Olsenella uli (DSM 7084, ATCC 49627, CIP 109912)

Name: Olsenella uli (DSM 7084, ATCC 49627, CIP 109912)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3059

Type strain

Strain Designation D76D-27C

Culture col. no. DSM 7084 ATCC 49627 CIP 109912 CCUG 31166 JCM 12494 5 more

NCBI tax ID(s) 633147 133926

Special Collections DSMZ CCUG JCM CIP

History <- ATCC <- VPI, D76D-27C CCUG 31166 <-- ATCC 49627 <-- VPI D76D-27C. CIP <- 2008, DSMZ <- ATCC <- E. Dewhirst, Harvard Med. School, Boston, USA: strain VPI, D76D-27C

Links

Olsenella uli D76D-27C is an obligate anaerobe, mesophilic, Gram-positive prokaryote that was isolated from human gingival crevice.

Gram-positive coccus-shaped obligate anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3384

LMG 11480,ATCC 49627,DSM 7084,NCFB 2895,CCUG 31166,NCIMB 702895,JCM 12494,KCTC 5039,CIP 109912

@ref 20215

Last LPSN update 2026-02-09 11:18:25

Domain Bacteria

Phylum Actinomycetota

Class Coriobacteriia

Order Coriobacteriales

Family Atopobiaceae

Genus Olsenella

Species Olsenella uli

Full scientific name Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001

Synonyms (1)

Lactobacillus uli

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123710	positive	coccus-shaped
125438			91.292
125439	negative		93.6

Colony morphology

50457

Incubation period3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2978	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
2978	MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)	Medium recipe at MediaDive	Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)2 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
2978	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
37683	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)
123710	CIP Medium 6	Medium recipe at CIP
123710	CIP Medium 137	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2978	positive	growth	37	mesophilic
37683	positive	growth	37	mesophilic
50457	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
2978	obligate anaerobe
50457	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.8

Murein

@ref	Murein short key	Type
2978	A21.04	A4ß L-Orn-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	+	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
123710	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
123710	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
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
123710	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	alkaline phosphatase	-	3.1.3.1	from API rID32A
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
68380	arginine dihydrolase	+	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
123710	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
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
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
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
123710	oxidase	-
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
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
68380	tyrosine arylamidase	+		from API rID32A
123710	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	acetate fermentation	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	palmitate biosynthesis	81.82	18 of 22
66794	hydrogen production	80	4 of 5
66794	serine metabolism	77.78	7 of 9
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	purine metabolism	69.15	65 of 94
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of sugar alcohols	68.75	11 of 16
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	oxidative phosphorylation	64.84	59 of 91
66794	proline metabolism	63.64	7 of 11
66794	histidine metabolism	62.07	18 of 29
66794	methylglyoxal degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	d-xylose degradation	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	isoprenoid biosynthesis	50	13 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	glutamate and glutamine metabolism	50	14 of 28
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	isoleucine metabolism	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	non-pathway related	47.37	18 of 38
66794	vitamin B1 metabolism	46.15	6 of 13
66794	leucine metabolism	46.15	6 of 13
66794	valine metabolism	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	tyrosine metabolism	42.86	6 of 14
66794	lipid metabolism	41.94	13 of 31
66794	arachidonate biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	lysine metabolism	38.1	16 of 42
66794	carnitine metabolism	37.5	3 of 8
66794	tryptophan metabolism	36.84	14 of 38
66794	vitamin B6 metabolism	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	flavin biosynthesis	33.33	5 of 15
66794	lipid A biosynthesis	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	glycine metabolism	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	arginine metabolism	25	6 of 24
66794	androgen and estrogen metabolism	25	4 of 16
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	cyclohexanol degradation	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	polyamine pathway	21.74	5 of 23
66794	glutathione metabolism	21.43	3 of 14

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
123710	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
2978	-	+	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	+	+	+	+	+	-	+	+	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
2978	human gingival crevice
50457	Human gingival crevice
67770	Saliva of periodontal patient
123710	Human, Gingival crevice

Taxonmaps

69479

Global distribution of 16S sequence AY005814 (>99% sequence identity) for Olsenella uli subclade from Microbeatlas

Aquatic Samples	150
Soil Samples	130
Animal Samples	8464
Plant Samples	55
Total Samples	8799

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2978	2	Risk group (German classification) According to TRBA 466
123710	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	ASM14384v1 assembly for Olsenella uli DSM 7084	complete	GCA_000143845	633147.4	648028047	633147	98.78
67770	ASM143758v1 assembly for Olsenella uli DSM 7084	scaffold	GCA_001437585	633147.7	2846506661	633147	70.23

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Olsenella uli 16S ribosomal RNA gene, partial sequence	AY005814	1481	633147
20218	Olsenella uli partial 16S rRNA gene, type strain DSM 7084T	FN178464	1428	633147
2978	Olsenella uli 16S ribosomal RNA gene, partial sequence	AF292373	1470	633147
124043	Olsenella uli JCM 12494 gene for 16S ribosomal RNA, partial sequence.	LC480796	1403	133926

