Porphyromonas catoniae (DSM 23684, ATCC 51270, CCUG 41358)

Name: Porphyromonas catoniae (DSM 23684, ATCC 51270, CCUG 41358)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12510

Type strain

Culture col. no. DSM 23684 ATCC 51270 CCUG 41358 JCM 13863 NCTC 13056 1 more

NCBI tax ID(s) 887901 41976

Special Collections DSMZ CCUG JCM

History <- JCM <- CCUG <- NCTC <- ATCC <- L. V. Moore, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI N3B-3 CCUG 41358 <-- NCTC 13056 <-- ATCC 51270 <-- L. V. Moore VPI N3B-3.

Links

Porphyromonas catoniae DSM 23684 is an anaerobe, mesophilic prokaryote that was isolated from human oral cavity; gingival crevice of adult patient with periodontitis.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42889

ATCC 51270,CCUG 41358,NCTC 13056,JCM 13863,DSM 23684

@ref 20215

Last LPSN update 2025-12-16 09:49:51

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Porphyromonadaceae

Genus Porphyromonas

Species Porphyromonas catoniae

Full scientific name Porphyromonas catoniae (Moore and Moore 1994) Willems and Collins 1995

Synonyms (1)

Oribaculum catoniae

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.728
125439	negative	97.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17342	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
17342	positive	growth	37	mesophilic
55031	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
17342	anaerobe
55031	anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		94.5
125439		99.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
17342	catalase	-	1.11.1.6
17342	cytochrome-c oxidase	-	1.9.3.1
68367	gelatinase	-		from API 20A
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
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
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
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	glycogen metabolism	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	NAD metabolism	66.67	12 of 18
66794	purine metabolism	65.96	62 of 94
66794	glycolysis	64.71	11 of 17
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	methylglyoxal degradation	60	3 of 5
66794	threonine metabolism	60	6 of 10
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	vitamin B6 metabolism	54.55	6 of 11
66794	phenylalanine metabolism	53.85	7 of 13
66794	suberin monomers biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	glutamate and glutamine metabolism	50	14 of 28
66794	citric acid cycle	50	7 of 14
66794	selenocysteine biosynthesis	50	3 of 6
66794	gluconeogenesis	50	4 of 8
66794	alanine metabolism	48.28	14 of 29
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	polyamine pathway	43.48	10 of 23
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	vitamin B1 metabolism	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	isoleucine metabolism	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	lysine metabolism	35.71	15 of 42
66794	non-pathway related	34.21	13 of 38
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	UDP-GlcNAc biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	valine metabolism	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	methionine metabolism	30.77	8 of 26
66794	myo-inositol biosynthesis	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	lipid metabolism	29.03	9 of 31
66794	tryptophan metabolism	28.95	11 of 38
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	heme metabolism	28.57	4 of 14
66794	degradation of hexoses	27.78	5 of 18
66794	arginine metabolism	25	6 of 24
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	leucine metabolism	23.08	3 of 13
66794	urea cycle	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
17342	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
17342	-	-	-	+/-	-	+	-	-	-	+/-	-	-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
17342	human oral cavity; gingival crevice of adult patient with periodontitis
55031	Human gingival crevice of adult patient
67770	Human gingival crevice of adult patient

Taxonmaps

69479

Global distribution of 16S sequence AB547656 (>99% sequence identity) for Porphyromonas catoniae subclade from Microbeatlas

Aquatic Samples	354
Soil Samples	334
Animal Samples	18353
Plant Samples	130
Total Samples	19171

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17342	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
67770	PcatATCC51270v1.0 assembly for Porphyromonas catoniae ATCC 51270	contig	GCA_000565015	887901.3	2558860281	887901	73.01

