{{Short description|Genus of bacteria}} {{Italic title}} {{Automatic_taxobox | image = Phytobacter diazotrophicus.jpg | image_caption = Colonies of ''P. diazotrophicus'' on MacConkey agar. | taxon = Phytobacter | authority = Zhang ''et al.'' 2008 | type_species = ''Phytobacter diazotrophicus'' | subdivision_ranks = Species | subdivision = ''P. diazotrophicus'' <br/> ''P. ursingii''<br/> ''P. palmae'' <br/> ''P. cepae'' <br/> ''P. massiliensis'' }}
'''''Phytobacter''''' is a genus of Gram-negative bacteria emerging from the grouping of isolates previously assigned to various genera of the family Enterobacteriaceae. This genus was first established on the basis of nitrogen fixing isolates from wild rice in China,<ref name=":0">{{Cite journal|title = Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov.|journal = Archives of Microbiology|date = May 2008|pmid = 18060384|pages = 431–439|volume = 189|issue = 5|doi = 10.1007/s00203-007-0333-7|first1 = Guo Xia|last1 = Zhang|first2 = Gui Xiang|last2 = Peng|first3 = En Tao|last3 = Wang|first4 = Hui|last4 = Yan|first5 = Qing Hua|last5 = Yuan|first6 = Wu|last6 = Zhang|first7 = Xu|last7 = Lou|first8 = Hui|last8 = Wu|first9 = Zhi Yuan |last9 =Tan|s2cid = 27236264}}</ref> but also includes a number of isolates obtained during a 2013 multi-state sepsis outbreak in Brazil<ref name=":1">{{Cite journal|title = Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.|journal = International Journal of Systematic and Evolutionary Microbiology|date = 2017-11-10|pmid = 29125457|pages = 176–184|volume = [Epub ahead of print]|issue = 1|doi = 10.1099/ijsem.0.002477|first1 = Marcelo|last1 = Pillonetto|first2 = Lavinia N.|last2 = Arend|first3 = Helisson|last3 = Faoro|first4 = Helena R.S.|last4 = D’Espindula|first5 = Jochen|last5 = Blom|first6 = Theo H.M.|last6 = Smits|first7 = Marcelo T.|last7 = Mira|first8 = Fabio|last8 = Rezzonico|doi-access = free}}</ref><ref>{{Cite journal|last1=Pillonetto|first1=Marcelo|last2=Arend|first2=Lavinia|last3=Gomes|first3=Suzie M. T.|last4=Oliveira|first4=Marluce A. A.|last5=Timm|first5=Loeci N.|last6=Martins|first6=Andreza F.|last7=Barth|first7=Afonso L.|last8=Mazzetti|first8=Alana|last9=Hersemann|first9=Lena|last10=Smits|first10=Theo H. M.|last11=Mira|first11=Marcelo T.|date=2018-08-13|title=Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil|journal=BMC Infectious Diseases|volume=18|issue=1|pages=397|doi=10.1186/s12879-018-3287-2|issn=1471-2334|pmc=6090600|pmid=30103698 |doi-access=free }}</ref> and, retrospectively, several clinical strains isolated in the 1970s in the United States that are still available in culture collections, which originally were grouped into Brenner's Biotype XII of the ''Erwinia herbicola''-''Enterobacter agglomerans''-Complex (EEC).<ref name=":2">{{Cite journal|last1=Rezzonico|first1=Fabio|last2=Smits|first2=Theo HM|last3=Montesinos|first3=Emilio|last4=Frey|first4=Jürg E.|last5=Duffy|first5=Brion|date=2009-01-01|title=Genotypic comparison of Pantoea agglomerans plant and clinical strains|journal=BMC Microbiology|volume=9|pages=204|doi=10.1186/1471-2180-9-204|issn=1471-2180|pmc=2764716|pmid=19772624 |doi-access=free }}</ref><ref>{{Cite journal|last1=Brenner|first1=Don J.|last2=Fanning|first2=G. Richard|last3=Leete Knutson|first3=Jean K.|last4=Steigerwalt|first4=Arnold G.|last5=Krichevsky|first5=Micah I.|date=1984|title=Attempts to Classify Herbicola Group-Enterobacter agglomerans Strains by Deoxyribonucleic Acid Hybridization and Phenotypic Tests|journal=International Journal of Systematic and Evolutionary Microbiology|volume=34|issue=1|pages=45–55|doi=10.1099/00207713-34-1-45|issn=1466-5026|doi-access=free}}</ref> Standard biochemical evaluation panels are lacking ''Phytobacter'' spp. from their database, thus often leading to misidentifications with other Enterobacterales species, especially ''Pantoea agglomerans''.<ref name=":1" /> Clinical isolates of the species have been identified as an important source of extended-spectrum β-lactamase and carbapenem-resistance genes, which are usually mediated by genetic mobile elements. Strong protection of co-infecting sensitive bacteria has also been reported.