GC content

@ref	GC-content (mol%)	Method
2978	53.0	thermal denaturation, midpoint method (Tm)
67770	65.5	high performance liquid chromatography (HPLC)
67770	64	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Olsenella uli DSM 7084
NCBI: GCA_000143845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	69.10	no
125439	gram_stain	BacteriaNetⓘ	negative	93.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	82.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Olsenella uli DSM 7084 DSM 7084
NCBI: GCA_000143845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.04	no
125438	anaerobic	anaerobicⓘ	yes	85.88	no
125438	aerobic	aerobicⓘ	no	95.85	no
125438	spore-forming	spore-formingⓘ	no	78.46	no
125438	thermophilic	thermophileⓘ	no	91.32	no
125438	flagellated	motile2+ⓘ	no	91.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A Systematic Approach to Discover New Natural Product Scaffolds Using Database-Derived Relative Mass Spectral Defects and Molecular Networking.	Cho HM, Boccia E, Rajwani R, O'Connor RD, Boshoff H, Barry C, Bifulco G, Bewley CA.	JACS Au	10.1021/jacsau.4c00889	2025
	The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme (CutD) for gut microbes and comparison with their TMA production levels.	Ramireddy L, Tsen HY, Chiang YC, Hung CY, Chen FC, Yen HT.	Curr Res Microb Sci	10.1016/j.crmicr.2021.100043	2021
	Mulberry leaf supplementation inhibits skatole deposition by regulating gut microbiota and upregulating liver cytochrome P450 1A1 expression in finishing pigs.	Sun Y, Men X, Lin T, Deng B, Zhong S, Huo J, Qin K, Lv Z, Xu Z, Li Y.	Anim Nutr	10.1016/j.aninu.2023.05.018	2024
Phylogeny	Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD.	Larsen JS, Miller M, Oakley AJ, Dixon NE, Lewis PJ.	Microbiologyopen	10.1002/mbo3.1251	2021
	Multiple variants of the type VII secretion system in Gram-positive bacteria.	Garrett SR, Higginson AB, Palmer T.	Microlife	10.1093/femsml/uqae013	2024
	Next generation sequencing data of a defined microbial mock community.	Singer E, Andreopoulos B, Bowers RM, Lee J, Deshpande S, Chiniquy J, Ciobanu D, Klenk HP, Zane M, Daum C, Clum A, Cheng JF, Copeland A, Woyke T.	Sci Data	10.1038/sdata.2016.81	2016
	Exploring Trimethylaminuria: Genetics and Molecular Mechanisms, Epidemiology, and Emerging Therapeutic Strategies.	Sidoti A, D'Angelo R, Castagnetti A, Viciani E, Scimone C, Alibrandi S, Giannini G.	Biology (Basel)	10.3390/biology13120961	2024
Pathogenicity	Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity.	Mendoza JL, Fischer S, Gee MH, Lam LH, Brackenridge S, Powrie FM, Birnbaum M, McMichael AJ, Garcia KC, Gillespie GM.	Elife	10.7554/elife.58128	2020
Metabolism	Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole.	Liu D, Wei Y, Liu X, Zhou Y, Jiang L, Yin J, Wang F, Hu Y, Nanjaraj Urs AN, Liu Y, Ang EL, Zhao S, Zhao H, Zhang Y.	Nat Commun	10.1038/s41467-018-06627-x	2018
	Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition.	Barratt MJ, Nuzhat S, Ahsan K, Frese SA, Arzamasov AA, Sarker SA, Islam MM, Palit P, Islam MR, Hibberd MC, Hibberd MC, Nakshatri S, Cowardin CA, Guruge JL, Byrne AE, Venkatesh S, Sundaresan V, Henrick B, Duar RM, Mitchell RD, Casaburi G, Prambs J, Flannery R, Mahfuz M, Rodionov DA, Osterman AL, Kyle D, Ahmed T, Gordon JI.	Sci Transl Med	10.1126/scitranslmed.abk1107	2022
Metabolism	Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.	Weagley JS, Zaydman M, Venkatesh S, Sasaki Y, Damaraju N, Yenkin A, Buchser W, Rodionov DA, Osterman A, Ahmed T, Barratt MJ, DiAntonio A, Milbrandt J, Gordon JI.	Cell Rep	10.1016/j.celrep.2022.110738	2022
	Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.	Lin HH, Liao YC.	Sci Rep	10.1038/srep24175	2016
Genetics	Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome.	Ravcheev DA, Moussu L, Smajic S, Thiele I.	Front Genet	10.3389/fgene.2019.00636	2019
Metabolism	Uncovering the Lactobacillus plantarum WCFS1 gallate decarboxylase involved in tannin degradation.	Jimenez N, Curiel JA, Reveron I, de Las Rivas B, Munoz R.	Appl Environ Microbiol	10.1128/aem.00840-13	2013
Phylogeny	Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification.	Salvetti E, Harris HMB, Felis GE, O'Toole PW.	Appl Environ Microbiol	10.1128/aem.00993-18	2018
Metabolism	Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.	Martinez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh PJ, Balskus EP.	mBio	10.1128/mbio.00042-15	2015
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Metabolism	Expression of the agmatine deiminase pathway in Enterococcus faecalis is activated by the AguR regulator and repressed by CcpA and PTS(Man) systems.	Suarez C, Espariz M, Blancato VS, Magni C.	PLoS One	10.1371/journal.pone.0076170	2013
