Leptotrichia shahii (DSM 19757, CCUG 47503, CIP 107916)

Name: Leptotrichia shahii (DSM 19757, CCUG 47503, CIP 107916)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17866

Type strain

Strain Designation LB 37

Culture col. no. DSM 19757 CCUG 47503 CIP 107916 LB 37 VPI N06A-34 1 more

NCBI tax ID(s) 1122172 157691

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- CIP <- CCUG <- I. Olsen; LB 37 <- W. E. C. Moore CCUG 47503 <-- I. Olsen LB 37 <-- W. E. C. Moore VPI N06A-34. CIP <- 2003, CCUG <- I. Olsen, Oslo, Norway: strain LB 37 <- W.E.C. Moore, VPI, Blacksburg, USA

Links

Leptotrichia shahii LB 37 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human gingivitis.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 131423

CCUG 47503,CIP 107916,DSM 19757,JCM 16776

@ref 20215

Last LPSN update 2026-02-09 11:22:19

Domain Bacteria

Phylum Fusobacteriota

Class Fusobacteriia

Order Fusobacteriales

Family Leptotrichiaceae

Genus Leptotrichia

Species Leptotrichia shahii

Full scientific name Leptotrichia shahii Eribe et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30006	negative	12.5 µm	0.7 µm	rod-shaped
122578	negative			rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8297	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
8297	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
33180	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122578	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8297	positive	growth	37
30006	positive	growth	25-37
30006	positive	optimum	37
33180	positive	growth	37
57723	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8297	anaerobe
30006	anaerobe
57723	anaerobe
122578	anaerobe
125439	anaerobe	99.5

Spore formation

30006

Spore formationno

Observation

30006

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30006	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
122578	17057 ChEBI	cellobiose	-	degradation
122578	17108 ChEBI	D-arabinose	+	degradation
122578	15824 ChEBI	D-fructose	-	degradation
122578	17634 ChEBI	D-glucose	-	degradation
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
122578	65327 ChEBI	D-xylose	+	degradation
30006	4853 ChEBI	esculin	+	hydrolysis
122578	4853 ChEBI	esculin	-	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
122578	17716 ChEBI	lactose	-	degradation
122578	17306 ChEBI	maltose	+	degradation
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
122578	17632 ChEBI	nitrate	-	reduction
122578	17632 ChEBI	nitrate	+	respiration
122578	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
122578	17814 ChEBI	salicin	+	degradation
122578	17992 ChEBI	sucrose	-	degradation
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
122578	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
122578	amylase	+
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
122578	beta-galactosidase	-	3.2.1.23
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
122578	caseinase	+	3.4.21.50
30006	catalase	+	1.11.1.6
122578	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
122578	gelatinase	-
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
122578	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
122578	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
122578	oxidase	-
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
122578	protease	-
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
122578	tween esterase	+
68380	tyrosine arylamidase	-		from API rID32A
122578	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122578	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
8297	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Gingiva

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
8297	human gingivitis	USA	USA	North America
57723	Human gingivitis
67770	Patient with gingivitis
122578	Human, Gingivitis

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
8297	yes, in single cases	1	Risk group (German classification) According to TRBA 466
122578		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM832782v1 assembly for Leptotrichia shahii JCM16776	complete	GCA_008327825	157691.3	8066215204	157691	98.87
67770	ASM37304v1 assembly for Leptotrichia shahii DSM 19757	scaffold	GCA_000373045	1122172.3	2515154071	1122172	75.32

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8297	Leptotrichia shahii strain LB37 16S ribosomal RNA gene, partial sequence	AY029806	1485		157691
67770	Leptotrichia shahii gene for 16S ribosomal RNA, partial sequence, strain: JCM 16776	AB558171	1473		157691

