Name: Faecalimonas umbilicata EGH7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140268

Type strain:

Species: Faecalimonas umbilicata

Strain Designation: EGH7

Culture col. no.: DSM 103426, JCM 30896

Strain history: M. Sakamoto; RIKEN BRC-JCM, Japan; EGH7.

NCBI tax ID(s): 1912855 (species)

SI-ID 407291

DSM 103426

Other strains from Faecalimonas umbilicata

F. umbilicata 9/1/43 B FAA, DSM 24431
F. umbilicata TSAH33, JCM 31370, DSM 103427
F. umbilicata JCM 31933

Section

Faecalimonas umbilicata EGH7 is an obligate anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from human faeces, healthy Japanese man .

coccus-shaped
colony-forming
Gram-positive
mesophilic
obligate anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Faecalimonas*
	Species	**Faecalimonas umbilicata**
	Full Scientific Name (LPSN)	Faecalimonas umbilicata Sakamoto et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43183]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43183]	Cell length	2.4 µm

[Ref.: #43183]	Cell width	0.8-1.5 µm

[Ref.: #43183]	Cell shape	coccus-shaped

[Ref.: #43183]	Motility	no

[Ref.: #43183]	Colony size	1-3 mm
[Ref.: #43183]	Colony color	white to ivory
[Ref.: #43183]	Colony shape	circular
[Ref.: #43183]	Incubation period	4 days
[Ref.: #43183]	Cultivation medium used	Eggerth-Gagnon (EG) agar (Merck)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43183]

Culture medium

Eggerth-Gagnon (EG) agar (Merck)

[Ref.: #43183]

Culture medium growth

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Culture medium

PYG broth

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Culture medium growth

[Ref.: #42875]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #42875]

Culture medium growth

[Ref.: #42875]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42875]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42875]	growth	37 °C
[Ref.: #43183]	optimum	37 °C
[Ref.: #43183]	growth	30-40 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #42875]	Temperature range	mesophilic
[Ref.: #43183]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43183]			optimum	7
[Ref.: #43183]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43183]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.63

[Ref.: #43183]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.501

[Ref.: #43183]	Name of tolerated compound	bile
[Ref.: #43183]	Tolerated concentration	20

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43183]	cellobiose ChEBI	-	builds acid from
[Ref.: #43183]	D-glucose ChEBI	+	builds acid from
[Ref.: #43183]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43183]	D-mannose ChEBI	-	builds acid from
[Ref.: #43183]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43183]	D-xylose ChEBI	+	builds acid from
[Ref.: #43183]	esculin ChEBI	+	hydrolysis
[Ref.: #43183]	gelatin ChEBI	-	degradation
[Ref.: #43183]	glycerol ChEBI	-	builds acid from
[Ref.: #43183]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43183]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43183]	lactose ChEBI	+	builds acid from
[Ref.: #43183]	maltose ChEBI	+	builds acid from
[Ref.: #43183]	mannose ChEBI	-	fermentation
[Ref.: #43183]	melezitose ChEBI	-	builds acid from
[Ref.: #43183]	nitrate ChEBI	+	reduction
[Ref.: #43183]	raffinose ChEBI	+	builds acid from
[Ref.: #43183]	raffinose ChEBI	+	fermentation
[Ref.: #43183]	salicin ChEBI	+	builds acid from
[Ref.: #43183]	sucrose ChEBI	+	builds acid from
[Ref.: #43183]	trehalose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43183]		hydrogen sulfide ChEBI	yes
[Ref.: #43183]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43183]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #43183]	acid phosphatase	+	3.1.3.2
[Ref.: #43183]	alanine arylamidase	+	3.4.11.2
[Ref.: #43183]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43183]	alpha-arabinosidase	-	3.2.1.55
[Ref.: #43183]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43183]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43183]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43183]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43183]	arginine arylamidase	+
[Ref.: #43183]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43183]	beta-galactosidase	+	3.2.1.23
[Ref.: #43183]	beta-glucosidase	+	3.2.1.21
[Ref.: #43183]	beta-glucuronidase	+	3.2.1.31
[Ref.: #43183]	catalase	-	1.11.1.6
[Ref.: #43183]	cystine arylamidase	-	3.4.11.3
[Ref.: #43183]	esterase	+
[Ref.: #43183]	esterase Lipase (C 8)	+
[Ref.: #43183]	glutamate decarboxylase	-	4.1.1.15
[Ref.: #43183]	glutamyl-glutamate arylamidase	-
[Ref.: #43183]	glycin arylamidase	-
[Ref.: #43183]	histidine arylamidase	+
[Ref.: #43183]	leucine arylamidase	+	3.4.11.1
[Ref.: #43183]	leucyl glycin arylamidase	-	3.4.11.1
[Ref.: #43183]	lipase	-
[Ref.: #43183]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43183]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43183]	phenylalanine arylamidase	+
[Ref.: #43183]	proline-arylamidase	-	3.4.11.5
[Ref.: #43183]	pyroglutamic acid arylamidase	-
[Ref.: #43183]	serine arylamidase	+
[Ref.: #43183]	trypsin	-	3.4.21.4
[Ref.: #43183]	tyrosine arylamidase	+
[Ref.: #43183]	urease	-	3.5.1.5
[Ref.: #43183]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43183]