Phylogeny	Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.	Sun Z, Harris HM, McCann A, Guo C, Argimon S, Zhang W, Yang X, Jeffery IB, Cooney JC, Kagawa TF, Liu W, Song Y, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O'Sullivan O, Ritari J, Douillard FP, Paul Ross R, Yang R, Briner AE, Felis GE, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui Y, Zhang H, O'Toole PW.	Nat Commun	10.1038/ncomms9322	2015
Enzymology	NarJ subfamily system specific chaperone diversity and evolution is directed by respiratory enzyme associations.	Bay DC, Chan CS, Turner RJ.	BMC Evol Biol	10.1186/s12862-015-0412-3	2015
	Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases.	Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe SG, Lelie Dv.	Biotechnol Biofuels	10.1186/1754-6834-4-23	2011
Genetics	A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.	Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.04.006	2020
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
	Dissemination of 6S RNA among bacteria.	Wehner S, Damm K, Hartmann RK, Marz M.	RNA Biol	10.4161/rna.29894	2014
Genetics	Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.	Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT.	PLoS One	10.1371/journal.pone.0030087	2012
Genetics	Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
Phylogeny	Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
Metabolism	Role of MurT C-Terminal Domain in the Amidation of Staphylococcus aureus Peptidoglycan.	Goncalves BV, Portela R, Lobo R, Figueiredo TA, Grilo IR, Ludovice AM, de Lencastre H, Dias JS, Sobral RG.	Antimicrob Agents Chemother	10.1128/aac.00957-19	2019
Phylogeny	Uncultivated phylotypes and newly named species associated with primary and persistent endodontic infections.	Siqueira JF, Rocas IN.	J Clin Microbiol	10.1128/jcm.43.7.3314-3319.2005	2005
	Comparative evaluation of light-emitting diode versus diode laser in photoactivated disinfection for endodontic retreatment: An in vivo study.	Yeli M, Naik B, Kulkarni RD, Bhat K, Moogi P, Tapashetti S, Karunakar P.	J Conserv Dent Endod	10.4103/jcde.jcde_93_25	2025
	Microbiota associated with caries and apical periodontitis: A next-generation sequencing study.	Tak EJ, Park OJ, Lee JS, Yoo YJ, Perinpanayagam H, Jeong YS, Lee JY, Bae JW, Kum KY, Han SH.	Int Endod J	10.1111/iej.14218	2025
	Comparative clinical characterization of microflora between primary and secondary endodontic infections-An in vivo cross sectional study.	Yeli M, Naik B, Kulkarni R, Kamath V, Moogi P, Patil S, Bhat K.	J Oral Biol Craniofac Res	10.1016/j.jobcr.2025.09.018	2025
	Comparative evaluation of light-emitting diode versus diode laser in photoactivated disinfection for endodontic retreatment: An in vivo study	Yeli M, Naik B, Kulkarni R, Bhat K, Moogi P, Tapashetti S, Karunakar P.	J Conserv Dent Endod		2025
Transcriptome	Metatranscriptome and Resistome of the Endodontic Microbiome.	Pinheiro ET, Karygianni L, Candeiro GTM, Vilela BG, Dantas LO, Pereira ACC, Gomes BPFA, Attin T, Thurnheer T, Russo G.	J Endod	10.1016/j.joen.2024.03.015	2024
	Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review.	Siqueira JF, Silva WO, Romeiro K, Gominho LF, Alves FRF, Rocas IN.	Int Endod J	10.1111/iej.14071	2024
Phylogeny	Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections.	Kesim B, Ulger ST, Aslan G, Cudal H, Ustun Y, Kucuk MO.	Clin Oral Investig	10.1007/s00784-023-04882-x	2023
	Association between root canals and gingival sulci microbiota in secondary and persistent endodontic infections.	Park DH, Tak EJ, Park OJ, Perinpanayagam H, Yoo YJ, Lee HJ, Jeong YS, Lee JY, Kim HS, Bae JW, Kum KY, Han SH.	Sci Rep	10.1038/s41598-025-95522-9	2025
	Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.	Bessa LJ, Egas C, Pires C, Proenca L, Mascarenhas P, Pais RJ, Barroso H, Machado V, Botelho J, Alcoforado G, Mendes JJ, Alves R.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1543100	2025
	Severe pneumonia with empyema due to multiple anaerobic infections: case report and literature review.	Yu F, Zhang X, Li Y, Gai W, Zheng Y, Cai X.	Front Med (Lausanne)	10.3389/fmed.2024.1435823	2024
	Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next-generation sequencing.	Hou Y, Wang L, Zhang L, Tan X, Huang D, Song D.	Int Endod J	10.1111/iej.13640	2022
	Challenging Diagnosis of Late Abdominal Pregnancy: A Case Study of Misdiagnosis and Fetal Death in the Third Trimester.	Alwafai Z, Kolbe C, Kruse-Wieczorek J, Khanji MN, Zygmunt M.	Am J Case Rep	10.12659/ajcr.943625	2024
Phylogeny	Coronal and Root Canal Microbiota in Apical Periodontitis with Different PAI.	Teofani A, Libonati A, Unida V, Biocca S, Desideri A, Campanella V.	Microorganisms	10.3390/microorganisms12081518	2024
	Trichomonas tenax detected in pleural effusion fluid: A case report.	Wang J, Zhao Q, Li D, Ning Y, Duan L, Zhang J, Yang Y, Ji A.	Biomed Rep	10.3892/br.2024.1909	2025
	Olsenella uli-induced pneumonia: a case report.	Yan Y, Li H, Li S, Liu S, Jia N, Liu Y, Liu Q, Li J, Han C.	Ann Clin Microbiol Antimicrob	10.1186/s12941-022-00499-2	2022
