Pelorhabdus rhamnosifermentans (DSM 111565, JCM 39158, BoRhaA)

Name: Pelorhabdus rhamnosifermentans (DSM 111565, JCM 39158, BoRhaA)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 169465

Type strain

Strain Designation BoRhaA

Culture col. no. DSM 111565 JCM 39158 BoRhaA

NCBI tax ID(s) 2772457

Special Collections JCM DSMZ

History DSMZ <- B. Schink, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; BoRhaA <- F. Gräßle; {2018}

Links

Pelorhabdus rhamnosifermentans BoRhaA is a bacterium that was isolated from sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406093

JCM 39158,DSM 111565

@ref 20215

Last LPSN update 2026-05-29 08:46:37

Domain Bacteria

Phylum Bacillota

Class Negativicutes

Order Selenomonadales

Family Sporomusaceae

Genus Pelorhabdus

Species Pelorhabdus rhamnosifermentans

Full scientific name Pelorhabdus rhamnosifermentans Gräßle et al. 2022

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
68748	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503) Composition: D-Glucose 4.98504 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
68748	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	96.511
125438	anaerobe	91.785

Spore formation

@ref	Spore formation	Confidence
125439		97.805

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
68748	sediment	Upper Lake Konstanz	Germany	DEU	Europe	47.6955	9.2141 47.6955/9.2141

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1883558v1 assembly for Pelorhabdus rhamnosifermentans BoRhaA	scaffold	GCA_018835585	2772457.3	2772457	30.85

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68748	Pelorhabdus rhamnosifermentans strain BoRhaA 16S ribosomal RNA gene, partial sequence	MW010209	1477		2772457

GC content

@ref	GC-content (mol%)	Method
68748	40.8	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1883558v1 assembly for Pelorhabdus rhamnosifermentans BoRhaA
NCBI: GCA_018835585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.81	no
125439	motility	BacteriaNetⓘ	no	81.85	no
125439	gram_stain	BacteriaNetⓘ	positive	52.53	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.51	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pelorhabdus rhamnosifermentans BoRhaA
NCBI: GCA_018835585.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	84.46	no
125438	anaerobic	anaerobicⓘ	yes	91.79	no
125438	aerobic	aerobicⓘ	no	91.97	no
125438	spore-forming	spore-formingⓘ	yes	65.39	no
125438	thermophilic	thermophileⓘ	no	88.94	yes
125438	flagellated	motile2+ⓘ	yes	75.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pelorhabdus rhamnosifermentans gen. nov., sp. nov., a strictly anaerobic rhamnose degrader from freshwater lake sediment.	Grassle F, Plugge C, Franchini P, Schink B, Schleheck D, Muller N	Syst Appl Microbiol	10.1016/j.syapm.2021.126225	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 )
#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) .
#68748	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 111565
#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

Pelorhabdus rhamnosifermentans (DSM 111565, JCM 39158, BoRhaA)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_018835585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media