Chitinophaga pinensis (DSM 2588, ATCC 43595, IFO 15968)

Name: Chitinophaga pinensis (DSM 2588, ATCC 43595, IFO 15968)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17740

Type strain

Culture col. no. DSM 2588 ATCC 43595 IFO 15968 NBRC 15968 UQM 2034 3 more

NCBI tax ID(s) 485918 79329

Special Collections DSMZ Literature strains CIP

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Chitinophaga pinensis DSM 2588 is an obligate aerobe, spore-forming, psychrophilic prokaryote that was isolated from pine litter.

spore-forming Gram-negative rod-shaped obligate aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 7622

LMG 13176,ATCC 43595,NCIB 11800,ACM 2034,IFO 15968,NCIMB 11800,KCTC 3412,NBRC 15968,DSM 2588,CIP 107364

@ref 20215

Last LPSN update 2025-12-16 09:51:10

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga pinensis

Full scientific name Chitinophaga pinensis Sangkhobol and Skerman 1981

BacDive ID	Other strains from **Chitinophaga pinensis** (1)	Type strain
17741	C. pinensis DSM 2589, IFO 15969, NBRC 15969, UQM 2036

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43362	negative	40 µm	0.5-0.8 µm	rod-shaped
125438	negative				92.565
121834	negative			rod-shaped

Colony morphology

Pigmentation

@ref	Production	Color	Name
43362		Yellowish	Unknown
121834			Flexirubin

Multimedia

@ref:	66793
multimedia content:	EM_DSM_2588_1.jpg
multimedia.multimedia content:	EM_DSM_2588_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1142	CY-AGAR (DSMZ Medium 67)	Medium recipe at MediaDive	Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
33117	MEDIUM 342 - for Flexibacter filiformis		Distilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Casitone (3.000 g)
121834	CIP Medium 35	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1142	positive	growth	22	psychrophilic
33117	positive	growth	22	psychrophilic
43362	positive	optimum	24	psychrophilic
43425	positive	growth	12-37
121834	negative	growth	41
121834	negative	growth	37
121834	negative	growth	15
121834	negative	growth	5
121834	positive	growth	22-30
121834	negative	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
43362	positive	optimum	7
43362	positive	growth	4-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

121834

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
43425	Diameter of 0.8-0.9 µm, formed upon aging	myxospore
125439				92.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43362	NaCl	positive	growth	0-1.5 %
121834	NaCl	positive	growth	0 %
121834	NaCl		growth	2 %
121834	NaCl		growth	4 %
121834	NaCl		growth	6 %
121834	NaCl		growth	8 %
121834	NaCl		growth	10 %

Observation

43425

ObservationResistant to 0.01 but not 0.1% sodium lauryl sulfate

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43425	2509 ChEBI	agar	-	hydrolysis
43362	58187 ChEBI	alginate	-	hydrolysis
43362		casein	+	hydrolysis
43362	62968 ChEBI	cellulose	-	hydrolysis
43362	17029 ChEBI	chitin	+	hydrolysis
43425	16991 ChEBI	dna	-	hydrolysis
121834	4853 ChEBI	esculin	+	hydrolysis
43362	5291 ChEBI	gelatin	+	hydrolysis
43362	17234 ChEBI	glucose	+	builds acid from
121834	606565 ChEBI	hippurate	+	hydrolysis
43362	17716 ChEBI	lactose	+	builds acid from
121834	15792 ChEBI	malonate	-	assimilation
43362	17632 ChEBI	nitrate	-	reduction
121834	17632 ChEBI	nitrate	-	reduction
121834	16301 ChEBI	nitrite	-	reduction
43362	28017 ChEBI	starch	-	hydrolysis
43362	17992 ChEBI	sucrose	+	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
121834		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
43362	17698	chloramphenicol	25 µg (disc)
43362	48923	erythromycin		5 µg (disc)
43362	6104	kanamycin		30 µg (disc)
43362	7507	neomycin		10 µg (disc)
43362	18208	penicillin g		4 Unit (disc)
43362	17076	streptomycin	10 µg (disc)
43362	27902	tetracycline	10 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite
43425	16136 ChEBI	hydrogen sulfide
43425	35581 ChEBI	indole
121834	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121834	15688 ChEBI	acetoin	-
121834	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121834	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121834	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
121834	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121834	caseinase	-	3.4.21.50
43362	catalase	+	1.11.1.6
121834	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
43362	cytochrome oxidase	+	1.9.3.1
121834	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
121834	gamma-glutamyltransferase	-	2.3.2.2
121834	gelatinase	-
121834	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
43425	lipase	+
121834	lipase	-
68382	lipase (C 14)	-		from API zym
43425	lipase (Tween 80)	+
121834	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121834	ornithine decarboxylase	-	4.1.1.17
121834	oxidase	-
121834	phenylalanine ammonia-lyase	-	4.3.1.24
43425	phenylalanine deaminase	-	4.3.1.5
68382	trypsin	+	3.4.21.4	from API zym
43425	tryptophan deaminase	-	4.1.99.1
121834	tryptophan deaminase	-
121834	tween esterase	-
43362	urease	+	3.5.1.5
121834	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	allantoin degradation	100	9 of 9
66794	kanosamine biosynthesis II	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	quinate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	acetate fermentation	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	ceramide biosynthesis	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	isoleucine metabolism	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	NAD metabolism	94.44	17 of 18
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	proline metabolism	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	tryptophan metabolism	78.95	30 of 38
66794	purine metabolism	78.72	74 of 94
66794	tyrosine metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	lipid metabolism	77.42	24 of 31
66794	vitamin B1 metabolism	76.92	10 of 13
66794	isoprenoid biosynthesis	76.92	20 of 26
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	degradation of hexoses	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	lysine metabolism	69.05	29 of 42
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	cyanate degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	carotenoid biosynthesis	54.55	12 of 22
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	cyclohexanol degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	phenol degradation	50	10 of 20
66794	phenylmercury acetate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	resorcinol degradation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	oxidative phosphorylation	47.25	43 of 91
66794	ascorbate metabolism	45.45	10 of 22
66794	arachidonic acid metabolism	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	chlorophyll metabolism	27.78	5 of 18
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121834	-	+	+	-	-	+	+	-	+	-	+	+	+	+	-	+	+	+	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121834	not determinedn.d.	+	-	+	+	+	-	+	+	-	+	+	+	+	-	-	+	+	+	+	-	+	+	+	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host	#Plants	#Decomposing plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
1142	pine litter	Brisbane, Alderley	Australia	AUS	Australia and Oceania
43362	from an infusion of litter from the base of a pine tree	Alderley, Brisbane	Australia	AUS	Australia and Oceania	-27	153 -27/153
121834	Pine needles	Adlerly, Queensland	Australia	AUS	Australia and Oceania			1979