<ref>{{Cite journal|last1=Zhang|first1=Zhao|last2=Li|first2=Daixi|last3=Shi|first3=Xing|last4=Zhai|first4=Yao|last5=Guo|first5=Yatao|last6=Zheng|first6=Yali|last7=Zhao|first7=Lili|last8=He|first8=Yukun|last9=Chen|first9=Yusheng|last10=Wang|first10=Zhanwei|last11=Su|first11=Jianrong|date=2020-04-15|title=Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient|journal=BMC Genomics|volume=21|issue=1|pages=297|doi=10.1186/s12864-020-6720-z|issn=1471-2164|pmc=7156906|pmid=32293254 |doi-access=free }}</ref> Bacteria belonging to this genus are not pigmented, chemoorganotrophic and able to fix nitrogen. They are lactose fermenting, cytochrome-oxidase negative and catalase positive. Glucose is fermented with the production of gas. Colonies growing on MacConkey agar (MAC) are circular, convex and smooth with non-entire margins and a usually elevated center. Five species are currently validly included in the genus ''Phytobacter,''<ref name=":1" /><ref name=":3">{{Cite journal|last1=Madhaiyan|first1=Munusamy|last2=Saravanan|first2=Venkatakrishnan Sivaraj|last3=Blom|first3=Jochen|last4=Smits|first4=Theo H. M.|last5=Rezzonico|first5=Fabio|last6=Kim|first6=Soo-Jin|last7=Weon|first7=Hang-Yeon|last8=Kwon|first8=Soon-Wo|last9=Whitman|first9=William B.|last10=Ji|first10=Lianghui|date=2020-02-01|title=Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.)|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=70|issue=2|pages=841–848|doi=10.1099/ijsem.0.003834|pmid=31829916|issn=1466-5026|doi-access=free}}</ref> which is still included within the ''Kosakonia'' clade in the lately reviewed family of Enterobacteriaceae.<ref>{{Cite journal|last1=Alnajar|first1=Seema|last2=Gupta|first2=Radhey S.|date=2017-10-01|title=Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family|journal=Infection, Genetics and Evolution|language=en|volume=54|pages=108–127|doi=10.1016/j.meegid.2017.06.024|pmid=28658607|issn=1567-1348}}</ref> The incorporation of ''Phytobacter massiliensis'' has been proposed via the unification of the genera ''Metakosakonia'' and ''Phytobacter''.<ref name=":4">{{Cite journal|last1=Ma|first1=Yuanyuan|last2=Yao|first2=Rong|last3=Li|first3=Yuanyuan|last4=Wu|first4=Xiuqin|last5=Li|first5=Shuying|last6=An|first6=Qianli|s2cid=216650629|date=2020-04-30|title=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.|journal=Current Microbiology|volume=77 |issue=8 |pages=1945–1954 |language=en|doi=10.1007/s00284-020-02004-4|pmid=32350604|issn=1432-0991}}</ref> More recently, a fifth species, ''Phytobacter cepae'', isolated from onion (''Allium cepa'') and characterized by phylogenomic analyses based on whole-genome sequencing, average nucleotide identity and in silico DNA–DNA hybridization, has been proposed.<ref name=":6" />
== Taxonomic history and synonymy == First described as ''Bacillus agglomerans'' in 1888 by M. W. Beijerinck<ref>{{Cite journal |last1=Edwards |first1=Jane |last2=Baque |first2=Ellen |last3=Tang |first3=Jane |date=2004-11-01 |title=Proposal to acknowledge Beijerinck as the original author of the species Pantoea agglomerans. Request for an Opinion |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=54 |issue=6 |pages=2437 |doi=10.1099/ijs.0.02955-0 |pmid=15545493 |issn=1466-5026|doi-access=free }}</ref> and later reclassified by Ewing and Fife as ''Enterobacter agglomerans'',<ref name=":5">{{Cite journal |last1=Gavini |first1=F. |last2=Mergaert |first2=J. |last3=Beji |first3=A. |last4=Mielcarek |first4=C. |last5=Izard |first5=D. |last6=Kersters |first6=K. |last7=De Ley |first7=J. |date=1989-07-01 |title=Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and Description of Pantoea dispersa sp. nov. |journal=International Journal of Systematic Bacteriology |language=en |volume=39 |issue=3 |pages=337–345 |doi=10.1099/00207713-39-3-337 |issn=0020-7713|doi-access=free }}</ref> the EEC has a history of many names changes and taxonomy updates that follows the evolution of taxonomy tools. In 1984, Brenner and coworkers, using DNA-DNA hybridization test, divided the EEC into thirtheen DNA relatedness groups (Biotypes), numbered from I to XIII.