currently this genus includes only one validly published species named dermabacter hominis 
 , which was formerly known as the coryneform bacteria of the centers for disease control groups 3 and 5 , .
members of this genus are gram - positive , non  spore forming , non  acid fast , nonmotile , short rods , facultatively anaerobic , catalase positive and oxidase negative .
d.  hominis has also been detected in clinical samples such as wound swabs , bronchial washings , abscesses and ear smears , , , .
recently , high - throughput genome sequencing and matrix - assisted laser desorption / ionization time - of - flight mass spectrometry ( maldi - tof ) analyses of bacteria have given unprecedented access to an abundance of genetic and proteomic information , .
thus , a polyphasic approach is currently proposed in our laboratory to describe new bacterial taxa , including their genome sequence , maldi - tof spectrum , and major phenotypic characteristics such as gram staining , culture conditions , metabolic characteristics , habitat and , if applicable , pathogenicity . here
in may 2014 , while working at dakar , the index finger of a researcher was bitten by a fish .
strain ff11 ( table  1 ) was isolated from this wound by culture on 5% sheep 's blood 
enriched columbia agar ( biomrieux , marcy letoile , france ) . in order to identify the strain ff11 ,
maldi - tof protein analysis was performed using a microflex lt ( bruker daltonics , leipzig , germany ) , as previously reported , .
the scores previously established by bruker to identify or validate species compared to the instrument 's database were applied . in short ,
a score of 2.000 with a species with a validly published name allows identification at the species level ; scores of 1.700 and < 2.000 allow identification at the genus level ; and a score of < 1.700 does not allow any identification to be made .
they were then imported into maldi biotyper software ( version 2.0 , bruker ) and analysed by standard pattern matching ( with default parameter settings ) against the main spectra .
scores ranging from 1.315 to 1.511 were obtained for ff11 , suggesting that this strain was not a member of any known species .
the reference mass spectrum from strain ff11 was incremented in our database ( fig .  1 ) .
moreover , strain ff11 exhibited 97.9% 16s rrna sequence similarity with dermabacter hominis 
  ( genbank accession no .
x91034 ) , the phylogenetically closest bacterial species with standing in the nomenclature ( fig .  2 ) .
this value was lower than the 98.7% 16s rrna sequence identity threshold recommended by meier - kolthoff et  al . 
  in 2013 to delineate a new species within the firmicutes phylum without carrying out dna - dna hybridization .
different growth temperatures ( 25 , 28 , 37 , 45 and 56c ) were tested .
growth of the strain was also tested under anaerobic and microaerophilic conditions using genbag anaer and genbag microaer systems ( biomrieux ) , respectively , and under aerobic conditions , with or without 5% co2 .
optimal growth was observed under aerobic and microaerophilic conditions , but weak growth was observed under anaerobic conditions at 37c .
strain ff11 shows white convex colonies measuring approximately 1  mm in diameter on 5% sheep 's blood  enriched columbia agar ( biomrieux ) .
cells are gram - positive , nonmotile , non  spore forming short rods ( fig .  3 ) .
the negative staining of the cells and observation under transmission electron microscopy ( fei company , hillsboro , oregon , usa ) displays cells lacking flagella ( fig .  4 ) .
dermabacter indicis is catalase positive and oxidase negative . using an api 50ch strip ( biomrieux ) ,
fermentation was observed for d - galactose , d - glucose , n - acetyl - d - glucosamine , d - lactose , d - saccharose , d - trehalose , d - melezitose , d - raffinose , starch and d - turanose . using the api coryne strip ( biomrieux ) , positive reactions were also observed for pyrazinecarboxamide , pyroglutamic acid--naphthylamide , esculin ferric citrate , urea and d - maltose .
negative reactions were noted for potassium nitrate ( reduction of nitrates ) , -glucuronidase , gelatin , d - ribose , d - xylose , d - mannitol and glycogen . using the api zym strip ( biomrieux ) , enzymatic reactions were observed for esterase , esterase 
lipase , lipase , acid phosphatase , alkaline phosphatase , naphthol - as - bi - phosphohydrolase , cystine arylamidase , trypsin , -glucosidase , -galactosidase , -mannosidase , -fucosidase and n - acetyl--glucosaminidase .
negative reactions were observed for leucine arylamidase , valine arylamidase , -glucosidase , -galactosidase and -glucuronidase .
strain ff11 is susceptible to ciprofloxacin , amoxicillin / clavulanic acid , ticarcillin , ceftriaxone , imipenem , doxycycline , gentamicin and cefalotin , but it is resistant to colistin , trimethoprim / sulfamethoxazole , erythromycin and nitrofurantoin .
a comparison of phenotypic characteristics with dermabacter hominis 
 , brachybacterium faecium 
 , brachybacterium muris 
 , and helcobacillus massiliensis 
  is summarized in table  2 .
the organism was selected for sequencing on the basis of its phylogenetic position , 16s rrna similarity and phenotypic differences with other members of the dermabacteraceae family . here
table  3 shows the project information and its association with migs ( minimum information about a genome sequence ) version 2.0 compliance .
dermabacter indicis strain ff11 (= csur p1488  =  dsm 100283 ) was grown on 5% sheep 's blood 
bacteria grown on four petri dishes were resuspended in 5    100 l of tris - edta buffer and 150 l of this suspension was diluted in : 350  l tris - edta buffer 10 , 25  l proteinase k and 50 l sodium dodecyl sulfate for lysis treatment .
extracted dna was then purified using three successive phenol  chloroform extractions and ethanol precipitations at  20c overnight .
the genomic dna concentration was measured at 69.3  ng/l using the qubit assay with the high sensitivity kit ( life technologies , carlsbad , ca , usa ) .
genomic dna ( gdna ) of dermabacter indicis ff11 was sequenced on the miseq technology ( illumina , san diego , ca , usa ) with the mate pair strategy .
the gdna was barcoded in order to be mixed with 11 other projects with the nextera mate pair sample prep kit ( illumina ) .
the mate pair library was prepared with 1.5  g of gdna using the nextera mate pair illumina guide .
the pattern of the fragmentation was validated on an agilent 2100 bioanalyzer ( agilent technologies , santa clara , ca , usa ) with a dna 7500 labchip .
the dna fragments are ranged in size from 1.5 to 11  kb with an optimal size at 6.730  kb .
no size selection was performed , and 636  ng of tagmented fragments were circularized .
the circularized dna was mechanically sheared into small fragments with an optimum at 653  bp on the covaris device s2 in t6 tubes ( covaris , woburn , ma , usa ) .
the library profile was visualized on a high sensitivity bioanalyzer labchip ( agilent ) , and the final concentration library was measured at 59.1  nmol / l .
after a denaturation step and dilution at 15  pm , the pool of libraries was loaded onto the reagent cartridge and then onto the instrument along with the flow cell . automated cluster generation and sequencing runs were performed in a single 39-hour run at a 2    251  bp read length .
total information of 5.9  gb was obtained from a 624k / mm cluster density with cluster passing quality control filters of 96.33% ( 12  040  000 clusters ) . within this run , the index representation for dermabacter indicis ff11
the 1  918  640 paired reads were filtered according to the read qualities .
open reading frames ( orfs ) were predicted using prodigal   with default parameters , but the predicted orfs were excluded if they spanned a sequencing gap region .
the predicted bacterial protein sequences were searched against the genbank database   and the clusters of orthologous groups ( cogs ) database using blastp .
the trnascan - se tool   was used to find trna genes , while ribosomal rnas were found using rnammer   and blastn against the genbank database .
orfans were identified if their blastp e value was lower than 1e-03 for an alignment length greater than 80 aa .
if alignment lengths were smaller than 80 aa , we used an e value of 1e-05 .
artemis   was used for data management and dna plotter   for the visualization of genomic features .
the mauve alignment tool ( version 2.3.1 ) was used for multiple genomic sequence alignment . briefly
, this software combines the proteinortho software   for detecting orthologous proteins in pairwise genomic comparisons , then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous orfs using the needleman - wunsch global alignment algorithm .
annotation and comparison processes were performed in the multi - agent software system dagobah , including figenix   libraries that provide pipeline analyses .
genome - to - genome distance calculator ( ggdc ) analysis was also performed using the ggdc web server as previously reported , . here , the genome of dermabacter indicis strain ff11 ( embl / ebi accession no .
