چکیده (انگلیسی):

As part of a culturomics study [1,2] of the human microbiome,
in 2015 we isolated from the urine of a 7-year-old boy hospitalized
for dental care under general anaesthesia a bacterial
strain that was not identified by matrix-assisted laser desorption–
ionization time-of-flight mass spectrometry (MALDI-TOF
MS) screening using a Microflex spectrometer (Bruker Daltonics,
Bremen, Germany) [3]. The patient’s parents provided
signed informed consent and the ethics committee of the
Institut Federatif de Recherche IFR48 validated the study under
number 09-022.
The initial growth was obtained after 10 days of incubation in
an anaerobic blood culture vial (Becton Dickinson, Le Pont-de-
Claix, France) supplemented with 5 mL of 0.2-μm filtered
rumen fluid. A subculture of strain FC2 was then obtained after
48 h of incubation at 37°C on 5% sheep blood–Columbia agar
medium (bioMérieux, Marcy l’Etoile, France) in anaerobic atmosphere
generated using the GENbag Anaer systems
(bioMérieux). Agar-grown colonies were microscopic and
translucent with a mean diameter of 1 μm. Bacterial cells were
Gram-positive cocci, ranging in length from 300 to 500 nm.
Strain FC2 was catalase and oxidase negative. The 16S rRNA
gene was sequenced using the fD1-rP2 primers as previously
described [4], using a 3130-XL sequencer (Applied Biosciences,
Saint Aubin, France). Strain FC2 exhibited a 91% sequence
identity with Peptoniphilus coxii strain RMA 16757T (GenBank
Accession number GU938836) [5], the phylogenetically closest
species with standing in nomenclature (Fig. 1), which putatively
classifies it as a new genus member of the family Peptoniphilaceae
in the phylum Firmicutes.
Strain FC2 presents a 16S rRNA gene sequence divergence
>5% with its phylogenetically closest species with standing in
nomenclature [6], so we propose the creation of the new genus
‘Urinacoccus’ gen. nov. (u.ri.na.coc’cus, N. L. masc. n. composed
of u.ri.na, L. N. gen. fem. urina, from urina, the Latin name of
urine and coc’cus. L. N. gen. masc. coccus, from coccus, the Latin
name of bacterium having a spherical or spheroidal shape) as
strain FC2 is a coccus and was first isolated from a paediatric
urine sample. We propose the new species ‘Urinacoccus massiliensis’
sp. nov. (mas.sil.ien’sis. L. Adj. gen. fem. massiliensis, of
massilia, the Latin name of Marseille) because strain FC2 was
first found in the city of Marseille.
New Microbe