Strain identifier
BacDive ID: 159777
Type strain:
Species: Mangrovicoccus ximenensis
Strain Designation: T1lg56
Strain history: <- Zhiliang Yu, Zhejiang Univ. of Technology
NCBI tax ID(s): 1911570 (species)
General
@ref: 66566
BacDive-ID: 159777
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped, colony-forming
description: Mangrovicoccus ximenensis T1lg56 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from the surface sediment sample of Ximen island mangrove forest.
NCBI tax id
- NCBI tax id: 1911570
- Matching level: species
strain history
- @ref: 67771
- history: <- Zhiliang Yu, Zhejiang Univ. of Technology
doi: 10.13145/bacdive159777.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Mangrovicoccus
- species: Mangrovicoccus ximenensis
- full scientific name: Mangrovicoccus ximenensis Yu et al. 2018
@ref: 66566
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Mangrovicoccus
species: Mangrovicoccus ximenensis
strain designation: T1lg56
type strain: yes
Morphology
cell morphology
- @ref: 66566
- gram stain: negative
- cell length: 0.7-1.1 µm
- cell shape: coccus-shaped
colony morphology
- @ref: 66566
- colony color: beige
- colony shape: circular
- medium used: Marine agar (MA)
Culture and growth conditions
culture medium
- @ref: 66566
- name: Marine agar (MA)
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
66566 | positive | optimum | 35 | mesophilic |
66566 | positive | growth | 18-42 | |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
66566 | positive | optimum | 6.5 | |
66566 | positive | growth | 6-9.5 | alkaliphile |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
66566 | NaCl | positive | growth | 0-15 %(w/v) |
66566 | NaCl | positive | growth | 2-5 %(w/v) |
observation
@ref | observation |
---|---|
66566 | divide through binary fission |
66566 | major respiratory quinone is Q-10 |
66566 | major polar lipids are PE, PG, DPG and PME |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
66566 | 8391 | D-gluconate | + | assimilation |
66566 | 12936 | D-galactose | + | assimilation |
66566 | 13705 | acetoacetate | + | assimilation |
66566 | 15588 | D-malate | + | assimilation |
66566 | 15589 | L-malate | + | assimilation |
66566 | 15740 | formate | + | assimilation |
66566 | 15748 | D-glucuronate | + | assimilation |
66566 | 15824 | D-fructose | + | assimilation |
66566 | 15971 | L-histidine | + | assimilation |
66566 | 15978 | glycerol 3-phosphate | + | assimilation |
66566 | 16024 | D-mannose | + | assimilation |
66566 | 16411 | acetic acid | + | assimilation |
66566 | 16651 | (S)-lactate | + | assimilation |
66566 | 16899 | D-mannitol | + | assimilation |
66566 | 17115 | L-serine | + | assimilation |
66566 | 17128 | adipate | + | assimilation |
66566 | 17164 | stachyose | + | assimilation |
66566 | 17268 | myo-inositol | + | assimilation |
66566 | 17306 | maltose | + | assimilation |
66566 | 17464 | L-galactonic acid gamma-lactone | + | assimilation |
66566 | 17634 | D-glucose | + | assimilation |
66566 | 17924 | D-sorbitol | + | assimilation |
66566 | 17925 | alpha-D-glucose | + | assimilation |
66566 | 17992 | sucrose | + | assimilation |
66566 | 18024 | D-galacturonic acid | + | assimilation |
66566 | 18333 | D-arabitol | + | assimilation |
66566 | 18401 | phenylacetate | + | assimilation |
66566 | 25115 | malate | + | assimilation |
66566 | 26490 | quinate | + | assimilation |
66566 | 27689 | decanoate | + | assimilation |
66566 | 28053 | melibiose | + | assimilation |
66566 | 28847 | D-fucose | + | assimilation |
66566 | 29985 | L-glutamate | + | assimilation |
66566 | 29991 | L-aspartate | + | assimilation |
