Aggregatibacter segnis (DSM 21418, ATCC 33393, CCUG 10787)

Name: Aggregatibacter segnis (DSM 21418, ATCC 33393, CCUG 10787)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11755

Type strain

Strain Designation HK316

Culture col. no. DSM 21418 ATCC 33393 CCUG 10787 CCUG 12838 CIP 103292 4 more

NCBI tax ID(s) 888057 739

Special Collections DSMZ CCUG KCTC CIP

Links

Aggregatibacter segnis HK316 is a microaerophile, mesophilic, rod-shaped prokaryote that was isolated from dental plaque.

rod-shaped microaerophile mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 47018

DSM 21418,KCTC 5968,ATCC 33393,NCTC 10977,CCUG 10787,CCUG 12838,CIP 103292,CCM 6052,LMG 25822

@ref 20215

Last LPSN update 2025-12-16 09:49:40

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Aggregatibacter

Species Aggregatibacter segnis

Full scientific name Aggregatibacter segnis (Kilian 1977) Nørskov-Lauritsen and Kilian 2006

Synonyms (1)

Haemophilus segnis

BacDive ID	Other strains from **Aggregatibacter segnis** (42)	Type strain
136051	A. segnis ANA 45, CIP 102164
137889	A. segnis 42-86, CIP 102120
137977	A. segnis 342-86, CIP 102350
138696	A. segnis 70-86, CIP 102141
139181	A. segnis 371.84, CIP 100870
139524	A. segnis 38.87, CIP 102796
142795	A. segnis CCUG 14859
142796	A. segnis CCUG 14860
142797	A. segnis CCUG 14861
142798	A. segnis CCUG 14862
143258	A. segnis CCUG 18088, MCCM 03015
143394	A. segnis CCUG 18888
143966	A. segnis CCUG 22129
144312	A. segnis CCUG 24524, MCCM 00313
144659	A. segnis CCUG 26123
144685	A. segnis CCUG 26210 A
145465	A. segnis CCUG 28604
145847	A. segnis CCUG 29771
147296	A. segnis CCUG 33321
148067	A. segnis CCUG 34757
148526	A. segnis CCUG 35594
148845	A. segnis CCUG 36144, MCCM 00286
149853	A. segnis CCUG 38557
150310	A. segnis CCUG 39605
150475	A. segnis CCUG 41394
150649	A. segnis CCUG 41855
151955	A. segnis CCUG 45340
152406	A. segnis CCUG 46700
152822	A. segnis CCUG 47710
153213	A. segnis CCUG 48771
153409	A. segnis CCUG 49495
153476	A. segnis CCUG 49706
153966	A. segnis CCUG 51794
153967	A. segnis CCUG 51795
153968	A. segnis CCUG 51796
153969	A. segnis CCUG 51797
153970	A. segnis CCUG 51798
153971	A. segnis CCUG 51799
154314	A. segnis CCUG 53043 A
154596	A. segnis CCUG 54525
155355	A. segnis CCUG 57436
156666	A. segnis CCUG 63997

Morphology

Cell morphology

@ref	Cell shape	Motility
67771	rod-shaped
67771	pleomorphic-shaped
67771
125439
125438
125438

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15694	HAEMOPHILUS MEDIUM (DSMZ Medium 804)	Medium recipe at MediaDive	Name: HAEMOPHILUS MEDIUM (DSMZ Medium 804) Composition: Mueller-Hinton broth 21.0 g/l Yeast extract 5.0 g/l Distilled water
40097	MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and Neisseria		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
122549	CIP Medium 10	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15694	positive	growth	37	mesophilic
40097	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
15694	microaerophile
67771	microaerophile
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.5
125438		90.988

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68377	15824 ChEBI	D-fructose	+	builds acid from	from API NH
68377	17634 ChEBI	D-glucose	+	builds acid from	from API NH
68377	17306 ChEBI	maltose	+	builds acid from	from API NH
68377	18257 ChEBI	ornithine	-	degradation	from API NH
68377	27897 ChEBI	tryptophan	-	energy source	from API NH
68377	16199 ChEBI	urea	-	hydrolysis	from API NH

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68377	35581 ChEBI	indole		from API NH

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68377	35581 ChEBI	indole	-	from API NH

Enzymes

@ref	Value	Activity	Ec
68377	beta-galactosidase	-	3.2.1.23	from API NH
68377	gamma-glutamyltransferase	-	2.3.2.2	from API NH
68377	ornithine decarboxylase	-	4.1.1.17	from API NH
68377	proline-arylamidase	-	3.4.11.5	from API NH
68377	tryptophan deaminase	-	4.1.99.1	from API NH
68377	urease	-	3.5.1.5	from API NH

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	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	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	purine metabolism	72.34	68 of 94
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	octane oxidation	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	NAD metabolism	61.11	11 of 18
66794	Entner Doudoroff pathway	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	glutathione metabolism	57.14	8 of 14
66794	leucine metabolism	53.85	7 of 13
66794	non-pathway related	52.63	20 of 38
66794	methionine metabolism	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	sulfopterin metabolism	50	2 of 4
66794	isoprenoid biosynthesis	50	13 of 26
66794	butanoate fermentation	50	2 of 4
66794	starch degradation	50	5 of 10
66794	adipate degradation	50	1 of 2
66794	glutamate and glutamine metabolism	50	14 of 28
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	oxidative phosphorylation	49.45	45 of 91
66794	tryptophan metabolism	47.37	18 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	d-mannose degradation	44.44	4 of 9
66794	lysine metabolism	42.86	18 of 42
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	citric acid cycle	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	formaldehyde oxidation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	urea cycle	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	propanol degradation	28.57	2 of 7
66794	histidine metabolism	27.59	8 of 29
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12
66794	phenol degradation	25	5 of 20
66794	toluene degradation	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

