Strain identifier

BacDive ID: 166147

Type strain: Yes

Species: Tabrizicola sediminis

Strain Designation: DRYC-M-16

NCBI tax ID(s): 2486418 (species)

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General

@ref: 68163

BacDive-ID: 166147

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative, rod-shaped, colony-forming

description: Tabrizicola sediminis DRYC-M-16 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sludge samples from saline Dangreyongcuo Lake.

NCBI tax id

  • NCBI tax id: 2486418
  • Matching level: species

doi: 10.13145/bacdive166147.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Tabrizicola
  • species: Tabrizicola sediminis
  • full scientific name: Tabrizicola sediminis Liu et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Pseudotabrizicola sediminis

@ref: 68163

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Tabrizicola

species: Tabrizicola sediminis

strain designation: DRYC-M-16

type strain: yes

Morphology

cell morphology

  • @ref: 68163
  • gram stain: negative
  • cell length: 0.8-1.2 µm
  • cell width: 0.6-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 68163
  • colony color: pink
  • colony shape: circular
  • incubation period: 2 days
  • medium used: 2216L agar

Culture and growth conditions

culture temp

@refgrowthtypetemperature
68163positivegrowth4-35
68163positiveoptimum20-25

culture pH

@refabilitytypepHPH range
68163positivegrowth7.0-9.0alkaliphile
68163positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 68163
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
68163NaClpositivegrowth1-2 %(w/v)
68163NaClpositiveoptimum1.5 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68163casein-hydrolysis
68163esculin-hydrolysis4853
68163starch-hydrolysis28017
68163tween 20-hydrolysis53424
68163tween 80-hydrolysis53426
68163glucose-fermentation17234
68163citrate-assimilation16947
68163nitrate-reduction17632
68163gelatin-hydrolysis5291
68163esculin ferric citrate+builds acid from
68163D-xylose+/-builds acid from65327
68163D-ribose-builds acid from16988
68163potassium 5-dehydro-D-gluconate-builds acid from
68163L-arabinose-builds acid from30849
68163D-tagatose-builds acid from16443
68163D-glucose+builds acid from17634
68163maltose+/-builds acid from17306
68163potassium 2-dehydro-D-gluconate-builds acid from
68163trehalose+/-builds acid from27082
68163turanose+builds acid from32528
68163D-galactose-builds acid from12936
68163D-fructose+builds acid from15824
68163sucrose+builds acid from17992
68163cellobiose+/-builds acid from17057
68163melibiose-builds acid from28053
68163arbutin-builds acid from18305
68163D-mannose+builds acid from16024
68163salicin+/-builds acid from17814
68163lactose-builds acid from17716
68163D-mannitol-builds acid from16899
68163glycogen-builds acid from28087
68163starch+builds acid from28017
68163D-arabinose-builds acid from17108
68163melezitose-builds acid from6731
68163L-fucose+/-builds acid from18287
68163L-rhamnose-builds acid from62345
68163gentiobiose+/-builds acid from28066
68163D-sorbitol-builds acid from17924
68163D-arabitol+/-builds acid from18333
68163D-lyxose-builds acid from62318
68163D-fucose+builds acid from28847
68163glycerol-builds acid from17754
68163N-acetylglucosamine+/-builds acid from59640
68163methyl alpha-D-glucopyranoside-builds acid from320061
68163myo-inositol-builds acid from17268
68163potassium gluconate-builds acid from32032
68163methyl beta-D-xylopyranoside-builds acid from74863
68163raffinose+builds acid from16634
68163amygdalin-builds acid from27613
68163methyl alpha-D-mannoside-builds acid from43943
68163erythritol-builds acid from17113
68163L-xylose-builds acid from65328
68163ribitol-builds acid from15963
68163L-sorbose-builds acid from17266
68163galactitol-builds acid from16813
68163inulin-builds acid from15443
68163xylitol-builds acid from17151
68163L-arabitol-builds acid from18403
68163maltose+carbon source17306
68163trehalose+carbon source27082
68163cellobiose+carbon source17057
68163gentiobiose+carbon source28066
68163sucrose+carbon source17992
68163turanose+carbon source32528
68163stachyose+carbon source17164
68163raffinose+carbon source16634
68163melibiose+carbon source28053
68163D-salicin+carbon source17814
68163alpha-D-glucose+carbon source17925
68163D-mannose+carbon source16024
68163D-galactose+carbon source12936
68163L-fucose+carbon source18287
68163inosine+carbon source17596
68163D-arabitol+carbon source18333
68163myo-inositol+carbon source17268
68163glycerol+carbon source17754
68163L-alanine+carbon source16977
68163L-aspartate+carbon source29991
68163L-glutamate+carbon source29985
68163L-serine+carbon source17115
68163D-galacturonic acid+carbon source18024
68163D-galactonic acid lactone+carbon source15895
68163D-gluconate+carbon source8391
68163beta-D-glucuronic acid+carbon source28860
68163glucuronamide+carbon source32323
68163methyl pyruvate+carbon source51850
68163L-lactate+carbon source
68163citrate+carbon source16947
68163D-malate+carbon source15588
68163L-malate+carbon source15589
68163bromosuccinate+carbon source73706
68163gamma-aminobutyric acid+carbon source16865
681633-hydroxybutyrate+carbon source37054
681632-hydroxybutyrate+carbon source64552
68163propionate+carbon source17272
68163acetic acid+carbon source16411
68163formate+carbon source15740
68163dextrin-carbon source23652
68163lactose-carbon source17716
68163N-acetyl-D-glucosamine-carbon source506227
68163N-acetyl-beta-D-mannosamine-carbon source63154
68163n-acetyl-D-galactosamine-carbon source28037
68163n-acetyl-neuraminic acid-carbon source
681633-O-methyl-D-glucose-carbon source73918
68163D-fucose-carbon source28847
68163D-fructose+carbon source15824
68163L-rhamnose-carbon source62345
68163D-sorbitol-carbon source17924
68163D-mannitol-carbon source16899
68163D-glucose 6-phosphate-carbon source14314
68163D-fructose 6-phosphate-carbon source78697
68163D-aspartate-carbon source29990
68163D-serine-carbon source16523
68163gelatin-carbon source5291
68163glycyl-L-proline-carbon source70744
68163L-arginine-carbon source16467
68163L-histidine-carbon source15971
68163L-pyroglutamic acid-carbon source18183
68163pectin-carbon source17309
68163galactarate-carbon source35390
68163(-)-quinic acid-carbon source17521
68163D-saccharate-carbon source33801
681634-hydroxyphenylacetic acid-carbon source18101
68163D-lactic acid methyl ester-carbon source
68163tween 40-carbon source53423
68163acetoacetate-carbon source13705

metabolite production

@refChebi-IDmetaboliteproduction
6816316136hydrogen sulfideno
6816335581indoleno
6816315688acetoinyes

metabolite tests

  • @ref: 68163
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
68163catalase+1.11.1.6
68163cytochrome oxidase+1.9.3.1
68163DNase-
68163urease-3.5.1.5
68163phenylalanine deaminase+/-4.3.1.5
68163ornithine decarboxylase-4.1.1.17
68163lysine decarboxylase-4.1.1.18
68163arginine dihydrolase-3.5.3.6
68163alkaline phosphatase+3.1.3.1
68163esterase (C 4)+
68163esterase Lipase (C 8)+
68163leucine arylamidase+3.4.11.1
68163valine arylamidase+
68163naphthol-AS-BI-phosphohydrolase+
68163alpha-galactosidase+3.2.1.22
68163beta-galactosidase+3.2.1.23
68163alpha-glucosidase+3.2.1.20
68163beta-glucosidase+3.2.1.21
68163acid phosphatase+/-3.1.3.2
68163lipase (C 14)-
68163cystine arylamidase-3.4.11.3
68163trypsin-3.4.21.4
68163alpha-chymotrypsin-3.4.21.1
68163beta-glucuronidase-3.2.1.31
68163N-acetyl-beta-glucosaminidase-3.2.1.52
68163alpha-mannosidase-3.2.1.24
68163alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68163C10:0 3OH2.5
    68163C14:01.2
    68163C15:1 anteiso A6.8
    68163C15:0 iso3
    68163C15:0 anteiso7.5
    68163C16:05
    68163C18:0 iso15.1
    68163C18:1 w9c1.2
    68163C18:04.1
    68163C18:1 w7c 11-methyl0.4
    68163C18:0 3OH1
    68163C20:1 w7c0.5
    68163C18:1 w7c/C18:1 w6c44.9
  • type of FA analysis: whole cell analysis
  • incubation medium: 2216 broth
  • incubation temperature: 25
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • instrument: 6890 N Agilent
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