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leptotrichia shahii DSM 19757
NCBI: GCA_000373045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no
125439	gram_stain	BacteriaNetⓘ	variable	76.80	no
125439	motility	BacteriaNetⓘ	yes	75.10	no
125439	spore_formation	BacteriaNetⓘ	yes	82.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Leptotrichia shahii JCM16776
NCBI: GCA_008327825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	88.67	yes
125438	anaerobic	anaerobicⓘ	yes	73.29	yes
125438	aerobic	aerobicⓘ	no	94.94	yes
125438	spore-forming	spore-formingⓘ	no	87.08	no
125438	thermophilic	thermophileⓘ	no	93.96	yes
125438	flagellated	motile2+ⓘ	no	86.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia.	Watanabe S, Cui B, Kiga K, Aiba Y, Tan XE, Sato'o Y, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Li FY, Azam AH, Nakada Y, Sasahara T, Cui L.	Front Microbiol	10.3389/fmicb.2019.02838	2019
Metabolism	C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.	Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F.	Science	10.1126/science.aaf5573	2016
	Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.	Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV.	Mol Cell	10.1016/j.molcel.2015.10.008	2015
Phylogeny	Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis.	Eisenberg T, Fawzy A, Nicklas W, Semmler T, Ewers C.	BMC Genomics	10.1186/s12864-016-3206-0	2016
Phylogeny	Comparative analysis of salivary cytokine profiles and oral microbial composition in caries-active and caries-free children.	Karched M, Alyahya A, Khalaf ME, Bhardwaj RG, Al-Sane M, Qudeimat MA.	J Dent	10.1016/j.jdent.2025.105611	2025
	In vitro investigation of the impact of contemporary restorative materials on cariogenic bacteria counts and gene expression.	Khalaf ME, Karched M, Shawaf NA, Qudeimat MA.	J Dent	10.1016/j.jdent.2023.104486	2023
Pathogenicity	Influence of Maqian essential oil on gut microbiota and immunoresponses in type 1 diabetes: In silico study.	Dahab M, Idris H, Zhang P, Aladhadh M, Alatawi EA, Ming LC, Goh KW, Ser HL.	Heliyon	10.1016/j.heliyon.2024.e29490	2024
Genetics	Genetic manipulation of bacteriophage T4 utilizing the CRISPR-Cas13b system.	Bhoobalan-Chitty Y, Stouf M, De Paepe M.	Front Genome Ed	10.3389/fgeed.2024.1495968	2024
	Diversity in the composition of pleural cavity and oral cavity microbiota in different bacterial empyema.	Huang Y, Gao QH, Liu CJ, Su T, Liu J, Liang ZY, Zhao ZJ, Chen LP, Yi YN, Li XR, He J.	Front Microbiol	10.3389/fmicb.2025.1566606	2025
Phylogeny	Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children.	Stephen AS, Worrall S, Somani C, Allaker RP, Davies J, Nibali L, Donos N.	J Clin Periodontol	10.1111/jcpe.14201	2025
	CRISPR/Cas13 sgRNA-Mediated RNA-RNA Interaction Mapping in Live Cells with APOBEC RNA Editing.	Diao LT, Xie SJ, Xu WY, Zhang HH, Hou YR, Hu YX, Liang XX, Liang JB, Zhang Q, Xiao ZD.	Adv Sci (Weinh)	10.1002/advs.202409004	2024
	Dental plaque microbiota profiles of children with caries-free and caries-active dentition.	Qudeimat MA, Alyahya A, Karched M, Behbehani J, Salako NO.	J Dent	10.1016/j.jdent.2020.103539	2021
	Implementation of RT-RAA and CRISPR/Cas13a for an NiV Point-of-Care Test: A Promising Tool for Disease Control.	Yin J, Cui J, Zheng H, Guo T, Wei R, Sha Z, Gu S, Ni B.	Viruses	10.3390/v17040483	2025