65595

Fatty acid	Percentage	ECL
C16:1 ω7c	29.2	15.819
C14:0	27.4	14
C16:0	25.4	16
C14:0 3OH/C16:1 ISO I	9.4	15.485
C18:2 ω6,9c/C18:0 ANTE	3.5	17.724
C18:1 ω9c	3	17.769
C18:0	0.7	18
C13:0 ISO 2OH	0.5	13.814
unknown 14.503	0.4	14.503
C12:0	0.3	12

Metadata FA analysis

@ref

65597

Fatty acid	Percentage	ECL
C16:1 ω7c	28	15.819
C14:0	26.8	14
C16:0	26.3	16
C14:0 3OH/C16:1 ISO I	7.7	15.485
C18:1 ω9c	4.3	17.769
C18:2 ω6,9c/C18:0 ANTE	3.3	17.724
C18:0	0.9	18
C12:0 ALDE ?	0.7	10.915
Unidentified	0.5	13.944
C13:0 ISO 2OH	0.5	13.814
unknown 14.503	0.4	14.503
C12:0	0.3	12
Unidentified	0.2	15.171
C16:1 ω5c	0.2	15.908
Unidentified	0.1	13.767

API NH

@ref	PEN	GLU	FRU	MAL	SAC	ODC	URE	LIP	PAL	beta GAL	ProA	GGT	IND
15694	+	+	+	+	-	-	-	+	-	-	-	-	-
15694	-	+	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
15694	dental plaque	Denmark	DNK	Europe
67771	From dental plaque	Denmark	DNK	Europe
122549	Other, Dental plate	Denmark	DNK	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15694	2	Risk group (German classification) According to TRBA 466
122549	2	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	53694_C01 assembly for Aggregatibacter segnis ATCC 33393 NCTC10977	complete	GCA_900476035	888057.20	2811995232	888057	99.6
124043	ASM1612711v1 assembly for Aggregatibacter segnis FDAARGOS_987	complete	GCA_016127115	739.212		739	99.19
66792	ASM18530v1 assembly for Aggregatibacter segnis ATCC 33393	scaffold	GCA_000185305	888057.3	649989906	888057	76.04

Genome browser: GCA_900476035

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15694	Aggregatibacter segnis ATCC 33393 16S ribosomal RNA gene, partial sequence	M75043	1479		888057

GC content

@ref	GC-content (mol%)	Method
67771	43.0-44.0	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aggregatibacter segnis ATCC 33393 NCTC 10977
NCBI: GCA_900476035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	55.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aggregatibacter segnis ATCC 33393 NCTC10977
NCBI: GCA_900476035.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	yes
125438	anaerobic	anaerobicⓘ	no	93.40	yes
125438	aerobic	aerobicⓘ	no	88.61	yes
125438	spore-forming	spore-formingⓘ	no	90.99	no
125438	thermophilic	thermophileⓘ	no	98.47	yes
125438	flagellated	motile2+ⓘ	no	93.42	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil.	Salam LB.	3 Biotech	10.1007/s13205-020-02219-z	2020
Pathogenicity	Longitudinal saliva omics responses to immune perturbation: a case study.	Mias GI, Singh VV, Rogers LRK, Xue S, Zheng M, Domanskyi S, Kanada M, Piermarocchi C, He J.	Sci Rep	10.1038/s41598-020-80605-6	2021
Genetics	Evaluation of Extraction Methods for Clinical Metagenomic Assay.	Farraj SA, El-Kafrawy SA, Kumosani TA, Yousef JM, Azhar EI.	Microorganisms	10.3390/microorganisms8081128	2020
	Laboratory Diagnosis of 37 Cases of Bartonella Endocarditis Based on Enzyme Immunoassay and Real-Time PCR.	Shapira L, Rasis M, Binsky Ehrenreich I, Maor Y, Katchman EA, Treves A, Velan A, Halutz O, Graidy-Varon M, Leibovitch C, Maisler N, Ephros M, Giladi M.	J Clin Microbiol	10.1128/jcm.02217-20	2021
Pathogenicity	The antibacterial activity of various saturated and unsaturated fatty acids against several oral pathogens.	Choi JS, Park NH, Hwang SY, Sohn JH, Kwak I, Cho KK, Choi IS	J Environ Biol		2013
Phylogeny	Reclassification of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, Haemophilus paraphrophilus and Haemophilus segnis as Aggregatibacter actinomycetemcomitans gen. nov., comb. nov., Aggregatibacter aphrophilus comb. nov. and Aggregatibacter segnis comb. nov., and emended description of Aggregatibacter aphrophilus to include V factor-dependent and V factor-independent isolates.	Norskov-Lauritsen N, Kilian M	Int J Syst Evol Microbiol	10.1099/ijs.0.64207-0	2006

References

#15694	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21418
#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 )
#40097	; Curators of the CIP;
#65595	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 10787
#65597	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12838
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68377	Automatically annotated from API NH .
#122549	Collection of Institut Pasteur ; Curators of the CIP; CIP 103292
#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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Aggregatibacter segnis (DSM 21418, ATCC 33393, CCUG 10787)

Name and taxonomic classification