Exiguobacterium algae sp. nov. and Exiguobacterium qingdaonense sp. nov., two novel moderately halotolerant bacteria isolated from the coastal algae.
Algae
Comparative genomics
Core genome
Exiguobacterium
Journal
Antonie van Leeuwenhoek
ISSN: 1572-9699
Titre abrégé: Antonie Van Leeuwenhoek
Pays: Netherlands
ID NLM: 0372625
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
received:
15
02
2021
accepted:
16
05
2021
pubmed:
13
7
2021
medline:
25
8
2021
entrez:
12
7
2021
Statut:
ppublish
Résumé
Two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial strains, S126
Identifiants
pubmed: 34251527
doi: 10.1007/s10482-021-01594-8
pii: 10.1007/s10482-021-01594-8
doi:
Substances chimiques
DNA, Bacterial
0
Fatty Acids
0
Phospholipids
0
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1399-1406Subventions
Organisme : National Natural Science Foundation of China
ID : 31670002
Organisme : National Natural Science Foundation of China
ID : 31970003 and 31770003
Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
Références
Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse HJ (1996) Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47:39–52
doi: 10.1016/0168-1656(96)01376-4
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917
pubmed: 13671378
doi: 10.1139/o59-099
pmcid: 13671378
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using diamond. Nat Methods 12:59–60
pubmed: 25402007
doi: 10.1038/nmeth.3176
pmcid: 25402007
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:1–9
doi: 10.1186/1471-2105-10-421
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The carbohydrate-active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37:D233-238
pubmed: 18838391
pmcid: 18838391
doi: 10.1093/nar/gkn663
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973
pubmed: 19505945
pmcid: 19505945
doi: 10.1093/bioinformatics/btp348
Chaturvedi P, Prabahar V, Manorama R, Pindi PK, Bhadra B, Begum Z, Shivaji S (2008) Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys. Antarct Int J Syst Evol MIcrobiol 58:2447–2453
doi: 10.1099/ijs.0.2008/000067-0
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X-W, Meye SD, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466
pubmed: 29292687
doi: 10.1099/ijsem.0.002516
pmcid: 29292687
Collins MD, Lund BM, Farrow JAE, Schleifer KH (1983) Chemotaxonomic study of an alkalophilic bacterium, Exiguobacterium aurantiacum gen. nov., sp. nov. J Gen Microbiol 129:2037–2042
Crapart S, Fardeau ML, Cayol JL, Thomas P, Sery C, Ollivier B, Combet-Blanc Y (2007) Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57:287–292
pubmed: 17267965
doi: 10.1099/ijs.0.64639-0
pmcid: 17267965
Dong XZ, Cai MY (eds) (2001) Determinative manual for routine bacteriology. Scientific Press, Beijing (English translation)
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
pubmed: 390337
pmcid: 390337
doi: 10.1093/nar/gkh340
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
doi: 10.1007/BF01734359
Fitch WM (1971) Toward defining the course of evolution: minimum changes for a specific tree topology. Syst Zool 20:406–416
doi: 10.2307/2412116
Fruhling A, Schumann P, Hippe H, Straubler B, Stackebrandt E (2002) Exiguobacterium undae sp. nov. and Exiguobacterium antarcticum sp. nov. Int J Syst Evol Microbiol 52:1171–1176
pubmed: 12148624
pmcid: 12148624
Jiang X, Xue Y, Wang L, Yu B, Ma Y (2013) Genome sequence of a novel polymer-grade L-lactate-producing alkaliphile, Exiguobacterium sp. strain 8–11-1. Genome Announc 1:e00616-e713
pubmed: 23950124
pmcid: 3744680
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Mering CV, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 34:2115–2122
pubmed: 28460117
pmcid: 5850834
doi: 10.1093/molbev/msx148
Kasana RC, Pandey CB (2018) Exiguobacterium: an overview of a versatile genus with potential in industry and agriculture. Crit Rev Biotechnol 38:141–156
pubmed: 28395514
doi: 10.1080/07388551.2017.1312273
pmcid: 28395514
Kim IG, Lee MH, Jung SY, Song JJ, Oh TK, Yoon JH (2005) Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55:885–889
pubmed: 15774680
doi: 10.1099/ijs.0.63308-0
pmcid: 15774680
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
pubmed: 27004904
pmcid: 8210823
doi: 10.1093/molbev/msw054
Konstantinidis KT, Rosselló-Móra R, Amann R (2017) Uncultivated microbesin need of their own taxonomy. ISME J 11:2399–4063
pubmed: 28731467
pmcid: 5649169
doi: 10.1038/ismej.2017.113
Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103
pubmed: 26585518
doi: 10.1099/ijsem.0.000760
pmcid: 26585518
Letunic I, Bork P (2019) Interactive tree of life (iTOL) V4: recent updates and new developments. Nucleic Acids Res 47:256–259
doi: 10.1093/nar/gkz239
