Abstract
The genus Metakosakonia, as the closest phylogenetic neighbor of the genus Kosakonia within the family Enterobacteriaceae, when proposed in 2017, consisted of M. massiliensis JC163T and Metakosakonia spp. strains CAV1151 and GT-16. The strain CAV1151 was later classified into a novel species Phytobacter ursingii. Here, we show that the strain GT-16 shares a digital DNA-DNA hybridization (DDH) similarity of 91.0% with P. diazotrophicus DSM 17806 T and thus also belongs to P. diazotrophicus. M. massiliensis and the strains within the genus Phytobacter formed a monophyletic cluster on a phylogenomic tree based on the core proteins of the family Enterobacteriaceae and on a phylogenetic tree based on the 16S rRNA genes. M. massiliensis and the genus Phytobacter share average amino acid identities of 86.80‒87.41% above the threshold (86%) for genus delimitation within the family Enterobacteriaceae. Moreover, they share conserved signature indels in the intracellular growth protein IgaA and the outer membrane assembly protein AsmA. Therefore, we propose to unite the genus Metakosakonia and the genus Phytobacter to a single genus. Because the genus Phytobacter was validly published earlier in 2017 than the genus Metakosakonia in 2017, the genus name Phytobacter has priority over Metakosakonia. We propose to unite the two genera under the name Phytobacter with the type species P. diazotrophicus and reclassify M. massiliensis as P. massiliensis comb. nov. In addition, the analyses of genome relatedness and phylogenomic relationship identified one potential novel species within the genus Phytobacter and three potential novel species within the genus Kosakonia.
Similar content being viewed by others
References
Adeolu M, Alnajar S, Naushad S, Gupta RS (2016) Genome based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 66:5575–5599
Alnajar S, Gupta RS (2017) Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. Infect Genet Evol 54:108–127
Lagier JC, El Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PE (2013) Noncontiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci 7:399–412
Oren A, Garrity GM (2014) Validation list No. 155. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 64:1–5
Oren A, Garrity GM (2017) Validation list No. 178. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 67:4291–4293
Tetz G, Tetz V (2016) Draft genome sequence of Kluyvera intestini strain GT-16 isolated from the stomach of a patient with gastric cancer. Genome Announc 22:e01432–e1516
Sheppard AE, Stoesser N, Wilson DJ et al (2016) Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC. Antimicrob Agents Chemother 60:3767–3778
Pillonetto M, Arend LN, Faoro H, D’Espindula HR, Blom J, Smits THM, Mira MT, Rezzonico F (2018) Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov. Int J Syst Evol Microbiol 68:176–184
Zhang GX, Peng GX, Wang ET, Yan H, Yuan QH, Zhang W, Lou X, Wu H, Tan ZY (2008) Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov. Arch Microbiol 189:431–439
Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L (2019) Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol 70:841–848
Brenner DJ, McWhorter AC, Knutson JK, Steigerwalt AG (1982) Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol 15:1133–1140
Sekizuka T, Matsui M, Takahashi T, Hayashi M, Suzuki S, Tokaji A, Kuroda M (2018) Complete genome sequence of blaIMP-6-positive Metakosakonia sp MRY16–398 isolate from the ascites of a diverticulitis patient. Front Microbiol 9:2853
Wang B, Huang B, Chen J, Li W, Yang L, Yao L, Niu Q (2019) Whole-genome analysis of the colonization-resistant bacterium Phytobacter sp. SCO41T isolated from Bacillus nematocida B16-fed adult Caenorhabditis elegans. Mol Biol Rep 46:1563–1575
Weingarten RA, Johnson RC, Conlan S et al (2018) Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. MBio 9:e02011–e2017
Thele R, Gumpert H, Christensen LB, Worning P, Schønning K, Westh H, Hansen TA (2017) Draft genome sequence of a Kluyvera intermedia isolate from a patient with a pancreatic abscess. J Glob Antimicrob Resist 10:1–2
Inoue K, Sugiyama K, Kosako Y, Sakazaki R, Yamai S (2000) Enterobacter cowanii sp. nov., a new species of the family Enterobacteriaceae. Curr Microbiol 41:417–420
Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P (2013) Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 36:309–319
Dennison NJ, Saraiva RG, Cirimotich CM, Mlambo G, Mongodin EF, Dimopoulos G (2016) Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence. Malar J 15:425