Fatty acid	Percentage	SD	ECL
C18:1ω9c	34.2	4.3
C16:0	21.3	0.9
C18:1ω9c DMA	15.2	0.9
unknown / C18:0ω11c/9t/6t FAME	6.9	0.7	17834
C14:0	5.8	0.4
C18:0	4.1	0.3
C16:0 DMA	3.1	0.7
unknown / C17:1ω8c	3.1	0.2	17
C18:2ω6,9c	2.7	0.5
C18:1ω7c DMA	2.6	1.6
C18:0 DMA	1.3	0.8
C12:0	1.3	0.1

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

[Ref.: #42875]	Sample type/isolated from	human faeces, healthy Japanese man (45-years-old)
[Ref.: #42875]	Geographic location (country and/or sea, region)	Tsukuba, Ibaraki
[Ref.: #42875]	Country	Japan
[Ref.: #42875]	Country ISO 3 Code	JPN
[Ref.: #42875]	Continent	Asia

[Ref.: #43183]	Sample type/isolated from	human faeces

[Ref.: #67770]	Sample type/isolated from	Feces of a man in the forties
* marker position based on {}

Isolation sources categories

#Host	#Human	#Male
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC192831 (>99% sequence identity) for Faecalimonas umbilicata subclade from Microbeatlas

Aquatic Samples	856
Soil Samples	369
Animal Samples	51940
Plant Samples	294
Total Samples	53459

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

[Ref.: #42875]

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.: #42875]	Faecalimonas umbilicata gene for 16S ribosomal RNA, partial sequence, strain: EGH7	LC192831	1492	ENA	1912855 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.: #67770]	Faecalimonas umbilicata EGH7	GCA_003402615	contig	GenBank	1912855 tax ID
[Ref.: #67770]	Faecalimonas umbilicata DSM 103426	GCA_004346095	scaffold	GenBank	1912855 tax ID
[Ref.: #66792]	Faecalimonas umbilicata strain DSM 103426	1912855.8	wgs	PATRIC	1912855 tax ID	*
[Ref.: #66792]	Faecalimonas umbilicata strain EGH7	1912855.5	wgs	PATRIC	1912855 tax ID	*
[Ref.: #66792]	Faecalimonas umbilicata EGH7	2832053327	draft	JGI IMG/M	1912855 tax ID	*
[Ref.: #66792]	Faecalimonas umbilicata DSM 103426	2784746781	draft	JGI IMG/M	1912855 tax ID	*

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GC-content

46.9 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Faecalimonas umbilicata DSM 103426 NCBI: GCA_004346095.1
[Ref.: #69481]	spore-forming	yes	55	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Faecalimonas umbilicata strain DSM 103426 PATRIC: 1912855.8
[Ref.: #69480]	motile	no	92.727	yes
[Ref.: #69480]	gram-positive	yes	96.079	no
[Ref.: #69480]	anaerobic	yes	99.499	no
[Ref.: #69480]	aerobic	no	98.157	no
[Ref.: #69480]	halophile	no	80.322	no
[Ref.: #69480]	spore-forming	no	72.075	yes
[Ref.: #69480]	glucose-util	yes	88.341	no
[Ref.: #69480]	flagellated	no	95.309	no
[Ref.: #69480]	thermophile	no	95.93	yes
[Ref.: #69480]	glucose-ferment	yes	73.375	no

Availability in culture collections External links

[Ref.: #42875]

Culture collection no.

DSM 103426, JCM 30896

[Ref.: #96574]

SI-ID 407291

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.	Sakamoto M, Iino T, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001790	2017	*
Genetics	Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.	Sakamoto M, Ikeyama N, Yuki M, Ohkuma M	Microbiol Resour Announc	10.1128/MRA.01091-18	2018	*

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 )

#42875

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103426

#43183

Mitsuo Sakamoto, Takao Iino, Moriya Ohkuma: Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.. IJSEM 67: 1219 - 1227 2017 ( DOI 10.1099/ijsem.0.001790 , PubMed 28556772 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96574

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-ID407291.1 )

* These data were automatically processed and therefore are not curated

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Faecalimonas umbilicata DSM 103426

Faecalimonas umbilicata strain DSM 103426

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