Paenibacillus ihumii (DSM 100664, CSUR 1981, CSUR P1981)

Name: Paenibacillus ihumii (DSM 100664, CSUR 1981, CSUR P1981)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132501

Type strain

Strain Designation AT5

Culture col. no. DSM 100664 CSUR 1981 CSUR P1981 AT5

NCBI tax ID(s) 687436

Special Collections DSMZ Cadoret human gut

Links

Paenibacillus ihumii AT5 is a mesophilic prokaryote that was isolated from human stool specimen, 33-year-old woman with morbid obesity.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 396945

DSM 100664

@ref 20215

Last LPSN update 2025-12-16 10:01:32

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus ihumii

Full scientific name Paenibacillus ihumii Togo et al. 2017

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24290	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24290	positive	growth	30	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		93
125438		92.73

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Specimen
#Host	#Human	#Female
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24290	human stool specimen, 33-year-old woman with morbid obesity	Marseille	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence LN881615 (>99% sequence identity) for Paenibacillus ihumii from Microbeatlas

Aquatic Samples	81
Soil Samples	266
Animal Samples	209
Plant Samples	96
Total Samples	652

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24290	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	Paenibacillus ihumii assembly for Paenibacillus ihumii AT5	scaffold	GCA_001403875	2775507040	687436	75.45

Genome browser: GCA_001403875

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24290	Paenibacillus sp. AT5 partial 16S rRNA gene, strain AT5	LN881615	1518		687436

GC content

@ref	GC-content (mol%)	Method
24290	50	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paenibacillus ihumii AT5
NCBI: GCA_001403875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	93.00	no
125439	motility	BacteriaNetⓘ	yes	89.00	no
125439	gram_stain	BacteriaNetⓘ	variable	86.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	88.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus ihumii AT5
NCBI: GCA_001403875.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	58.54	no
125438	anaerobic	anaerobicⓘ	no	96.23	no
125438	aerobic	aerobicⓘ	no	52.73	no
125438	spore-forming	spore-formingⓘ	yes	92.73	no
125438	thermophilic	thermophileⓘ	no	90.20	yes
125438	flagellated	motile2+ⓘ	yes	81.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Systematically investigating and identifying bacteriocins in the human gut microbiome.	Zhang D, Zou Y, Shi Y, Zhang J, Liu J, Wu G, Zhang J, Gao Y, Chen M, Li YX.	Cell Genom	10.1016/j.xgen.2025.100983	2025
Genetics	Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5.	Togo AH, Khelaifia S, Lagier JC, Caputo A, Robert C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M	New Microbes New Infect	10.1016/j.nmni.2016.01.013	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 )
#24290	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100664
#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 .
#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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Paenibacillus ihumii (DSM 100664, CSUR 1981, CSUR P1981)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001403875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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