Taxonmaps

69479

Global distribution of 16S sequence AB681008 (>99% sequence identity) for Chitinophaga pinensis subclade from Microbeatlas

Aquatic Samples	723
Soil Samples	4418
Animal Samples	378
Plant Samples	1270
Total Samples	6789

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1142	1	Risk group (German classification) According to TRBA 466
43425	1
121834	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2400v1 assembly for Chitinophaga pinensis DSM 2588	complete	GCA_000024005	485918.6	644736340	485918	97.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Chitinophaga pinensis gene for 16S rRNA, partial sequence, strain: NBRC 15968	AB681008	1451		79329
124043	Chitinophaga pinensis 16S ribosomal RNA gene, partial sequence.	AF078775	1458		485918

GC content

@ref	GC-content (mol%)	Method
1142	44.6
43425	44.58	thermal denaturation, midpoint method (Tm)
1142	45.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga pinensis DSM 2588
NCBI: GCA_000024005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.90	no
125439	motility	BacteriaNetⓘ	no	64.20	no
125439	gram_stain	BacteriaNetⓘ	negative	87.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	63.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga pinensis DSM 2588 DSM 2588
NCBI: GCA_000024005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.57	no
125438	anaerobic	anaerobicⓘ	no	98.31	no
125438	aerobic	aerobicⓘ	yes	88.58	yes
125438	spore-forming	spore-formingⓘ	no	63.05	yes
125438	thermophilic	thermophileⓘ	no	98.49	no
125438	flagellated	motile2+ⓘ	no	87.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequences of Chitinophaga sp. strain MM2321 and Microbacterium sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany.	Eisenhut M, Schulze T, Matten FNJ, Sengewald A, Bohner P, Falk D, Klinge CV, Langschwager R, Lohoff S, Meyer N, Ponomarchuk V, Punter F, Sherlock J, Pschik D, Klages LJ, Busche T, Wobbe L, Brautigam A, Laker B.	Microbiol Resour Announc	10.1128/mra.00700-24	2024
	Engineering an antimicrobial chimeric endolysin that targets the phytopathogen Pseudomonas syringae pv. actinidiae.	Warring SL, Sisson HM, Randall G, Grimon D, Dams D, Gutierrez D, Fellner M, Fagerlund RD, Briers Y, Jackson SA, Fineran PC.	J Biol Chem	10.1016/j.jbc.2025.110224	2025
	The Impact of Chitinase Binding Domain Truncation on the Properties of CaChi18B from Chitinilyticum aquatile CSC-1.	Gu C, Chen J, Huang X, Jiang Y, Ou N, Yang D, Jiang M, Pan L.	Mar Drugs	10.3390/md23030093	2025
	Chryseobacterium herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau.	Zhang L, Wang Y, Kong D, Ma Q, Li Y, Xing Z, Ruan Z.	Microorganisms	10.3390/microorganisms11082017	2023
	Comparative genomic analysis of azasugar biosynthesis.	Beal HE, Horenstein NA.	AMB Express	10.1186/s13568-021-01279-5	2021
	LolA and LolB are conserved in Bacteroidota and are crucial for gliding motility and Type IX secretion.	De Smet T, Baland E, Giovannercole F, Mignon J, Lizen L, Dugauquier R, Lauber F, Dieu M, Lima-Mendez G, Michaux C, Devos D, Renzi F.	Commun Biol	10.1038/s42003-025-07817-2	2025
	18-Hydroxydolabella-3,7-diene synthase - a diterpene synthase from Chitinophaga pinensis.	Dickschat JS, Rinkel J, Rabe P, Beyraghdar Kashkooli A, Bouwmeester HJ.	Beilstein J Org Chem	10.3762/bjoc.13.171	2017
	The chemistry and biology of natural ribomimetics and related compounds.	Tsunoda T, Tanoeyadi S, Proteau PJ, Mahmud T.	RSC Chem Biol	10.1039/d2cb00019a	2022
	Unusual Class I Lanthipeptides from the Marine Bacteria Thalassomonas viridans.	Vermeulen R, Van Staden ADP, van Zyl LJ, Dicks LMT, Trindade M.	ACS Synth Biol	10.1021/acssynbio.2c00480	2022
Genetics	Genomic and Chemical Decryption of the Bacteroidetes Phylum for Its Potential to Biosynthesize Natural Products.	Brinkmann S, Kurz M, Patras MA, Hartwig C, Marner M, Leis B, Billion A, Kleiner Y, Bauer A, Toti L, Poverlein C, Hammann PE, Vilcinskas A, Glaeser J, Spohn M, Schaberle TF.	Microbiol Spectr	10.1128/spectrum.02479-21	2022
	Potential of tellurite resistance in heterotrophic bacteria from mining environments.	Farias P, Francisco R, Morais PV.	iScience	10.1016/j.isci.2022.104566	2022
Genetics	Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces.	Park JS, Kim DE, Hong SC, Kim SY, Kwon HC, Hyun CG, Choi J.	Microorganisms	10.3390/microorganisms9091802	2021
Metabolism	Focused Metabolism of beta-Glucans by the Soil Bacteroidetes Species Chitinophaga pinensis.	McKee LS, Martinez-Abad A, Ruthes AC, Vilaplana F, Brumer H.	Appl Environ Microbiol	10.1128/aem.02231-18	2019
Metabolism	Initiation of the flexirubin biosynthesis in Chitinophaga pinensis.	Schoner TA, Fuchs SW, Schonau C, Bode HB.	Microb Biotechnol	10.1111/1751-7915.12110	2014
	Differential gliding motility responses of Chryseobacterium sp. strain PMSZPI isolated from uranium ore deposit on hard and soft substrates.	Yermunja L, Acharya C.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100309	2024
	Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.	Shivaji S, Ara S, Begum Z, Srinivas TN, Singh A, Kumar Pinnaka A.	Genome Announc	10.1128/genomea.00240-13	2013
Pathogenicity	Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays.	Yergeau E, Lawrence JR, Waiser MJ, Korber DR, Greer CW.	Appl Environ Microbiol	10.1128/aem.00873-10	2010
Enzymology	Cloning, Expression and 3D Structure Prediction of Chitinase from Chitinolyticbacter meiyuanensis SYBC-H1.	Hao Z, Wu H, Yang M, Chen J, Xi L, Zhao W, Yu J, Liu J, Liao X, Huang Q.	Int J Mol Sci	10.3390/ijms17060825	2016
Metabolism	New Vocabulary for Bacterial Communication.	Tobias NJ, Brehm J, Kresovic D, Brameyer S, Bode HB, Heermann R.	Chembiochem	10.1002/cbic.201900580	2020
Metabolism	Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 beta-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation.	McKee LS, Brumer H.	PLoS One	10.1371/journal.pone.0139932	2015
	Mechanistic investigations on six bacterial terpene cyclases.	Rabe P, Schmitz T, Dickschat JS.	Beilstein J Org Chem	10.3762/bjoc.12.173	2016
Transcriptome	In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria.	Marsh AJ, O'Sullivan O, Ross RP, Cotter PD, Hill C.	BMC Genomics	10.1186/1471-2164-11-679	2010
Metabolism	Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis.	Suroto DA, Kitani S, Arai M, Ikeda H, Nihira T.	PLoS One	10.1371/journal.pone.0190973	2018
	Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides.	Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L.	ACS Bio Med Chem Au	10.1021/acsbiomedchemau.2c00062	2023
Metabolism	Discovery of Lysine Hydroxylases in the Clavaminic Acid Synthase-Like Superfamily for Efficient Hydroxylysine Bioproduction.	Hara R, Yamagata K, Miyake R, Kawabata H, Uehara H, Kino K.	Appl Environ Microbiol	10.1128/aem.00693-17	2017
Phylogeny	Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.	Shulse CN, Allen EE.	PLoS One	10.1371/journal.pone.0020146	2011
Transcriptome	Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space.	Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, Henrissat B.	Proc Natl Acad Sci U S A	10.1073/pnas.1815791116	2019
	Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.	Asplund-Samuelsson J, Bergman B, Larsson J.	PLoS One	10.1371/journal.pone.0049888	2012
	Structural properties of 2/2 hemoglobins: the group III protein from Helicobacter hepaticus.	Nothnagel HJ, Winer BY, Vuletich DA, Pond MP, Lecomte JT.	IUBMB Life	10.1002/iub.430	2011
	In silico characterization of pectate lyase protein sequences from different source organisms.	Dubey AK, Yadav S, Kumar M, Singh VK, Sarangi BK, Yadav D.	Enzyme Res	10.4061/2010/950230	2010
Enzymology	Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria.	Spero MA, Aylward FO, Currie CR, Donohue TJ.	mBio	10.1128/mbio.00389-15	2015
	3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis.	Nofiani R, Philmus B, Nindita Y, Mahmud T.	Medchemcomm	10.1039/c9md00162j	2019
Genetics	How genome complexity can explain the difficulty of aligning reads to genomes.	Phan V, Gao S, Tran Q, Vo NS.	BMC Bioinformatics	10.1186/1471-2105-16-s17-s3	2015
	Veillonella, Firmicutes: Microbes disguised as Gram negatives.	Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.	Stand Genomic Sci	10.4056/sigs.2981345	2013
Metabolism	The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis.	Gattis SG, Chung HS, Trent MS, Raetz CR.	J Biol Chem	10.1074/jbc.m113.453324	2013
Genetics	Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library.	McGarvey KM, Queitsch K, Fields S.	Appl Environ Microbiol	10.1128/aem.06759-11	2012
