Paenibacillus abyssi (DSM 26238, CGMCC 1.12987, SCSIO N0306)

Name: Paenibacillus abyssi (DSM 26238, CGMCC 1.12987, SCSIO N0306)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130515

Type strain

Culture col. no. DSM 26238 CGMCC 1.12987 SCSIO N0306

NCBI tax ID(s) 1340531

Special Collections DSMZ

History <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO N0306 <- X.-P. Tian and X.-F. Huang

Links

Paenibacillus abyssi DSM 26238 is a bacterium that was isolated from abyssal sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407547

DSM 26238

@ref 20215

Last LPSN update 2026-02-09 11:31:14

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus abyssi

Full scientific name Paenibacillus abyssi Huang et al. 2015

Morphology

Cell morphology

@ref	Motility	Confidence
125439		90.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21717	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21717	positive	growth	28

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		94.1
125438		94.137

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
21717	abyssal sediment	(10.0575°N; 82.985°E) at a depth of 3636 m	10.0575	82.985 10.0575/82.985

Taxonmaps

69479

Global distribution of 16S sequence KC978082 (>99% sequence identity) for Paenibacillus abyssi subclade from Microbeatlas

Aquatic Samples	47
Soil Samples	345
Animal Samples	41
Plant Samples	13
Total Samples	446

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21717	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4264738v1 assembly for Paenibacillus abyssi CGMCC 1.12987	contig	GCA_042647385			1340531	74.17
66792	ASM1464029v1 assembly for Paenibacillus abyssi CGMCC 1.12987	contig	GCA_014640295	1340531.3	2996646784	1340531	68.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21717	Paenibacillus abyssi strain SCSIO N0306 16S ribosomal RNA gene, partial sequence	KC978082	1453		1340531

GC content

@ref	GC-content (mol%)	Method
21717	45.5	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: Paenibacillus abyssi CGMCC 1.12987
NCBI: GCA_014640295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	94.10	no
125439	motility	BacteriaNetⓘ	yes	90.10	no
125439	gram_stain	BacteriaNetⓘ	variable	88.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	79.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus abyssi strain CGMCC 1.12987
PATRIC: 1340531.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	66.66	no
125438	anaerobic	anaerobicⓘ	no	91.31	no
125438	spore-forming	spore-formingⓘ	yes	94.14	no
125438	aerobic	aerobicⓘ	yes	75.87	no
125438	thermophilic	thermophileⓘ	no	86.51	no
125438	flagellated	motile2+ⓘ	yes	85.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Marinicrinis lubricantis sp. nov., isolated from a coolant lubricant.	Kampfer P, Busse HJ, Glaeser SP.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002603	2018
Phylogeny	Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean.	Huang XF, Wang FZ, Zhang W, Li J, Ling J, Yang J, Dong JD, Tian XP	Antonie Van Leeuwenhoek	10.1007/s10482-014-0277-2	2014

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 )
#21717	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26238
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 abyssi (DSM 26238, CGMCC 1.12987, SCSIO N0306)

Name and taxonomic classification

Morphology

Cell 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_042647385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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