Name: Ammoniphilus resinae CC-RT-E
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132587

Type strain:

Species: Ammoniphilus resinae

Strain Designation: CC-RT-E

Culture col. no.: DSM 24738, BCRC 80314

Strain history: <- C. C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC-RT-E <- Y.-H. Wu

NCBI tax ID(s): 861532 (species)

SI-ID 405331

DSM 24738

Special Collections

Section

When using BacDive for research please cite our paper

Ammoniphilus resinae CC-RT-E is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from aged resin.

colony-forming
Gram-variable
rod-shaped
spore-forming
facultative anaerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Paenibacillaceae*
	Genus	*Ammoniphilus*
	Species	**Ammoniphilus resinae**
	Full Scientific Name (LPSN)	Ammoniphilus resinae Lin et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43085]	Gram stain	variable

[Ref.: #43085]	Cell length	2.8-3.4 µm

[Ref.: #43085]	Cell width	0.5-0.6 µm

[Ref.: #43085]	Cell shape	rod-shaped

[Ref.: #43085]	Colony color	white
[Ref.: #43085]	Colony shape	circular
[Ref.: #43085]	Incubation period	2 days
[Ref.: #43085]	Cultivation medium used	nutritient agar (NA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43085]

Culture medium

nutritient agar (NA)

[Ref.: #43085]

Culture medium growth

[Ref.: #24376]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #24376]

Culture medium growth

[Ref.: #24376]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24376]

Culture medium composition

expand / minimize

[Ref.: #43085]

Culture medium

ammonium-based medium (OM-2)

[Ref.: #43085]

Culture medium growth

		Temperature
[Ref.: #24376]	growth	28 °C
[Ref.: #43085]	optimum	30 °C
[Ref.: #43085]	growth	20-37 °C

	pH	Kind of pH		pH
[Ref.: #43085]			optimum	7
[Ref.: #43085]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43085]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %90.2

[Ref.: #43085]	Spore description	ellipsoidal spores at terminal position
[Ref.: #43085]	Type of spore	endospore
[Ref.: #43085]	Ability of spore formation	yes
[Ref.: #125438]	Ability of spore formation	yes Confidence in %91.119

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43085]		NaCl		growth	0-2	%(w/v)
[Ref.: #43085]		NaCl		optimum	1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43085]	(+)-D-glycogen	+	builds acid from
[Ref.: #43085]	4-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43085]	beta-d-glucose ChEBI	+	builds acid from
[Ref.: #43085]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43085]	casein	-	hydrolysis
[Ref.: #43085]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43085]	D-arabitol ChEBI	+	builds acid from
[Ref.: #43085]	D-galactose ChEBI	+	builds acid from
[Ref.: #43085]	D-glucose ChEBI	+	assimilation
[Ref.: #43085]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43085]	D-mannitol ChEBI	-	assimilation
[Ref.: #43085]	D-mannose ChEBI	+	assimilation
[Ref.: #43085]	D-ribose ChEBI	+	builds acid from
[Ref.: #43085]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43085]	D-xylose ChEBI	+	builds acid from
[Ref.: #43085]	esculin ChEBI	+	hydrolysis
[Ref.: #43085]	gelatin ChEBI	-	hydrolysis
[Ref.: #43085]	L-arabinose ChEBI	+	carbon source
[Ref.: #43085]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43085]	L-fucose ChEBI	+	builds acid from
[Ref.: #43085]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43085]	lactose ChEBI	+	builds acid from
[Ref.: #43085]	malate ChEBI	+	assimilation
[Ref.: #43085]	maltose ChEBI	+	builds acid from
[Ref.: #43085]	maltose ChEBI	-	assimilation
[Ref.: #43085]	nitrate ChEBI	+	reduction
[Ref.: #43085]	nitrite ChEBI	+	reduction
[Ref.: #43085]	potassium gluconate ChEBI	+	assimilation
[Ref.: #43085]	sodium citrate ChEBI	-	assimilation
[Ref.: #43085]	starch ChEBI	+	hydrolysis
[Ref.: #43085]	succinamate ChEBI	+	carbon source
[Ref.: #43085]	trehalose ChEBI	+	builds acid from
[Ref.: #43085]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43085]	tween 40 ChEBI	-	hydrolysis
[Ref.: #43085]	tween 60 ChEBI	-	hydrolysis
[Ref.: #43085]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43085]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43085]	acetoin ChEBI	yes
[Ref.: #43085]	hydrogen sulfide ChEBI	yes
[Ref.: #43085]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43085]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #43085]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43085]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43085]	beta-galactosidase	-	3.2.1.23
[Ref.: #43085]	beta-glucosidase	+	3.2.1.21
[Ref.: #43085]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43085]	catalase	+	1.11.1.6
[Ref.: #43085]	cystine arylamidase	+	3.4.11.3
[Ref.: #43085]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43085]	DNase	-
[Ref.: #43085]	esterase (C 4)	+
[Ref.: #43085]	esterase Lipase (C 8)	+
[Ref.: #43085]	leucine arylamidase	+	3.4.11.1
[Ref.: #43085]	naphthol-AS-BI-phosphohydrolase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43085]