Metabolism	PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System.	Heath JE, Seers CA, Veith PD, Butler CA, Nor Muhammad NA, Chen YY, Slakeski N, Peng B, Zhang L, Dashper SG, Cross KJ, Cleal SM, Moore C, Reynolds EC.	PLoS One	10.1371/journal.pone.0164313	2016
	Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes.	Yutin N, Koonin EV.	Virol J	10.1186/1743-422x-9-161	2012
	A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins.	Pawlowski K, Muszewska A, Lenart A, Szczepinska T, Godzik A, Grynberg M.	BMC Genomics	10.1186/1471-2164-11-590	2010
	Environmental and gut bacteroidetes: the food connection.	Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G.	Front Microbiol	10.3389/fmicb.2011.00093	2011
Genetics	Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.	Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT.	PLoS One	10.1371/journal.pone.0030087	2012
Genetics	Microbiome of fungus-growing termites: a new reservoir for lignocellulase genes.	Liu N, Yan X, Zhang M, Xie L, Wang Q, Huang Y, Zhou X, Wang S, Zhou Z.	Appl Environ Microbiol	10.1128/aem.01521-10	2011
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Genetics	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.	Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Goker M.	Front Microbiol	10.3389/fmicb.2019.02083	2019
Enzymology	Skeletal Rearrangements in the Enzyme-Catalysed Biosynthesis of Coral-Type Diterpenes from Chitinophaga pinensis.	Tabekoueng GB, Li H, Goldfuss B, Schnakenburg G, Dickschat JS.	Angew Chem Int Ed Engl	10.1002/anie.202413860	2024
	Multiple enzymatic approaches to hydrolysis of fungal beta-glucans by the soil bacterium Chitinophaga pinensis.	Lu Z, Ramgard C, Ergenlioglu I, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS.	FEBS J	10.1111/febs.16720	2023
	A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and beta-glucans found in fungal cell walls.	Lu Z, Kvammen A, Li H, Hao M, Inman AR, Bulone V, McKee LS.	mSphere	10.1128/msphere.00244-23	2023
	Evolutionary history of the DNA repair protein, Ku, in eukaryotes and prokaryotes.	Rijal S, Mainali A, Acharya S, Bhattarai HK.	PLoS One	10.1371/journal.pone.0308593	2025
	Valorisation of wheat bran to produce natural pigments using selected microorganisms.	Cassarini M, Besaury L, Remond C.	J Biotechnol	10.1016/j.jbiotec.2021.08.003	2021
	Construction of the reduced nicotinamide adenine dinucleotide salvage pathway in artificial cells and its application in amino acid synthesis.	Liu Y, Du S, Zhang X, Li C, Li S, Xu W, Zhao J, Mu W, Han X.	Chem Sci	10.1039/d5sc00852b	2025
	Transcriptomic analyses of bacterial growth on fungal necromass reveal different microbial community niches during degradation.	Novak JK, Kennedy PG, Gardner JG.	Appl Environ Microbiol	10.1128/aem.01062-24	2024
	Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops.	Chai YN, Futrell S, Schachtman DP.	Front Microbiol	10.3389/fmicb.2022.791110	2022
Enzymology	Carboxy-terminal glycosyl hydrolase 18 domain of a carbohydrate active protein of Chitinophaga pinensis is a non-processive exochitinase.	Ramakrishna B, Vaikuntapu P, Mallakuntla MK, Bhuvanachandra B, Sivaramakrishna D, Uikey S, Podile AR.	Int J Biol Macromol	10.1016/j.ijbiomac.2018.04.159	2018
	Fungal and bacterial pathogenic co-infections mainly lead to the assembly of microbial community in tobacco stems.	Wang C, Xiao Z, Cao Z, Sheng F, Xiang P, Mu T, Ma Y, Lin X, Xiao M, Zhu Q, Wu S, Tan L.	Open Life Sci	10.1515/biol-2025-1103	2025
	Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures.	Neves ALA, Chen Y, Le Cao KA, Mandal S, Sharpton TJ, McAllister T, Guan LL.	Animal	10.1017/s1751731119002453	2020
	Functional analysis of a novel endo-beta-1,6-glucanase MoGlu16 and its application in detecting cell wall beta-1,6-glucan of Magnaporthe oryzae.	Wang Y, Li D, Li Z, Cui Z, Ye X.	Front Microbiol	10.3389/fmicb.2024.1429065	2024
Metabolism	Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis.	Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS.	J Proteomics	10.1016/j.jprot.2017.01.003	2017
	Organic amendments shift the phosphorus-correlated microbial co-occurrence pattern in the peanut rhizosphere network during long-term fertilization regimes	Chen Y, Sun R, Sun T, Liang Y, Jiang Y, Sun B.	Appl Soil Ecol	10.1016/j.apsoil.2017.11.023	2018
Enzymology	Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis.	Shimizu H, Nakajima M, Miyanaga A, Takahashi Y, Tanaka N, Kobayashi K, Sugimoto N, Nakai H, Taguchi H.	Biochemistry	10.1021/acs.biochem.8b00385	2018
