Strain identifier

BacDive ID: 158714

Type strain: Yes

Species: Amnibacterium endophyticum

Strain Designation: 1T4Z-3

Strain history: <- Fei-Na Li, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

NCBI tax ID(s): 2109337 (species)

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General

@ref: 65456

BacDive-ID: 158714

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Amnibacterium endophyticum 1T4Z-3 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from a piece of branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao.

NCBI tax id

  • NCBI tax id: 2109337
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Fei-Na Li, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

doi: 10.13145/bacdive158714.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Amnibacterium
  • species: Amnibacterium endophyticum
  • full scientific name: Amnibacterium endophyticum Li et al. 2018

@ref: 65456

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Amnibacterium

species: Amnibacterium endophyticum

strain designation: 1T4Z-3

type strain: yes

Morphology

cell morphology

  • @ref: 65456
  • gram stain: positive
  • cell length: 1.0-1.5 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65456
  • colony size: 0.2-0.3 mm
  • colony color: brilliant yellow
  • colony shape: circular
  • medium used: International Streptomyces Project 2 agar

Culture and growth conditions

culture medium

@refnamegrowthcomposition
65456International Streptomyces Project agaryesl^-1 distilled water: 4.0 g glucose, 4.0 g yeast extract powder, 5.0 g malt extract powder, vitamin mixture (0.001 g vitamin B1 , 0.001 g vitamin B2 , 0.001 g vitamin B3 , 0.001 g vitamin B 6 , 0.001 g phenylalanine, 0.001 g alanine, 0.0005 g biotin), trace salt mixture (0.2 g FeSO4 7H2O, 0.1 g ZnSO4 7H2O, 0.1 g MnCl2 4H2O), 18.0 g agar, pH 7.2] supplemented with 1 % (v/v) plant tissue extract
65456International Streptomyces Project 2 agaryes
65456Trypticase soy agaryes
65456Reasoner's 2A agaryes
65456Nutrient agar (NA)yes
65456LB (Luria-Bertani) MEDIUMno
65456ISP 4 agarno
65456ISP 5 agarno

culture temp

@refgrowthtypetemperaturerange
65456positivegrowth10-35
65456positiveoptimum28-30mesophilic
67771positivegrowth28-30mesophilic

culture pH

@refabilitytypepH
65456positivegrowth6-8
65456positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65456aerobe
67771aerobe

spore formation

  • @ref: 65456
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65456NaClpositivegrowth0-4.9 %(w/v)
65456NaClpositiveoptimum0-1 %(w/v)

observation

@refobservation
65456diagnostic cellwall diamino acid is L-2,4-diaminobutyric acid
65456predominant menaquinones are MK-11 and MK-12
65456major polar lipids contain DPG, PG, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
654563-O-methyl alpha-D-glucopyranoside+builds acid from
65456amygdalin+builds acid from27613
65456arbutin+builds acid from18305
65456cellobiose+builds acid from17057
65456D-arabinose+builds acid from17108
65456D-fructose+builds acid from15824
65456D-galactose+builds acid from12936
65456D-glucose+assimilation17634
65456D-glucose+builds acid from17634
65456D-lyxose+builds acid from62318
65456D-mannitol+assimilation16899
65456D-mannitol+builds acid from16899
65456D-mannose+builds acid from16024
65456D-ribose+assimilation16988
65456D-ribose+builds acid from16988
65456D-sorbitol+assimilation17924
65456D-sorbitol+builds acid from17924
65456D-tagatose+builds acid from16443
65456D-xylose+builds acid from65327
65456galactitol+builds acid from16813
65456esculin+builds acid from4853
65456gelatin-assimilation5291
65456gentiobiose+builds acid from28066
65456glycerol+builds acid from17754
65456glycogen+builds acid from28087
65456L-arabinose+assimilation30849
65456L-arabinose+builds acid from30849
65456L-rhamnose+assimilation62345
65456L-sorbose+builds acid from17266
65456L-xylose+builds acid from65328
65456lactose+builds acid from17716
65456maltose+assimilation17306
65456maltose+builds acid from17306
65456melezitose+builds acid from6731
65456melibiose+assimilation28053
65456melibiose+builds acid from28053
65456methyl beta-D-xylopyranoside+builds acid from74863
65456milk-assimilation
65456N-acetylglucosamine+assimilation506227
65456N-acetylglucosamine+builds acid from506227
65456potassium 5-dehydro-D-gluconate+builds acid from
65456potassium gluconate+builds acid from32032
65456raffinose+builds acid from16634
65456salicin+assimilation17814
65456salicin+builds acid from17814
65456starch+builds acid from28017
65456starch+hydrolysis28017
65456sucrose+assimilation17992
65456sucrose+builds acid from17992
65456sulfide-assimilation15138
65456trehalose+builds acid from27082
65456turanose+builds acid from32528
65456tween 20-hydrolysis53424
65456tween 40+hydrolysis53423
65456tween 80-hydrolysis53426
65456xylitol+builds acid from17151