Liao H, Lin XL, Li YQ, Qu MM, Tian Y (2020) Reclassification of the taxonomic framework of orders Cellvibrionales, Oceanospirillales, Pseudomonadales and Alteromonadales in class Gammaproteobacteria through phylogenomic tree analysis. Msystems 15:e00543-e620
Liu H, Xin B, Zheng J, Zhong H, Yu Y, Peng D, Sun M (2021) Build a bioinformatic analysis platform and apply it to routine analysis of microbial genomics and comparative genomics. Protoc Exch. https://doi.org/10.21203/rs.2.21224/v5
doi: 10.21203/rs.2.21224/v5
Liu SW, Ye JJ, Lu QP, Cheema MT, Abbas M, Huang DL, Sajid I, Sun CH (2020) Motilibacter deserti sp. nov. and Motilibacter aurantiacus sp. nov., two novel actinobacteria isolated from soil of Cholistan Desert and emended description of the genus Motilibacter. Syst Appl Microbiol 43:126150
pubmed: 33099259
doi: 10.1016/j.syapm.2020.126150
pmcid: 33099259
Lopez-Cortes A, Schumann P, Pukall R, Stackebrandt E (2006) Exiguobacterium mexicanum sp. nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana. Syst Appl Microbiol 29:183–190
pubmed: 16564954
doi: 10.1016/j.syapm.2005.09.007
pmcid: 16564954
Margesin R, Gander S, Zacke G, Gounot AM, Schinner F (2003) Hydrocarbon degradation and enzyme activities of cold-adapted bacteria and yeasts. Extremophiles 7:451–458
pubmed: 12942349
doi: 10.1007/s00792-003-0347-2
pmcid: 12942349
Meng X, Chang YQ, Zhou LY, Du ZJ (2020) Exiguobacterium flavidum sp. nov., isolated from the Red Maple Lake. Int J Syst Evol Microbiol 70:2359–2365
pubmed: 32065575
doi: 10.1099/ijsem.0.004048
pmcid: 32065575
Mohan Kulshreshtha N, Kumar R, Begum Z, Shivaji S, Kumar A (2013) Exiguobacterium alkaliphilum sp. nov. isolated from alkaline wastewater drained sludge of a beverage factory. Int J Syst Evol Microbiol 63:4374–4379
pubmed: 23838447
doi: 10.1099/ijs.0.039123-0
pmcid: 23838447
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274
pubmed: 25371430
doi: 10.1093/molbev/msu300
pmcid: 25371430
Raichand R, Pareek S, Singh NK, Mayilraj S (2012) Exiguobacterium aquaticum sp. nov., a member of the genus Exiguobacterium. Int J Syst Evol Microbiol 62:2150–2155
pubmed: 22058319
doi: 10.1099/ijs.0.035790-0
pmcid: 22058319
Rodrigues DF, Goris J, Vishnivetskaya T, Gilichinsky D, Thomashow MF, Tiedje JM (2006) Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles 10:285–294
pubmed: 16489412
doi: 10.1007/s00792-005-0497-5
pmcid: 16489412
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101.Newark, DE: MIDI Inc
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schumann P (2011) Peptidoglycan structure. Methods Microbiol 38:101–129
doi: 10.1016/B978-0-12-387730-7.00005-X
Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
doi: 10.1016/S0580-9517(08)70474-4
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069
pubmed: 24642063
doi: 10.1093/bioinformatics/btu153
pmcid: 24642063
Singh NK, Raichand R, Kaur I, Kaur C, Pareek S, Mayilraj S (2013) Exiguobacterium himgiriensis sp. nov. a novel member of the genus Exiguobacterium, isolated from the Indian Himalayas. Antonie Van Leeuwenhoek 103:789–796
pubmed: 23229437
doi: 10.1007/s10482-012-9861-5
pmcid: 23229437
Srivastava AK, Srivastava R, Sharma A, Bharati AP, Tiwari PK, Singh AK, Srivastava AK, Chakdar H, Kashyap PL, Saxena AK (2020) Pan-genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum PHM 11. Environ Microbiol Rep 12:639–650
pubmed: 32996243
doi: 10.1111/1758-2229.12890
pmcid: 32996243
Stolz A, Busse HJ, Kämpfer P (2007) Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57:572–576
pubmed: 17329787
doi: 10.1099/ijs.0.64761-0
pmcid: 17329787
Tindall BJ (1990a) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202
doi: 10.1111/j.1574-6968.1990.tb03996.x
Tindall BJ (1990b) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130
doi: 10.1016/S0723-2020(11)80158-X
Vishnivetskaya TA, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce DC, Goodwin LA, Pitluck S, Saunders E, Brettin T, Detter C, Han C, Larimer F, Land ML, Hauser LJ, Kyrpides NC, Ovchinnikova G, Kathariou S, Ramaley RF, Rodrigues DF, Hendrix C, Richardson P, Tiedje JM (2011) Complete genome sequence of the thermophilic bacterium Exiguobacterium sp. AT1b. J Bacteriol 193:2880
pubmed: 21460088
pmcid: 3133134
doi: 10.1128/JB.00303-11
Vishnivetskaya TA, Kathariou S, Tiedje JM (2009) The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 13:541–555
pubmed: 19381755
doi: 10.1007/s00792-009-0243-5
pmcid: 19381755
Wang Q, Liu F, Zhang DC (2020) Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount. Int J Syst Evol Microbiol 70:4569–4575
pubmed: 32634089
doi: 10.1099/ijsem.0.004315
pmcid: 32634089
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
pubmed: 28005526
pmcid: 28005526
doi: 10.1099/ijsem.0.001755
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46:95–101
doi: 10.1093/nar/gky418