Name: Microbacterium halimionae PA36
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130413

Type strain:

Species: Microbacterium halimionae

Strain Designation: PA36

Culture col. no.: DSM 27576, CECT 8593

Strain history: <- A. Alves, Univ. de Aveiro, Dep. de Biologia, Portugal; PA36

NCBI tax ID(s): 1526413 (species)

SI-ID 395106

CECT 8593, DSM 27576

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

Microbacterium halimionae PA36 is a mesophilic bacterium that was isolated from surface sterilized aerial parts of sea purslane , a salt-marsh halophyte.

mesophilic
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microbacterium*
	Species	**Microbacterium halimionae**
	Full Scientific Name (LPSN)	Microbacterium halimionae Alves et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	positive Confidence in %90.617

[Ref.: #125438]	Motility	no Confidence in %93.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21666]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #21666]

Culture medium growth

[Ref.: #21666]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21666]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21666]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %98.7

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

[Ref.: #21666]	Sample type/isolated from	surface sterilized aerial parts of sea purslane (Halimione portulacoides), a salt-marsh halophyte
[Ref.: #21666]	Host species	Halimione portulacoides
[Ref.: #21666]	Geographic location (country and/or sea, region)	Murtosa, Largo do Laranjo, Ria de Aveiro (40°43'48.0''N 8°36'45.5''W)
[Ref.: #21666]	Country	Portugal
[Ref.: #21666]	Country ISO 3 Code	PRT
[Ref.: #21666]	Continent	Europe
[Ref.: #21666]	Geographic location	40.7300°/-8.6126°
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

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

[Ref.: #21666]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21666]	Microbacterium halimionae strain PA36 16S ribosomal RNA gene, partial sequence	KJ920278	1438	GenBank ENA	1526413 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microbacterium halimionae CECT 8593	GCA_011761265	scaffold	GenBank ENA	1526413 tax ID	*
[Ref.: #66792]	Microbacterium halimionae DSM 27576	GCA_014137985	contig	GenBank ENA	1526413 tax ID	*
[Ref.: #66792]	Microbacterium halimionae strain CECT 8593	1526413.3	wgs	PATRIC	1526413 tax ID	*
[Ref.: #66792]	Microbacterium halimionae strain DSM 27576	1526413.4	wgs	PATRIC	1526413 tax ID	*
[Ref.: #66792]	Microbacterium halimionae DSM 27576	2820985940	draft	JGI IMG/M	1526413 tax ID	*
[Ref.: #66792]	Microbacterium halimionae CECT 8593	2824251017	draft	JGI IMG/M	1526413 tax ID	*

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: Microbacterium halimionae CECT 8593 NCBI: GCA_011761265.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	90.617	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.306	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	76.219	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	78.098	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.429	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	93.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbacterium halimionae CECT 8593 NCBI: GCA_011761265
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	87.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	50.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	55.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.7

Availability in culture collections External links

[Ref.: #21666]

Culture collection no.

DSM 27576, CECT 8593

[Ref.: #88945]

SI-ID 395106

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium.	Alves A, Correia A, Igual JM, Trujillo ME	Syst Appl Microbiol	10.1016/j.syapm.2014.08.004	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 )

#21666

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27576

#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) .

#88945

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-ID395106.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Microbacterium halimionae CECT 8593

Microbacterium halimionae CECT 8593

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