66566 | 30612 | D-glucarate | + | assimilation |
66566 | 30849 | L-arabinose | + | assimilation |
66566 | 32032 | potassium gluconate | + | assimilation |
66566 | 32323 | glucuronamide | + | assimilation |
66566 | 51850 | methyl pyruvate | + | assimilation |
66566 | 53071 | L-galactonate | + | assimilation |
66566 | 53258 | sodium citrate | + | assimilation |
66566 | 59640 | N-acetylglucosamine | + | assimilation |
66566 | 62345 | L-rhamnose | + | assimilation |
66566 | 64552 | 2-hydroxybutyrate | + | assimilation |
66566 | 70744 | glycine-proline | + | assimilation |
66566 | 73706 | bromosuccinate | + | assimilation |
66566 | 78697 | D-fructose 6-phosphate | + | assimilation |
66566 | alpha-hydroxybutyrate | + | assimilation | |
66566 | L-alanine 4-nitroanilide | + | assimilation | |
66566 | 27082 | trehalose | - | builds acid from |
66566 | 28017 | starch | - | builds acid from |
66566 | 12936 | D-galactose | + | builds acid from |
66566 | 17306 | maltose | + | builds acid from |
66566 | 17716 | lactose | + | builds acid from |
66566 | 17992 | sucrose | + | builds acid from |
66566 | 16899 | D-mannitol | + | fermentation |
66566 | 17234 | glucose | + | fermentation |
66566 | 17268 | myo-inositol | + | fermentation |
66566 | 17634 | D-glucose | + | fermentation |
66566 | 17924 | D-sorbitol | + | fermentation |
66566 | 17992 | sucrose | + | fermentation |
66566 | 27613 | amygdalin | + | fermentation |
66566 | 28053 | melibiose | + | fermentation |
66566 | 30849 | L-arabinose | + | fermentation |
66566 | 62345 | L-rhamnose | + | fermentation |
66566 | 4853 | esculin | + | hydrolysis |
66566 | 17632 | nitrate | - | reduction |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. | is sensitive | sensitivity conc. |
---|---|---|---|---|---|---|---|
66566 | 6472 | lincomycin | yes | yes | 2 µg | ||
66566 | 100147 | nalidixic acid | yes | yes | 30 µg | ||
66566 | 2676 | amoxicillin | yes | yes | 20 µg | ||
66566 | 28971 | ampicillin | yes | yes | 10 µg | ||
66566 | 3393 | carbenicillin | yes | yes | 100 µg (disc) | ||
66566 | 3534 | cephalexin | yes | yes | 30 µg (disc) | ||
66566 | 8309 | polymyxin b | yes | yes | 300 Unit | ||
66566 | 474053 | cefazolin | yes | yes | 30 µg (disc) | ||
66566 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
66566 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
66566 | 7507 | neomycin | yes | yes | 30 µg (disc) | ||
66566 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
66566 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
66566 | 28001 | vancomycin | yes | yes | 30 µg (disc) | ||
66566 | 18208 | penicillin g | yes | yes | 10 µg (disc) | ||
66566 | 28077 | rifampicin | yes | yes | 5 µg (disc) | ||
66566 | 7731 | ofloxacin | yes | yes | 5 µg (disc) | ||
66566 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
66566 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
66566 | 7809 | oxacillin | yes | yes | 30 µg (disc) |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
66566 | 15688 | acetoin | yes |
66566 | 35581 | indole | yes |
66566 | 16136 | hydrogen sulfide | no |
66566 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
66566 | alpha-chymotrypsin | - | 3.4.21.1 |
66566 | alpha-fucosidase | - | 3.2.1.51 |
66566 | alpha-galactosidase | - | 3.2.1.22 |
66566 | alpha-glucosidase | - | 3.2.1.20 |
66566 | alpha-mannosidase | - | 3.2.1.24 |
66566 | arginine dihydrolase | - | 3.5.3.6 |
66566 | beta-galactosidase | - | 3.2.1.23 |
66566 | beta-glucosidase | - | 3.2.1.21 |
66566 | beta-glucuronidase | - | 3.2.1.31 |
66566 | gelatinase | - | |
66566 | lysine decarboxylase | - | 4.1.1.18 |
66566 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