enzymes

@refvalueactivityec
65456catalase+1.11.1.6
65456cytochrome oxidase-1.9.3.1
65456alkaline phosphatase+3.1.3.1
65456esterase (C 4)+
65456esterase Lipase (C 8)+
65456leucine arylamidase+3.4.11.1
65456valine arylamidase+
65456cystine arylamidase+3.4.11.3
65456acid phosphatase+3.1.3.2
65456naphthol-AS-BI-phosphohydrolase+
65456alpha-galactosidase+3.2.1.22
65456beta-galactosidase+3.2.1.23
65456alpha-mannosidase+3.2.1.24
65456alpha-glucosidase+3.2.1.20
65456beta-glucosidase+3.2.1.21
65456lipase (C 14)+
65456trypsin+3.4.21.4
65456alpha-chymotrypsin+3.4.21.1
65456beta-glucuronidase+3.2.1.31
65456N-acetyl-beta-glucosaminidase+3.2.1.52
65456alpha-fucosidase+3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65456C16:0 iso46.6
    65456C15:0 anteiso27.3
    65456C17:0 anteiso9.6
    65456C14:0 iso5.1
    65456C16:02.6
    65456C15:0 iso1.7
    65456C20:1ω9t1.3
    65456C18:01
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • agar/liquid: agar
  • incubation temperature: 30
  • software version: Sherlock 6.2
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • instrument: Agilent 7890B
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typelatitudelongitudeenrichment culture durationenrichment culture temperatureisolation proceduregeographic locationcountryorigin.countrycontinent
65456a piece of branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao22.1397113.5522 weeks28The branch of Aegiceras corniculatum was surface-sterilized as described by Qin et al.. After drying in the hood for 2 days, the surface-sterilized branch was ground into a powder using a micromill and distributed on modified International Streptomyces Project (ISP) 2 agar medium
67771From plantMacaoChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Stem (Branch)
#Host#Plants#Tree

Sequence information

16S sequences

  • @ref: 65456
  • description: 16S rRNA gene sequence
  • accession: MG065698
  • database: nuccore

GC content

  • @ref: 65456
  • GC-content: 71.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65456

culture collection no.: KCTC 39983, CGMCC 1.16066

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29498617Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum.Li FN, Tuo L, Lee SM, Jin T, Liao S, Li W, Yan X, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0026762018Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, Primulaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny31332634Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail.Kim I, Chhetri G, Kim J, Seo TAntonie Van Leeuwenhoek10.1007/s10482-019-01302-72019Actinobacteria/*classification/genetics/*isolation & purification, Aerobiosis, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Glycolipids/analysis, Locomotion, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Setaria Plant/*microbiologyEnzymology

Reference

@idauthorstitledoi/urljournalpubmed
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
65456Fei-Na Li, Li Tuo, Simon Ming-Yuen Lee, Tao Jin, Shuilin Liao, Wenlian Li, Xinyu Yan, Cheng-Hang SunAmnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum10.1099/ijsem.0.002676IJSEM 68: 1327-1332 201829498617
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc