Name: Rhodoligotrophos defluvii lm1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 166282

Type strain:

Species: Rhodoligotrophos defluvii

Strain Designation: lm1

Culture col. no.: CCTCC AB 2019071, KCTC 72156

NCBI tax ID(s): 2561934 (species)

Special Collections

Section

Rhodoligotrophos defluvii lm1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from PO saponification wastewater activated sludge.

colony-forming
Gram-negative
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Parvibaculaceae*
	Genus	*Rhodoligotrophos*
	Species	**Rhodoligotrophos defluvii**
	Full Scientific Name (LPSN)	Rhodoligotrophos defluvii Liu et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #68241]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.571

[Ref.: #68241]	Cell length	0.8-1.2 µm

[Ref.: #68241]	Cell width	0.3-0.5 µm

[Ref.: #68241]	Cell shape	rod-shaped

[Ref.: #68241]	Colony size	1.5 mm
[Ref.: #68241]	Colony color	red
[Ref.: #68241]	Colony shape	circular
[Ref.: #68241]	Incubation period	4 days
[Ref.: #68241]	Cultivation medium used	LB (Luria-Bertani) agar

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #68241]			growth	15-45 °C
[Ref.: #68241]			optimum	40 °C

	pH	Kind of pH		pH
[Ref.: #68241]			optimum	8
[Ref.: #68241]			growth	4-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68241]

Oxygen tolerance

aerobe

[Ref.: #68241]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68241]		NaCl		growth	0-4	%(w/v)
[Ref.: #68241]		NaCl		optimum	1-2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68241]	(-)-quinic acid ChEBI	-	carbon source
[Ref.: #68241]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #68241]	2-oxoglutarate ChEBI	+/-	carbon source
[Ref.: #68241]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #68241]	4-hydroxyphenylacetic acid ChEBI	-	carbon source
[Ref.: #68241]	acetic acid ChEBI	+	carbon source
[Ref.: #68241]	acetoacetate ChEBI	+/-	carbon source
[Ref.: #68241]	alpha-D-glucose ChEBI	+/-	carbon source
[Ref.: #68241]	alpha-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68241]	amygdalin ChEBI	-	builds acid from
[Ref.: #68241]	arbutin ChEBI	+/-	builds acid from
[Ref.: #68241]	aspartate ChEBI	-	carbon source
[Ref.: #68241]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68241]	bromosuccinate ChEBI	-	carbon source
[Ref.: #68241]	cellobiose ChEBI	-	builds acid from
[Ref.: #68241]	cellobiose ChEBI	-	carbon source
[Ref.: #68241]	citrate ChEBI	+	assimilation
[Ref.: #68241]	citrate ChEBI	-	carbon source
[Ref.: #68241]	D-arabinose ChEBI	+	builds acid from
[Ref.: #68241]	D-arabitol ChEBI	-	builds acid from
[Ref.: #68241]	D-arabitol ChEBI	-	carbon source
[Ref.: #68241]	D-fructose ChEBI	+	builds acid from
[Ref.: #68241]	D-fructose ChEBI	-	carbon source
[Ref.: #68241]	D-fructose 6-phosphate ChEBI	+/-	carbon source
[Ref.: #68241]	D-fucose ChEBI	-	builds acid from
[Ref.: #68241]	D-fucose ChEBI	-	carbon source
[Ref.: #68241]	D-galactonic acid lactone ChEBI	-	carbon source
[Ref.: #68241]	D-galactose ChEBI	-	builds acid from
[Ref.: #68241]	D-galactose ChEBI	-	carbon source
[Ref.: #68241]	D-galacturonic acid ChEBI	-	carbon source
[Ref.: #68241]	D-gluconate ChEBI	-	carbon source
[Ref.: #68241]	D-glucose ChEBI	-	builds acid from
[Ref.: #68241]	D-glucose 6-phosphate ChEBI	+/-	carbon source
[Ref.: #68241]	D-glucuronate ChEBI	-	carbon source
[Ref.: #68241]	D-lactic acid methyl ester	-	carbon source
[Ref.: #68241]	D-lyxose ChEBI	+	builds acid from
[Ref.: #68241]	D-malate ChEBI	-	carbon source
[Ref.: #68241]	D-mannitol ChEBI	-	carbon source
[Ref.: #68241]	D-mannose ChEBI	-	builds acid from
[Ref.: #68241]	D-mannose ChEBI	-	carbon source
[Ref.: #68241]	D-ribose ChEBI	+	builds acid from
[Ref.: #68241]	D-saccharate ChEBI	-	carbon source
[Ref.: #68241]	D-salicin ChEBI	-	carbon source
[Ref.: #68241]	D-serine ChEBI	-	carbon source
[Ref.: #68241]	D-sorbitol ChEBI	-	carbon source
[Ref.: #68241]	D-tagatose ChEBI	+	builds acid from
[Ref.: #68241]	D-xylose ChEBI	+	builds acid from
[Ref.: #68241]	dextrin ChEBI	-	carbon source
[Ref.: #68241]	erythritol ChEBI	+	builds acid from
[Ref.: #68241]	esculin ChEBI	+	builds acid from
[Ref.: #68241]	formate ChEBI	+	carbon source
[Ref.: #68241]	galactarate ChEBI	-	carbon source
[Ref.: #68241]	galactitol ChEBI	-	builds acid from
[Ref.: #68241]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #68241]	gelatin ChEBI	-	carbon source
[Ref.: #68241]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68241]	gentiobiose ChEBI	-	carbon source
[Ref.: #68241]	glucuronamide ChEBI	+/-	carbon source
[Ref.: #68241]	glycerol ChEBI	-	carbon source
[Ref.: #68241]	glycogen ChEBI	-	builds acid from
[Ref.: #68241]	glycyl-L-proline ChEBI	-	carbon source
[Ref.: #68241]	inosine ChEBI	-	carbon source
[Ref.: #68241]	inulin ChEBI	-	builds acid from
[Ref.: #68241]	L-alanine ChEBI	+	carbon source
[Ref.: #68241]	L-arabinose ChEBI	+	builds acid from
[Ref.: #68241]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68241]	L-arginine ChEBI	-	carbon source
[Ref.: #68241]	L-aspartate ChEBI	-	carbon source
[Ref.: #68241]	L-fucose ChEBI	-	builds acid from
[Ref.: #68241]	L-fucose ChEBI	-	carbon source
[Ref.: #68241]	L-glutamate ChEBI	-	carbon source
[Ref.: #68241]	L-histidine ChEBI	-	carbon source
[Ref.: #68241]	L-lactate	-	carbon source
[Ref.: #68241]	L-malate ChEBI	+/-	carbon source
[Ref.: #68241]	L-pyroglutamic acid ChEBI	+/-	carbon source
[Ref.: #68241]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68241]	L-rhamnose ChEBI	-	carbon source
[Ref.: #68241]	L-serine ChEBI	+	carbon source
[Ref.: #68241]	L-sorbose ChEBI	+	builds acid from
[Ref.: #68241]	L-xylose ChEBI	+	builds acid from
[Ref.: #68241]	lactose ChEBI	-	builds acid from
[Ref.: #68241]	lactose ChEBI	-	carbon source
[Ref.: #68241]	maltose ChEBI	-	builds acid from
[Ref.: #68241]	maltose ChEBI	-	carbon source
[Ref.: #68241]	mannitol ChEBI	+	builds acid from
[Ref.: #68241]	mannitol ChEBI	-	builds acid from
[Ref.: #68241]	melezitose ChEBI	-	builds acid from
[Ref.: #68241]	melibiose ChEBI	-	builds acid from
[Ref.: #68241]	melibiose ChEBI	-	carbon source
[Ref.: #68241]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #68241]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #68241]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #68241]	methyl D-glucoside ChEBI	-	carbon source
[Ref.: #68241]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #68241]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68241]	myo-inositol ChEBI	-	carbon source
[Ref.: #68241]	N-acetyl-beta-D-mannosamine ChEBI	-	carbon source
[Ref.: #68241]	n-acetyl-D-galactosamine ChEBI	-	carbon source
[Ref.: #68241]	N-acetyl-D-glucosamine ChEBI	-	builds acid from
[Ref.: #68241]	N-acetyl-D-glucosamine ChEBI	-	carbon source
[Ref.: #68241]	n-acetyl-neuraminic acid	-	carbon source
[Ref.: #68241]	pectin ChEBI	-	carbon source
[Ref.: #68241]	potassium 2-dehydro-D-gluconate	+/-	builds acid from
[Ref.: #68241]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #68241]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #68241]	propionate ChEBI	+	carbon source
[Ref.: #68241]	raffinose ChEBI	-	builds acid from
[Ref.: #68241]	raffinose ChEBI	-	carbon source
[Ref.: #68241]	ribitol ChEBI	-	builds acid from
[Ref.: #68241]	salicin ChEBI	-	builds acid from
[Ref.: #68241]	sorbitol ChEBI	-	builds acid from
[Ref.: #68241]	stachyose ChEBI	-	carbon source
[Ref.: #68241]	starch ChEBI	-	builds acid from
[Ref.: #68241]	sucrose ChEBI	-	builds acid from
[Ref.: #68241]	sucrose ChEBI	-	carbon source
[Ref.: #68241]	trehalose ChEBI	-	builds acid from
[Ref.: #68241]	trehalose ChEBI	-	carbon source
[Ref.: #68241]	turanose ChEBI	+/-	builds acid from
[Ref.: #68241]	turanose ChEBI	+/-	carbon source
[Ref.: #68241]	tween 40 ChEBI	-	carbon source
[Ref.: #68241]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #68241]	ampicillin ChEBI	yes
[Ref.: #68241]	cefoperazone ChEBI	yes
[Ref.: #68241]	chloramphenicol ChEBI	yes
[Ref.: #68241]	erythromycin ChEBI		yes
[Ref.: #68241]	gentamicin ChEBI	yes
[Ref.: #68241]	kanamycin ChEBI	yes
[Ref.: #68241]	lincomycin ChEBI	yes
[Ref.: #68241]	lincomycin ChEBI		yes
[Ref.: #68241]	minocycline ChEBI		yes
[Ref.: #68241]	neomycin ChEBI	yes
[Ref.: #68241]	paromomycin sulfate ChEBI	yes
[Ref.: #68241]	penicillin ChEBI		yes
[Ref.: #68241]	rifamycin ChEBI		yes
[Ref.: #68241]	spectinomycin ChEBI	yes
[Ref.: #68241]	streptomycin ChEBI	yes
[Ref.: #68241]	tetracycline ChEBI	yes
[Ref.: #68241]	troleandomycin ChEBI		yes
[Ref.: #68241]	vancomycin ChEBI		yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68241]	acetoin ChEBI	no
[Ref.: #68241]	hydrogen sulfide ChEBI	no
[Ref.: #68241]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #68241]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68241]	acid phosphatase	+	3.1.3.2
[Ref.: #68241]	alkaline phosphatase	+/-	3.1.3.1
[Ref.: #68241]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68241]	alpha-glucosidase	-	3.2.1.20
[Ref.: #68241]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68241]	arginine dihydrolase	+	3.5.3.6
[Ref.: #68241]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #68241]	beta-galactosidase	-	3.2.1.23
[Ref.: #68241]	beta-glucosidase	-	3.2.1.21
[Ref.: #68241]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68241]	catalase	+	1.11.1.6
[Ref.: #68241]	chymotrypsin	+	3.4.4.5
[Ref.: #68241]	cystine arylamidase	+	3.4.11.3
[Ref.: #68241]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68241]	esterase (C 4)	+/-
[Ref.: #68241]	esterase Lipase (C 8)	+/-
[Ref.: #68241]	gelatinase	+
[Ref.: #68241]	leucine arylamidase	+	3.4.11.1
[Ref.: #68241]	lipase (C 14)	+/-
[Ref.: #68241]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68241]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68241]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68241]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68241]	trypsin	+	3.4.21.4
[Ref.: #68241]	tryptophan deaminase	-	4.1.99.1
[Ref.: #68241]	urease	+	3.5.1.5
[Ref.: #68241]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #68241]