Phylogeny	Microbiome analysis of bile samples in patients with choledocholithiasis and hepatobiliary disorders.	Azimirad M, Sadeghi A, Hosseinkhan N, Mirbagheri SZ, Alebouyeh M.	Germs	10.18683/germs.2023.1390	2023
	De novo biosynthesis and nicotinamide biotransformation of nicotinamide mononucleotide by engineered yeast cells.	Ren Y, Han B, Wang S, Wang X, Liu Q, Cai M.	Microb Biotechnol	10.1111/1751-7915.70048	2024
	Boosting Biocatalytic Efficiency: Engineering of Chitinase Chit33 with Chitin and Cellulose Binding Domains for Sustainable Chitin Conversion.	Martinez-Ranz M, Kidibule PE, Jimenez-Ortega E, Valcarcel J, Vazquez JA, Sanz-Aparicio J, Fernandez-Lobato M.	J Agric Food Chem	10.1021/acs.jafc.4c10364	2025
	MakC and MakD are two proteins associated with a tripartite toxin of Vibrio cholerae.	Bodra N, Toh E, Nadeem A, Wai SN, Persson K.	Front Microbiol	10.3389/fmicb.2024.1457850	2024
	The microbiome of pseudomyxoma peritonei: a scoping review.	Portela DS, Jain A, Flood M, Lavelle A, Guerra G, Patel M, Aziz O, Warrier S, Heriot A, Mohan H.	Pleura Peritoneum	10.1515/pp-2024-0016	2025
Enzymology	Functional characterisation of twelve terpene synthases from actinobacteria.	Chhalodia AK, Xu H, Tabekoueng GB, Gu B, Taizoumbe KA, Lauterbach L, Dickschat JS.	Beilstein J Org Chem	10.3762/bjoc.19.100	2023
	Pinensins: the first antifungal lantibiotics.	Mohr KI, Volz C, Jansen R, Wray V, Hoffmann J, Bernecker S, Wink J, Gerth K, Stadler M, Muller R.	Angew Chem Int Ed Engl	10.1002/anie.201500927	2015
Enzymology	Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis.	Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS.	Data Brief	10.1016/j.dib.2017.02.032	2017
Metabolism	Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters.	Nkosi BVZ, Padayachee T, Gront D, Nelson DR, Syed K.	Int J Mol Sci	10.3390/ijms23095057	2022
Enzymology	A First Expression, Purification and Characterization of Endo-beta-1,3-Glucanase from Penicillium expansum.	Wang K, Huai S, Tan Z, Ngea GLN, Godana EA, Shi J, Yang Q, Zhang X, Zhao L, Zhang H.	J Fungi (Basel)	10.3390/jof9100961	2023
Enzymology	Diterpene Biosynthesis from Geranylgeranyl Diphosphate Analogues with Changed Reactivities Expands Skeletal Diversity.	Li H, Dickschat JS.	Angew Chem Int Ed Engl	10.1002/anie.202211054	2022
	Functional and structural analysis of a cyclization domain in a cyclic beta-1,2-glucan synthase.	Tanaka N, Saito R, Kobayashi K, Nakai H, Kamo S, Kuramochi K, Taguchi H, Nakajima M, Masaike T.	Appl Microbiol Biotechnol	10.1007/s00253-024-13013-9	2024
	High impact of bacterial predation on cyanobacteria in soil biocrusts.	Bethany J, Johnson SL, Garcia-Pichel F.	Nat Commun	10.1038/s41467-022-32427-5	2022
	In Vitro Fermentation Characteristics of Fungal Polysaccharides Derived from Wolfiporia cocos and Their Effect on Human Fecal Microbiota.	Ma KL, Kei N, Yang F, Lauw S, Chan PL, Chen L, Cheung PCK.	Foods	10.3390/foods12214014	2023
Metabolism	A widely distributed phosphate-insensitive phosphatase presents a route for rapid organophosphorus remineralization in the biosphere.	Lidbury IDEA, Scanlan DJ, Murphy ARJ, Christie-Oleza JA, Aguilo-Ferretjans MM, Hitchcock A, Daniell TJ.	Proc Natl Acad Sci U S A	10.1073/pnas.2118122119	2022
	New glycoside hydrolase families of beta-1,2-glucanases.	Nakajima M, Tanaka N, Motouchi S, Kobayashi K, Shimizu H, Abe K, Hosoyamada N, Abara N, Morimoto N, Hiramoto N, Nakata R, Takashima A, Hosoki M, Suzuki S, Shikano K, Fujimaru T, Imagawa S, Kawadai Y, Wang Z, Kitano Y, Nihira T, Nakai H, Taguchi H.	Protein Sci	10.1002/pro.70147	2025
Metabolism	Bagasse minority pathway expression: Real time study of GH2 beta-mannosidases from bacteroidetes.	Leonel TF, Pepe ESG, Castellane TCL, Vantini JDS, Funnicelli MIG, Lemos EGM.	PLoS One	10.1371/journal.pone.0247822	2021
	Discovery of Novel Tyrosine Ammonia Lyases for the Enzymatic Synthesis of p-Coumaric Acid.	Brack Y, Sun C, Yi D, Bornscheuer UT.	Chembiochem	10.1002/cbic.202200062	2022
Enzymology	A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil.	Hu XP, Heath C, Taylor MP, Tuffin M, Cowan D.	Extremophiles	10.1007/s00792-011-0407-y	2012
