol Biotechnol	10.1007/s00253-021-11693-1	2021	Bacillus coagulans, Fermentation, Hydrolysis, Lactic Acid, Wine

Reference

@id	authors	catalogue	doi/url	title
1042	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2314)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-2314
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
70325	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID92159.1	StrainInfo: A central database for resolving microbial strain identifiers
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

compound production

Isolation, sampling and environmental information

isolation

isolation source categories

Safety information

risk assessment

Sequence information

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference