Alloscardovia omnicolens (DSM 21503, CCUG 31649, LMG 23792)

Name: Alloscardovia omnicolens (DSM 21503, CCUG 31649, LMG 23792)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1767

Type strain

Culture col. no. DSM 21503 CCUG 31649 LMG 23792 CIP 109610

NCBI tax ID(s) 1120979 419015

Special Collections DSMZ CCUG CIP Literature strains

History <- CCUG; CCUG 31649 <- K. Ericson, PHL Kristianstad, Sweden;

Links

Alloscardovia omnicolens DSM 21503 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from human tonsil, 25-yr-old woman.

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 51942

CCUG 31649,LMG 23792,DSM 21503

@ref 20215

Last LPSN update 2026-02-09 11:18:10

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Alloscardovia

Species Alloscardovia omnicolens

Full scientific name Alloscardovia omnicolens Huys et al. 2007

BacDive ID	Other strains from **Alloscardovia omnicolens** (18)	Type strain
139088	A. omnicolens CIP 101708
141805	A. omnicolens CCUG 7132
142574	A. omnicolens CCUG 13112 B
143345	A. omnicolens CCUG 18650
144874	A. omnicolens CCUG 26938
145014	A. omnicolens CCUG 27412 A
146657	A. omnicolens CCUG 31736
147893	A. omnicolens CCUG 34444
151349	A. omnicolens CCUG 43818
151516	A. omnicolens CCUG 44187
151740	A. omnicolens CCUG 44766
153182	A. omnicolens CCUG 48667
153671	A. omnicolens CCUG 50589
153978	A. omnicolens CCUG 51831
154585	A. omnicolens CCUG 54474
155855	A. omnicolens CCUG 59476
156789	A. omnicolens CCUG 65230
156981	A. omnicolens CCUG 68090

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
32013	positive	rod-shaped
125438				94.5

Multimedia

@ref:	66793
multimedia content:	EM_DSM_21503_1.jpg
multimedia.multimedia content:	EM_DSM_21503_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21503_2.jpg
multimedia.multimedia content:	EM_DSM_21503_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21503_3.jpg
multimedia.multimedia content:	EM_DSM_21503_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21503_4.jpg
multimedia.multimedia content:	EM_DSM_21503_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21503_5.jpg
multimedia.multimedia content:	EM_DSM_21503_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15682	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
15682	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15682	positive	growth	37	mesophilic
32013	positive	growth	28-45
32013	positive	optimum	36.5	mesophilic
50672	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
15682	anaerobe
32013	facultative anaerobe
50672	microaerophile
125439	obligate aerobe	93.8

Spore formation

@ref	Spore formation	Confidence
32013
125439		99.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32013	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
32013	4853 ChEBI	esculin	+	hydrolysis
32013	17234 ChEBI	glucose	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
32013	17306 ChEBI	maltose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
32013	16634 ChEBI	raffinose	+	carbon source
32013	17814 ChEBI	salicin	+	carbon source
32013	17992 ChEBI	sucrose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
32013	18222 ChEBI	xylose	+	carbon source

Metabolite production

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

Metabolite tests

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

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-fucosidase	-	3.2.1.51	from API rID32A
32013	alpha-galactosidase	+	3.2.1.22
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-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate 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	N-acetyl-beta-glucosaminidase	-	3.2.1.52	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

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
15682	-	-	+	-	-	+	+/-	+/-	-	-	-	+/-	-	-	-	-	-	+	+	-	+	+	-	+	-	+	+	-	+
15682	-	-	+	+/-	-	+	+	+	-	-	-	+	-	-	-	-	-	+	+	-	+	+	-	+	-	+/-	+/-	-	+
50672	-	-	+	+	-	+	+	+	-	-	-	+	-	-	-	-	-	+	+	-	+	+	-	+	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
15682	human tonsil, 25-yr-old woman			Sweden	SWE	Europe
50672	Human tonsil,25-yr-old woman	1993-06-15	Kristianstad	Sweden	SWE	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM419460 (>99% sequence identity) for Alloscardovia omnicolens subclade from Microbeatlas

Aquatic Samples	686
Soil Samples	356
Animal Samples	42333
Plant Samples	140
Total Samples	43515

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15682	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
66792	ASM42050v1 assembly for Alloscardovia omnicolens DSM 21503	contig	GCA_000420505	1120979.4	2523533599	1120979	69.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15682	Alloscardovia omnicolens partial 16S rRNA gene, strain CCUG 31649T	AM419460	1482		419015
124043	Alloscardovia omnicolens strain DSM 21503 16S-23S ribosomal RNA intergenic spacer, partial sequence.	KT343136	300		419015

GC content

@ref	GC-content (mol%)
15682	48.0
32013	47.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alloscardovia omnicolens DSM 21503
NCBI: GCA_000420505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.80	no
125439	gram_stain	BacteriaNetⓘ	negative	79.00	no
125439	motility	BacteriaNetⓘ	no	64.60	no
125439	spore_formation	BacteriaNetⓘ	no	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alloscardovia omnicolens DSM 21503
PATRIC: 1120979.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.53	yes
125438	anaerobic	anaerobicⓘ	yes	75.67	no
125438	spore-forming	spore-formingⓘ	no	87.52	no
125438	aerobic	aerobicⓘ	no	95.04	no
125438	thermophilic	thermophileⓘ	no	91.47	no
125438	flagellated	motile2+ⓘ	no	94.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discrimination of Gardnerella Species by Combining MALDI-TOF Protein Profile, Chaperonin cpn60 Sequences, and Phenotypic Characteristics.	Bulavaite A, Maier T, Pleckaityte M.	Pathogens	10.3390/pathogens10030277	2021
Phylogeny	Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome.	Hill JE, Albert AYK, Albert AYK, VOGUE Research Group.	Infect Immun	10.1128/iai.00532-19	2019
Genetics	Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.	Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiri K, van Sinderen D, Ventura M.	BMC Genomics	10.1186/s12864-017-3955-4	2017
	Impact of bovine lactoferrin supplementation and reduced iron in formula on infant oral microbiome: a randomized controlled trial.	Anticona C, Esberg A, Berglund SK, Bjormsjo M, Hernell O, Lonnerdal B, Johansson I, Holgerson PL.	J Oral Microbiol	10.1080/20002297.2025.2561212	2025
	Thoracic empyema caused by Alloscardovia omnicolens and Bifidobacteriumdentium.	Takiguchi Y, Nagayoshi M, Matsuura Y, Yokota S, Kajiwara Y, Akiba Y.	J Infect Chemother	10.1016/j.jiac.2022.07.021	2022
	A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.	Thomas-White K, Hilt EE, Olmschenk G, Gong M, Phillips CD, Jarvis C, Sanford N, White J, Navarro P.	Diagnostics (Basel)	10.3390/diagnostics14182039	2024
	Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data	Zhang Y, Zhang H, Liu B, Ning K.	iScience		2024
	Genitourinary microbiomes and prostate cancer: a systematic review and meta-analysis of tumorigeneses and cancer characteristics.	Parizi MK, Matsukawa A, Alimohammadi A, Klemm J, Tsuboi I, Fazekas T, Laukhtina E, Chiujdea S, Karakiewicz PI, Shariat SF.	Cent European J Urol	10.5173/ceju.2024.80	2024
	Alloscardovia omnicolens emerging presence in premature rupture of membranes.	Cardona-Benavides I, Puertas-Prieto A, Pinilla-Martin FJ, Navarro-Mari JM, Gutierrez-Fernandez J.	New Microbiol		2019
