Name: Algoriphagus lutimaris S1-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133541

Type strain:

Species: Algoriphagus lutimaris

Strain Designation: S1-3

Culture col. no.: KCTC 22630, CCUG 57608

Strain history: <- Jung-Hoon Yoon, KRIBB

NCBI tax ID(s): 613197 (species)

SI-ID 411629

CCUG 57608

Special Collections

Section

When using BacDive for research please cite our paper

Algoriphagus lutimaris S1-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Cyclobacteriaceae*
	Genus	*Algoriphagus*
	Species	**Algoriphagus lutimaris**
	Full Scientific Name (LPSN)	Algoriphagus lutimaris Park et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29415]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.1
[Ref.: #125438]	Gram stain	negative Confidence in %96.989

[Ref.: #29415]	Cell length	2.7 µm

[Ref.: #29415]	Cell width	0.55 µm

[Ref.: #29415]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29415]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %90.5

[Ref.: #29415]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #29415]	growth	04-40 °C
[Ref.: #29415]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29415]			optimum	7.5
[Ref.: #29415]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29415]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %94.9

[Ref.: #29415]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29415]		NaCl		growth	0-8	%
[Ref.: #29415]		NaCl		optimum	2	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29415]		galactose ChEBI	+	carbon source
[Ref.: #29415]		trehalose ChEBI	+	carbon source

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #61387]

Fatty acid	Percentage	ECL
C15:0 ISO	27.4	14.621
C16:1 ω7c	12.8	15.819
C17:1 ω9c ISO	11.3	16.416
C16:1 ω7c/C15:0 ISO 2OH	9.9	15.85
C17:0 iso 3OH	6.6	18.161
C16:0 iso	5.2	15.626
C16:1 ω5c	4.8	15.908
C15:0 ANTEISO	4.1	14.711
C17:1 ω6c	2.6	16.862
C17:1 ISO I/C16:0 DMA	2.5	16.481
C16:1 ISO H	2.3	15.461
C11:0 ANTEISO	1.7	10.693
C15:0	1.4	15
C15:0 ISO 3OH	1.4	16.135
C16:0 iso 3OH	1.3	17.145
unknown 14.966	0.8	14.966
C16:0	0.8	16
C15:1 ω6c	0.7	14.856
C17:1 ω8c	0.6	16.792
unknown 16.580	0.6	16.58
C17:0 iso	0.6	16.629
C11:0 iso	0.5	10.605
C14:0 ISO	0.5	13.618

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

[Ref.: #29415]	Sample type/isolated from	marine sediment

[Ref.: #61387]	Sample type/isolated from	Tidal flat sediment
[Ref.: #61387]	Sampling date	2007-01-01
[Ref.: #61387]	Geographic location (country and/or sea, region)	Saemankum
[Ref.: #61387]	Country	Republic of Korea
[Ref.: #61387]	Country ISO 3 Code	KOR
[Ref.: #61387]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sediment of a tidal flat
[Ref.: #67771]	Geographic location (country and/or sea, region)	Saemankum on the west coast
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ669216 (>99% sequence identity) for Algoriphagus from Microbeatlas

Aquatic Samples	282
Soil Samples	82
Animal Samples	32
Plant Samples	24
Total Samples	420

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.: #29415]	Algoriphagus lutimaris strain S1-3 16S ribosomal RNA gene, partial sequence	FJ669216	1475	GenBank ENA	613197 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Algoriphagus lutimaris KCTC 22630	GCA_017051705	scaffold	GenBank ENA	613197 tax ID	*
[Ref.: #66792]	Algoriphagus lutimaris strain KCTC 22630	613197.3	wgs	PATRIC	613197 tax ID	*

[Ref.: #29415]	GC-content	41.4 mol%
[Ref.: #67771]	GC-content	41.4 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Algoriphagus lutimaris KCTC 22630 NCBI: GCA_017051705.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.989	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.895	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	83.84	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.941	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.922	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Algoriphagus lutimaris KCTC 22630 NCBI: GCA_017051705
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	82.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	70.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	94.9

Availability in culture collections External links

[Ref.: #29415]

Culture collection no.

KCTC 22630, CCUG 57608

[Ref.: #91494]

SI-ID 411629

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment.	Kang H, Weerawongwiwat V, Jung MY, Myung SC, Kim W	Int J Syst Evol Microbiol	10.1099/ijs.0.039214-0	2012	*
Phylogeny	Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate.	Alegado RA, Grabenstatter JD, Zuzow R, Morris A, Huang SY, Summons RE, King N	Int J Syst Evol Microbiol	10.1099/ijs.0.038646-0	2012	*
Phylogeny	Algoriphagus namhaensis sp. nov., isolated from seawater.	Oh KH, Kang SJ, Lee SY, Park S, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.030791-0	2011	*
Phylogeny	Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment.	Park S, Kang SJ, Oh KH, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.012682-0	2009	*

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 )

#29415

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25822 (see below)

#61387 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57608

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#91494

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-ID411629.1 )

#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 .

#25822

IJSEM 200 2010 ( DOI 10.1099/ijs.0.012682-0 , PubMed 19648320 )

* These data were automatically processed and therefore are not curated

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Algoriphagus lutimaris KCTC 22630

Algoriphagus lutimaris KCTC 22630

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