Name: Chitinophaga costaii A37T2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134894

Type strain:

Species: Chitinophaga costaii

Strain Designation: A37T2

Culture col. no.: CIP 110584, UCCCB37, LMG 27458

Strain history: CIP <- 2013, P.V.Morais, Coimbra Univ., Coimbra, Portugal: strain A37T2

NCBI tax ID(s): 1335309 (species)

SI-ID 387454

LMG 27458, CIP 110584

Special Collections

CIP
UCCCB

Section

Chitinophaga costaii A37T2 is a Gram-negative, motile, rod-shaped bacterium of the family Chitinophagaceae.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Chitinophaga*
	Species	**Chitinophaga costaii**
	Full Scientific Name (LPSN)	Chitinophaga costaii Proença et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #33557]	Gram stain	negative

[Ref.: #33557]	Cell shape	rod-shaped

[Ref.: #33557]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33557]

Culture medium

MEDIUM 407 - for Limnobacter thiooxidans

[Ref.: #33557]

Culture medium growth

[Ref.: #33557]

Culture medium composition

expand / minimize

[Ref.: #33557]

Culture medium

CIP Medium 407

[Ref.: #33557]

Culture medium growth

[Ref.: #33557]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #33557]	growth	30 °C
[Ref.: #67772]	optimum	26-30 °C
[Ref.: #67772]	minimum	15 °C
[Ref.: #67772]	maximum	45 °C

		pH
[Ref.: #67772]	maximum	8.0
[Ref.: #67772]	minimum	5.5
[Ref.: #67772]	optimum	7.0

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67772]	Sample type/isolated from	Endophytic microbial community of Pinus pinaster
[Ref.: #67772]	Sampling date	2009
[Ref.: #67772]	Geographic location (country and/or sea, region)	Coimbra, Avô
[Ref.: #67772]	Country	Portugal
[Ref.: #67772]	Country ISO 3 Code	PRT
[Ref.: #67772]	Continent	Europe

[Ref.: #33557]	Sample type/isolated from	Plant, Pine tree
[Ref.: #33557]	Geographic location (country and/or sea, region)	Coimbra
[Ref.: #33557]	Country	Portugal
[Ref.: #33557]	Country ISO 3 Code	PRT
[Ref.: #33557]	Continent	Europe
[Ref.: #33557]	Isolation date	2009

[Ref.: #33557]	Geographic location (country and/or sea, region)	Coimbra
[Ref.: #33557]	Country	Portugal
[Ref.: #33557]	Country ISO 3 Code	PRT
[Ref.: #33557]	Continent	Europe
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence KC922450 (>99% sequence identity) for Chitinophaga costaii subclade from Microbeatlas

Aquatic Samples
Soil Samples	18
Animal Samples	3
Plant Samples	19
Total Samples	40

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #67772]	Biosafety level	1
[Ref.: #33557]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67772]	Chitinophaga costaii strain A37T2 from Portugal 16S ribosomal RNA gene, partial sequence	KC922450	1503	GenBank ENA	1335309 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67772]	Chitinophaga costaii A37T2	GCA_900094705	contig	GenBank ENA	1335309 tax ID
[Ref.: #66792]	Chitinophaga costaii A37T2	GCA_003071385	contig	GenBank ENA	1335309 tax ID	*
[Ref.: #66792]	Chitinophaga costaii A37T2	2840984945	draft	JGI IMG/M	1335309 tax ID	*
[Ref.: #66792]	Chitinophaga costaii A37T2	2671180112	draft	JGI IMG/M	1335309 tax ID	*

Availability in culture collections External links

[Ref.: #33557]

Culture collection no.

CIP 110584, UCCCB37, LMG 27458

[Ref.: #92333]

SI-ID 387454

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga parva sp. nov., a new member of the family Chitinophagaceae, isolated from soil in a chemical factory.	Ke Z, Yang MJ, Jia WB, Mu Y, Li JL, Chen D, Chen K, Jiang JD	Int J Syst Evol Microbiol	10.1099/ijsem.0.003006	2018	*
Genetics	Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2(T).	Proenca DN, Whitman WB, Shapiro N, Woyke T, Kyrpides NC, Morais PV	Stand Genomic Sci	10.1186/s40793-017-0262-2	2017	*
Phylogeny	Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis.	Proenca DN, Nobre MF, Morais PV	Int J Syst Evol Microbiol	10.1099/ijs.0.053454-0	2014	*

References

#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 )

#33557 Collection of Institut Pasteur ; Curators of the CIP; CIP 110584

#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 )

#67772 The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;

#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 .

#92333

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID387454.1 )

* These data were automatically processed and therefore are not curated

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