Fatty acid	Percentage
C19:0 cyclo w8c	44.2
C18:1 w7c	29
C16:0	17
C16:1 w7c/C16:1 w6c	3.3
C18:0	1.6
C14:0	0.7
C15:0 iso	0.6
C17:0 cyclo	0.5
C12:0	0.5
C18:1 w5c	0.2
C15:0 anteiso	0.2
C8:0 3OH	0.2
C16:0 2OH	0.2
C17:1 w8c	0.1
C16:0 iso	0.1
C17:0 anteiso	0.1

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

[Ref.: #68241]	Sample type/isolated from	PO saponification wastewater activated sludge
[Ref.: #68241]	Geographic location (country and/or sea, region)	Binzhou, Shandong Province
[Ref.: #68241]	Country	China
[Ref.: #68241]	Country ISO 3 Code	CHN
[Ref.: #68241]	Continent	Asia
[Ref.: #68241]	Geographic location	37.6564°/118.1180°
[Ref.: #68241]	Enrichment culture	LB
[Ref.: #68241]	Enrichment culture duration	1 week
[Ref.: #68241]	Enrichment culture temperature	37 ̊C
* marker position based on {}

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.: #68241]	Rhodoligotrophos defluvii strain lm1 16S ribosomal RNA gene, partial sequence	MK124546	1359	GenBank ENA	1969729 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #68241]	Rhodoligotrophos defluvii lm1	GCA_005281615	contig	GenBank ENA	2561934 tax ID

[Ref.: #68241]

GC-content

64.4 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoligotrophos defluvii lm1 NCBI: GCA_005281615.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.571	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.71	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.484	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	81.25	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.21	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	52.191	no

Availability in culture collections External links

[Ref.: #68241]

Culture collection no.

CCTCC AB 2019071, KCTC 72156

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodoligotrophos defluvii sp. nov., isolated from activated sludge.	Liu YL, Meng D, Li RR, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.003691	2019	*

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 )

#68241

Yu-Ling Liu, Dong Meng, Rui-Rui Li, Peng-Fei Gu, Xiang-Yu Fan, Zhao-Song Huang, Zong-Jun Du and Qiang Li: Rhodoligotrophos defluvii sp. nov., isolated from activated sludge. IJSEM 69: 3830 - 3836 2019 ( DOI 10.1099/ijsem.0.003691 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

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