	Four-Year Longitudinal Epidemiological Study on the Association Between a Multi-Item Saliva Testing System and Oral and Gut Microbiota.	Sato S, Chinda D, Mikami K, Tobinai M, Ishidoya N, Furusawa K, Miyashiro K, Yoshida K, Iino C, Sawada K, Mikami T, Nakaji S, Murashita K, Sakuraba H.	Microorganisms	10.3390/microorganisms13112483	2025
	A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review.	Putrino A, Marinelli E, Galeotti A, Ferrazzano GF, Ciribe M, Zaami S.	Microorganisms	10.3390/microorganisms12050902	2024
Genetics	Role of immunostimulatory deoxycytidylate-phosphate-deoxyguanylate (CpG) motifs in oral bacteria associated with oral diseases.	Charoenwongwatthana P, Caroline OS, Ahmed H, Coulter J, Chang CY.	J Oral Microbiol	10.1080/20002297.2025.2486639	2025
	Functional and taxonomic dysbiosis of the supragingival plaque metagenome in Behçet's disease.	Sapthanakorn T, Choopong P, Sermsripong W, Boriboonhirunsarn C, Khamwachirapitak C, Krasaesin A, Sutthiboonyaphan P, Siripaiboonpong N, Mahanonda R, Wiriyakijja P, Pelekos G, Porntaveetus T, Srithanyarat SS.	J Oral Microbiol	10.1080/20002297.2025.2552165	2025
	Probiotics in the management of radiation-induced oral mucositis.	Li Y, Li Z, Zheng S, Xu X.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1477143	2024
	Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants.	Nagaraj SK, Joy CM, Shiraz R, Narayan R, Kaur S, Khatun O, Dubey S, Ng J, Mishra N, Tripathi S.	Npj Viruses	10.1038/s44298-025-00158-1	2025
	Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.	Sun Y, Guo K, Tang J, Zhao J, Zhang X, Yan Y, Yuan L, Zhang Y, Qiu C, Luo J, Zhang W, Fang H, Chen J.	Ann Med	10.1080/07853890.2025.2514093	2025
	Exploring Relationships Within the Microbiome of Root Canal Infections and the Influence of Associated Clinical Parameters.	Mominkhan D, Brito LCN, Yakubu AR, Larson E, Martin L, Patel M, Tavares WLF, Ribeiro-Sobrinho A, Teles F.	Int Endod J	10.1111/iej.70011	2025
Genetics	Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.	Rehner J, Gund M, Becker SL, Hannig M, Rupf S, Schattenberg JM, Keller A, The Imagine Consortium, Molano LG, Keller V.	Nutrients	10.3390/nu17223527	2025
Phylogeny	Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.	Nardello LCL, Amado PPP, Franco DC, Cazares RXR, Nogales CG, Mayer MPA, Karygianni L, Thurnheer T, Pinheiro ET.	J Endod	10.1016/j.joen.2020.05.004	2020
Genetics	Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.	Nassar R, Nassar M, Mohamed L, Senok A, Williams D.	Int Endod J	10.1111/iej.14227	2025
	Anti-inflammatory and antimicrobial efficacy of coconut oil for periodontal pathogens: a triple-blind randomized clinical trial.	Pardinas Lopez S, Garcia-Caro ME, Vallejo JA, Aja-Macaya P, Conde-Perez K, Nion-Cabeza P, Khouly I, Bou G, Cendal AIR, Diaz-Prado S, Poza M.	Clin Oral Investig	10.1007/s00784-025-06267-8	2025
	Potential Association of the Oral Microbiome with Trimethylamine N-Oxide Quantification in Mexican Patients with Myocardial Infarction.	Hernandez-Ruiz P, Escalona Montano AR, Amezcua-Guerra LM, Gonzalez-Pacheco H, Niccolai E, Amedei A, Aguirre-Garcia MM.	Mediators Inflamm	10.1155/2024/3985731	2024
Phylogeny	Identification and characterization of pancreatic infections in severe and critical acute pancreatitis patients using 16S rRNA gene next generation sequencing.	Sun N, Chen Y, Zhang J, Cao J, Huang H, Wang J, Guo W, Li X.	Front Microbiol	10.3389/fmicb.2023.1185216	2023
Phylogeny	Bacterial genera in the fluids from apical periodontitis-related radicular cysts: An observational study.	Szaraz D, Bohm J, Cerulova S, Bodokyova L, Danek Z, Machacek C, Borilova Linhartova P.	Int Endod J	10.1111/iej.14220	2025
	[Acute apical abscess and associated factors in patients during the covid-19 pandemic in a health center in Acapulco, Mexico.]	Juarez-Medel CA, Rodriguez-Gonzalez E, Mendoza-Figueroa AN.	Rev Cient Odontol (Lima)	10.21142/2523-2754-1202-2024-193	2024
Pathogenicity	Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus.	MacCann R, Li J, Leon AAG, Negi R, Alalwan D, Tinago W, McGettrick P, Cotter AG, Landay A, Sabin C, O'Toole PW, Mallon PWG, Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group .	J Infect Dis	10.1093/infdis/jiaf043	2025
	Roseburia hominis improves host metabolism in diet-induced obesity.	Huang W, Zhu W, Lin Y, Chan FKL, Xu Z, Ng SC.	Gut Microbes	10.1080/19490976.2025.2467193	2025
	Unveiling Therapeutic Potential: Targeting Fusobacterium nucleatum's Lipopolysaccharide Biosynthesis for Endodontic Infections-An In Silico Screening Study.	Boreak N, Alrajab EA, Nahari RA, Najmi LE, Masmali MA, Ghawi AA, Al Moaleem MM, Alhazmi MY, Maqbul AA.	Int J Mol Sci	10.3390/ijms25084239	2024
	Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry.	Fu B, Yang H, Kountz DJ, Lundahl MN, Beller HR, Broderick WE, Broderick JB, Hoffman BH, Balskus EP.	J Am Chem Soc	10.1021/jacs.4c10348	2024