cyug00000000 ) is compared to those of dermabacter hominis strain 1368 ( jdrs00000000 ) , brachybacterium faecium strain dsm 4810 ( cp001643 ) , brachybacterium paraconglomeratum strain lc44 ( agso00000000 ) , brachybacterium squillarum strain m-6 - 3 ( agbx00000000 ) and brachybacterium muris strain ucd - ay4 ( aorc00000000 ) .
the embl / ebi bioproject number is prjeb10922 and consists of 248 large contigs . finally , the draft genome of d.  indicis ff11 generated a 2  222  902  bp long genome with a 63.2% g+c content ( fig .  5 ) . of the 2124 predicted genes , 2074 were protein - coding genes and 50 were rnas ( three 5s rrna genes , one 16s rrna gene , one 23s rrna gene and 45 trna genes ) .
the remaining genes were annotated as hypothetical proteins . the properties and statistics of the genome
the draft genome of d.  indicis is smaller than d.  hominis , b. faecium , b. paraconglomeratum , b. squillarum and b.  muris ( 2.22 , 2.51 , 3.61 , 3.78 , 3.19 and 3.26 mb respectively ) .
the g+c content of d.  indicis is higher than that of d.  hominis ( 63.2 and 62.7% , respectively ) but lower than that of b.  faecium , b. paraconglomeratum , b. squillarum and b.  muris ( 72.0 , 72.4 , 72.8 and 70.0% respectively ) . the gene content of d.  indicis is smaller than that of d.  hominis , b. faecium , b. paraconglomeratum , b. squillarum and b.  muris ( 2124 , 2302 , 3191 , 3432 , 2869 and 2914 respectively ) .
the distribution of genes into cogs categories was similar in all the genomes compared ( fig .  6 ) .
in addition , d.  indicis shared 2074 , 2226 , 3068 , 3341 , 2765 and 2806 orthologous genes with d.  hominis , b. faecium , b. paraconglomeratum , b. squillarum and b.  muris ( fig .  6 ) . the genomic similarity between strain ff11 and the closely related brachybacterium species
the results of phenotypic , phylogenetic and genomic analyses allow us to propose the creation of dermabacter indicis sp . nov . , which contains strain ff11 .
n. indicis , pertaining to the latin name of the index finger , from which the type strain was isolated ) .
strain ff11 is a gram - positive bacterium , facultatively anaerobic , with small ( 1  mm ) and white colonies on 5% sheep 's blood  enriched columbia agar .
strain ff11 is nonmotile , non  spore forming , oxidase negative and catalase positive .
strain ff11 presents positive reactions for d - galactose , d - glucose , d - trehalose , d - melezitose , d - raffinose , starch , d - turanose , esterase , esterase - lipase , pyrazinecarboxamide , pyroglutamic acid--naphthylamide , esculin ferric citrate , urea , d - lactose , d - maltose , d - saccharose , acid phosphatase , naphthol - as - bi - phosphohydrolase , cystine arylamidase , trypsin , -glucosidase , -galactosidase , -mannosidase , -fucosidase and n - acetyl--glucosaminidase .
dermabacter indicis strain ff11 is susceptible to ciprofloxacin , amoxicillin / clavulanic acid , ticarcillin , ceftriaxone , imipenem , doxycycline , gentamicin and cefalotin but resistant to colistin , trimethoprim / sulfamethoxazole , erythromycin and nitrofurantoin .
the 16s rrna and genome sequences are deposited in genbank under accession numbers ln810502 and cyug00000000 , respectively .
the type strain ff11 (= csur p1488  =  dsm 100283 ) was isolated from a human finger wound in dakar , senegal .
 strain ff11 t was isolated from the wound on a researcher 's finger who had been bitten by a fish ( protopterus annectens ) in senegal . 
 analysis by matrix - assisted laser desorption / ionization time - of - flight mass spectrometry did not provide any identification , but the 16s rrna sequence exhibited 97.9% identity with dermabacter hominis . 
 phenotypic and genomic analyses demonstrated that strain ff11 t is gram - positive , facultatively anaerobic , nonmotile and non  spore forming ; it exhibited a genome of 2  222  902  bp encoding 2074 protein - coding and 50 rna genes , with a 63.2% g+c content . 
 we consequently proposed the creation of dermabacter indicis strain ff11 t . 
Introduction
Classification and features
Genome sequencing information
Genome properties
Conclusion
Taxonomic and nomenclatural proposals