	Characterization of a GH36 beta-L-Arabinopyranosidase in Bifidobacterium adolescentis.	Sasaki Y, Togo N, Kitahara K, Fujita K.	J Appl Glycosci (1999)	10.5458/jag.jag.jag-2018_001	2018
	Enzyme-Catalysed Formation of Hydrocarbon Scaffolds from Geranylgeranyl Diphosphate Analogs with Shifted Double Bonds.	Li H, Goldfuss B, Dickschat JS.	Chemistry	10.1002/chem.202500712	2025
	Efficient and scalable synthesis of 1,5-diamino-2-hydroxy-pentane from L-lysine via cascade catalysis using engineered Escherichia coli.	Li Y, Zhang A, Hu S, Chen K, Ouyang P.	Microb Cell Fact	10.1186/s12934-022-01864-8	2022
	Interplay between the microalgae Micrasterias radians and its symbiont Dyadobacter sp. HH091.	Astafyeva Y, Gurschke M, Streit WR, Krohn I.	Front Microbiol	10.3389/fmicb.2022.1006609	2022
	Structural Analysis of Class I Lanthipeptides from Pedobacter lusitanus NL19 Reveals an Unusual Ring Pattern.	Bothwell IR, Caetano T, Sarksian R, Mendo S, van der Donk WA.	ACS Chem Biol	10.1021/acschembio.1c00106	2021
Genetics	Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.	Sumida T, Hiraoka S, Usui K, Ishiwata A, Sengoku T, Stubbs KA, Tanaka K, Deguchi S, Fushinobu S, Nunoura T.	Nat Commun	10.1038/s41467-024-47653-2	2024
	In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography.	Kaplan M, Chreifi G, Metskas LA, Liedtke J, Wood CR, Oikonomou CM, Nicolas WJ, Subramanian P, Zacharoff LA, Wang Y, Chang YW, Beeby M, Dobro MJ, Zhu Y, McBride MJ, Briegel A, Shaffer CL, Jensen GJ.	Elife	10.7554/elife.73099	2021
	Identification of enzymatic functions of osmo-regulated periplasmic glucan biosynthesis proteins from Escherichia coli reveals a novel glycoside hydrolase family.	Motouchi S, Kobayashi K, Nakai H, Nakajima M.	Commun Biol	10.1038/s42003-023-05336-6	2023
Enzymology	The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy.	Ma JE, Jiang HY, Li LM, Zhang XJ, Li GY, Li HM, Jin XJ, Chen JP.	Front Microbiol	10.3389/fmicb.2018.02793	2018
	Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms.	Doty SL, Joubert PM, Firrincieli A, Sher AW, Tournay R, Kill C, Parikh SS, Okubara P.	Pathogens	10.3390/pathogens12010013	2022
Genetics	CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain.	Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M.	Front Microbiol	10.3389/fmicb.2021.628055	2021
Metabolism	Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era.	Hetrick KJ, van der Donk WA.	Curr Opin Chem Biol	10.1016/j.cbpa.2017.02.005	2017
Metabolism	Optimization of the biotechnological production of a novel class of anti-MRSA antibiotics from Chitinophaga sancti.	Beckmann A, Huttel S, Schmitt V, Muller R, Stadler M.	Microb Cell Fact	10.1186/s12934-017-0756-z	2017
Genetics	Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.	Alteio LV, Schulz F, Seshadri R, Varghese N, Rodriguez-Reillo W, Ryan E, Goudeau D, Eichorst SA, Malmstrom RR, Bowers RM, Katz LA, Blanchard JL, Woyke T.	mSystems	10.1128/msystems.00768-19	2020
Phylogeny	Phylogenetic position of Chitinophaga pinensis in the Flexibacter-Bacteroides-Cytophaga phylum.	Sly LI, Taghavi M, Fegan M.	Int J Syst Bacteriol	10.1099/00207713-49-2-479	1999
	From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase.	Fernandes GC, Sierra EGM, Brear P, Pereira MR, Lemos EGM.	Microorganisms	10.3390/microorganisms9020393	2021
	Synthetic microbes and biocatalyst designs in Thailand.	Trisrivirat D, Tinikul R, Chaiyen P.	Biotechnol Notes	10.1016/j.biotno.2023.02.003	2023
	Enzymatic Cascade Reactions for the Synthesis of Chiral Amino Alcohols from L-lysine.	Fossey-Jouenne A, Vergne-Vaxelaire C, Zaparucha A.	J Vis Exp	10.3791/56926	2018
Phylogeny	Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment.	Costa PS, Reis MP, Avila MP, Leite LR, de Araujo FM, Salim AC, Oliveira G, Barbosa F, Chartone-Souza E, Nascimento AM.	PLoS One	10.1371/journal.pone.0119465	2015
	Changes of Fusarium oxysporum f.sp. lactucae levels and soil microbial community during soil biosolarization using chitin as soil amendment.	Randall TE, Fernandez-Bayo JD, Harrold DR, Achmon Y, Hestmark KV, Gordon TR, Stapleton JJ, Simmons CW, VanderGheynst JS.	PLoS One	10.1371/journal.pone.0232662	2020
Transcriptome	Metatranscriptomic dynamics after Verticillium dahliae infection and root damage in Olea europaea.	Marti JM, Arias-Giraldo LF, Diaz-Villanueva W, Arnau V, Rodriguez-Franco A, Garay CP.	BMC Plant Biol	10.1186/s12870-019-2185-0	2020