	Dietary Polycan, a beta-glucan originating from Aureobasidium pullulansSM-2001, attenuates high-fat-diet-induced intestinal barrier damage in obese mice by modulating gut microbiota dysbiosis.	Ko GP, Unno T, Kim YS, Kim J.	Food Sci Nutr	10.1002/fsn3.4235	2024
	Microbial profiling of peri-implantitis compared to the periodontal microbiota in health and disease using 16S rRNA sequencing.	Kim HJ, Ahn DH, Yu Y, Han H, Kim SY, Joo JY, Chung J, Na HS, Lee JY.	J Periodontal Implant Sci	10.5051/jpis.2202080104	2023
	Bacteria in the apical root canals of teeth with apical periodontitis.	Lee LW, Lee YL, Hsiao SH, Lin HP.	J Formos Med Assoc	10.1016/j.jfma.2016.08.010	2017
	Orofacial fascial space abscess disguised as temporomandibular disorder: a report of 3 cases and literature review.	Kim TS, Lee YH.	BMC Oral Health	10.1186/s12903-023-03800-7	2024
	Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors.	Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJN, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ.	iScience	10.1016/j.isci.2024.110122	2024
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
	Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer.	Fu B, Nazemi A, Levin BJ, Yang Z, Kulik HJ, Balskus EP.	J Am Chem Soc	10.1021/jacs.1c13580	2022
	Evaluation of Bacteriological Profile in the Apical Root Segment of the Patients with Primary Apical Periodontitis.	Tatikonda A, Sudheep N, Biswas KP, Gowtham K, Pujari S, Singh P.	J Contemp Dent Pract	10.5005/jp-journals-10024-1986	2017
Phylogeny	Oral microbiome in older adults with mild cognitive impairment.	Da D, Zhao Q, Zhang H, Wu W, Zeng X, Liang X, Jiang Y, Xiao Z, Yu J, Ding S, Zheng L, Zhang Y, Xu X, Ding D.	J Oral Microbiol	10.1080/20002297.2023.2173544	2023
	Environmental Impact on Differential Composition of Gut Microbiota in Indoor Chickens in Commercial Production and Outdoor, Backyard Chickens.	Seidlerova Z, Kubasova T, Faldynova M, Crhanova M, Karasova D, Babak V, Rychlik I.	Microorganisms	10.3390/microorganisms8050767	2020
Enzymology	Dynamics and diversity of the 'Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of 'Atopobium cluster' isolates.	Thorasin T, Hoyles L, McCartney AL.	Microbiology (Reading)	10.1099/mic.0.000016	2015
Phylogeny	Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis.	Zakaria MN, Takeshita T, Shibata Y, Maeda H, Wada N, Akamine A, Yamashita Y.	Int Endod J	10.1111/iej.12361	2015
Metabolism	A Co-Association of Streptococcus mutans and Veillonella parvula/dispar in Root Caries Patients and In Vitro Biofilms.	Abram AM, Szewczyk MM, Park SG, Sam SS, Eldana HB, Koria FJ, Ferracciolo JM, Young LA, Qadir H, Bonham AJ, Yang F, Zora JS, Abdulelah SA, Patel NA, Koleilat A, Saleh MA, Alhabeil JA, Khan S, Tripathi A, Palanci JG, Krukonis ES.	Infect Immun	10.1128/iai.00355-22	2022
Phylogeny	Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance.	Vieira Colombo AP, Magalhaes CB, Hartenbach FA, Martins do Souto R, Maciel da Silva-Boghossian C.	Microb Pathog	10.1016/j.micpath.2015.09.009	2016
	Association of specific microorganisms with endodontic signs and symptoms. A comparative study.	Singh KK, Kumar P, Das P, Marandi M, Panda S, Mahajan A, Kumar D.	J Family Med Prim Care	10.4103/jfmpc.jfmpc_523_20	2020
	Analysis of gastric microbiota and Helicobacter pylori infection in gastroesophageal reflux disease.	Sugihartono T, Fauzia KA, Miftahussurur M, Waskito LA, Rejeki PS, I'tishom R, Alfaray RI, Doohan D, Amalia R, Savitri CMA, Rezkitha YAA, Akada J, Matsumoto T, Yamaoka Y.	Gut Pathog	10.1186/s13099-022-00510-3	2022
	Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species.	Mann AE, Chakraborty B, O'Connell LM, Nascimento MM, Burne RA, Richards VP.	Microbiol Spectr	10.1128/spectrum.01445-23	2024
	Acute Endophthalmitis Caused by Leuconostoc spp. following Intravitreal Bevacizumab Injection.	Singh S, Patel CV, Kishore K.	Case Rep Ophthalmol	10.1159/000480727	2017
	Epigallocatechin-3-Gallate Decreases Plasma and Urinary Levels of p-Cresol by Modulating Gut Microbiota in Mice.	Unno T, Ichitani M.	ACS Omega	10.1021/acsomega.2c04731	2022
	Evaluation of the antimicrobial efficacy of 20% Punica granatum, 0.2% chlorhexidine gluconate, and 2.5% sodium hypochlorite used alone or in combinations against Enterococcus faecalis: An in-vitro study.	Mallya L, Shenoy R, Mala K, Shenoy S.	J Conserv Dent	10.4103/jcd.jcd_43_19	2019
	Microbiome and metabolome associated with white spot lesions in patients treated with clear aligners.	Song Z, Fang S, Guo T, Wen Y, Liu Q, Jin Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1119616	2023
	Clinical Quantitative Antibacterial Potency of Garlic-Lemon Against Sodium Hypochlorite in Infected Root Canals: A Double-blinded, Randomized, Controlled Clinical Trial.	Siddique R, Ranjan M, Jose J, Srivastav A, Rajakeerthi R, Kamath A.	J Int Soc Prev Community Dent	10.4103/jispcd.jispcd_287_20	2020
