Faecalimonas umbilicata (DSM 103426, JCM 30896, EGH7)

Name: Faecalimonas umbilicata (DSM 103426, JCM 30896, EGH7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140268

Type strain

Strain Designation EGH7

Culture col. no. DSM 103426 JCM 30896 EGH7

NCBI tax ID(s) 1912855

Special Collections DSMZ JCM Literature strains

History <- M. Sakamoto, RIKEN BRC-JCM, Japan; EGH7 M. Sakamoto; RIKEN BRC-JCM, Japan; EGH7.

Links

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

Gram-positive coccus-shaped colony-forming obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407291

JCM 30896,DSM 103426

@ref 20215

Last LPSN update 2026-02-09 11:33:34

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Faecalimonas

Species Faecalimonas umbilicata

Full scientific name Faecalimonas umbilicata Sakamoto et al. 2017

BacDive ID	Other strains from **Faecalimonas umbilicata** (3)	Type strain
160749	F. umbilicata 9/1/43 B FAA, DSM 24431
164043	F. umbilicata TSAH33, JCM 31370, DSM 103427
164157	F. umbilicata JCM 31933

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43183	positive	2.4 µm	0.8-1.5 µm	coccus-shaped
125439						90.3

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43183	1-3 mm	white to ivory	circular	4 days	Eggerth-Gagnon (EG) agar (Merck)

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43183	Eggerth-Gagnon (EG) agar (Merck)
43183	PYG broth
42875	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42875	positive	growth	37
43183	positive	optimum	37
43183	positive	growth	30-40
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
43183	positive	optimum	7
43183	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43183	obligate anaerobe
125439	facultative anaerobe	99.5

Spore formation

@ref	Spore formation	Confidence
43183
125439		91.3

Tolerance

@ref	Compound	Concentration
43183	bile	20.0 % (w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43183	17057 ChEBI	cellobiose	-	builds acid from
43183	17634 ChEBI	D-glucose	+	builds acid from
43183	16899 ChEBI	D-mannitol	-	builds acid from
43183	16024 ChEBI	D-mannose	-	builds acid from
43183	17924 ChEBI	D-sorbitol	-	builds acid from
43183	65327 ChEBI	D-xylose	+	builds acid from
43183	4853 ChEBI	esculin	+	hydrolysis
43183	5291 ChEBI	gelatin	-	degradation
43183	17754 ChEBI	glycerol	-	builds acid from
43183	30849 ChEBI	L-arabinose	-	builds acid from
43183	62345 ChEBI	L-rhamnose	-	builds acid from
43183	17716 ChEBI	lactose	+	builds acid from
43183	17306 ChEBI	maltose	+	builds acid from
43183	37684 ChEBI	mannose	-	fermentation
43183	6731 ChEBI	melezitose	-	builds acid from
43183	17632 ChEBI	nitrate	+	reduction
43183	16634 ChEBI	raffinose	+	builds acid from
43183	16634 ChEBI	raffinose	+	fermentation
43183	17814 ChEBI	salicin	+	builds acid from
43183	17992 ChEBI	sucrose	+	builds acid from
43183	27082 ChEBI	trehalose	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43183	16136 ChEBI	hydrogen sulfide
43183	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43183	6-phospho-beta-galactosidase	-	3.2.1.85
43183	acid phosphatase	+	3.1.3.2
43183	alanine arylamidase	+	3.4.11.2
43183	alkaline phosphatase	+	3.1.3.1
43183	alpha-arabinosidase	-	3.2.1.55
43183	alpha-chymotrypsin	-	3.4.21.1
43183	alpha-galactosidase	+	3.2.1.22
43183	alpha-glucosidase	+	3.2.1.20
43183	alpha-mannosidase	-	3.2.1.24
43183	arginine arylamidase	+
43183	arginine dihydrolase	-	3.5.3.6
43183	beta-galactosidase	+	3.2.1.23
43183	beta-glucosidase	+	3.2.1.21
43183	beta-glucuronidase	+	3.2.1.31
43183	catalase	-	1.11.1.6
43183	cystine arylamidase	-	3.4.11.3
43183	esterase	+
43183	esterase Lipase (C 8)	+
43183	glutamate decarboxylase	-	4.1.1.15
43183	glutamyl-glutamate arylamidase	-
43183	glycin arylamidase	-
43183	histidine arylamidase	+
43183	leucine arylamidase	+	3.4.11.1
43183	leucyl glycin arylamidase	-	3.4.11.1
43183	lipase	-
43183	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43183	naphthol-AS-BI-phosphohydrolase	+
43183	phenylalanine arylamidase	+
43183	proline-arylamidase	-	3.4.11.5
43183	pyroglutamic acid arylamidase	-
43183	serine arylamidase	+
43183	trypsin	-	3.4.21.4
43183	tyrosine arylamidase	+
43183	urease	-	3.5.1.5
43183	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	#Male
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
42875	human faeces, healthy Japanese man (45-years-old)	Tsukuba, Ibaraki	Japan	JPN	Asia
43183	human faeces
67770	Feces of a man in the forties

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42875	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM340261v1 assembly for Faecalimonas umbilicata EGH7	contig	GCA_003402615	1912855.5	2832053327	1912855	76.05
67770	ASM434609v1 assembly for Faecalimonas umbilicata DSM 103426	scaffold	GCA_004346095	1912855.8	2784746781	1912855	65.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42875	Faecalimonas umbilicata gene for 16S ribosomal RNA, partial sequence, strain: EGH7	LC192831	1492		1912855

GC content

@ref	GC-content (mol%)	Method
42875	46.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Faecalimonas umbilicata DSM 103426
NCBI: GCA_004346095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	91.30	no
125439	motility	BacteriaNetⓘ	yes	90.30	no
125439	gram_stain	BacteriaNetⓘ	positive	75.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Faecalimonas umbilicata strain DSM 103426
PATRIC: 1912855.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.20	yes
125438	anaerobic	anaerobicⓘ	yes	88.87	yes
125438	spore-forming	spore-formingⓘ	no	53.57	no
125438	aerobic	aerobicⓘ	no	97.86	yes
125438	thermophilic	thermophileⓘ	no	92.84	no
125438	flagellated	motile2+ⓘ	no	84.44	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
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
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

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 )
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Faecalimonas umbilicata (DSM 103426, JCM 30896, EGH7)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Tolerance

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003402615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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