Enzymology	Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.	Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, Taguchi H.	J Biol Chem	10.1074/jbc.m116.762724	2017
	An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae).	Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE.	Front Microbiol	10.3389/fmicb.2017.00350	2017
Genetics	GROOLS: reactive graph reasoning for genome annotation through biological processes.	Mercier J, Josso A, Medigue C, Vallenet D.	BMC Bioinformatics	10.1186/s12859-018-2126-1	2018
	Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages.	Kobayashi K, Shimizu H, Tanaka N, Kuramochi K, Nakai H, Nakajima M, Taguchi H.	J Biol Chem	10.1016/j.jbc.2022.101606	2022
Biotechnology	Evolution-aided engineering of plant specialized metabolism.	Irfan M, Chavez B, Rizzo P, D'Auria JC, Moghe GD.	aBIOTECH	10.1007/s42994-021-00052-3	2021
Metabolism	Heterologous expression and characterization of an Arabidopsis beta-l-arabinopyranosidase and alpha-d-galactosidases acting on beta-l-arabinopyranosyl residues.	Imaizumi C, Tomatsu H, Kitazawa K, Yoshimi Y, Shibano S, Kikuchi K, Yamaguchi M, Kaneko S, Tsumuraya Y, Kotake T.	J Exp Bot	10.1093/jxb/erx279	2017
	Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).	Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N.	Stand Genomic Sci	10.4056/sigs.3117229	2012
	Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsia bacterial endosymbionts.	Duron O.	Heredity (Edinb)	10.1038/hdy.2013.56	2013
	Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.	Martinez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P.	Nat Microbiol	10.1038/s41564-020-00794-8	2021
	An investigation of bacterial protein interactions as a primary research project in a sophomore-level molecular biology course.	Cardinale JA.	J Microbiol Biol Educ	10.1128/jmbe.v12i2.327	2011
	Linking microbial community structure to beta-glucosidic function in soil aggregates.	Bailey VL, Fansler SJ, Stegen JC, McCue LA.	ISME J	10.1038/ismej.2013.87	2013
	Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.	Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A.	BMC Bioinformatics	10.1186/1471-2105-15-196	2014
Lipids	The catalytic and structural basis of archaeal glycerophospholipid biosynthesis.	de Kok NAW, Driessen AJM.	Extremophiles	10.1007/s00792-022-01277-w	2022
Phylogeny	Marine and giant viruses as indicators of a marine microbial community in a riverine system.	Dann LM, Rosales S, McKerral J, Paterson JS, Smith RJ, Jeffries TC, Oliver RL, Mitchell JG.	Microbiologyopen	10.1002/mbo3.392	2016
Enzymology	Identification and Characterization of Heptaprenylglyceryl Phosphate Processing Enzymes in Bacillus subtilis.	Linde M, Peterhoff D, Sterner R, Babinger P.	J Biol Chem	10.1074/jbc.m115.711994	2016
Enzymology	Structural basis for the formation of acylalkylpyrones from two beta-ketoacyl units by the fungal type III polyketide synthase CsyB.	Mori T, Yang D, Matsui T, Hashimoto M, Morita H, Fujii I, Abe I.	J Biol Chem	10.1074/jbc.m114.626416	2015
	Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes.	Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ.	Genes (Basel)	10.3390/genes1030371	2010
	Multiple conversion between the genes encoding bacterial class-I release factors.	Ishikawa SA, Kamikawa R, Inagaki Y.	Sci Rep	10.1038/srep12406	2015
Metabolism	Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes.	McBride MJ, Zhu Y.	J Bacteriol	10.1128/jb.01962-12	2013
	Deciphering unusual uncultured magnetotactic multicellular prokaryotes through genomics.	Abreu F, Morillo V, Nascimento FF, Werneck C, Cantao ME, Ciapina LP, de Almeida LG, Lefevre CT, Bazylinski DA, de Vasconcelos AT, Lins U.	ISME J	10.1038/ismej.2013.203	2014
Metabolism	Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing.	Anantharaman V, Iyer LM, Aravind L.	Mol Biosyst	10.1039/c2mb25239b	2012
Metabolism	Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains.	Anantharaman V, Iyer LM, Aravind L.	Biol Direct	10.1186/1745-6150-5-43	2010
Enzymology	Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.	Tanaka N, Nakajima M, Narukawa-Nara M, Matsunaga H, Kamisuki S, Aramasa H, Takahashi Y, Sugimoto N, Abe K, Terada T, Miyanaga A, Yamashita T, Sugawara F, Kamakura T, Komba S, Nakai H, Taguchi H.	J Biol Chem	10.1074/jbc.ra118.007087	2019