Enzymology	Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis.	Rocas IN, Siqueira JF.	PLoS One	10.1371/journal.pone.0190469	2018
Genetics	Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study.	Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R.	Microorganisms	10.3390/microorganisms11102437	2023
	Alterations of the Intestinal Permeability are Reflected by Changes in the Urine Metabolome of Young Autistic Children: Preliminary Results.	Piras C, Mussap M, Noto A, De Giacomo A, Cristofori F, Spada M, Fanos V, Atzori L, Francavilla R.	Metabolites	10.3390/metabo12020104	2022
	Apical root canal microbiota as determined by reverse-capture checkerboard analysis of cryogenically ground root samples from teeth with apical periodontitis.	Rocas IN, Alves FR, Santos AL, Rosado AS, Siqueira JF.	J Endod	10.1016/j.joen.2010.07.001	2010
	Identification of bacteria enduring endodontic treatment procedures by a combined reverse transcriptase-polymerase chain reaction and reverse-capture checkerboard approach.	Rocas IN, Siqueira JF.	J Endod	10.1016/j.joen.2009.10.022	2010
Phylogeny	The microbiota of acute apical abscesses.	Siqueira JF, Rocas IN.	J Dent Res	10.1177/0022034508328124	2009
Genetics	Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities.	Wang Y, Wang S, Wu C, Chen X, Duan Z, Xu Q, Jiang W, Xu L, Wang T, Su L, Wang Y, Chen Y, Zhang J, Huang Y, Tong S, Zhou C, Deng S, Qin N.	mSystems	10.1128/msystems.00450-19	2019
	Why do lactic acid bacteria thrive in chain elongation microbiomes?	Ulcar B, Regueira A, Podojstersek M, Boon N, Ganigue R.	Front Bioeng Biotechnol	10.3389/fbioe.2023.1291007	2023
Enzymology	Bacteria in the apical root canal of teeth with primary apical periodontitis.	Siqueira JF, Rocas IN, Alves FR, Silva MG.	Oral Surg Oral Med Oral Pathol Oral Radiol Endod	10.1016/j.tripleo.2009.01.042	2009
Pathogenicity	Response to alkaline stress by root canal bacteria in biofilms.	Chavez de Paz LE, Bergenholtz G, Dahlen G, Svensater G.	Int Endod J	10.1111/j.1365-2591.2006.01226.x	2007
	Oral health status in historic population: Macroscopic and metagenomic evidence.	Willmann C, Mata X, Hanghoej K, Tonasso L, Tisseyre L, Jeziorski C, Cabot E, Chevet P, Crubezy E, Orlando L, Esclassan R, Theves C.	PLoS One	10.1371/journal.pone.0196482	2018
Enzymology	Species-directed 16S rRNA gene nested PCR detection of Olsenella species in association with endodontic diseases.	Rocas IN, Siqueira JF.	Lett Appl Microbiol	10.1111/j.1472-765x.2005.01723.x	2005
Pathogenicity	Insight into the intestinal microbiome of farrowing sows following the administration of garlic (Allium sativum) extract and probiotic bacteria cultures under farming conditions.	Satora M, Magdziarz M, Rzasa A, Rypula K, Ploneczka-Janeczko K.	BMC Vet Res	10.1186/s12917-020-02659-y	2020
Enzymology	Detection of novel oral species and phylotypes in symptomatic endodontic infections including abscesses.	Rocas IN, Siqueira JF.	FEMS Microbiol Lett	10.1016/j.femsle.2005.07.017	2005
	Gut mobilization improves behavioral symptoms and modulates urinary p-cresol in chronically constipated autistic children: A prospective study.	Turriziani L, Ricciardello A, Cucinotta F, Bellomo F, Turturo G, Boncoddo M, Mirabelli S, Scattoni ML, Rossi M, Persico AM.	Autism Res	10.1002/aur.2639	2022
	Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience.	Lee E, Park S, Um S, Kim S, Lee J, Jang J, Jeong HO, Shin J, Kang J, Lee S, Jeong T.	Diagnostics (Basel)	10.3390/diagnostics11081324	2021
Phylogeny	Gram-positive rods prevailing in teeth with apical periodontitis undergoing root canal treatment.	Chavez de Paz LE, Molander A, Dahlen G.	Int Endod J	10.1111/j.1365-2591.2004.00845.x	2004
Metabolism	Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites.	Saito Y, Sato T, Nomoto K, Tsuji H.	FEMS Microbiol Ecol	10.1093/femsec/fiy125	2018
	Robust cross-cohort gut microbiome associations with COVID-19 severity.	Li J, Li J, Ghosh TS, McCann R, Mallon P, Hill C, Draper L, Schult D, Fanning LJ, Shannon R, Sadlier C, Horgan M, O'Mahony L, O'Toole PW.	Gut Microbes	10.1080/19490976.2023.2242615	2023
	The Use of Different Irrigation Techniques to Decrease Bacterial Loads in Healthy and Diabetic Patients with Asymptomatic Apical Periodontitis.	Ghoneim M, Saber SE, El-Badry T, Obeid M, Hassib N.	Open Access Maced J Med Sci	10.3889/oamjms.2016.124	2016
	Streptococci from root canals in teeth with apical periodontitis receiving endodontic treatment.	Chavez de Paz L, Chavez de Paz L, Svensater G, Dahlen G, Bergenholtz G.	Oral Surg Oral Med Oral Pathol Oral Radiol Endod	10.1016/j.tripleo.2004.10.008	2005
	Gut Anaerobes Capable of Chicken Caecum Colonisation.	Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, Matiasovicova J, Faldynova M, Sisak F, Babak V, Pokorna A, Cizek A, Rychlik I.	Microorganisms	10.3390/microorganisms7120597	2019
