Gemmiger gallinarum (JCM 34595, DSM 109015, Cla-CZ-245)

Name: Gemmiger gallinarum (JCM 34595, DSM 109015, Cla-CZ-245)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160187

Type strain

Strain Designation Cla-CZ-245

Culture col. no. JCM 34595 DSM 109015 Cla-CZ-245

NCBI tax ID(s) 2779354 2049027

Special Collections DSMZ JCM Chicken DZIF

History DSMZ <- T. Clavel, RWTH Aachen; Cla-CZ-245 <- C. Zenner, LMU, München; JCM <-- B. Abt; DSMZ, Germany; Cla-CZ-245 <-- T. Clavel; RWTH Aachen, Germany.

Links

Gemmiger gallinarum Cla-CZ-245 is a bacterium that was isolated from chicken cecal content, adult.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401403

JCM 34595,DSM 109015

@ref 20215

Last LPSN update 2026-05-29 08:44:23

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Gemmiger

Species Gemmiger gallinarum

Full scientific name Gemmiger gallinarum Zenner et al. 2021

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.345

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
67091	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
67091	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
67091	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	anaerobe	93.338
125439	obligate anaerobe	98.151

Spore formation

@ref	Spore formation	Confidence
125439		99.554

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68367	catalase	-	1.11.1.6	from API 20A
68367	gelatinase	-		from API 20A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
67091	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67091	chicken cecal content, adult	Munich	Germany	DEU	Europe	48.1502	11.5856 48.1502/11.5856
67770	Cecal content of an M11-layer chicken	Munich	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN055967 (>99% sequence identity) for Eubacteriales from Microbeatlas

Aquatic Samples	30
Soil Samples	35
Animal Samples	801
Plant Samples	2
Total Samples	868

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1498280v1 assembly for Gemmiger gallinarum DSM 109015	contig	GCA_014982805	2779354.3	2910495024	2779354	74.07

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67091	Gemmiger gallinarum strain Cla-CZ-245 16S ribosomal RNA gene, partial sequence	MN055967.1	1472		2779354
67770	Gemmiger gallinarum strain Cla-CZ-245 16S ribosomal RNA gene, partial sequence	MN055967	1472		2779354

GC content

@ref	GC-content (mol%)	Method
67770	59.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1498280v1 assembly for Gemmiger gallinarum DSM 109015
BV-BRC: 2779354.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.15	no
125439	gram_stain	BacteriaNetⓘ	negative	96.35	no
125439	motility	BacteriaNetⓘ	no	60.78	no
125439	spore_formation	BacteriaNetⓘ	no	99.55	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Subdoligranulum sp. DSM 109015
PATRIC: 2779354.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	73.32	no
125438	anaerobic	anaerobicⓘ	yes	93.34	no
125438	spore-forming	spore-formingⓘ	no	57.91	no
125438	aerobic	aerobicⓘ	no	98.80	no
125438	thermophilic	thermophileⓘ	no	90.12	yes
125438	flagellated	motile2+ⓘ	no	88.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Is Intestinal Microbiota Fully Restored After Chickens Have Recovered from Coccidiosis?	Guo J, Zhao Z, Broadwater C, Tobin I, Liu J, Whitmore M, Zhang G.	Pathogens	10.3390/pathogens14010081	2025
Phylogeny	Immunoglobulin secretion influences the composition of chicken caecal microbiota.	Volf J, Kaspers B, Schusser B, Crhanova M, Karasova D, Stepanova H, Babak V, Rychlik I.	Sci Rep	10.1038/s41598-024-76856-2	2024
Metabolism	Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.	Park S, Li C, Wu X, Zhang T.	Int J Mol Sci	10.3390/ijms241713329	2023
	Changes in the intestinal microbiota of broiler chicken induced by dietary supplementation of the diatomite-bentonite mixture.	Wesierska E, Micek P, Adamski MG, Gondek K, Lis M, Trela M, Wojtysiak D, Kowal J, Wyrobisz-Papiewska A, Kunstman G, Mosiolek S, Smoron K.	BMC Vet Res	10.1186/s12917-024-04439-4	2025
	Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria.	Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S, Buhl EM, Abt B, Neuhaus K, Velge P, Overmann J, Kaspers B, Clavel T.	mSystems	10.1128/msystems.01300-20	2021

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 )
#67091	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 109015
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#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 )

Rate our new design

Content

About us

Gemmiger gallinarum (JCM 34595, DSM 109015, Cla-CZ-245)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014982805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media