Metabolism	UPF0586 Protein C9orf41 Homolog Is Anserine-producing Methyltransferase.	Drozak J, Piecuch M, Poleszak O, Kozlowski P, Chrobok L, Baelde HJ, de Heer E.	J Biol Chem	10.1074/jbc.m115.640037	2015
Metabolism	Flavobacterium johnsoniae GldK, GldL, GldM, and SprA are required for secretion of the cell surface gliding motility adhesins SprB and RemA.	Shrivastava A, Johnston JJ, van Baaren JM, McBride MJ.	J Bacteriol	10.1128/jb.00333-13	2013
Phylogeny	Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.	Shlykov MA, Zheng WH, Chen JS, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2011.12.005	2012
	Flavobacterium johnsoniae sprB is part of an operon spanning the additional gliding motility genes sprC, sprD, and sprF.	Rhodes RG, Nelson SS, Pochiraju S, McBride MJ.	J Bacteriol	10.1128/jb.01203-10	2011
Phylogeny	Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats.	Schauer M, Hahn MW.	Appl Environ Microbiol	10.1128/aem.71.4.1931-1940.2005	2005
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
Metabolism	Functional Analysis of a Gene Cluster from Chitinophaga pinensis Involved in Biosynthesis of the Pyrrolidine Azasugar DAB-1.	Nunez C, Horenstein NA	J Nat Prod	10.1021/acs.jnatprod.9b00758	2019
Phylogeny	In Silico Characterization of a Unique Plant-Like "Loopful" GH19 Chitinase from Newly Isolated Chitinophaga sp. YS-16.	Sharma S, Singh R, Kaur R	Curr Microbiol	10.1007/s00284-020-02022-2	2020
Genetics	Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).	Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S	Stand Genomic Sci	10.4056/sigs.661199	2010
	Fixed-target serial crystallography at the Structural Biology Center.	Sherrell DA, Lavens A, Wilamowski M, Kim Y, Chard R, Lazarski K, Rosenbaum G, Vescovi R, Johnson JL, Akins C, Chang C, Michalska K, Babnigg G, Foster I, Joachimiak A	J Synchrotron Radiat	10.1107/S1600577522007895	2022
Phylogeny	Chitinophaga pollutisoli sp. nov., isolated from contaminated sediment.	Lee DS, Lee JK, Han DM, Baek JH, Jeon CO.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006447	2024
Phylogeny	Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.	Kampfer P, Young CC, Sridhar KR, Arun AB, Lai WA, Shen FT, Rekha PD.	Int J Syst Evol Microbiol	10.1099/ijs.0.64359-0	2006
Phylogeny	Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana.	Zhang XJ, Feng GD, Yang F, Zhu H, Yao Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.005118	2021
Phylogeny	Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.	Lee SA, Heo J, Kim TW, Sang MK, Song J, Kwon SW, Weon HY	Arch Microbiol	10.1007/s00203-020-02066-9	2020
Phylogeny	Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts.	Ike F, Sakamoto M, Ohkuma M, Kajita A, Matsushita S, Kokubo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.000685	2015
Phylogeny	Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes.	Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB	Int J Syst Evol Microbiol	10.1099/ijs.0.057463-0	2014
Phylogeny	Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).	Chung EJ, Park TS, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.036442-0	2012
Phylogeny	Chitinophaga eiseniae sp. nov., isolated from vermicompost.	Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.023028-0	2010

References

#1142	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2588
#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 )
#33117	; Curators of the CIP;
#43362	Tijana Glavina Del Rio, Birte Abt, Stefan Spring, Alla Lapidus, Matt Nolan, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Susan Lucas: Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci 2: 87 - 95 2010 ( DOI 10.1099/00207713-31-3-285 )
#43425	Vullapa Sangkhobol, V. B. D. Skerman: Chitinophaga, a New Genus of Chitinolytic Myxobacteria. IJSEM 31: 285 - 293 1981 ( DOI 10.4056/sigs.661199 , PubMed 21304681 )
#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 )
#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 )
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#121834	Collection of Institut Pasteur ; Curators of the CIP; CIP 107364
#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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Chitinophaga pinensis (DSM 2588, ATCC 43595, IFO 15968)

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