Pathogenicity	Effects of subgingival air-polishing with trehalose powder on oral biofilm during periodontal maintenance therapy: a randomized-controlled pilot study.	Kruse AB, Maamar R, Akakpo DL, Woelber JP, Wittmer A, Vach K, Ratka-Kruger P, Al-Ahmad A.	BMC Oral Health	10.1186/s12903-020-01111-9	2020
Pathogenicity	The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut.	Wong EO, Brownlie EJE, Ng KM, Kathirgamanathan S, Yu FB, Merrill BD, Huang KC, Martin A, Tropini C, Navarre WW.	mBio	10.1128/mbio.02949-21	2022
	Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria.	Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S, Buhl EM, Abt B, Neuhaus K, Velge P, Overmann J, Kaspers B, Clavel T.	mSystems	10.1128/msystems.01300-20	2021
Genetics	2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.	Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Tessmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ.	BMC Biol	10.1186/s12915-020-00839-8	2020
Phylogeny	Microbiologic profile of endodontic infections from HIV- and HIV+ patients using multiple-displacement amplification and checkerboard DNA-DNA hybridization.	Brito LC, Sobrinho AP, Teles RP, Socransky SS, Haffajee AD, Vieira LQ, Teles FR.	Oral Dis	10.1111/j.1601-0825.2012.01908.x	2012
	Metagenomic identification, purification and characterisation of the Bifidobacterium adolescentis BgaC beta-galactosidase.	Mulualem DM, Agbavwe C, Ogilvie LA, Jones BV, Kilcoyne M, O'Byrne C, Boyd A.	Appl Microbiol Biotechnol	10.1007/s00253-020-11084-y	2021
	Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species.	Li G, Yin B, Li J, Wang J, Wei W, Bolnick DI, Wan X, Zhu B, Zhang Z.	ISME J	10.1038/s41396-020-0646-y	2020
	The Subgingival Microbiome Relationship to Periodontal Disease in Older Women.	Genco RJ, LaMonte MJ, McSkimming DI, Buck MJ, Li L, Hovey KM, Andrews CA, Sun Y, Tsompana M, Zheng W, Banack HR, Murugaiyan V, Wactawski-Wende J.	J Dent Res	10.1177/0022034519860449	2019
Genetics	Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria.	Shen H, Ye F, Xie L, Yang J, Li Z, Xu P, Meng F, Li L, Chen Y, Bo X, Ni M, Zhang X.	Sci Rep	10.1038/srep17450	2015
Phylogeny	Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures.	Lau SK, Ng KH, Woo PC, Yip KT, Fung AM, Woo GK, Chan KM, Que TL, Yuen KY.	J Clin Pathol	10.1136/jcp.2004.025247	2006
Genetics	Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.	Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, Ngan CY, Cheng JF, Tringe SG, Woyke T.	BMC Genomics	10.1186/s12864-015-2063-6	2015
	Development of a species-specific TaqMan-MGB real-time PCR assay to quantify Olsenella scatoligenes in pigs offered a chicory root-based diet.	Li X, Jensen BB, Hojberg O, Noel SJ, Canibe N.	AMB Express	10.1186/s13568-018-0627-y	2018
Metabolism	Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage.	Harrison MA, Kaur H, Wren BW, Dawson LF.	Front Cell Infect Microbiol	10.3389/fcimb.2021.757599	2021
Enzymology	Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication.	Niazi SA, Al Kharusi HS, Patel S, Bruce K, Beighton D, Foschi F, Mannocci F.	Clin Oral Investig	10.1007/s00784-016-1739-x	2016
	Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice.	Lei M, Menon R, Manteiga S, Alden N, Hunt C, Alaniz RC, Lee K, Jayaraman A.	mSystems	10.1128/msystems.00724-19	2019
Metabolism	Time-resolved DNA stable isotope probing links Desulfobacterales- and Coriobacteriaceae-related bacteria to anaerobic degradation of benzene under methanogenic conditions.	Noguchi M, Kurisu F, Kasuga I, Furumai H.	Microbes Environ	10.1264/jsme2.me13104	2014
Phylogeny	Root canal microbiota of teeth with chronic apical periodontitis.	Rocas IN, Siqueira JF.	J Clin Microbiol	10.1128/jcm.00431-08	2008
	Usefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles.	Woo PC, Ng KH, Lau SK, Yip KT, Fung AM, Leung KW, Tam DM, Que TL, Yuen KY.	J Clin Microbiol	10.1128/jcm.41.5.1996-2001.2003	2003
Phylogeny	High-resolution phylogenetic microbial community profiling.	Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T.	ISME J	10.1038/ismej.2015.249	2016
Genetics	Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis.	Ai D, Huang R, Wen J, Li C, Zhu J, Xia LC.	BMC Genomics	10.1186/s12864-016-3254-5	2017
Metabolism	Scottish soldiers from the Battle of Dunbar 1650: A prosopographical approach to a skeletal assemblage.	Millard AR, Annis RG, Caffell AC, Dodd LL, Fischer R, Gerrard CM, Graves CP, Hendy J, Mackenzie L, Montgomery J, Nowell GM, Radini A, Beaumont J, Koon HEC, Speller CF.	PLoS One	10.1371/journal.pone.0243369	2020
	Interkingdom networking within the oral microbiome.	Nobbs AH, Jenkinson HF.	Microbes Infect	10.1016/j.micinf.2015.03.008	2015