	From Origin to the Present: Establishment, Mechanism, Evolutions and Biomedical Applications of the CRISPR/Cas-Based Macromolecular System in Brief.	Yuan Z.	Molecules	10.3390/molecules30040947	2025
Genetics	Novel potential biomarkers for predicting childhood caries via metagenomic analysis.	Zhang H, Zheng X, Huang Y, Zou Y, Zhang T, Repo MA, Yin M, You Y, Jie Z, Xu WA.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1522970	2025
	tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector.	Jain I, Kolesnik M, Kuznedelov K, Minakhin L, Morozova N, Shiriaeva A, Kirillov A, Medvedeva S, Livenskyi A, Kazieva L, Makarova KS, Koonin EV, Borukhov S, Severinov K, Semenova E.	Sci Adv	10.1126/sciadv.adl0164	2024
	De novo design of hypercompact transcript degraders by engineering substrate-specific toxins and Cas6-CBS system.	Chen PR, Qin PP, Wang YN, Liu PF, Zhang XY, Qian T, Ye BC, Yin BC.	Nat Commun	10.1038/s41467-025-63166-y	2025
Genetics	Effect of implant abutment surface treatments on bacterial biofilm composition and structure.	Anitua E, Murias-Freijo A, Tierno R, Tejero R, Hamdan Alkhraisat M.	J Oral Microbiol	10.1080/20002297.2025.2459922	2025
	HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome.	Mann AE, Aumend C, Crull S, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Rowe M, Blouin T, Soule A, Kelly C, DOMHaIN Study Team, Burne RA, Coker MO, Richards VP.	Microbiome	10.1186/s40168-025-02123-9	2025
	Molecular mechanism for target RNA recognition and cleavage of Cas13h.	Chen F, Zhang C, Xue J, Wang F, Li Z.	Nucleic Acids Res	10.1093/nar/gkae324	2024
	Programmable RNA N⁶-methyladenosine editing with CRISPR/dCas13a in plants.	Shi C, Zou W, Liu X, Zhang H, Li X, Fu G, Fei Q, Qian Q, Shang L.	Plant Biotechnol J	10.1111/pbi.14307	2024
	Developed and Validated Capillary Isotachophoresis Method for the Rapid Determining Organic Acids in Children's Saliva.	Dobrowolska-Iwanek J, Jamka-Kasprzyk M, Rusin M, Pasko P, Grekh S, Jurczak A.	Molecules	10.3390/molecules28031092	2023
	Applications of CRISPR/Cas13-Based RNA Editing in Plants.	Kavuri NR, Ramasamy M, Qi Y, Mandadi K.	Cells	10.3390/cells11172665	2022
	Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a.	Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G.	Nucleic Acids Res	10.1093/nar/gkad1127	2024
	Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages.	Johnson MC, Hille LT, Kleinstiver BP, Meeske AJ, Bondy-Denomy J.	Mol Cell	10.1016/j.molcel.2022.05.002	2022
	A CRISPR-Cas13a Based Strategy That Tracks and Degrades Toxic RNA in Myotonic Dystrophy Type 1.	Zhang N, Bewick B, Xia G, Furling D, Ashizawa T.	Front Genet	10.3389/fgene.2020.594576	2020
	Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants.	Yu L, Zou J, Hussain A, Jia R, Fan Y, Liu J, Nie X, Zhang X, Jin S.	Genome Biol	10.1186/s13059-024-03448-8	2024
	Structural principles of CRISPR-Cas enzymes used in nucleic acid detection.	Das A, Goswami HN, Whyms CT, Sridhara S, Li H.	J Struct Biol	10.1016/j.jsb.2022.107838	2022
	CRISPR-Cas Gene Editing Technology in Potato	Sapakhova Z, Kanat R, Choi K, Daurov D, Daurova A, Zhambakin K, Shamekova M.	Int J Mol Sci		2025
	Broad-spectrum resistance against multiple PVY-strains by CRSIPR/Cas13 system in Solanum tuberosum crop.	Noureen A, Zuhaib Khan M, Amin I, Zainab T, Ahmad N, Haider S, Mansoor S.	GM Crops Food	10.1080/21645698.2022.2080481	2022
