Lacrimispora indolis (CCUG 55582, JCM 1380, NCTC 11811)

Name: Lacrimispora indolis (CCUG 55582, JCM 1380, NCTC 11811)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2602

Type strain

Strain Designation 7, strain 7

Culture col. no. CCUG 55582 JCM 1380 NCTC 11811 KCTC 5151 BCRC 11667 8 more

NCBI tax ID(s) 1304881 69825

Special Collections DSMZ CCUG JCM KCTC

Links

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

spore-forming Gram-positive anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:47:21

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Lacrimispora

Species Lacrimispora indolis

Full scientific name Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020

Synonyms (3)

Clostridium indolis
"Eubacterium indolis"
Clostridium methoxybenzovorans

Morphology

Cell morphology

67771

Gram stainpositive

Colony morphology

60650

Incubation period1 day

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
427	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
427	positive	growth	37	mesophilic
60650	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
427	anaerobe
60650	anaerobe
67771	anaerobe
125438	anaerobe
125439	anaerobe

Spore formation

@ref	Type of spore	Spore formation
67771	spore

Isolation, sampling and environmental information

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
427	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67771	ASM52699v1 assembly for Lacrimispora indolis DSM 755	contig	GCA_000526995	1304881.3	2524614838	1304881	76.65
67771	NCTC11811 assembly for Lacrimispora indolis NCTC11811	contig	GCA_900618075	69825.3	8116823654	69825	49.22

Genome browser: GCA_000526995

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium indolis strain DSM 755 16S ribosomal RNA gene, partial sequence	HM245946	839	69825
427	Clostridium indolis 16S rRNA gene, partial, strain DSM 755	Y18184	1488	69825
67770	[Clostridium] indolis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1380	AB971794	1494	69825

GC content

@ref	GC-content (mol%)
427	44.0
67770	44
67771	44.93
67771	44.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] indolis DSM 755
NCBI: GCA_000526995

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	88.10	no
125439	motility	BacteriaNetⓘ	yes	84.50	no
125439	gram_stain	BacteriaNetⓘ	variable	72.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium indolis DSM 755
PATRIC: 1304881.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	60.38	yes
125438	anaerobic	anaerobicⓘ	yes	91.32	yes
125438	spore-forming	spore-formingⓘ	yes	73.66	yes
125438	aerobic	aerobicⓘ	no	93.80	yes
125438	thermophilic	thermophileⓘ	no	95.20	no
125438	flagellated	motile2+ⓘ	yes	74.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999.	Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma M, Tohno M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004951	2021
	Characterization of the Gut Microbiome in Healthy Dogs and Dogs with Diabetes Mellitus.	Kwong TC, Chau ECT, Mak MCH, Choy CT, Chan LT, Pang CK, Zhou J, Poon PHC, Guan Y, Tsui SKW, Chan SW, Leung GPH, Tai WCS, Kwan YW.	Animals (Basel)	10.3390/ani13152479	2023
	Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.	Ahn JS, Han EJ, Chung HJ.	Front Microbiol	10.3389/fmicb.2025.1533580	2025
	Identification of the Intestinal Microbes Associated with Locomotion.	Ahn JS, Choi YJ, Kim HB, Chung HJ, Hong ST.	Int J Mol Sci	10.3390/ijms241411392	2023
Phylogeny	Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa.	Haas KN, Blanchard JL.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003698	2020
Phylogeny	Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes.	Kardos G, Laczko L, Kaszab E, Timmer B, Szarka K, Prepost E, Banyai K.	Antibiotics (Basel)	10.3390/antibiotics13070573	2024
Enzymology	Reduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats.	Yao Y, Fu B, Han D, Zhang Y, Wei Z, Liu H.	Environ Microbiol Rep	10.1111/1758-2229.13129	2023
Metabolism	The alternative coproporphyrinogen III oxidase (CgoN) catalyzes the oxygen-independent conversion of coproporphyrinogen III into coproporphyrin III.	Mingers T, Barthels S, Mass V, Acuna JMB, Biedendieck R, Cooke A, Dailey TA, Gerdes S, Blankenfeldt W, Dailey HA, Warren MJ, Jahn M, Jahn D.	Front Microbiol	10.3389/fmicb.2024.1378989	2024
	Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.	Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y.	Nat Commun	10.1038/s41467-022-34771-y	2022
	Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.	Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T.	ISME Commun	10.1038/s43705-021-00017-z	2021
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	Lacrimispora brassicae sp. nov. isolated from fermented cabbage, and proposal of Clostridium indicum Gundawar et al. 2019 and Clostridium methoxybenzovorans Mechichi et al. 1999 as heterotypic synonyms of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020, respectively.	Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma M, Tohno M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006456	2024
Biotechnology	Lacrimispora sinapis sp. nov., isolated from pickled potherb mustard (Brassica juncea Coss.).	Ren Q, Wang D, Han J, Liu Z, Wu Z.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006675	2025
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
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
#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 .
#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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Lacrimispora indolis (CCUG 55582, JCM 1380, NCTC 11811)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000526995

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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