Name: Lacrimispora indolis 7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2602

Type strain:

Species: Lacrimispora indolis

Strain Designation: 7

Culture col. no.: CCUG 55582, JCM 1380, NCTC 11811, KCTC 5151, BCRC 11667, DSM 755, ATCC 25771, NCIB 9731, NCIMB 9731, VPI 4520, VTT E-042445

Strain history: <- DSM <- NCIB <- RH Vaughn, 7

NCBI tax ID(s): 69825 (species)

SI-ID 125932

ATCC 25771, NCIB 9731, DSM 755, JCM 1380, CCRC 11667, NCIMB 9731, NCTC 11811, BCRC 11667, KCTC 5151, VTT E-042445, CCUG 55582

Section

Lacrimispora indolis 7 is an anaerobe, spore-forming, mesophilic bacterium of the family Lachnospiraceae.

Gram-positive
spore-forming
anaerobe
mesophilic
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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Lacrimispora*
	Species	**Lacrimispora indolis**
	Full Scientific Name (LPSN)	Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020

Synonym

Clostridium indolis

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #60650]

Incubation period

1 day

Information on culture and growth conditions Culture and growth conditions

[Ref.: #427]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #427]

Culture medium growth

[Ref.: #427]

Culture medium link

Medium recipe at MediaDive

[Ref.: #427]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #427]	growth	37 °C
[Ref.: #60650]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #427]	Temperature range	mesophilic
[Ref.: #60650]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #427]	Oxygen tolerance	anaerobe
[Ref.: #60650]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.113

[Ref.: #67771]	Type of spore	spore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %99
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.448

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

[Ref.: #69479]

Global distribution of 16S sequence Y18184 (>99% sequence identity) for Lacrimispora from Microbeatlas

Aquatic Samples	207
Soil Samples	195
Animal Samples	3154
Plant Samples	52
Total Samples	3608

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

[Ref.: #427]

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.: #67770]	[Clostridium] indolis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1380	AB971794	1494	ENA	69825 tax ID
[Ref.: #427]	Clostridium indolis 16S rRNA gene, partial, strain DSM 755	Y18184	1488	ENA	69825 tax ID
[Ref.: #20218]	Clostridium indolis strain DSM 755 16S ribosomal RNA gene, partial sequence	HM245946	839	ENA	69825 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	[Clostridium] indolis DSM 755	GCA_000526995	contig	GenBank	1304881 tax ID
[Ref.: #67771]	Lacrimispora indolis NCTC11811	GCA_900618075	contig	GenBank	69825 tax ID
[Ref.: #66792]	Clostridium indolis DSM 755	1304881.3	wgs	PATRIC	1304881 tax ID	*
[Ref.: #66792]	[Clostridium] indolis strain NCTC11811	69825.3	wgs	PATRIC	69825 tax ID	*
[Ref.: #66792]	Clostridium indolis DSM 755	2524614838	draft	JGI IMG/M	1304881 tax ID	*

[Ref.: #427]	GC-content	44.0 mol%
[Ref.: #67770]	GC-content	44 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67771]	GC-content	44.93 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	44.0 mol%	thermal denaturation, midpoint method (Tm)

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: Clostridium indolis DSM 755 PATRIC: 1304881.3
[Ref.: #69481]	spore-forming	yes	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium indolis DSM 755 PATRIC: 1304881.3
[Ref.: #69480]	motile	yes	84.448	no
[Ref.: #69480]	gram-positive	yes	61.037	no
[Ref.: #69480]	anaerobic	yes	98.181	no
[Ref.: #69480]	halophile	no	93.396	no
[Ref.: #69480]	spore-forming	yes	88.472	yes
[Ref.: #69480]	thermophile	no	99.641	yes
[Ref.: #69480]	glucose-util	yes	87.276	no
[Ref.: #69480]	aerobic	no	97.89	yes
[Ref.: #69480]	flagellated	yes	55.765	no
[Ref.: #69480]	glucose-ferment	yes	75.163	no

Availability in culture collections External links

[Ref.: #427]

Culture collection no.

CCUG 55582, JCM 1380, NCTC 11811, KCTC 5151, BCRC 11667, DSM 755, ATCC 25771, NCIB 9731, NCIMB 9731, VPI 4520, VTT E-042445

[Ref.: #72133]

SI-ID 125932

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium indicum sp. nov., a novel anaerobic bacterium isolated from the sludge of an industrial effluent.	Gundawar K, Kumari S, Sharma S, Grover V, Patil PB, Korpole S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003199	2019	*
Genetics	The complete genome sequence of Clostridium indolis DSM 755(T.).	Biddle AS, Leschine S, Huntemann M, Han J, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Schaumberg A, Pati A, Stamatis D, Reddy T, Lobos E, Goodwin L, Nordberg HP, Cantor MN, Hua SX, Woyke T, Blanchard JL	Stand Genomic Sci	10.4056/sigs.5281010	2014	*
Phylogeny	Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).	Kwon MJ, Wei N, Millerick K, Popovic J, Finneran K	Curr Microbiol	10.1007/s00284-014-0531-x	2014	*

References

#427	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 755

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#60650 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55582

#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;

#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 )

#72133

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-ID125932.1 )

* These data were automatically processed and therefore are not curated

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Clostridium indolis DSM 755

Clostridium indolis DSM 755

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