	A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae.	Zhang Y, Ge H, Marchisio MA.	Front Bioeng Biotechnol	10.3389/fbioe.2022.922949	2022
	Structure-based design of gRNA for Cas13.	Bandaru S, Tsuji MH, Shimizu Y, Usami K, Lee S, Takei NK, Yoshitome K, Nishimura Y, Otsuki T, Ito T.	Sci Rep	10.1038/s41598-020-68459-4	2020
	Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems.	Wang B, Zhang T, Yin J, Yu Y, Xu W, Ding J, Patel DJ, Yang H.	Mol Cell	10.1016/j.molcel.2020.12.033	2021
	CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria.	Ko SC, Woo HM.	Nucleic Acids Res	10.1093/nar/gkad1130	2024
	Engineering CRISPR immune systems conferring GLRaV-3 resistance in grapevine.	Jiao B, Hao X, Liu Z, Liu M, Wang J, Liu L, Liu N, Song R, Zhang J, Fang Y, Xu Y.	Hortic Res	10.1093/hr/uhab023	2022
	Precise editing of FGFR3-TACC3 fusion genes with CRISPR-Cas13a in glioblastoma.	Wu Y, Jin W, Wang Q, Zhou J, Wang Y, Tan Y, Cui X, Tong F, Yang E, Wang J, Kang C.	Mol Ther	10.1016/j.ymthe.2021.07.002	2021
Genetics	Raising Climate-Resilient Crops: Journey From the Conventional Breeding to New Breeding Approaches.	Gaba Y, Pareek A, Singla-Pareek SL.	Curr Genomics	10.2174/1389202922666210928151247	2021
	Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis.	Wang Q, Chen X, Hu H, Wei X, Wang X, Peng Z, Ma R, Zhao Q, Zhao J, Liu J, Deng F.	Sci Rep	10.1038/s41598-021-82709-z	2021
	Multimodal Data Integration Reveals Mode of Delivery and Snack Consumption Outrank Salivary Microbiome in Association With Caries Outcome in Thai Children.	Wu TT, Xiao J, Manning S, Saraithong P, Pattanaporn K, Paster BJ, Chen T, Vasani S, Gilbert C, Zeng Y, Li Y.	Front Cell Infect Microbiol	10.3389/fcimb.2022.881899	2022
Transcriptome	Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis.	Aman R, Mahas A, Butt H, Aljedaani F, Mahfouz M.	Viruses	10.3390/v10120732	2018
	RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems.	Meeske AJ, Marraffini LA.	Mol Cell	10.1016/j.molcel.2018.07.013	2018
Phylogeny	From Mouth to Brain: Distinct Supragingival Plaque Microbiota Composition in Cerebral Palsy Children With Caries.	Liu M, Shi Y, Wu K, Xie W, Ser HL, Jiang Q, Wu L.	Front Cell Infect Microbiol	10.3389/fcimb.2022.814473	2022
Metabolism	Urease and Dental Plaque Microbial Profiles in Children.	Morou-Bermudez E, Rodriguez S, Bello AS, Dominguez-Bello MG.	PLoS One	10.1371/journal.pone.0139315	2015
Enzymology	Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status.	Richards VP, Alvarez AJ, Luce AR, Bedenbaugh M, Mitchell ML, Burne RA, Nascimento MM.	Infect Immun	10.1128/iai.00106-17	2017
	Expanding the plant genome editing toolbox with recently developed CRISPR-Cas systems.	Wada N, Osakabe K, Osakabe Y.	Plant Physiol	10.1093/plphys/kiac027	2022
Pathogenicity	Genome Editing Strategies to Protect Livestock from Viral Infections.	Sollner JH, Mettenleiter TC, Petersen B.	Viruses	10.3390/v13101996	2021
	Epidemiological and Microbiome Characterization of Black Tooth Stain in Preschool Children.	Zhang Y, Yu R, Zhan JY, Cao GZ, Feng XP, Chen X.	Front Pediatr	10.3389/fped.2022.751361	2022
Genetics	CRISPR-Cas9: From a bacterial immune system to genome-edited human cells in clinical trials.	Kick L, Kirchner M, Schneider S.	Bioengineered	10.1080/21655979.2017.1299834	2017