Fatty acid	Percentage
C15:0 anteiso	33.3
C15:0 iso	18
C16:1ω7c / C16:1ω6c	13.5
C14:0	12.3
C16:0	6.4
C14:0 iso	2.8
C17:0 cyclo	2.8
C15:1ω6c	1.6
C16:1ω5c	1.4
C13:0 iso	1
C13:0 3-OH / iso-C15:1H	1
C16:0 iso	1

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

[Ref.: #24376]	Sample type/isolated from	aged resin
[Ref.: #24376]	Geographic location (country and/or sea, region)	tropical rainforest
[Ref.: #24376]	Country	Indonesia
[Ref.: #24376]	Country ISO 3 Code	IDN
[Ref.: #24376]	Continent	Asia

[Ref.: #43085]	Sample type/isolated from	resin sample from tropical forest
[Ref.: #43085]	Country	Indonesia
[Ref.: #43085]	Country ISO 3 Code	IDN
[Ref.: #43085]	Continent	Asia
[Ref.: #43085]	Enrichment culture	nutrient agar (NA; Hi-Media)
[Ref.: #43085]	Enrichment culture duration	3 days
[Ref.: #43085]	Enrichment culture temperature	30 ̊C
[Ref.: #43085]	Isolation/enrichment procedure	standard serial dilution-plating technique
* marker position based on {}

Isolation sources categories

#Host Body-Site

#Plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HM193518 (>99% sequence identity) for Ammoniphilus resinae subclade from Microbeatlas

Aquatic Samples	60
Soil Samples	565
Animal Samples	117
Plant Samples	37
Total Samples	779

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

[Ref.: #24376]

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.: #24376]	Ammoniphilus resinae strain CC-RT-E 16S ribosomal RNA gene, partial sequence	HM193518	1497	GenBank ENA	861532 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ammoniphilus resinae DSM 24738	GCA_017873965	contig	GenBank ENA	861532 tax ID	*
[Ref.: #66792]	Ammoniphilus resinae strain DSM 24738	861532.3	wgs	PATRIC	861532 tax ID	*
[Ref.: #66792]	Ammoniphilus resinae DSM 24738	2913422633	draft	JGI IMG/M	861532 tax ID	*

[Ref.: #24376]

GC-content

39.2 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: Ammoniphilus resinae strain DSM 24738 PATRIC: 861532.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	53.522	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	90.136	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	65.128	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	91.119	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	82.101	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	80.878	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ammoniphilus resinae DSM 24738 NCBI: GCA_017873965
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	89.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	82.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	86
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	90.2

Availability in culture collections External links

[Ref.: #24376]

Culture collection no.

DSM 24738, BCRC 80314

[Ref.: #90904]

SI-ID 405331

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ammoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments.	Lin SY, Wu YH, Hameed A, Liu YC, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001137	2016	*

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 )

#24376

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24738

#43085

Shih-Yao Lin, Yun-Hsuan Wu, Asif Hameed, You-Cheng Liu, Chiu-Chung Young: Ammoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments. IJSEM 66: 3010 - 3016 2016 ( DOI 10.1099/ijsem.0.001137 , PubMed 27151144 )

#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) .

#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 .

#90904

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-ID405331.1 )

#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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Ammoniphilus resinae strain DSM 24738

Ammoniphilus resinae DSM 24738

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