Myroides indicus (DSM 28213, NCIM 5555, UKS 3)

Name: Myroides indicus (DSM 28213, NCIM 5555, UKS 3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131511

Type strain

Culture col. no. DSM 28213 NCIM 5555 UKS 3

NCBI tax ID(s) 1323422

Special Collections DSMZ

Myroides indicus DSM 28213 is a prokaryote that was isolated from garden soil.

genome sequence 16S sequence

Name and taxonomic classification

Culture Collection Numbers

DSM 28213 NCIM 5555 UKS 3

@ref 20215

Last LPSN update 2025-12-16 10:01:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Myroides

Species Myroides indicus

Full scientific name Myroides indicus Ram et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	94.4
125438		91.5
125438	negative	98.5

Culture and growth conditions

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		94.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	suberin monomers biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	alanine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	purine metabolism	67.02	63 of 94
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	histidine metabolism	65.52	19 of 29
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	leucine metabolism	61.54	8 of 13
66794	arachidonate biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	threonine metabolism	60	6 of 10
66794	glycolysis	58.82	10 of 17
66794	tryptophan metabolism	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	vitamin B6 metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	phenylalanine metabolism	53.85	7 of 13
66794	lipid metabolism	51.61	16 of 31
66794	biotin biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	isoleucine metabolism	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	heme metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	oxidative phosphorylation	46.15	42 of 91
66794	urea cycle	46.15	6 of 13
66794	valine metabolism	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	vitamin B1 metabolism	38.46	5 of 13
66794	pentose phosphate pathway	36.36	4 of 11
66794	proline metabolism	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	degradation of hexoses	27.78	5 of 18
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	butanoate fermentation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin B12 metabolism	23.53	8 of 34
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Garden

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22738	garden soil	University of Delhi, Department of Botany, North Campus	India	IND	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC906253 (>99% sequence identity) for Myroides indicus subclade from Microbeatlas

Aquatic Samples	138
Soil Samples	103
Animal Samples	387
Plant Samples	34
Total Samples	662

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM436457v1 assembly for Myroides indicus DSM 28213	scaffold	GCA_004364575	1323422.3	2739367659	1323422	56.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22738	Myroides indicus strain UKS3 16S ribosomal RNA gene, partial sequence	KC906253	1388		1323422

GC content

@ref	GC-content (mol%)	Method
22738	36.8	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: Myroides indicus DSM 28213
NCBI: GCA_004364575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.40	no
125439	motility	BacteriaNetⓘ	no	69.10	no
125439	gram_stain	BacteriaNetⓘ	negative	94.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	81.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Myroides indicus DSM 28213
NCBI: GCA_004364575.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	95.15	no
125438	aerobic	aerobicⓘ	yes	83.02	no
125438	spore-forming	spore-formingⓘ	no	89.69	no
125438	thermophilic	thermophileⓘ	no	96.08	no
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Myroides indicus sp. nov., isolated from garden soil.	Ram H, Kumar A, Thomas L, Dastager SG, Mawlankar R, Singh VP	Int J Syst Evol Microbiol	10.1099/ijsem.0.000530	2015

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 )
#22738	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28213
#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 )
#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 .
#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 .

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Myroides indicus (DSM 28213, NCIM 5555, UKS 3)

Name and taxonomic classification

Culture Collection Numbers

Morphology

Cell morphology

Culture and growth conditions

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004364575

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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