Enzymology	Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing.	Jing X, Xie B, Chen L, Zhang N, Jiang Y, Qin H, Wang H, Hao P, Yang S, Li X.	Nucleic Acids Res	10.1093/nar/gky433	2018
	CRISPR-based strategies in infectious disease diagnosis and therapy.	Binnie A, Fernandes E, Almeida-Lousada H, de Mello RA, Castelo-Branco P.	Infection	10.1007/s15010-020-01554-w	2021
Genetics	Structure and engineering of the minimal type VI CRISPR-Cas13bt3.	Nakagawa R, Kannan S, Altae-Tran H, Takeda SN, Tomita A, Hirano H, Kusakizako T, Nishizawa T, Yamashita K, Zhang F, Nishimasu H, Nureki O.	Mol Cell	10.1016/j.molcel.2022.08.001	2022
	Bacterial Composition and Metabolomics of Dental Plaque From Adolescents.	Havsed K, Stensson M, Jansson H, Carda-Dieguez M, Pedersen A, Neilands J, Svensater G, Mira A.	Front Cell Infect Microbiol	10.3389/fcimb.2021.716493	2021
	Genome Editing for Resistance to Insect Pests: An Emerging Tool for Crop Improvement.	Tyagi S, Kesiraju K, Saakre M, Rathinam M, Raman V, Pattanayak D, Sreevathsa R.	ACS Omega	10.1021/acsomega.0c01435	2020
	Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review.	Wang D, Jin S, Lu Q, Chen Y.	J Fungi (Basel)	10.3390/jof9030362	2023
	The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes.	Hong BY, Hoare A, Cardenas A, Dupuy AK, Choquette L, Salner AL, Schauer PK, Hegde U, Peterson DE, Dongari-Bagtzoglou A, Strausbaugh LD, Diaz PI.	J Dent Res	10.1177/0022034520915879	2020
Genetics	Prokaryotic Argonaute Proteins as a Tool for Biotechnology.	Kropocheva EV, Lisitskaya LA, Agapov AA, Musabirov AA, Kulbachinskiy AV, Esyunina DM.	Mol Biol	10.1134/s0026893322060103	2022
	Three New Cs for CRISPR: Collateral, Communicate, Cooperate.	Varble A, Marraffini LA.	Trends Genet	10.1016/j.tig.2019.03.009	2019
Transcriptome	RNA virus interference via CRISPR/Cas13a system in plants.	Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M.	Genome Biol	10.1186/s13059-017-1381-1	2018
	Generation of virus-resistant potato plants by RNA genome targeting.	Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock R, Nie B, Zhang J.	Plant Biotechnol J	10.1111/pbi.13102	2019
Metabolism	Abrogation of PRRSV infectivity by CRISPR-Cas13b-mediated viral RNA cleavage in mammalian cells.	Cui J, Techakriengkrai N, Nedumpun T, Suradhat S.	Sci Rep	10.1038/s41598-020-66775-3	2020
	Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction.	Bayoumi M, Munir M.	Front Microbiol	10.3389/fmicb.2021.743580	2021
	Not Only Editing: A Cas-Cade of CRISPR/Cas-Based Tools for Functional Genomics in Plants and Animals.	Devillars A, Magon G, Pirrello C, Palumbo F, Farinati S, Barcaccia G, Lucchin M, Vannozzi A.	Int J Mol Sci	10.3390/ijms25063271	2024
	CRISPR-Cas13: A new technology for the rapid detection of pathogenic microorganisms.	Huang Z, Fang J, Zhou M, Gong Z, Xiang T.	Front Microbiol	10.3389/fmicb.2022.1011399	2022
	Programmable System of Cas13-Mediated RNA Modification and Its Biological and Biomedical Applications.	Tang T, Han Y, Wang Y, Huang H, Qian P.	Front Cell Dev Biol	10.3389/fcell.2021.677587	2021
	A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13.	Vialetto E, Yu Y, Collins SP, Wandera KG, Barquist L, Beisel CL.	Cell Host Microbe	10.1016/j.chom.2022.05.013	2022