  • @ref: 68163
  • sample type: sludge samples from saline Dangreyongcuo Lake
  • geographic location: Tibet
  • country: China
  • origin.country: CHN
  • continent: Asia
  • enrichment culture: marine agar 2216
  • enrichment culture temperature: 22

taxonmaps

  • @ref: 69479
  • File name: preview.99_66307.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3953;97_4863;98_46797;99_66307&stattab=map
  • Last taxonomy: Rhodobacteraceae
  • 16S sequence: MK693145
  • Sequence Identity:
  • Total samples: 357
  • soil counts: 15
  • aquatic counts: 295
  • animal counts: 44
  • plant counts: 3

Sequence information

16S sequences

  • @ref: 68163
  • description: Tabrizicola sp. strain DRYC_M_16 16S ribosomal RNA gene, partial sequence
  • accession: MK693145
  • length: 1338
  • database: ena
  • NCBI tax ID: 2005166

Genome sequences

  • @ref: 68163
  • description: Pseudotabrizicola sediminis DRYC-M-16
  • accession: GCA_004745575
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2486418

GC content

  • @ref: 68163
  • GC-content: 63
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno69.415no
flagellatedno88.459yes
gram-positiveno98.572yes
anaerobicno97.024yes
aerobicyes85.855no
halophileno77.347yes
spore-formingno94.799no
glucose-utilyes88.104no
thermophileno98.593no
glucose-fermentno88.652no

External links

@ref: 68163

culture collection no.: CGMCC 1.13881, KCTC 72015

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny31219417Tabrizicola sediminis sp. nov., one aerobic anoxygenic photoheterotrophic bacteria from sediment of saline lake.Liu ZX, Dorji P, Liu HC, Li AH, Zhou YGInt J Syst Evol Microbiol10.1099/ijsem.0.0035422019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, *Salinity, Sequence Analysis, DNA, Tibet, Ubiquinone/chemistryTranscriptome
Phylogeny32038006Tabrizicola piscis sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Acheilognathus koreensis.Han JE, Kang W, Lee JY, Sung H, Hyun DW, Kim HS, Kim PS, Tak EJ, Jeong YS, Lee JY, Lee SY, Yun JH, Jung MJ, Shin NR, Whon TW, Kang MS, Lee KE, Lee BH, Bae JWInt J Syst Evol Microbiol10.1099/ijsem.0.0040342020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fishes/*microbiology, Fresh Water, Gastrointestinal Tract/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny35099369Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake.Szuroczki S, Abbaszade G, Boka K, Schumann P, Neumann-Schaal M, Toth EInt J Syst Evol Microbiol10.1099/ijsem.0.0052192022*Alkalies, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, *Lakes/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodobacteraceae/classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
68163Zi-Xuan Liu, Phurbu Dorji, Hong-Can Liu, Ai-Hua Li and Yu-Guang ZhouTabrizicola sediminis sp. nov., one aerobic anoxygenic photoheterotrophic bacteria from sediment of saline lake10.1099/ijsem.0.003542IJSEM 69: 2565-2570 2019
69479João 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 betahttps://microbeatlas.org/