Name: Phyllobacterium catacumbae CECT 5680
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134109

Type strain:

Species: Phyllobacterium catacumbae

Culture col. no.: CECT 5680, LMG 22520, CSC 19, CIP 108923

Strain history: CIP <- 2005, CECT <- 2004, S. Jimenez, Italy: strain CSC19

NCBI tax ID(s): 281785 (species)

SI-ID 131920

LMG 22520, CECT 5680, CIP 108923

Section

Phyllobacterium catacumbae CECT 5680 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Tuff walls of Roman Catacombs of St Callixtus.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria

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	*Phyllobacteriaceae*
	Genus	*Phyllobacterium*
	Species	**Phyllobacterium catacumbae**
	Full Scientific Name (LPSN)	Phyllobacterium catacumbae Jurado et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31361]	Gram stain	negative
[Ref.: #117210]	Gram stain	negative

[Ref.: #31361]	Cell length	1.15 µm

[Ref.: #31361]	Cell width	0.55 µm

[Ref.: #31361]	Cell shape	rod-shaped
[Ref.: #117210]	Cell shape	rod-shaped

[Ref.: #31361]	Motility	yes
[Ref.: #117210]	Motility	yes

[Ref.: #31361]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #38367]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #38367]

Culture medium growth

[Ref.: #38367]

Culture medium composition

expand / minimize

[Ref.: #117210]

Culture medium

CIP Medium 72

[Ref.: #117210]

Culture medium growth

[Ref.: #117210]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #31361]			optimum	28 °C
[Ref.: #38367]			growth	30 °C

[Ref.: #31361]	Temperature range	mesophilic
[Ref.: #38367]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31361]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31361]		NaCl		growth	<2	%

[Ref.: #31361]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31361]	arabinose ChEBI	+	carbon source
[Ref.: #31361]	arginine ChEBI	+	carbon source
[Ref.: #31361]	cellobiose ChEBI	+	carbon source
[Ref.: #31361]	esculin ChEBI	+	hydrolysis
[Ref.: #31361]	fructose ChEBI	+	carbon source
[Ref.: #31361]	fucose ChEBI	+	carbon source
[Ref.: #31361]	galactose ChEBI	+	carbon source
[Ref.: #31361]	glucose ChEBI	+	carbon source
[Ref.: #31361]	maltose ChEBI	+	carbon source
[Ref.: #31361]	mannitol ChEBI	+	carbon source
[Ref.: #31361]	mannose ChEBI	+	carbon source
[Ref.: #31361]	melibiose ChEBI	+	carbon source
[Ref.: #31361]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31361]	nitrate ChEBI	+	reduction
[Ref.: #117210]	nitrate ChEBI	+	reduction
[Ref.: #117210]	nitrite ChEBI	-	reduction
[Ref.: #31361]	rhamnose ChEBI	+	carbon source
[Ref.: #31361]	ribose ChEBI	+	carbon source
[Ref.: #31361]	sodium citrate ChEBI	+	carbon source
[Ref.: #31361]	sorbitol ChEBI	+	carbon source
[Ref.: #31361]	sucrose ChEBI	+	carbon source
[Ref.: #31361]	trehalose ChEBI	+	carbon source
[Ref.: #31361]	urea ChEBI	+	carbon source
[Ref.: #31361]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #31361]		hydrogen sulfide ChEBI	yes
[Ref.: #117210]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #117210]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31361]	catalase	+	1.11.1.6
[Ref.: #117210]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31361]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #117210]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #117210]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #117210]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #31361]	urease	+	3.5.1.5
[Ref.: #117210]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #117210]	11552	-	-	+	-	-	+	-	-	+	-	+	+	-	-	-	-	-	+	-	-

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

[Ref.: #117210]	Sample type/isolated from	Tuff walls of Roman Catacombs of St Callixtus
[Ref.: #117210]	Geographic location (country and/or sea, region)	Rome
[Ref.: #117210]	Country	Italy
[Ref.: #117210]	Country ISO 3 Code	ITA
[Ref.: #117210]	Continent	Europe
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AY636000 (>99% sequence identity) for Phyllobacterium from Microbeatlas

Aquatic Samples	44
Soil Samples	78
Animal Samples	85
Plant Samples	51
Total Samples	258

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

[Ref.: #117210]

Biosafety level

Risk group (French classification)

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.: #31361]	Phyllobacterium catacumbae strain CSC19 16S ribosomal RNA gene, partial sequence	AY636000	1412	GenBank	281785 tax ID

[Ref.: #31361]

GC-content

55.9 mol%

Availability in culture collections External links

[Ref.: #31361]

Culture collection no.

CECT 5680, LMG 22520, CSC 19, CIP 108923

[Ref.: #91714]

SI-ID 131920

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phyllobacterium catacumbae sp. nov., a member of the order 'Rhizobiales' isolated from Roman catacombs.	Jurado V, Laiz L, Gonzalez JM, Hernandez-Marine M, Valens M, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.63402-0	2005	*

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 )

#31361

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 #27674 (see below)

#38367 ; Curators of the CIP;

#68382

Automatically annotated from API zym .

#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 .

#91714

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-ID131920.1 )

#117210 Collection of Institut Pasteur ; Curators of the CIP; CIP 108923

#27674

IJSEM 1487 2005 ( DOI 10.1099/ijs.0.63402-0 , PubMed 16014469 )

* These data were automatically processed and therefore are not curated

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