	Biosynthesis of Arabinoside from Sucrose and Nucleobase via a Novel Multi-Enzymatic Cascade.	Liu Y, Yang E, Zhang X, Liu X, Tang X, Wang Z, Wang H.	Biomolecules	10.3390/biom14091107	2024
Genetics	Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.	Kumari V S S, Potdar V, Shinde M, Parashar D, Alagarasu K, Cherian S, Lavania M.	J Oral Microbiol	10.1080/20002297.2025.2569523	2025
	Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs.	Wang D, Haley E, Luke N, Mathur M, Festa RA, Zhao X, Anderson LA, Allison JL, Stebbins KL, Diaz MJ, Baunoch D.	Infect Drug Resist	10.2147/idr.s429990	2023
	The Vaginal Microbiota, Human Papillomavirus, and Cervical Dysplasia-A Review.	Kazlauskaite J, Zukiene G, Rudaitis V, Bartkeviciene D.	Medicina (Kaunas)	10.3390/medicina61050847	2025
Genetics	A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.	Ferneyhough B, Roddis M, Millington S, Quirk J, Clements C, West S, Schilizzi R, Fischer MD, Parkinson NJ.	BMC Urol	10.1186/s12894-025-01723-9	2025
	The effects of fresh mango consumption on gut health and microbiome - Randomized controlled trial.	Asuncion P, Liu C, Castro R, Yon V, Rosas M, Hooshmand S, Kern M, Hong MY.	Food Sci Nutr	10.1002/fsn3.3243	2023
	Comparative analysis of the postadmission and antemortem oropharyngeal and rectal swab microbiota of ICU patients.	Petrilla A, Nemeth P, Fauszt P, Szilagyi-Racz A, Mikolas M, Szilagyi-Tolnai E, David P, Stagel A, Gal F, Gal K, Sohajda R, Pham T, Stundl L, Biro S, Remenyik J, Paholcsek M.	Sci Rep	10.1038/s41598-024-78102-1	2024
	Distinctive salivary oral microbiome in patients with burning mouth syndrome depending on pain intensity compared to healthy subjects.	Ju HM, Ahn YW, Ok SM, Jeong SH, Na HS, Chung J.	J Dent Sci	10.1016/j.jds.2024.05.022	2025
	Comparing Prescribing Behaviors and Clinician Experiences Between Multiplex PCR/Pooled Antibiotic Susceptibility Testing and Standard Urine Culture in Complicated UTI Cases.	Haley E, Luke N, Korman H, Rao GS, Baunoch D, Chen X, Havrilla J, Mathur M.	J Clin Med	10.3390/jcm13237453	2024
	Perinatal factors influencing the earliest establishment of the infant microbiome.	Linehan K, Healy K, Hurley E, O'Shea CA, Ryan CA, Ross RP, Stanton C, Dempsey EM.	Microbiome Res Rep	10.20517/mrr.2024.92	2025
	Acute Pyelonephritis with Bacteremia in an 89-Year-Old Woman Caused by Two Slow-Growing Bacteria: Aerococcus urinae and Actinotignum schaalii.	Lotte L, Durand C, Chevalier A, Gaudart A, Cheddadi Y, Ruimy R, Lotte R.	Microorganisms	10.3390/microorganisms11122908	2023
	Marking the Profile of the Microflora of the Endometrium and Uterine Cervix in Women as a Potential Factor Determining the Effectiveness of In Vitro Fertilization.	Bednarska-Czerwinska A, Czerwinski M, Czerwinski M, Morawiec E, Lach A, Ziaja A, Kusaj A, Straczynska P, Sagan D, Boron D, Grabarek BO.	J Clin Med	10.3390/jcm11123348	2022
Phylogeny	The role of the vaginal microbiome in distinguishing female chronic pelvic pain caused by endometriosis/adenomyosis.	Chao X, Liu Y, Fan Q, Shi H, Wang S, Lang J.	Ann Transl Med	10.21037/atm-20-4586	2021
	Seasonal variations in blood culture numbers and time to positivity and potential impact of reducing incubation periods.	de Ponfilly GP, Lourtet-Hascoet J, Porcheret H, Cambau E, Le Monnier A, Jacquier H, Vasse M, Farfour E.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-021-04248-9	2021
	Using the Sysmex UF-4000 urine flow cytometer for rapid diagnosis of urinary tract infection in the clinical microbiological laboratory.	Korsten K, de Gier A, Leenders A, Wever PC, Kolwijck E.	J Clin Lab Anal	10.1002/jcla.25004	2024
	The Past, Present, and Future of Biomarkers for the Early Diagnosis of Pancreatic Cancer.	Vitale F, Zileri Dal Verme L, Paratore M, Negri M, Nista EC, Ainora ME, Esposto G, Mignini I, Borriello R, Galasso L, Alfieri S, Gasbarrini A, Zocco MA, Nicoletti A.	Biomedicines	10.3390/biomedicines12122840	2024
Pathogenicity	In vitro antimicrobial susceptibility of Alloscardovia omnicolens and molecular mechanisms of acquired resistance.	Isnard C, Lienhard R, Reissier S, Rodriguez S, Krahenbuhl J, Liassine N, Guerin F, Cattoir V.	Diagn Microbiol Infect Dis	10.1016/j.diagmicrobio.2015.08.009	2016
Enzymology	Significant increase in cultivation of Gardnerella vaginalis, Alloscardovia omnicolens, Actinotignum schaalii, and Actinomyces spp. in urine samples with total laboratory automation.	Klein S, Nurjadi D, Horner S, Heeg K, Zimmermann S, Burckhardt I.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-018-3250-6	2018
	Pooled Antibiotic Susceptibility Testing for Polymicrobial UTI Performs Within CLSI Validation Standards.	Festa RA, Cockerill FR, Pesano RL, Haley E, Luke N, Mathur M, Chen X, Havrilla J, Percaccio M, Magallon J, Erickson S, Ghashghaie M, Rosas A, Baunoch D.	Antibiotics (Basel)	10.3390/antibiotics14020143	2025
	Presence and Relevance of Emerging Microorganisms in Clinical Genitourinary Samples.	Rosales-Castillo A, Exposito-Ruiz M, Gutierrez-Soto M, Navarro-Mari JM, Gutierrez-Fernandez J.	Microorganisms	10.3390/microorganisms11040915	2023
	Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms.	Prasanchit P, Pongchaikul P, Lertsittichai P, Tantitham C, Manonai J.	Sci Rep	10.1038/s41598-024-58118-3	2024
Pathogenicity	Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains.	Barberis C, Budia M, Palombarani S, Rodriguez CH, Ramirez MS, Arias B, Bonofiglio L, Famiglietti A, Mollerach M, Almuzara M, Vay C.	J Glob Antimicrob Resist	10.1016/j.jgar.2016.11.007	2017
Phylogeny	Natal factors influencing newborn's oral microbiome diversity.	Kim YH, Lee TY, Kim HY, Jeong SJ, Han JH, Shin JE, Lee JH, Kang CM.	Sci Rep	10.1038/s41598-024-78609-7	2024
	Mechanisms by which the intestinal microbiota affects gastrointestinal tumours and therapeutic effects.	He J, Li H, Jia J, Liu Y, Zhang N, Wang R, Qu W, Liu Y, Jia L.	Mol Biomed	10.1186/s43556-023-00157-9	2023
	Emerging Presence of Culturable Microorganisms in Clinical Samples of the Genitourinary System: Systematic Review and Experience in Specialized Care of a Regional Hospital.	Rosales-Castillo A, Jimenez-Guerra G, Ruiz-Gomez L, Exposito-Ruiz M, Navarro-Mari JM, Gutierrez-Fernandez J.	J Clin Med	10.3390/jcm11051348	2022
	Female reproductive dysfunctions and the gut microbiota.	Chadchan SB, Singh V, Kommagani R.	J Mol Endocrinol	10.1530/jme-21-0238	2022
	The gut microbiota in persistent post-operative pain following breast cancer surgery.	Masaud K, Collins JM, Rubio RC, Corrigan M, Cotter PD, O'Brien N, Bluett R, Jimenez CK, O'Mahony SM, Shorten GD.	Sci Rep	10.1038/s41598-024-62397-1	2024
Pathogenicity	Stability of saliva microbiota during moderate consumption of red wine.	Barroso E, Martin V, Martinez-Cuesta MC, Pelaez C, Requena T.	Arch Oral Biol	10.1016/j.archoralbio.2015.09.015	2015
	Urine biomarkers individually and as a consensus model show high sensitivity and specificity for detecting UTIs.	Akhlaghpour M, Haley E, Parnell L, Luke N, Mathur M, Festa RA, Percaccio M, Magallon J, Remedios-Chan M, Rosas A, Wang J, Jiang Y, Anderson L, Baunoch D.	BMC Infect Dis	10.1186/s12879-024-09044-2	2024
	Endometriosis specific vaginal microbiota links to urine and serum N-glycome.	MacSharry J, Kovacs Z, Xie Y, Adamczyk B, Walsh C, Reidy F, McAuliffe FM, Kilbane MT, Twomey PJ, Rudd PM, Wingfield M, Butler M, van Sinderen D, Glover L, Saldova R.	Sci Rep	10.1038/s41598-024-76125-2	2024
	Emerging Technologies for the Diagnosis of Urinary Tract Infections: Advances in Molecular Detection and Resistance Profiling.	Baimakhanova B, Sadanov A, Berezin V, Baimakhanova G, Trenozhnikova L, Orasymbet S, Seitimova G, Kalmakhanov S, Xetayeva G, Shynykul Z, Seidakhmetova A, Turgumbayeva A.	Diagnostics (Basel)	10.3390/diagnostics15192469	2025
	Elevated UTI Biomarkers in Symptomatic Patients with Urine Microbial Densities of 10,000 CFU/mL Indicate a Lower Threshold for Diagnosing UTIs.	Parnell LKS, Luke N, Mathur M, Festa RA, Haley E, Wang J, Jiang Y, Anderson L, Baunoch D.	Diagnostics (Basel)	10.3390/diagnostics13162688	2023
Genetics	Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.	Li Y, Pan G, Wang S, Li Z, Yang R, Jiang Y, Chen Y, Li SC, Shen B.	Brief Bioinform	10.1093/bib/bbae620	2024
	The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis.	De Seta F, Campisciano G, Zanotta N, Ricci G, Comar M.	Front Microbiol	10.3389/fmicb.2019.02451	2019
	Concordance Between Antibiotic Resistance Genes and Susceptibility in Symptomatic Urinary Tract Infections.	Baunoch D, Luke N, Wang D, Vollstedt A, Zhao X, Ko DSC, Huang S, Cacdac P, Sirls LT.	Infect Drug Resist	10.2147/idr.s323095	2021
	Gut Microbiota in Diagnosis, Therapy and Prognosis of Cholangiocarcinoma and Gallbladder Carcinoma-A Scoping Review.	Lederer AK, Rasel H, Kohnert E, Kreutz C, Huber R, Badr MT, Dellweg PKE, Bartsch F, Lang H.	Microorganisms	10.3390/microorganisms11092363	2023
Phylogeny	[Correlations Between Gut Microbiota Changes and Cognitive Function in Patients with Post-Stroke Cognitive Impairment in the Early Stage].	Li YM, Yu Q, Huang L, Fu J, Feng RJ.	Sichuan Da Xue Xue Bao Yi Xue Ban	10.12182/20220960105	2022
	Microbiota as a state-of-the-art approach in precision medicine for pancreatic cancer management: A comprehensive systematic review.	Hesami Z, Sabzehali F, Khorsand B, Alipour S, Sadeghi A, Asri N, Pazienza V, Houri H.	iScience	10.1016/j.isci.2025.112314	2025
Metabolism	Metagenome association study of the gut microbiome revealed biomarkers linked to chemotherapy outcomes in locally advanced and advanced lung cancer.	Zhao Z, Fei K, Bai H, Wang Z, Duan J, Wang J.	Thorac Cancer	10.1111/1759-7714.13711	2021
	Endometrial microbiota in women with and without adenomyosis: A pilot study.	Lin Q, Duan H, Wang S, Guo Z, Wang S, Chang Y, Chen C, Shen M, Shou H, Zhou C.	Front Microbiol	10.3389/fmicb.2023.1075900	2023
Pathogenicity	Antimicrobial Susceptibility Patterns of Anaerobic Bacterial Clinical Isolates From 2014 to 2016, Including Recently Named or Renamed Species.	Byun JH, Kim M, Lee Y, Lee K, Chong Y.	Ann Lab Med	10.3343/alm.2019.39.2.190	2019