<ref>{{Cite journal |last1=Brenner |first1=D. J. |last2=Fanning |first2=G. R. |last3=Leete Knutson |first3=J. K. |last4=Steigerwalt |first4=A. G. |last5=Krichevsky |first5=M. I. |date=1984-01-01 |title=Attempts to Classify Herbicola Group-Enterobacter agglomerans Strains by Deoxyribonucleic Acid Hybridization and Phenotypic Tests |journal=International Journal of Systematic Bacteriology |language=en |volume=34 |issue=1 |pages=45–55 |doi=10.1099/00207713-34-1-45 |issn=0020-7713|doi-access=free }}</ref> In 1989, Françoise Gavini and coworkers proposed to rename ''Enterobacter agglomerans'' (previously included in Biotypes I and XIII) as ''Pantoea agglomerans,''<ref name=":5" /> while the genus ''Phytobacter'' emerged from the characterization of Biotype XII.<ref name=":1" />
Mislabelled genome sequences in public databases have also contributed to taxonomic confusion within the genus. For example, genomes deposited under the names "''Citrobacter bitternis''" and "''Kluyvera intestini''" have been shown by phylogenomic analyses to belong to ''Phytobacter diazotrophicus'' and have been proposed as heterotypic synonyms of that species.<ref>{{Citation |last=Rezzonico |first=Fabio |title=“ Citrobacter bitternis ” Ko et al., 2015 and “ Kluyvera intestini ” Tetz and Tetz, 2016 are heterotypic synonyms of Phytobacter diazotrophicus Zhang et al., 2017 |date=2025-08-11 |url=http://biorxiv.org/lookup/doi/10.1101/2025.08.11.669625 |access-date=2026-03-13 |language=en |doi=10.1101/2025.08.11.669625 |last2=Smits |first2=Theo H. M.|hdl=11475/35010 |hdl-access=free }}</ref>
== Species == *''Phytobacter diazotrophicus'' is the most common ''Phytobacter'' species recovered from the environment and humans and is an opportunistic pathogen associated with contaminated catheters or the use of total parenteral nutrition.<ref name=":1" /><ref name=":2" /> * ''Phytobacter ursingii'' can biochemically be differentiated from ''Phytobacter diazotrophicus'' on the basis of its ability to metabolize d-serine and l-sorbose. Despite the presence of nitrogen-fixation genes suggests an environmental origin, only clinical isolates of the species have been reported so far.''<ref name=":1" />'' *''Phytobacter palmae'' is a species with high nitrogen fixing ability that was first identified in Singapore in leaf tissues of oil palm (''Elaeis guineensis'').<ref name=":3" /> *''Phytobacter cepae'', which was isolated from onion bulbs in the United States along to other Enterobacteriaceae and does not possess nitrogen-fixation (''nif'') genes.<ref name=":6">{{Cite journal |last=Jordan |first=Sara |last2=Pothier |first2=Joël F. |last3=Rezzonico |first3=Fabio |last4=Kvitko |first4=Brian H. |last5=Coutinho |first5=Teresa A. |last6=Smits |first6=Theo H. M. |date=2026-01-23 |title=Kosakonia beeri sp. nov. and Phytobacter cepae sp. nov. isolated from onion (Allium cepa) |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.007043 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=76 |issue=1 |doi=10.1099/ijsem.0.007043 |issn=1466-5026|url-access=subscription |hdl=11475/35228 |hdl-access=free }}</ref> *''Phytobacter massiliensis'', whose type strain JC163<sup>T</sup> was isolated from the fecal flora of a healthy Senegalese patient. This species also appears not to harbour the ''nif'' operon.<ref name=":4" /><ref>{{Cite journal|last1=Lagier|first1=Jean-Christophe|last2=El Karkouri|first2=Khalid|last3=Mishra|first3=Ajay Kumar|last4=Robert|first4=Catherine|last5=Raoult|first5=Didier|last6=Fournier|first6=Pierre-Edouard|date=2013-02-22|title=Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov.|journal=Standards in Genomic Sciences|language=en|volume=7|issue=3|pages=399–412|doi=10.4056/sigs.3396830|issn=1944-3277|pmc=3764934|pmid=24019988}}</ref>
== In popular culture == The 2025 documentary [https://www.youtube.com/watch?v=aU0XDB3hn6M A saga do ''Phytobacter''], which is available on YouTube, recounts the history of the discovery of the genus ''Phytobacter'' and its growing relevance as an opportunistic human pathogen.
== References == <!-- Inline citations added to your article will automatically display here. See https://en.wikipedia.org/wiki/WP:REFB for instructions on how to add citations. --> {{Reflist}}
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Category:Bacteria genera Category:Gram-negative bacteria