Accepted Manuscript
“Phoenicibacter massiliensis” gen. nov., sp. nov. , a new bacterium isolated from the human gut of a pygmy woman
Melhem Bilen, Frédéric Cadoret, Gregory Dubourg, Pierre-Edouard Fournier, Ziad Daoud, Didier Raoult
PII: S2052-2975(17)30033-1 DOI: 10.1016/j.nmni.2017.04.003 Reference: NMNI 321
To appear in: New Microbes and New Infections Received Date: 13 February 2017
Revised Date: 5 April 2017 Accepted Date: 10 April 2017
Please cite this article as: Bilen M, Cadoret F, Dubourg G, Fournier P-E, Daoud Z, Raoult D,
“Phoenicibacter massiliensis” gen. nov., sp. nov. , a new bacterium isolated from the human gut of a pygmy woman, New Microbes and New Infections (2017), doi: 10.1016/j.nmni.2017.04.003.
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human gut of a pygmy woman
Running title: Phoenicibacter massiliensis
Melhem Bilen1,2, Frédéric Cadoret1, Gregory Dubourg1, Pierre-Edouard Fournier1, Ziad Daoud2 and Didier Raoult1,3*
1Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
• 2Clinical Microbiology Laboratory, Saint George University Hospital, Faculty of Health Sciences, University of Balamand, Beirut, Lebanon.
• 3Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
* Corresponding author. E-mail address: [email protected]
Keywords: Culturomics, “Phoenicibacter massiliensis”, Emerging bacteria, Gut microbiota, Human microbiota.
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Abstract:
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This study supports the main characteristics of the new genus and new species “Phoenicibacter 3
massiliensis” strain Marseille-P3241T (CSUR P3241); a new bacterium that was isolated from a 4
stool sample of a healthy 47-year-old pygmy woman.
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In 2015, stool samples were collected in Congo for analysis as part of project of the human 7
microbiome description via culturomics [1]. Prior of the start up, an approval was taken from the 8
ethic committee of the Institut Federatif de Recherche IFR48 (Marseille, France) under the 9
number 09-022. Thus, 1 mL of phosphate buffer saline was used to dilute stool samples ahead of 10
inoculation in a blood culture media supplemented with 5mL of filtered rumen and 5mL of sheep 11
blood. Culture bottle was incubated at 37°C under anaerobic conditions. After 10 days of growth, 12
strain Marseille-P3241 was isolated on 5% blood–enriched Columbia agar (bioMérieux, Marcy 13
l'Etoile, France). Colonies were smooth with a diameter ranging between of 0.1-0.5 mm. Strain 14
Marseille-P3241 cells are cocco-bacillus, Gram positive, catalase and oxidase negative with a 15
diameter of an average of 2.9 µm. This strain could not be identified using our systematic matrix- 16
assisted laser desorption-ionization time-of-flight (MALDI-TOF) screening on a Microflex 17
spectrometer (Bruker Daltonics, Brenen, Germany) [2]. Therefore, sequencing of the 16S rRNA 18
gene was performed by the mean of the fD1-rP2 primers as previously described (Eurogentec, 19
Seraing, Belgium), using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) [3].
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Strain Marseille-P3241 exhibited an 87.7% sequence identity with Gordonibacter pamelaeae the 21
phylogenetically closest species, published with standing nomenclature (Fig. 1). Having a 16S 22
rRNA gene sequence similarity <5% with the phylogentically closest species with sanding in 23
nomenclature, we propose the creation of the new genus [4] named “Phoenicibacter” (Phoe.
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ni.ci.bac’ter N.L. masc. gen. n, “Phoenicibacter”, for Phoenician, the ancestor culture of the 25
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species “Phoenicibacter massiliensis” gen. nov., sp. nov. (mas.il.i.en’sis. L. gen. masc. n.
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massiliensis pertaining to Massilia, the antic name of the city of Marseille where this bacteria has 28
been discovered.
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MALDI-TOF MS spectrum accession number. The MALDI-TOF MS spectrum of P.
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massiliensis is available online (http://www.mediterranee- 31
infection.com/article.php?laref=256&titre=urms-database) 32
Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in 33
Genbank under accession number LT725668.
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Deposit in a culture collection. Strain Marseille-P3241T was deposited in the Collection de 35
Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3241.
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Conflict of interest:
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None to declare.
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Funding sources:
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This work was funded by Mediterrannée-Infection Foundation.
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Figure 1: This phylogenetic tree shows the positioning of “P. massiliensis” strain Marseille- 41
P3241 among its phylogenetically closest species. Sequences alignment was performed by 42
CLUSTALW and phylogenetic inferences were generated using the Mega software with the 43
maximum-likelihood approach. Yet, 500 repeats were used for the bootstrap values generation 44
and are shown on the nodes. A minimum of 90% bootstrap value was only considered for the 45
tree. The scale bar indicates a 2% nucleotide sequence divergence.
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Reference list 48
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Figure 1 :