Niu S, Ma W, Jin M, Chen J, Li S, Zou X (2019) Complete genome sequence of Kosakonia sp. strain CCTCC M2018092, a fucose-rich exopolysaccharide producer. Microbiol Resour Announc 8:e00567–e619
Wang D, Han CS, Dichosa AE, Gleasner CD, Johnson SL, Daligault HE, Davenport KW, Li PE, Pierson EA, Pierson LS 3rd (2014) Draft genome sequence of Enterobacter cloacae strain S611. Genome Announc 2:e00710–e714
Hardoim PR, Nazir R, Sessitsch A, Elhottová D, Korenblum E, van Overbeek LS, van Elsas JD (2013) The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice. BMC Microbiol 13:164
Li CY, Zhou YL, Ji J, Gu CT (2016) Reclassification of Enterobacter oryziphilus and Enterobacter oryzendophyticus as Kosakonia oryziphila comb. nov. and Kosakonia oryzendophytica comb. nov. Int J Syst Evol Microbiol 66:2780–2783
Ji K, Wang W, Zeng B, Chen S, Zhao Q, Chen Y, Li G, Ma T (2016) Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07. Sci Rep 6:21863
Zhu B, Zhou Q, Lin L, Hu C, Shen P, Yang L, An Q, Xie G, Li Y (2013) Enterobacter sacchari sp. nov. a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.). Int J Syst Evol Microbiol 63:2577–2582
Gu CT, Li CY, Yang LJ, Huo GC (2014) Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari. Int J Syst Evol Microbiol 64:2650–2656
Kämpfer P, McInroy JA, Doijad S, Chakraborty T, Glaeser SP (2016) Kosakonia pseudosacchari sp. nov., an endophyte of Zea mays. Syst Appl Microbiol 39:1–7
Meng X, Bertani I, Abbruscato P, Piffanelli P, Licastro D, Wang C, Venturi V (2015) Draft genome sequence of rice endophyte-associated isolate Kosakonia oryzae KO348. Genome Announc 3:e00594–e615
Madhaiyan M, Peng N, Ji L (2013) Complete genome sequence of Enterobacter sp. strain R4–368, an endophytic N-fixing gammaproteobacterium isolated from surface-sterilized roots of Jatropha curcas L. Genome Announc 1:e00544–e613
Wang C, Wu W, Wei L, Feng Y, Kang M, Xie Y, Zong Z (2019) Kosakonia quasisacchari sp. nov. recovered from human wound secretion in China. Int J Syst Evol Microbiol 69:3164–3169
Kämpfer P, Ruppel S, Remus R (2005) Enterobacter radicincitans sp. nov., a plant growth promoting species of the family Enterobacteriaceae. Syst Appl Microbiol 28:213–221
Peng G, Zhang W, Luo H, Xie H, Lai W, Tan Z (2009) Enterobacter oryzae sp. nov, a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia. Int J Syst Evol Microbiol 59:1650–1655
Bergottini VM, Filippidou S, Junier T, Johnson S, Chain PS, Otegui MB, Zapata PD, Junier P (2015) Genome sequence of Kosakonia radicincitans strain YD4, a plant growth-promoting rhizobacterium isolated from yerba mate (Ilex paraguariensis St. Hill.). Genome Announc 3:e00239–e315
Madhaiyan M, Poonguzhali S, Lee J-S, Saravanan VS, LeeSanthanakrishnan KCP (2010) Enterobacter arachidis sp. nov., a plant-growth-promoting diazotrophic bacterium isolated from rhizosphere soil of groundnut. Int J Syst Evol Microbiol 60:1559–1564
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75
Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J (2012) PGAP: pan-genomes analysis pipeline. Bioinformatics 28:416–418
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552
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
Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242–W245
Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer K-H, Glöckner FO, Rosselló-Móra R (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118
Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:e73
Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264
Rosselló-Móra R, Whitman WB (2019) Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 42:5–14
Oren A, Garrity GM (2017) Validation list No. 175. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 67:1095–1098
Parker CT, Tindall BJ, Garrity GM (2019) International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69:S1–S111
Funding
This work was supported by the National Natural Science Foundation of China (31471449), Zhejiang Provincial Natural Science Foundation of China (LY14C010002).
Author information
Authors and Affiliations
Contributions
YL and SL analyzed WGSs released before April 2017. RY and XW analyzed WGSs released before April 2018. YM analyzed WGSs released before July 2019. QA designed this work and wrote the manuscript.
Corresponding author
Ethics declarations
Conflicts of interest
The authors declare that there are no conflicts of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ma, Y., Yao, R., Li, Y. et al. Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov.. Curr Microbiol 77, 1945–1954 (2020). https://doi.org/10.1007/s00284-020-02004-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-020-02004-4