Strain identifier

BacDive ID: 132412

Type strain: Yes

Species: Pontibacter ummariensis

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; NKM1 <- N. Kumar Mahato

NCBI tax ID(s): 1610492 (species)

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General

@ref: 24201

BacDive-ID: 132412

DSM-Number: 100161

keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, Gram-negative, rod-shaped

description: Pontibacter ummariensis DSM 100161 is an aerobe, heterotroph, Gram-negative bacterium that was isolated from hexachlorocyclohexane contaminated soil.

NCBI tax id

  • NCBI tax id: 1610492
  • Matching level: species

strain history

  • @ref: 24201
  • history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; NKM1 <- N. Kumar Mahato

doi: 10.13145/bacdive132412.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Pontibacter
  • species: Pontibacter ummariensis
  • full scientific name: Pontibacter ummariensis Mahato et al. 2016

@ref: 24201

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Pontibacter

species: Pontibacter ummariensis

full scientific name: Pontibacter ummariensis Mahato et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 44034
  • gram stain: negative
  • cell length: 0.8-1.7 µm
  • cell width: 0.5-1.0 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 44034
  • colony color: pinkish red
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowth
44034LB (Luria-Bertani) MEDIUMyes
44034Marine agar (MA)yes
44034Nutrient agar (NA)yes
44034tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
44034positivegrowth25-45
44034positiveoptimum28mesophilic

culture pH

  • @ref: 44034
  • ability: positive
  • type: optimum
  • pH: 8.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 44034
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 44034
  • type: heterotroph

halophily

  • @ref: 44034
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4403416947citrate-assimilation
4403417113erythritol-assimilation
4403417368hypoxanthine-assimilation
4403415963ribitol-growth
4403417108D-arabinose-growth
4403415824D-fructose-growth
4403412936D-galactose-growth
4403416988D-ribose-growth
4403465327D-xylose-growth
4403416813galactitol-growth
4403417754glycerol-growth
4403428087glycogen-growth
4403417268myo-inositol-growth
4403430849L-arabinose-growth
4403462345L-rhamnose-growth
4403417266L-sorbose-growth
4403465328L-xylose-growth
4403474863methyl beta-D-xylopyranoside-growth
44034506227N-acetylglucosamine-growth
440345291gelatin-hydrolysis
4403453426tween 80-hydrolysis
4403416199urea-hydrolysis
4403417128adipate-oxidation
4403427689decanoate-oxidation
4403425115malate-oxidation
44034506227N-acetylglucosamine-oxidation
4403418401phenylacetate-oxidation
4403432032potassium gluconate-oxidation
4403453258sodium citrate-oxidation
4403417632nitrate-reduction
4403427613amygdalin+assimilation
4403418305arbutin+assimilation
4403417814salicin+assimilation
4403428017starch+assimilation
4403415318xanthine+assimilation
4403417057cellobiose+builds acid from
4403417634D-glucose+builds acid from
4403416899D-mannitol+builds acid from
4403416024D-mannose+builds acid from
4403428066gentiobiose+builds acid from
4403430849L-arabinose+builds acid from
4403417716lactose+builds acid from
4403417306maltose+builds acid from
4403428053melibiose+builds acid from
4403416634raffinose+builds acid from
4403417992sucrose+builds acid from
4403427082trehalose+builds acid from
4403430911sorbitol+fermentation
440344853esculin+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
44034100241ciprofloxacinyesyes5 µg (disc)
4403428077rifampicinyesyes5 µg (disc)
4403418208penicillin gyesyes10 µg (disc)
4403417833gentamicinyesyes10 µg (disc)
4403427902tetracyclineyesyes30 µg (disc)
4403427701oxytetracyclineyesyes30 µg (disc)
4403417698chloramphenicolyesyes30 µg (disc)
44034100147nalidixic acidyesyes30 µg (disc)
4403428001vancomycinyesyes30 µg (disc)
440348309polymyxin byesyes30 µg (disc)
440346104kanamycinyesyes30 µg (disc)
4403428971ampicillinyesyes10 µg (disc)
440342637amikacinyesyes30 µg (disc)

metabolite production

  • @ref: 44034
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44034catalase+1.11.1.6
44034cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    4403410-methyl C16:0 / iso-C17:1ω9c0.42
    44034C15:0 anteiso30.72
    44034C17:0 anteiso5.26
    44034C13:0 3-OH / iso-C15:1H0.55
    44034C14:01.75
    44034C16:011.07
    44034C16:1ω7c / C16:1ω6c5.66
    44034C17:1ω8c1.24
    44034C18:1ω6c / C18:1ω7c0.35
    44034C18:1ω9c10.39
    44034C15:0 iso19.76
    44034C16:0 iso2.15
    44034C17:0 iso1.38
    44034iso-C17:1B / iso-C17:1I0.83
  • type of FA analysis: whole cell analysis
  • incubation medium: trypticase soy agar
  • incubation time: 1
  • library/peak naming table: TSBA60
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
24201hexachlorocyclohexane contaminated soilUttar Pradesh, Lucknow, Ummari village (27° 0' 24.264'' N 81° 8' 57.588'' E)IndiaINDAsia27.006781.1493
44034soil sample contaminated with hexachlorocyclohexaneUmmari village, Lucknow, Uttar PradeshIndiaINDAsia27.006781.14932014-06-29LB agarwith nystatin (20 mg/ml) and streptomycin (10 mg/ml)48 hours28serially diluted with sterile 0.9 % NaCl

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_23328.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_1325;97_14246;98_17581;99_23328&stattab=map
  • Last taxonomy: Pontibacter ummariensis subclade
  • 16S sequence: KP265297
  • Sequence Identity:
  • Total samples: 39
  • soil counts: 25
  • aquatic counts: 11
  • animal counts: 1
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 24201
  • description: Pontibacter ummariensis strain NKM1 16S ribosomal RNA gene, partial sequence
  • accession: KP265297
  • length: 1441
  • database: ena
  • NCBI tax ID: 1610492

Genome sequences

  • @ref: 66792
  • description: Pontibacter ummariensis DSM 100161
  • accession: 2728369279
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1610492

GC content

@refGC-contentmethod
4403458.6Thermal denaturation, fluorometry
2420158.6fluorimetric

External links

@ref: 24201

culture collection no.: DSM 100161, KCTC 42944, MCC 2777, NKM 1

literature

  • topic: Phylogeny
  • Pubmed-ID: 26652923
  • title: Pontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil.
  • authors: Mahato NK, Tripathi C, Nayyar N, Singh AK, Lal R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000840
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24201Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100161Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100161)
44034N. K. Mahato, C. Tripathi, N. Nayyar, A. K. Singh and R. LalPontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil10.1099/ijsem.0.000840IJSEM 66: 1080-1087 201626652923
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/