unclassified bacterium (DSM 11001, LD64)

Name: unclassified bacterium (DSM 11001, LD64)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2511

Type strain

Strain Designation LD64

Culture col. no. DSM 11001 LD64

NCBI tax ID(s) 1869227

Special Collections DSMZ

History DSMZ <- N. O. van Gylswyk, Swedish Univ. Agric. Sci., Uppsala, Sweden; LD64 (Sarcina sp.) <- N. O. van Gylswyk {1991}

unclassified bacterium LD64 is an anaerobe prokaryote that was isolated from cow rumen, grass-silage diet.

anaerobe genome sequence 16S sequence

Name and taxonomic classification

Culture Collection Numbers

DSM 11001 LD64

@ref 4155

Phylum Not assigned to order

Class Not assigned to order

Order Clostridiales

Family Not assigned to family

Genus unclassified

Species unclassified bacterium

Full scientific name unclassified bacterium

Strain designation LD64

Type strain no

BacDive ID	Other strains from unclassified bacterium (64)	Type strain
174674	u. bacterium KA00274, DSM 112988 (type strain)
174675	u. bacterium UPII 610-J, DSM 112989 (type strain)
23365	u. bacterium SIO, DSM 2170, ATCC 19263, CCM 326, NCMB ...
23366	u. bacterium 008-523, DSM 3039
23368	u. bacterium Re10, DSM 4661
23369	u. bacterium Wo021, DSM 5672
23370	u. bacterium KN032, DSM 5673
23371	u. bacterium US2, DSM 5848
23374	u. bacterium FlGlyM, DSM 6945
23376	u. bacterium 16AV, DSM 8385
23378	u. bacterium Ia3, DSM 10066
23379	u. bacterium LFR, DSM 10174, ATCC 51258
23386	u. bacterium mXyS1, DSM 12567
23387	u. bacterium PB90-2, DSM 12558
23389	u. bacterium XB90, DSM 12595
23390	u. bacterium 72Chol, DSM 12783
23392	u. bacterium NapHS2, DSM 14454
23394	u. bacterium EbS7, DSM 15769
23395	u. bacterium MLMS-1, DSM 17814
23396	u. bacterium 95, DSM 30001, ATCC 19103, IAM 1433
24688	u. bacterium EL-44, DSM 11444
24711	u. bacterium agV6, DSM 13281
24712	u. bacterium AZD10A1, DSM 17878, CCUG 52015
24713	u. bacterium AP57, DSM 18372, CECT 7177
130784	u. bacterium CH 1359, DSM 12902
130785	u. bacterium DSM 14861, HEL Hel43, HEL 43
130786	u. bacterium JWIYJL-CPRB 1, JW/YJL-CPRB1, DSM 17738
130792	u. bacterium G.Slu-02, DSM 21096
130793	u. bacterium L-1031, DSM 22395
130970	u. bacterium CHL6 7, DSM 10147
130971	u. bacterium CHL6 8, DSM 10148
132009	u. bacterium DSM 17195, Jamm 0065
132016	u. bacterium FSW06-301, DSM 27188
132022	u. bacterium SB2, CSURP1926, DSM 100743, CSUR P1926
132029	u. bacterium P2414, CSURP2414, DSM 102218, CSUR P2414
132035	u. bacterium CSURP2434, DSM 102883, CSUR P2434, Marseille-2434
132037	u. bacterium LC8, DSM 103728
139746	u. bacterium CB Cb502, CB 502, DSM 53758
139748	u. bacterium FGR15-07, DSM 26766, KACC 15970
139749	u. bacterium DSM 27371, WR 21
139751	u. bacterium UV 2.5, DSM 100784
139754	u. bacterium 2-bin, DSM 105719, KCTC 32235, CFCC 10925
157746	u. bacterium RS22 G, DSM 23554
157753	u. bacterium HV4-6-A5C, DSM 104144
157759	u. bacterium f-CSY, f_CSY, DSM 107475
157760	u. bacterium f-RGN, f_RGN, DSM 107527
157766	u. bacterium H2-39, H2_39, DSM 108347
159078	u. bacterium DSM 23666, CAT 12a
159091	u. bacterium HV4-5-C5C, DSM 103941
159093	u. bacterium H3_16, DSM 108225
160193	u. bacterium KNH, DSM 24760
169308	u. bacterium D16, 4/1/38B, DSM 27791, BEI HM-79
169310	u. bacterium 7D4C2, DSM 110548
169311	u. bacterium NM08_P-01, NM08, P-01, DSM 110563
174669	u. bacterium ING2-ESF, DSM 28740
174670	u. bacterium F4-6, DSM 29277
174671	u. bacterium MO-YS, DSM 29925
174672	u. bacterium CSURP1934, Mt11, DSM 100589, CSUR P1934
174676	u. bacterium NC2008, DSM 116427
174677	u. bacterium KH1P17, DSM 116970
174678	u. bacterium MA2020, DSM 116971
176606	u. bacterium AN20T, DSM 111154, CCM 9041
176607	u. bacterium AN421T, DSM 111155, CCM 9040
176608	u. bacterium AN502, DSM 111156

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4155	SUCCINICLASTICUM MEDIUM (DSMZ Medium 666)		Medium recipe at MediaDive	Name: SUCCINICLASTICUM MEDIUM (DSMZ Medium 666; with strain-specific modifications) Composition: NaHCO3 6.4 g/l NaCl 0.45 g/l (NH4)2SO4 0.45 g/l Na2S x 9 H2O 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l KH2PO4 0.23 g/l K2HPO4 0.23 g/l MgSO4 x 7 H2O 0.09 g/l CaCl2 x 2 H2O 0.06 g/l Indigocarmine 0.005 g/l Rumen fluid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4155	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4155	anaerobe
125439	anaerobe	94.097

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4155	cow rumen, grass-silage diet	Sweden	SWE	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN336244 (>99% sequence identity) for Lachnospiraceae from Microbeatlas

Aquatic Samples	178
Soil Samples	432
Animal Samples	5606
Plant Samples	218
Total Samples	6434

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2608642105 annotated assembly for Sarcina sp. DSM 11001	scaffold	GCA_900101015	1798184.3	2608642105	1798184	51.82
66792	RUG30296 assembly for Sarcina sp. DSM 11001	contig	GCA_905235985	1798184.6		1798184	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4155	Bacterium strain DSM _11001 16S ribosomal RNA gene, partial sequence	MN336244	1518		1869227

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2608642105 annotated assembly for Sarcina sp. DSM 11001
NCBI: GCA_900101015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	94.10	no
125439	gram_stain	BacteriaNetⓘ	variable	51.31	no
125439	motility	BacteriaNetⓘ	no	74.40	no
125439	spore_formation	BacteriaNetⓘ	no	83.39	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sarcina sp. DSM 11001 DSM 11001
NCBI: GCA_900101015.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.12	no
125438	anaerobic	anaerobicⓘ	yes	85.67	no
125438	aerobic	aerobicⓘ	no	90.80	yes
125438	spore-forming	spore-formingⓘ	no	59.16	no
125438	thermophilic	thermophileⓘ	no	85.97	yes
125438	flagellated	motile2+ⓘ	no	76.75	no

Literature

References

#4155	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11001
#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 .

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