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Porphyromonas catoniae gene for 16S ribosomal RNA, partial sequence, strain: JCM 13863	AB547656	1451	887901
17342	O.catoniae 16S rRNA gene	X82823	1470	887901
124043	Porphyromonas catoniae ATCC 51270 gene for 16S rRNA, partial sequence.	LC752304	579	887901
124043	Porphyromonas catoniae JCM 13863 gene for 16S rRNA, partial sequence.	LC752377	579	887901
124043	Porphyromonas catoniae ATCC 51270 16S ribosomal RNA gene, partial sequence.	PQ763941	1470	887901

GC content

@ref	GC-content (mol%)	Method
17342	49
17342	51.0	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Porphyromonas catoniae ATCC 51270
NCBI: GCA_000565015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.30	no
125439	motility	BacteriaNetⓘ	yes	55.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	78.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Porphyromonas catoniae ATCC 51270
PATRIC: 887901.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.73	no
125438	anaerobic	anaerobicⓘ	yes	65.74	yes
125438	aerobic	aerobicⓘ	no	86.90	no
125438	spore-forming	spore-formingⓘ	no	94.50	no
125438	thermophilic	thermophileⓘ	no	92.78	yes
125438	flagellated	motile2+ⓘ	no	89.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic diversity in Porphyromonas: evidence of Porphyromonas catoniae commensality in lungs.	Velo-Suarez L, Moalic Y, Guilloux CA, Ame J, Lamoureux C, Gouriou S, Le Berre R, Beauruelle C, Hery-Arnaud G.	Microb Genom	10.1099/mgen.0.001411	2025
Enzymology	Gastric acid inhibitor aggravates indomethacin-induced small intestinal injury via reducing Lactobacillus johnsonii.	Nadatani Y, Watanabe T, Suda W, Nakata A, Matsumoto Y, Kosaka S, Higashimori A, Otani K, Hosomi S, Tanaka F, Nagami Y, Kamata N, Taira K, Yamagami H, Tanigawa T, Hattori M, Fujiwara Y.	Sci Rep	10.1038/s41598-019-53559-7	2019
	Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health.	Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ.	BMC Med Genomics	10.1186/1755-8794-4-22	2011
Phylogeny	Concatenated 16S rRNA sequence analysis improves bacterial taxonomy.	Paul B.	F1000Res	10.12688/f1000research.128320.3	2022
	Evaluation of antimicrobial-antibiofilm activity of a hydrogen peroxide decontaminating system used in dental unit water lines.	Orru G, Del Nero S, Tuveri E, Laura Ciusa M, Pilia F, Erriu M, Orru G, Liciardi M, Piras V, Denotti G.	Open Dent J	10.2174/1874210601004010140	2010
	Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.	Soares-Castro P, Araujo-Rodrigues H, Godoy-Vitorino F, Ferreira M, Covelo P, Lopez A, Vingada J, Eira C, Santos PM.	Sci Rep	10.1038/s41598-019-50139-7	2019
	Usefulness of real time PCR for the differentiation and quantification of 652 and JP2 Actinobacillus actinomycetemcomitans genotypes in dental plaque and saliva.	Orru G, Marini MF, Ciusa ML, Isola D, Cotti M, Baldoni M, Piras V, Pisano E, Montaldo C.	BMC Infect Dis	10.1186/1471-2334-6-98	2006
	Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks.	Pozhitkov A, Chernov B, Yershov G, Noble PA.	Appl Environ Microbiol	10.1128/aem.71.12.8663-8676.2005	2005
Phylogeny	The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.	Gao P, Yuan H, Mei Z, Yin X, Zeng Y, Liu Z, Yang X, Xue J, Liu Z, Jiang Y, Ye W, Lu M, Suo C, Chen X.	Cell Rep Med	10.1016/j.xcrm.2025.102431	2025
	Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.	Ali MJ.	Ophthalmic Plast Reconstr Surg	10.1097/iop.0000000000002931	2025
Pathogenicity	Metagenomics of the lacrimal sac in primary acquired nasolacrimal duct obstruction: the Lacriome paper 1.	Ali MJ.	Br J Ophthalmol	10.1136/bjophthalmol-2021-319677	2023
	Bacteria of healthy periodontal tissues as candidates of probiotics: a systematic review.	Del Pilar Angarita-Diaz M, Fong C, Medina D.	Eur J Med Res	10.1186/s40001-024-01908-2	2024
	Association Between Oral Dysbiosis and Alzheimer's Disease: A Systematic Review.	Martinez-Martinez V, Rodriguez-Lozano FJ, Pecci-Lloret MP, Perez-Guzman N.	J Clin Med	10.3390/jcm14103415	2025
	Carcinogenesis of Male Oral Submucous Fibrosis Alters Salivary Microbiomes.	Chen MY, Chen JW, Wu LW, Huang KC, Chen JY, Wu WS, Chiang WF, Shih CJ, Tsai KN, Hsieh WT, Ho YH, Wong TY, Wu JH, Chen YL.	J Dent Res	10.1177/0022034520968750	2021
	Supra- and Subgingival Microbiome in Gingivitis and Impact of Biofilm Control: A Comprehensive Review	Iniesta M, Vasconcelos V, Sanz M, Herrera D.	Antibiotics (Basel)		2024
	Alterations in serum metabolomics during the first seizure and after effective control of epilepsy.	Lian X, Liu Z, Liu S, Jin L, Wu T, Chen Y, Li S, Kang W, Lian Y, Jiang Y, Ren Z.	Sci Rep	10.1038/s41598-024-68966-8	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
	Microbiome Shifts in Peri-Implantitis: Longitudinal Characterization of Dysbiosis and Resolution.	Anuntakarun S, Thaweesapphithak S, Krasaesin A, Prommanee S, Arunyanak S, Kungsadalpipob K, Acharya A, Porntaveetus T, Mattheos N.	Int Dent J	10.1016/j.identj.2025.100951	2025
	Comparison of the Oral Microbiota Structure among People from the Same Ethnic Group Living in Different Environments.	Ma G, Qiao Y, Shi H, Zhou J, Li Y.	Biomed Res Int	10.1155/2022/6544497	2022
	Linking Microbiota Profiles to Disease Characterization in Common Variable Immunodeficiency: The Case of Granulomatous-Lymphocytic Interstitial Lung Disease.	Cabanero-Navalon MD, Carda-Dieguez M, Moral Moral P, Mira A, Balastegui-Martin H, Salavert-Lleti M, Garcia-Bustos V.	Biomedicines	10.3390/biomedicines12102239	2024
Phylogeny	Full-length 16S rDNA sequencing based on Oxford Nanopore Technologies revealed the association between gut-pharyngeal microbiota and tuberculosis in cynomolgus macaques.	Sawaswong V, Chanchaem P, Klomkliew P, Rotcheewaphan S, Meesawat S, Kemthong T, Kaewparuehaschai M, Noradechanon K, Ekatat M, Kanitpun R, Srilohasin P, Warit S, Chaiprasert A, Malaivijitnond S, Payungporn S.	Sci Rep	10.1038/s41598-024-53880-w	2024
	HmuY proteins of the Porphyromonas genus show diversity in heme-binding properties.	Smiga M, Olczak T.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1560779	2025
	Oral microbial dysbiosis in patients with oral cavity cancers.	Unlu O, Demirci M, Paksoy T, Eden AB, Tansuker HD, Dalmizrak A, Aktan C, Senel F, Sunter AV, Yigit O, Cakir BO, Kantarci A.	Clin Oral Investig	10.1007/s00784-024-05770-8	2024
	Identification of a growth factor required for culturing specific fastidious oral bacteria.	Murugkar P, Dimise E, Stewart E, Viala SN, Clardy J, Dewhirst FE, Lewis K.	J Oral Microbiol	10.1080/20002297.2022.2143651	2023
	Influence of orthodontic appliances and nitrate on the oral microbiota.	Reichardt E, Eigenthaler M, Jost-Brinkmann PG, Stellzig-Eisenhauer A, Verna C, Plumeier I, Kahl S, Junca H, Vilchez-Vargas R, Pieper DH.	Appl Microbiol Biotechnol	10.1007/s00253-025-13496-0	2025
Phylogeny	Candida albicans enriched in orthodontic derived white spot lesions and shaped focal supragingival bacteriome.	Yang H, Ma Y, Xie X, Wang H, Li X, Fang D, Bai Y.	Front Microbiol	10.3389/fmicb.2023.1084850	2023
	The Global Trends and Advances in Oral Microbiome Research on Oral Squamous Cell Carcinoma: A Systematic Review.	Dumitrescu R, Bolchis V, Fratila AD, Jumanca D, Buzatu BLR, Sava-Rosianu R, Alexa VT, Galuscan A, Balean O.	Microorganisms	10.3390/microorganisms13020373	2025
Phylogeny	Periodontal dysbiosis associates with reduced CSF Abeta42 in cognitively normal elderly.	Kamer AR, Pushalkar S, Gulivindala D, Butler T, Li Y, Annam KRC, Glodzik L, Ballman KV, Corby PM, Blennow K, Zetterberg H, Saxena D, de Leon MJ.	Alzheimers Dement (Amst)	10.1002/dad2.12172	2021
	Microbiome at sites of gingival recession in children with Hutchinson-Gilford progeria syndrome.	Bassir SH, Chase I, Paster BJ, Gordon LB, Kleinman ME, Kieran MW, Kim DM, Sonis A.	J Periodontol	10.1002/jper.17-0351	2018
Metabolism	Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation.	Olivares M, Hernandez-Calderon P, Cardenas-Brito S, Liebana-Garcia R, Sanz Y, Benitez-Paez A.	Genome Biol	10.1186/s13059-024-03325-4	2024
	Optimization of conditions for in vitro modeling of subgingival normobiosis and dysbiosis.	Baraniya D, Do T, Chen T, Albandar JM, Chialastri SM, Devine DA, Marsh PD, Al-Hebshi NN.	Front Microbiol	10.3389/fmicb.2022.1031029	2022
Metabolism	Oral probiotic activities and biosafety of Lactobacillus gasseri HHuMIN D.	Mann S, Park MS, Johnston TV, Ji GE, Hwang KT, Ku S.	Microb Cell Fact	10.1186/s12934-021-01563-w	2021
Phylogeny	Subgingival microbiome of experimental gingivitis: shifts associated with the use of chlorhexidine and N-acetyl cysteine mouthwashes.	Al-Kamel A, Baraniya D, Al-Hajj WA, Halboub E, Abdulrab S, Chen T, Al-Hebshi NN.	J Oral Microbiol	10.1080/20002297.2019.1608141	2019
	Geographic Variation Did Not Affect the Predictive Power of Salivary Microbiota for Caries in Children With Mixed Dentition.	Li S, Huang S, Guo Y, Zhang Y, Zhang L, Li F, Tan K, Lu J, Chen Z, Guo Q, Tang Y, Teng F, Yang F.	Front Cell Infect Microbiol	10.3389/fcimb.2021.680288	2021
	Microbiological assessment of success and failure in pulp revitalization: a randomized clinical trial using calcium hydroxide and chlorhexidine gluconate in traumatized immature necrotic teeth.	Wikstrom A, Romani Vestman N, Rakhimova O, Lazaro Gimeno D, Tsilingaridis G, Brundin M.	J Oral Microbiol	10.1080/20002297.2024.2343518	2024
	Analysis of airway microbiota in adults from a Brazilian cystic fibrosis center.	Leite CCF, de Freitas FAD, de Cassia Firmida M, Leao RS, Albano RM, Marques EA.	Braz J Microbiol	10.1007/s42770-020-00381-3	2020
	Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease.	Muggeo A, Perotin JM, Brisebarre A, Dury S, Dormoy V, Launois C, Ancel J, Mulette P, de Champs C, Deslee G, Guillard T.	Front Microbiol	10.3389/fmicb.2021.781797	2021
	Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children.	Hurley E, Barrett MPJ, Kinirons M, Whelton H, Ryan CA, Stanton C, Harris HMB, O'Toole PW.	BMC Oral Health	10.1186/s12903-018-0693-1	2019
	Electronic Cigarette Use Promotes a Unique Periodontal Microbiome.	Thomas SC, Xu F, Pushalkar S, Lin Z, Thakor N, Vardhan M, Flaminio Z, Khodadadi-Jamayran A, Vasconcelos R, Akapo A, Queiroz E, Bederoff M, Janal MN, Guo Y, Aguallo D, Gordon T, Corby PM, Kamer AR, Li X, Saxena D.	mBio	10.1128/mbio.00075-22	2022
	Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.	Islam SMS, Ryu HM, Sohn S.	Cells	10.3390/cells11121903	2022
Genetics	Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis.	O'Flynn C, Deusch O, Darling AE, Eisen JA, Wallis C, Davis IJ, Harris SJ.	Genome Biol Evol	10.1093/gbe/evv220	2015
	Changes in abundance of Lactobacillus spp. and Streptococcus suis in the stomach, jejunum and ileum of piglets after weaning.	Su Y, Yao W, Perez-Gutierrez ON, Smidt H, Zhu WY.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2008.00529.x	2008
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
	Site- and Time-Dependent Compositional Shifts in Oral Microbiota Communities.	Esberg A, Eriksson L, Johansson I.	Front Oral Health	10.3389/froh.2022.826996	2022
Genetics	Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight.	Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra MA, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina JS, Houerbi N, Meydan C, Wain Hirschberg J, Qiu J, Kleinman AS, Al-Ghalith GA, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead BP, Beyaz S, Venkateswaran KJ, Wiseman K, Moreno J, Boddicker AM, Zhao J, Lajoie BR, Scott RT, Altomare A, Kruglyak S, Levy S, Church GM, Mason CE.	Nat Microbiol	10.1038/s41564-024-01635-8	2024
Phylogeny	Microbiome succession with increasing age in three oral sites.	Liu S, Wang Y, Zhao L, Sun X, Feng Q.	Aging (Albany NY)	10.18632/aging.103108	2020
Phylogeny	Comparison of oral microbial profiles between children with severe early childhood caries and caries-free children using the human oral microbe identification microarray.	Ma C, Chen F, Zhang Y, Sun X, Tong P, Si Y, Zheng S.	PLoS One	10.1371/journal.pone.0122075	2015
	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
	Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.	Relvas M, Regueira-Iglesias A, Balsa-Castro C, Salazar F, Pacheco JJ, Cabral C, Henriques C, Tomas I.	Sci Rep	10.1038/s41598-020-79875-x	2021
Pathogenicity	Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.	Islam SMS, Ryu HM, Sayeed HM, Byun HO, Jung JY, Kim HA, Suh CH, Sohn S.	Front Immunol	10.3389/fimmu.2021.712312	2021
Phylogeny	Enrichment of periodontal pathogens from the biofilms of healthy adults.	Naginyte M, Do T, Meade J, Devine DA, Marsh PD.	Sci Rep	10.1038/s41598-019-41882-y	2019
Transcriptome	Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing.	Regueira-Iglesias A, Vazquez-Gonzalez L, Balsa-Castro C, Blanco-Pintos T, Vila-Blanco N, Carreira MJ, Tomas I.	Microbiol Spectr	10.1128/spectrum.04398-22	2023
Genetics	CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice.	Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, Nagarkatti M.	Eur J Immunol	10.1002/eji.201646792	2017
	The Oral-Gut Axis: Periodontal Diseases and Gastrointestinal Disorders.	Lam GA, Albarrak H, McColl CJ, Pizarro A, Sanaka H, Gomez-Nguyen A, Cominelli F, Paes Batista da Silva A.	Inflamm Bowel Dis	10.1093/ibd/izac241	2023
	Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis.	Vieira J, Jesudasen S, Bringhurst L, Sui HY, McIver L, Whiteson K, Hanselmann K, O'Toole GA, Richards CJ, Sicilian L, Neuringer I, Lai PS.	mSystems	10.1128/msystems.00364-22	2022
Phylogeny	Reclassification of Oribaculum catoniae (Moore and Moore 1994) as Porphyromonas catoniae comb. nov. and emendation of the genus Porphyromonas.	Willems A, Collins MD.	Int J Syst Bacteriol	10.1099/00207713-45-3-578	1995
Phylogeny	Subgingival microbiota in health compared to periodontitis and the influence of smoking.	Camelo-Castillo AJ, Mira A, Pico A, Nibali L, Henderson B, Donos N, Tomas I.	Front Microbiol	10.3389/fmicb.2015.00119	2015
Enzymology	Establishment of oral anaerobes during the first year of life.	Kononen E, Kanervo A, Takala A, Asikainen S, Jousimies-Somer H.	J Dent Res	10.1177/00220345990780100801	1999
	Grade C molar-incisor pattern periodontitis subgingival microbial profile before and after treatment.	Velsko IM, Harrison P, Chalmers N, Barb J, Huang H, Aukhil I, Shaddox L.	J Oral Microbiol	10.1080/20002297.2020.1814674	2020
Metabolism	Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses.	Yost S, Stashenko P, Choi Y, Kukuruzinska M, Genco CA, Salama A, Weinberg EO, Kramer CD, Frias-Lopez J.	Int J Oral Sci	10.1038/s41368-018-0037-7	2018
	Sex-specific differences in the salivary microbiome of caries-active children.	Ortiz S, Herrman E, Lyashenko C, Purcell A, Raslan K, Khor B, Snow M, Forsyth A, Choi D, Maier T, Machida CA.	J Oral Microbiol	10.1080/20002297.2019.1653124	2019
Genetics	Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis.	Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, van Gils E, Bruin J, Montijn R, Bonten M, Sanders E.	PLoS One	10.1371/journal.pone.0017035	2011
	Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity.	Hall MW, Singh N, Ng KF, Lam DK, Goldberg MB, Tenenbaum HC, Neufeld JD, G Beiko R, Senadheera DB.	NPJ Biofilms Microbiomes	10.1038/s41522-016-0011-0	2017
	Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population.	Al-Hebshi NN, Abdulhaq A, Albarrag A, Basode VK, Chen T.	J Oral Microbiol	10.3402/jom.v8.31444	2016
	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
Metabolism	The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity.	Lynch A, Crowley E, Casey E, Cano R, Shanahan R, McGlacken G, Marchesi JR, Clarke DJ.	Sci Rep	10.1038/s41598-017-13774-6	2017
Enzymology	Detection of the amoeba Entamoeba gingivalis in periodontal pockets.	Bonner M, Amard V, Bar-Pinatel C, Charpentier F, Chatard JM, Desmuyck Y, Ihler S, Rochet JP, Roux de La Tribouille V, Saladin L, Verdy M, Girones N, Fresno M, Santi-Rocca J.	Parasite	10.1051/parasite/2014029	2014
	Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.	Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE, Daniels TW, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.	ISME J	10.1038/ismej.2015.198	2016
Phylogeny	Culture-independent identification of periodontitis-associated Porphyromonas and Tannerella populations by targeted molecular analysis.	de Lillo A, Booth V, Kyriacou L, Weightman AJ, Wade WG.	J Clin Microbiol	10.1128/jcm.42.12.5523-5527.2004	2004
Genetics	Host genetic variation and its microbiome interactions within the Human Microbiome Project.	Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C.	Genome Med	10.1186/s13073-018-0515-8	2018
Enzymology	Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay.	Dzidic M, Collado MC, Abrahamsson T, Artacho A, Stensson M, Jenmalm MC, Mira A.	ISME J	10.1038/s41396-018-0204-z	2018
Enzymology	Beta-lactamase production by oral anaerobic gram-negative species in infants in relation to previous antimicrobial therapy.	Nyfors S, Kononen E, Takala A, Jousimies-Somer H.	Antimicrob Agents Chemother	10.1128/aac.43.7.1591	1999
	The microbiota of the mother at birth and its influence on the emerging infant oral microbiota from birth to 1 year of age: a cohort study.	Hurley E, Mullins D, Barrett MP, O'Shea CA, Kinirons M, Ryan CA, Stanton C, Whelton H, Harris HMB, O'Toole PW.	J Oral Microbiol	10.1080/20002297.2019.1599652	2019
	Analysis of the salivary microbiome using culture-independent techniques.	Lazarevic V, Whiteson K, Gaia N, Gizard Y, Hernandez D, Farinelli L, Osteras M, Francois P, Schrenzel J.	J Clin Bioinforma	10.1186/2043-9113-2-4	2012
Phylogeny	The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation.	Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, Gamonal J, Diaz PI.	ISME J	10.1038/ismej.2012.174	2013
Genetics	Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis.	Scher JU, Ubeda C, Equinda M, Khanin R, Buischi Y, Viale A, Lipuma L, Attur M, Pillinger MH, Weissmann G, Littman DR, Pamer EG, Bretz WA, Abramson SB.	Arthritis Rheum	10.1002/art.34539	2012
	A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.	Davis IJ, Wallis C, Deusch O, Colyer A, Milella L, Loman N, Harris S, Harris S.	PLoS One	10.1371/journal.pone.0083158	2013
Phylogeny	High-resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis.	Szafranski SP, Wos-Oxley ML, Vilchez-Vargas R, Jauregui R, Plumeier I, Klawonn F, Tomasch J, Meisinger C, Kuhnisch J, Sztajer H, Pieper DH, Wagner-Dobler I.	Appl Environ Microbiol	10.1128/aem.03534-14	2015
	Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.	Biesbroek G, Sanders EA, Roeselers G, Wang X, Caspers MP, Trzcinski K, Bogaert D, Keijser BJ.	PLoS One	10.1371/journal.pone.0032942	2012
Phylogeny	Cultivable anaerobic microbiota of severe early childhood caries.	Tanner AC, Mathney JM, Kent RL, Chalmers NI, Hughes CV, Loo CY, Pradhan N, Kanasi E, Hwang J, Dahlan MA, Papadopolou E, Dewhirst FE.	J Clin Microbiol	10.1128/jcm.02427-10	2011
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
Genetics	Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.	Togo AH, Diop A, Dubourg G, Nguyen TT, Andrieu C, Caputo A, Couderc C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2016.07.010	2016
Phylogeny	Porphyromonas pogonae sp. nov., an anaerobic but low concentration oxygen adapted coccobacillus isolated from lizards (Pogona vitticeps) or human clinical specimens, and emended description of the genus Porphyromonas Shah and Collins 1988.	Kawamura Y, Kuwabara S, Kania SA, Kato H, Hamagishi M, Fujiwara N, Sato T, Tomida J, Tanaka K, Bemis DA.	Syst Appl Microbiol	10.1016/j.syapm.2014.11.004	2015
Phylogeny	Porphyromonas somerae sp. nov., a pathogen isolated from humans and distinct from porphyromonas levii.	Summanen PH, Durmaz B, Vaisanen ML, Liu C, Molitoris D, Eerola E, Helander IM, Finegold SM.	J Clin Microbiol	10.1128/jcm.43.9.4455-4459.2005	2005
Phylogeny	Porphyromonas pasteri sp. nov., isolated from human saliva.	Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.000294	2015
Phylogeny	Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic gram-negative bacilli from the human gingival crevice.	Moore LV, Moore WE	Int J Syst Bacteriol	10.1099/00207713-44-2-187	1994

References

#17342	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23684
#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 )
#55031	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 41358
#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;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#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 .
#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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Porphyromonas catoniae (DSM 23684, ATCC 51270, CCUG 41358)

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