Metabolism	Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition.	Charbonneau MR, O'Donnell D, Blanton LV, Totten SM, Davis JC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR, Muehlbauer MJ, Ilkayeva O, Wu C, Struckmeyer T, Barile D, Mangani C, Jorgensen J, Fan YM, Maleta K, Dewey KG, Ashorn P, Newgard CB, Lebrilla C, Mills DA, Gordon JI.	Cell	10.1016/j.cell.2016.01.024	2016
Phylogeny	A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.	Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernandez SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischoder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Sproer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-020-19929-w	2020
	A taxonomy of bacterial microcompartment loci constructed by a novel scoring method.	Axen SD, Erbilgin O, Kerfeld CA.	PLoS Comput Biol	10.1371/journal.pcbi.1003898	2014
Phylogeny	PCR-based identification of bacteria associated with endodontic infections.	Fouad AF, Barry J, Caimano M, Clawson M, Zhu Q, Carver R, Hazlett K, Radolf JD.	J Clin Microbiol	10.1128/jcm.40.9.3223-3231.2002	2002
	Gene expression of bacterial collagenolytic proteases in root caries.	Dame-Teixeira N, Parolo CCF, Maltz M, Rup AG, Devine DA, Do T	J Oral Microbiol	10.1080/20002297.2018.1424475	2018
Genetics	Complete genome sequence of Olsenella uli type strain (VPI D76D-27C).	Goker M, Held B, Lucas S, Nolan M, Yasawong M, Glavina Del Rio T, Tice H, Cheng JF, Bruce D, Detter JC, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Pukall R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.1082860	2010
Genetics	Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool.	Bilen M, Cadoret F, Richez M, Tomei E, Daoud Z, Raoult D, Fournier PE.	New Microbes New Infect	10.1016/j.nmni.2017.11.001	2018
Genetics	Taxono-genomics description of Olsenella lakotia SW165 ^T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken.	Wongkuna S, Ghimire S, Janvilisri T, Doerner K, Chankhamhaengdecha S, Scaria J.	F1000Res	10.12688/f1000research.25823.1	2020
Genetics	Olegusella massiliensis gen. nov., sp. nov., strain KHD7^T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis.	Diop K, Diop A, Bretelle F, Cadoret F, Michelle C, Richez M, Cocallemen JF, Raoult D, Fournier PE, Fenollar F.	Anaerobe	10.1016/j.anaerobe.2017.02.012	2017
Phylogeny	Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa.	Kraatz M, Wallace RJ, Svensson L.	Int J Syst Evol Microbiol	10.1099/ijs.0.022954-0	2011
Phylogeny	Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov.	Dewhirst FE, Paster BJ, Tzellas N, Coleman B, Downes J, Spratt DA, Wade WG.	Int J Syst Evol Microbiol	10.1099/00207713-51-5-1797	2001
Phylogeny	Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov.	Bilen M, Beye M, Mbogning Fonkou MD, Khelaifia S, Cadoret F, Armstrong N, Nguyen TT, Delerce J, Daoud Z, Raoult D, Fournier PE.	Microbiologyopen	10.1002/mbo3.580	2018
Genetics	Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut.	Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD, Tall ML, Michelle C, Yasir M, Ibraheem Azhar E, Bibi F, Bittar F, Jiman-Fatani AA, Daoud Z, Cadoret F, Fournier PE, Edouard S.	Microbiologyopen	10.1002/mbo3.758	2019
Phylogeny	Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu.	Lu LF, Yang Y, Zheng L, Zhang R, Liu GQ, Tu TY, Xu T, Luo X, Ran MF, Zhang LQ, Wang ST, Shen CH, Zhang YG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005192	2021
Phylogeny	Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces.	Han KI, Lee KC, Eom MK, Kim JS, Suh MK, Park SH, Lee JH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003469	2019
Phylogeny	Parolsenella catena gen. nov., sp. nov., isolated from human faeces.	Sakamoto M, Iino T, Hamada M, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002645	2018
Phylogeny	Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces.	Li X, Jensen RL, Hojberg O, Canibe N, Jensen BB	Int J Syst Evol Microbiol	10.1099/ijs.0.000083	2015
Phylogeny	Lactobacillus uli sp. nov. and Lactobacillus rimae sp. nov. from the human gingival crevice and emended descriptions of lactobacillus minutus and Streptococcus parvulus.	Olsen I, Johnson JL, Moore LV, Moore WE	Int J Syst Bacteriol	10.1099/00207713-41-2-261	1991

References

#2978	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7084
#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 )
#37683	; Curators of the CIP;
#50457	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 31166
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#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 .
#123710	Collection of Institut Pasteur ; Curators of the CIP; CIP 109912
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Olsenella uli (DSM 7084, ATCC 49627, CIP 109912)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

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Murein

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Metabolite tests

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