'Ndongobacter massiliensis' gen. nov., sp. nov., a new bacterial genus isolated from a human urine sample after de novo kidney transplantation.

We report the main characteristics of 'Ndongobacter massiliensis' strain Marseille-P3170T (= CSUR P3170), which was isolated from the urine sample of a 37-year-old man who had just received a kidney transplant for genetic focal segmental glomerulosclerosis.

As a part of the study exploreing the diversity of the urinary microbiota by culturomics [1], [2], we investigated urine samples collected from adult kidney transplant recipients. The bacterial strain Marseille-P3170, which was not identified by our systematic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) screening on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) [3], was isolated from a urine sample of a 37-year-old man, after kidney transplantation for genetic focal segmental glomerulosclerosis. The patient provided signed informed consent, and the agreement of the local ethics committee of the IFR48 (Marseille, France) was obtained under number 09-022. We initially pre-incubated the urine sample at 37°C for 10 days in an anaerobic blood-culture bottle (BACTEC™ Lytic/10 Anaerobic/F Culture Vials; Becton-Dickinson, Pont de Claix, France) enriched with 5% sterilized rumen by microfiltration (0.2-μm pore diameter). Then, the pre-incubated sample was seeded on 5% sheep blood Columbia agar medium (bioMérieux, Marcy l’Étoile, France). A pure culture of the strain Marseille-P3170 was obtained after 3 days of incubation at 37°C in an anaerobic atmosphere (AnaeroGen™, Oxoid Ltd, Dardilly, France). Agar-grown microcolonies were translucent glistening with a mean diameter <0.5 mm. The strain Marseille-P3170 cells were Gram-negative cocci, non-motile, ranging in diameter from 400 to 600 nm and did not exhibit oxidase or catalase activities.

The complete 16S rRNA gene was sequenced using fD1-rP2 primers as previously described [4] and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). The strain Marseille-P3170 exhibited sequence similarity of 89.7% with Murdochiella massiliensis strain SIT12 (GenBank Accession number LN866998), which is the phylogenetically closest published species (Fig. 1). The genus Murdochiella was first discovered and published by Ulger-Toprak et al. in 2010, the strain was isolated from a sacral pilonidal cyst aspirate from an immunocompetent patient, the cells were cocci, Gram-positive staining, non-motile and obligate anaerobic [5]. Murdochiella massiliensis was first isolated by Vicino et al. in May 2015 from the stool of a healthy 2-year-old Senegalese boy, by cultivation on marine medium in anaerobic atmosphere after 21 days of incubation. Murdochiella massiliensis is a Gram-positive, coccus-shaped, non-motile, non-spore-forming bacterium [6].

Fig. 1

Phylogenetic tree showing the position of ‘Ndongobacter massiliensis’ strain Marseille-P3170T relative to other phylogenetically close neighbours. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only bootstrap scores of at least 90% were retained. The scale bar indicates a 2% nucleotide sequence divergence.

As the strain Marseille-P3170 showed a 16S rRNA gene sequence divergence >5% from its phylogenetically closest species with standing in nomenclature [7], it is putatively classified as a new representative strain of the new genus ‘Ndongobacter’ among the Firmicutes phylum. We propose the creation of the new genus ‘Ndongobacter’ gen. nov. (N.don.go.bacʹter N. L. masc. n. Ndongo referring to the microbiologist Sokhna Ndongo N.L. masc. n. bacter, a rod). The strain Marseille-P3170T is the type strain of ‘Ndongobacter massiliensis’ gen. nov., sp. nov., the first representative species of this new genus (mas.si.li.en’sis, L., fem. adj., massiliensis for Massilia, the Latin name of Marseille, France, where the organism was first isolated).

MALDI-TOF MS spectrum accession number. The MALDI-TOF MS spectrum of ‘Ndongobacter massiliensis’ strain Marseille-P3170T is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).

Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LT598585.

Deposit in a culture collection Strain Marseille-P3170T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3170

Transparency declaration

The authors have no conflicts of interest to declare.

Funding

This work was funded by the Fondation Méditerranée Infection.