Metabolism	Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.	Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA.	Nat Struct Mol Biol	10.1038/nsmb.3466	2017
	Prenatal and postnatal determinants in shaping offspring's microbiome in the first 1000 days: study protocol and preliminary results at one month of life.	Raspini B, Porri D, De Giuseppe R, Chieppa M, Liso M, Cerbo RM, Civardi E, Garofoli F, Monti MC, Vacca M, De Angelis M, Cena H.	Ital J Pediatr	10.1186/s13052-020-0794-8	2020
Phylogeny	A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, species differentiation, and drug-resistance genotyping.	Cunningham CH, Hennelly CM, Lin JT, Ubalee R, Boyce RM, Mulogo EM, Hathaway N, Thwai KL, Phanzu F, Kalonji A, Mwandagalirwa K, Tshefu A, Juliano JJ, Parr JB.	EBioMedicine	10.1016/j.ebiom.2021.103415	2021
	Engineered materials for in vivo delivery of genome-editing machinery.	Tong S, Moyo B, Lee CM, Leong K, Bao G.	Nat Rev Mater	10.1038/s41578-019-0145-9	2019
Genetics	Current trends of clinical trials involving CRISPR/Cas systems.	Zhang S, Wang Y, Mao D, Wang Y, Zhang H, Pan Y, Wang Y, Teng S, Huang P.	Front Med (Lausanne)	10.3389/fmed.2023.1292452	2023
	Establishing RNA virus resistance in plants by harnessing CRISPR immune system.	Zhang T, Zheng Q, Yi X, An H, Zhao Y, Ma S, Zhou G.	Plant Biotechnol J	10.1111/pbi.12881	2018
Metabolism	Guide RNA engineering for versatile Cas9 functionality.	Nowak CM, Lawson S, Zerez M, Bleris L.	Nucleic Acids Res	10.1093/nar/gkw908	2016
Enzymology	Association between Oral Candida and Bacteriome in Children with Severe ECC.	Xiao J, Grier A, Faustoferri RC, Alzoubi S, Gill AL, Feng C, Liu Y, Quivey RG, Kopycka-Kedzierawski DT, Koo H, Gill SR.	J Dent Res	10.1177/0022034518790941	2018
	CRISPR/Cas9 therapeutics: progress and prospects.	Li T, Yang Y, Qi H, Cui W, Zhang L, Fu X, He X, Liu M, Li PF, Yu T.	Signal Transduct Target Ther	10.1038/s41392-023-01309-7	2023
Metabolism	Efficient RNA Virus Targeting via CRISPR/CasRx in Fish.	Wang Q, Liu Y, Han C, Yang M, Huang F, Duan X, Wang S, Yu Y, Liu J, Yang H, Lu D, Zhao H, Zhang Y, Qin Q.	J Virol	10.1128/jvi.00461-21	2021
	Temporal development of the oral microbiome and prediction of early childhood caries.	Dashper SG, Mitchell HL, Le Cao KA, Carpenter L, Gussy MG, Calache H, Gladman SL, Bulach DM, Hoffmann B, Catmull DV, Pruilh S, Johnson S, Gibbs L, Amezdroz E, Bhatnagar U, Seemann T, Mnatzaganian G, Manton DJ, Reynolds EC.	Sci Rep	10.1038/s41598-019-56233-0	2019
	CRISPR technology in human diseases.	Feng Q, Li Q, Zhou H, Wang Z, Lin C, Jiang Z, Liu T, Wang D.	MedComm (2020)	10.1002/mco2.672	2024
Metabolism	A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases.	Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J.	Nature	10.1038/s41586-019-1786-y	2020
Genetics	Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era.	Shelake RM, Pramanik D, Kim JY.	Microorganisms	10.3390/microorganisms7080269	2019
	The Microbiome in Populations with a Low and High Prevalence of Caries.	Johansson I, Witkowska E, Kaveh B, Lif Holgerson P, Tanner AC.	J Dent Res	10.1177/0022034515609554	2016
	CRISPR/Cas systems usher in a new era of disease treatment and diagnosis.	Li R, Wang Q, She K, Lu F, Yang Y.	Mol Biomed	10.1186/s43556-022-00095-y	2022
