Archive BacDiveID:10.13145/bacdive14708.20230509.8.1

Strain identifier

BacDive ID: 14708

Type strain:

Species: Lactococcus piscium

Strain Designation: HR1A-68

Strain history: DSM 6634 <-- NCFB 2778 <-- J. L. Fryer <-- R. A. Holt HR1A-68.

NCBI tax ID(s): 1364 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 2640

BacDive-ID: 14708

DSM-Number: 6634

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Lactococcus piscium HR1A-68 is an anaerobe, mesophilic bacterium that was isolated from diseased Rainbow yearling.

NCBI tax id

NCBI tax id: 1364
Matching level: species

strain history

@ref	history
2640	<- NCFB <- J.L. Fryer <- R.A. Holt, HR1A-68
67770	DSM 6634 <-- NCFB 2778 <-- J. L. Fryer <-- R. A. Holt HR1A-68.

doi: 10.13145/bacdive14708.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Bacilli
order: Lactobacillales
family: Streptococcaceae
genus: Lactococcus
species: Lactococcus piscium
full scientific name: Lactococcus piscium Williams et al. 1990

@ref: 2640

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Lactococcus

species: Lactococcus piscium

full scientific name: Lactococcus piscium Williams et al. 1990

strain designation: HR1A-68

type strain: yes

Morphology

colony morphology

@ref: 51145
incubation period: >2 days

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
2640	ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412)	yes	https://mediadive.dsmz.de/medium/412	Name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412) Composition: NaHCO3 6.0 g/l Na-acetate 5.0 g/l Glucose 4.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.255 g/l (NH4)2SO4 0.255 g/l K2HPO4 0.225 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Distilled water
2640	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	yes	https://mediadive.dsmz.de/medium/92	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
2640	positive	growth	30	mesophilic
2640	positive	growth	28	mesophilic
51145	positive	growth	25	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
2640	anaerobe
51145	aerobe

murein

@ref: 2640
murein short key: A11.05
type: A3alpha L-Lys-L-Ala₂

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
2640	diseased Rainbow yearling
51145	Trout,diseased rainbow trout
67770	Diseased yearling rainbow trout	Hood River, OR	USA	USA	North America

isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease
#Host	#Fishes	#Salmonidae

taxonmaps

@ref: 69479
File name: preview.99_3069.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_58;96_1605;97_1917;98_2358;99_3069&stattab=map
Last taxonomy: Lactococcus piscium subclade
16S sequence: LC519868
Sequence Identity:
Total samples: 24593
soil counts: 3484
aquatic counts: 4463
animal counts: 15578
plant counts: 1068

Safety information

risk assessment

@ref: 2640
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Lactococcus piscium strain CCUG 32732 16S ribosomal RNA gene, partial sequence	DQ343754	1436	ena	1364
20218	Lactococcus piscium 16S rRNA	X53905	1483	ena	1364
67770	Lactococcus piscium JCM 16647 gene for 16S rRNA, partial sequence	LC519868	1479	ena	1364

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Lactococcus piscium DSM 6634	GCA_002441695	scaffold	ncbi	1364
66792	Lactococcus piscium strain DSM 6634	1364.33	wgs	patric	1364
66792	Lactococcus piscium DSM 6634	2871629740	draft	img	1364

GC content

@ref	GC-content	method
2640	39.0	thermal denaturation, midpoint method (Tm)
67770	38.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
flagellated	no	97.408	no
gram-positive	yes	94.703	no
anaerobic	no	93.669	no
aerobic	no	97.869	no
halophile	yes	78.662	no
spore-forming	no	92.548	no
thermophile	no	99.896	yes
glucose-util	yes	88.831	no
motile	no	95.25	no
glucose-ferment	yes	90.679	no

External links

@ref: 2640

culture collection no.: DSM 6634, CIP 104371, JCM 16647, NCFB 2778, CCUG 32732, LMG 11463, JCM 11055, ATCC 700018, CCM 4494, CECT 4493, KCTC 3639, LMG 23383, NBRC 100935, NCIMB 13196

straininfo link

@ref: 83827
straininfo: 3458

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	1692000	Lactococcus piscium sp. nov. a new Lactococcus species from salmonid fish.	Williams AM, Fryer JL, Collins MD	FEMS Microbiol Lett	10.1016/0378-1097(90)90134-c	1990	Animals, Base Sequence, DNA, Bacterial/analysis, Fatty Acids/analysis, Molecular Sequence Data, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Salmonidae/microbiology, Sequence Homology, Nucleic Acid, Streptococcus/*classification/genetics	Genetics
Phylogeny	29300157	Lactococcus reticulitermitis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus.	Yuki M, Sakamoto M, Nishimura Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002549	2018	Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/microbiology, Isoptera/microbiology, Lactococcus/classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome
Phylogeny	32614762	Lactococcus insecticola sp. nov. and Lactococcus hodotermopsidis sp. nov., isolated from the gut of the wood-feeding lower termite Hodotermopsis sjostedti.	Noda S, Koyama F, Aihara C, Ikeyama N, Yuki M, Ohkuma M, Sakamoto M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004309	2020	Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/microbiology, Genes, Bacterial, Isoptera/microbiology, Lactococcus/classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wood	Transcriptome
Biotechnology	35190348	Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat.	Werum V, Ehrmann M, Vogel R, Hilgarth M	Microbiol Res	10.1016/j.micres.2022.126982	2022	Animals, Anti-Infective Agents/metabolism, Food Microbiology, Food Packaging, Lactococcus, Meat/microbiology, Phylogeny	Phylogeny

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2640	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6634)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-6634
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
51145	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 32732)	https://www.ccug.se/strain?id=32732
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
83827	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID3458.1	StrainInfo: A central database for resolving microbial strain identifiers