66566 | ornithine decarboxylase | - | 4.1.1.17 |
66566 | trypsin | - | 3.4.21.4 |
66566 | 2-nitrophenyl beta-D-galactopyranoside | + | 3.2.1.52 |
66566 | acid phosphatase | + | 3.1.3.2 |
66566 | alkaline phosphatase | + | 3.1.3.1 |
66566 | catalase | + | 1.11.1.6 |
66566 | cystine arylamidase | + | 3.4.11.3 |
66566 | cytochrome oxidase | + | 1.9.3.1 |
66566 | esterase (C 4) | + | |
66566 | esterase Lipase (C 8) | + | |
66566 | leucine arylamidase | + | 3.4.11.1 |
66566 | lipase (C 14) | + | |
66566 | naphthol-AS-BI-phosphohydrolase | + | |
66566 | tryptophan deaminase | + | 4.1.99.1 |
66566 | urease | + | 3.5.1.5 |
66566 | valine arylamidase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | isolation procedure |
---|---|---|---|---|---|
66566 | the surface sediment sample (10 cm depth) of Ximen island mangrove forest | China | CHN | Asia | The marine sediment sample was serially diluted with artificial seawater (ASW; 3 % sea salts), spread on marine agar 2216 (MA; Difco) |
67771 | From sediment sample, Xiamen island mangrove forest | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Mangrove |
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_14957.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_5364;97_9230;98_11320;99_14957&stattab=map
- Last taxonomy: Mangrovicoccus ximenensis subclade
- 16S sequence: KY012060
- Sequence Identity:
- Total samples: 2062
- soil counts: 326
- aquatic counts: 1388
- animal counts: 270
- plant counts: 78
Sequence information
16S sequences
- @ref: 66566
- description: Myxococcus sp. T1lg56 16S ribosomal RNA gene, partial sequence
- accession: KY012060
- length: 1368
- database: ena
- NCBI tax ID: 1911570
Genome sequences
- @ref: 66792
- description: Mangrovicoccus ximenensis T1lg56
- accession: GCA_003056725
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1911570
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 89.571 | no |
gram-positive | no | 97.711 | yes |
anaerobic | no | 95.901 | yes |
halophile | yes | 58.908 | no |
spore-forming | no | 96.723 | no |
glucose-util | yes | 90.75 | yes |
aerobic | yes | 91.495 | yes |
thermophile | no | 98.557 | yes |
motile | no | 58.633 | no |
glucose-ferment | no | 82.471 | yes |
External links
@ref: 66566
culture collection no.: CCTCC AB 2016238, KCTC 52623
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29767617 | Mangrovicoccus ximenensis gen. nov., sp. nov., isolated from mangrove forest sediment. | Yu Z, Cao Y, Zhou G, Yin J, Qiu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002796 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *Wetlands | Transcriptome |
Phylogeny | 34662266 | Mangrovicoccus algicola sp. nov., an alginate lyase - producing marine bacterium. | Shi L, Mo K, Bao S, Wu Q, Xue C, Huang H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004844 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phaeophyta/*microbiology, Phospholipids, *Phylogeny, *Polysaccharide-Lyases, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/enzymology/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Enzymology |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
66566 | Zhiliang Yu, Yang Cao, Guoqiang Zhou, Jianhua Yin, Juanping Qiu | Mangrovicoccus ximenensis gen. nov., sp. nov., isolated from mangrove forest sediment | 10.1099/ijsem.0.002796 | IJSEM 68: 2172-2177 2018 | 29767617 |
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) | https://diaspora-project.de/progress.html#genomes | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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 | https://microbeatlas.org/ |