Enzymology	Lactobacillus and Bifidobacterium diversity in horse feces, revealed by PCR-DGGE.	Endo A, Futagawa-Endo Y, Dicks LM.	Curr Microbiol	10.1007/s00284-009-9498-4	2009
	Multi-site microbiota alteration is a hallmark of kidney stone formation.	Al KF, Joris BR, Daisley BA, Chmiel JA, Bjazevic J, Reid G, Gloor GB, Denstedt JD, Razvi H, Burton JP.	Microbiome	10.1186/s40168-023-01703-x	2023
	Metataxonomic and metabolomic evidence of biofilm homeostasis disruption related to caries: An in vitro study.	Sanchez MC, Velapatino A, Llama-Palacios A, Valdes A, Cifuentes A, Ciudad MJ, Collado L.	Mol Oral Microbiol	10.1111/omi.12363	2022
	Lifestyle Factors and the Microbiome in Urolithiasis: A Narrative Review.	Koudonas A, Tsiakaras S, Tzikoulis V, Papaioannou M, de la Rosette J, Anastasiadis A, Dimitriadis G.	Nutrients	10.3390/nu17030465	2025
	Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment.	Sawhney SS, Johnson C, Shupe A, Fine J, Dantas G, Burnham CD, Yarbrough ML.	Clin Chem	10.1093/clinchem/hvab199	2021
	The Neuro-Endo-Microbio-Ome Study: A Pilot Study of Neurobiological Alterations Pre- Versus Post-Bariatric Surgery.	Agarwal K, Maki KA, Vizioli C, Carnell S, Goodman E, Hurley M, Harris C, Colwell R, Steele K, Joseph PV.	Biol Res Nurs	10.1177/10998004221085976	2022
Metabolism	Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease.	Wu IW, Gao SS, Chou HC, Yang HY, Chang LC, Kuo YL, Dinh MCV, Chung WH, Yang CW, Lai HC, Hsieh WP, Su SC.	Theranostics	10.7150/thno.41725	2020
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
	Altered oral microbiome in Sudanese Toombak smokeless tobacco users carries a newly emerging risk of squamous cell carcinoma development and progression.	Sami A, Elimairi I, Ryan CA, Stanton C, Patangia D, Ross RP.	Sci Rep	10.1038/s41598-023-32892-y	2023
	Modeling Normal and Dysbiotic Subgingival Microbiomes: Effect of Nutrients.	Baraniya D, Naginyte M, Chen T, Albandar JM, Chialastri SM, Devine DA, Marsh PD, Al-Hebshi NN.	J Dent Res	10.1177/0022034520902452	2020
Enzymology	Site and clinical significance of Alloscardovia omnicolens and Bifidobacterium species isolated in the clinical laboratory.	Mahlen SD, Clarridge JE.	J Clin Microbiol	10.1128/jcm.00555-09	2009
Enzymology	Strategy using a new antigenic test for rapid diagnosis of Streptococcus pneumoniae infection in respiratory samples from children consulting at hospital.	Haddar CH, Joly J, Carricajo A, Verhoeven PO, Grattard F, Mory O, Begaud E, Germani Y, Cantais A, Pozzetto B.	BMC Microbiol	10.1186/s12866-020-01764-0	2020
Enzymology	The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms.	Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C, Brubaker L, Wolfe AJ, Mueller ER, Schreckenberger PC.	J Clin Microbiol	10.1128/jcm.00044-16	2016
Genetics	Evolutionary relationships among bifidobacteria and their hosts and environments.	Rodriguez CI, Martiny JBH.	BMC Genomics	10.1186/s12864-019-6435-1	2020
Metabolism	Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria.	Li Y, Huang Y.	Microbiol Spectr	10.1128/spectrum.02380-21	2022
	Microorganisms Identified in the Maternal Bladder: Discovery of the Maternal Bladder Microbiota.	Jacobs KM, Thomas-White KJ, Hilt EE, Wolfe AJ, Waters TP.	AJP Rep	10.1055/s-0037-1606860	2017
	A faecal microbiota signature with high specificity for pancreatic cancer.	Kartal E, Schmidt TSB, Molina-Montes E, Rodriguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gomez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Marquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, MAGIC Study investigators, PanGenEU Study investigators, Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P.	Gut	10.1136/gutjnl-2021-324755	2022
	Phylogeny-guided microbiome OTU-specific association test (POST).	Huang C, Callahan BJ, Wu MC, Holloway ST, Brochu H, Lu W, Peng X, Tzeng JY.	Microbiome	10.1186/s40168-022-01266-3	2022
Genetics	Understanding the Conundrum of Pancreatic Cancer in the Omics Sciences Era.	Nicoletti A, Paratore M, Vitale F, Negri M, Quero G, Esposto G, Mignini I, Alfieri S, Gasbarrini A, Zocco MA, Zileri Dal Verme L.	Int J Mol Sci	10.3390/ijms25147623	2024
Phylogeny	Isolation and identification of bifidobacteriaceae from human saliva.	Beighton D, Gilbert SC, Clark D, Mantzourani M, Al-Haboubi M, Ali F, Ransome E, Hodson N, Fenlon M, Zoitopoulos L, Gallagher J.	Appl Environ Microbiol	10.1128/aem.00895-08	2008
	A multicentre study investigating parameters which influence direct bacterial identification from urine.	Zboromyrska Y, Bosch J, Aramburu J, Cuadros J, Garcia-Riestra C, Guzman-Puche J, Liebana Martos C, Loza E, Munoz-Algarra M, Ruiz de Alegria C, Sanchez-Hellin V, Vila J.	PLoS One	10.1371/journal.pone.0207822	2018
Phylogeny	Research of the potential biomarkers in vaginal microbiome for persistent high-risk human papillomavirus infection.	Chao X, Sun T, Wang S, Tan X, Fan Q, Shi H, Zhu L, Lang J.	Ann Transl Med	10.21037/atm.2019.12.115	2020
	Amixicile depletes the ex vivo periodontal microbiome of anaerobic bacteria.	Gui Q, Ramsey KW, Hoffman PS, Lewis JP.	J Oral Biosci	10.1016/j.job.2020.03.004	2020
Phylogeny	Recurrent urinary infection with Bifidobacterium scardovii.	Barberis CM, Cittadini RM, Almuzara MN, Feinsilberg A, Famiglietti AM, Ramirez MS, Vay CA.	J Clin Microbiol	10.1128/jcm.06027-11	2012
	Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos.	Mei Z, Chen GC, Wang Z, Usyk M, Yu B, Baeza YV, Humphrey G, Benitez RS, Li J, Williams-Nguyen JS, Daviglus ML, Hou L, Cai J, Zheng Y, Knight R, Burk RD, Boerwinkle E, Kaplan RC, Qi Q.	Am J Clin Nutr	10.1093/ajcn/nqab001	2021
Enzymology	Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory.	Schulthess B, Bloemberg GV, Zbinden R, Bottger EC, Hombach M.	J Clin Microbiol	10.1128/jcm.02399-13	2014
Enzymology	Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study.	Gao W, Weng J, Gao Y, Chen X.	BMC Infect Dis	10.1186/1471-2334-13-271	2013
Metabolism	Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients.	Tian N, Faller L, Leffler DA, Kelly CP, Hansen J, Bosch JA, Wei G, Paster BJ, Schuppan D, Helmerhorst EJ.	Appl Environ Microbiol	10.1128/aem.03330-16	2017
	Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle.	Chaban B, Links MG, Jayaprakash TP, Wagner EC, Bourque DK, Lohn Z, Albert AY, van Schalkwyk J, Reid G, Hemmingsen SM, Hill JE, Money DM.	Microbiome	10.1186/2049-2618-2-23	2014
	Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer.	Guest C, Harris R, Sfanos KS, Shrestha E, Partin AW, Trock B, Mangold L, Bader R, Kozak A, Mclean S, Simons J, Soule H, Johnson T, Lee WY, Gao Q, Aziz S, Stathatou PM, Thaler S, Foster S, Mershin A.	PLoS One	10.1371/journal.pone.0245530	2021