Genetics	Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops.	Tussipkan D, Manabayeva SA.	Front Plant Sci	10.3389/fpls.2021.747476	2021
Pathogenicity	CRISPR-Cas13d mediates robust RNA virus interference in plants.	Mahas A, Aman R, Mahfouz M.	Genome Biol	10.1186/s13059-019-1881-2	2019
	Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria.	Kiga K, Tan XE, Ibarra-Chavez R, Watanabe S, Aiba Y, Sato'o Y, Li FY, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penades JR, Cui L.	Nat Commun	10.1038/s41467-020-16731-6	2020
	The Impact of Maltitol-Sweetened Chewing Gum on the Dental Plaque Biofilm Microbiota Composition.	Keijser BJF, van den Broek TJ, Slot DE, van Twillert L, Kool J, Thabuis C, Ossendrijver M, van der Weijden FA, Montijn RC.	Front Microbiol	10.3389/fmicb.2018.00381	2018
	A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila.	Huynh N, Depner N, Larson R, King-Jones K.	Genome Biol	10.1186/s13059-020-02193-y	2020
	CRISPR-Cas9/Cas12a biotechnology and application in bacteria.	Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y.	Synth Syst Biotechnol	10.1016/j.synbio.2018.09.004	2018
Pathogenicity	CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy.	Chen S, Yu X, Guo D.	Viruses	10.3390/v10010040	2018
	CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants.	Abdullah, Jiang Z, Hong X, Zhang S, Yao R, Xiao Y.	Synth Syst Biotechnol	10.1016/j.synbio.2020.08.003	2020
	Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis.	Liao C, Ttofali F, Slotkowski RA, Denny SR, Cecil TD, Leenay RT, Keung AJ, Beisel CL.	Nat Commun	10.1038/s41467-019-10747-3	2019
Genetics	Gene editing and CRISPR in the clinic: current and future perspectives.	Hirakawa MP, Krishnakumar R, Timlin JA, Carney JP, Butler KS.	Biosci Rep	10.1042/bsr20200127	2020
Metabolism	Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases.	Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ.	Nucleic Acids Res	10.1093/nar/gkw803	2016
	Progress and Prospects of CRISPR/Cas Systems in Insects and Other Arthropods.	Sun D, Guo Z, Liu Y, Zhang Y.	Front Physiol	10.3389/fphys.2017.00608	2017
	CRISPR Technology for Breast Cancer: Diagnostics, Modeling, and Therapy.	Mintz RL, Gao MA, Lo K, Lao YH, Li M, Leong KW.	Adv Biosyst	10.1002/adbi.201800132	2018
	Leptotrichia species in human infections II.	Eribe ERK, Olsen I.	J Oral Microbiol	10.1080/20002297.2017.1368848	2017
Phylogeny	Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.	Eribe ERK, Paster BJ, Caugant DA, Dewhirst FE, Stromberg VK, Lacy GH, Olsen I	Int J Syst Evol Microbiol	10.1099/ijs.0.02819-0	2004

References

#8297	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19757
#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 )
#26370	IJSEM 583 2004 ( DOI 10.1099/ijs.0.02819-0 , PubMed 15023979 )
#30006	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26370
#33180	; Curators of the CIP;
#57723	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 47503
#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;
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#122578	Collection of Institut Pasteur ; Curators of the CIP; CIP 107916
#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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Leptotrichia shahii (DSM 19757, CCUG 47503, CIP 107916)

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