Phylogeny	The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women.	Freitas AC, Chaban B, Bocking A, Rocco M, Yang S, Hill JE, Money DM, VOGUE Research Group.	Sci Rep	10.1038/s41598-017-07790-9	2017
	Microbiota of severe early childhood caries before and after therapy.	Tanner AC, Kent RL, Holgerson PL, Hughes CV, Loo CY, Kanasi E, Chalmers NI, Johansson I.	J Dent Res	10.1177/0022034511421201	2011
Genetics	Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.	Arzamasov AA, van Sinderen D, Rodionov DA.	Front Microbiol	10.3389/fmicb.2018.00776	2018
	Longitudinal study of the dynamics of vaginal microflora during two consecutive menstrual cycles.	Santiago GL, Cools P, Verstraelen H, Trog M, Missine G, El Aila N, Verhelst R, Tency I, Claeys G, Temmerman M, Vaneechoutte M.	PLoS One	10.1371/journal.pone.0028180	2011
Genetics	Resolution and characterization of distinct cpn60-based subgroups of Gardnerella vaginalis in the vaginal microbiota.	Paramel Jayaprakash T, Schellenberg JJ, Hill JE.	PLoS One	10.1371/journal.pone.0043009	2012
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Pathogenicity	Bacteremia secondary to Alloscardovia omnicolens urinary tract infection.	Ogawa Y, Koizumi A, Kasahara K, Lee ST, Yamada Y, Nakano R, Yano H, Mikasa K	J Infect Chemother	10.1016/j.jiac.2015.12.013	2016
Phylogeny	Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada).	Modesto M, Satti M, Watanabe K, Sciavilla P, Felis GE, Sandri C, Spiezio C, Arita M, Mattarelli P	Int J Syst Evol Microbiol	10.1099/ijsem.0.003584	2019
Phylogeny	Alloscardovia venturai sp. nov., a fructose 6-phosphate phosphoketolase-positive species isolated from the oral cavity of a guinea-pig (Cavia aperea f. porcellus).	Sechovcova H, Killer J, Pechar R, Geigerova M, Svejstil R, Salmonova H, Mekadim C, Rada V, Vlkova E, Kofronova O, Benada O	Int J Syst Evol Microbiol	10.1099/ijsem.0.002031	2017
Phylogeny	Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica).	Pechar R, Killer J, Svejstil R, Salmonova H, Geigerova M, Bunesova V, Rada V, Benada O	Int J Syst Evol Microbiol	10.1099/ijsem.0.001972	2017
Phylogeny	Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.	Killer J, Rockova S, Vlkova E, Rada V, Havlik J, Kopecny J, Bunesova V, Benada O, Kofronova O, Pechar R, Profousova I	Int J Syst Evol Microbiol	10.1099/ijs.0.051326-0	2013
Phylogeny	Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees.	Killer J, Kopecny J, Mrazek J, Havlik J, Koppova I, Benada O, Rada V, Kofronova O	Syst Appl Microbiol	10.1016/j.syapm.2010.08.002	2010
Phylogeny	Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples.	Huys G, Vancanneyt M, D'Haene K, Falsen E, Wauters G, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.64812-0	2007

References

#15682	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21503
#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 )
#28266	IJSEM 1442 2007 ( DOI 10.1099/ijs.0.64812-0 , PubMed 17625172 )
#32013	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28266
#50672	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 31649
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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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Alloscardovia omnicolens (DSM 21503, CCUG 31649, LMG 23792)

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