paenibacillus species were originally classified within the bacillus genus . members of this genus are often gram variable , facultatively anaerobic , and endospore forming .
these bacteria are frequently isolated from environments such as soil , water , vegetable matter , forage , larvae and insects but could be detected from clinical samples , , .
bacteria belonging to this genus are able to produce polysaccharide - degrading enzymes and proteases , are beneficial to agriculture and horticulture and have industrial and medical applications . some species of this genus may be involved in human infections , , , .
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 to describe new bacterial taxa that includes their genome sequence , maldi - tof spectrum and major phenotypic characteristics such as gram staining , culture , metabolic characteristics , habitat and , if applicable , pathogenicity .
the strain ff9 (= csur p1429  =  dsm 29777 ) was isolated from a blood culture of a 16-month - old child presenting at the hpital principal de dakar , senegal .
strain ff9 is a gram - variable bacterium , facultatively anaerobic , motile and rod shaped .
here we present a summary classification and a set of features for paenibacillus dakarensis sp .
in march 2014 a blood culture was performed on a 16-month - old child presenting at the hpital principal de dakar , senegal .
strain ff9 ( table  1 ) was isolated from this blood culture by culture on 5% sheep 's blood 
enriched columbia agar ( biomrieux , marcy letoile , france ) . identification was not obtained using maldi - tof because the scores obtained by this strain were low .
moreover , strain ff9 exhibited 98.18% 16s rrna sequence similarity with paenibacillus uliginis 
  ( genbank accession no .
fn556467 ) , the phylogenetically closest bacterial species with standing in nomenclature ( fig .  1 ) .
these values were lower than the 98.7% 16s rrna sequence 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 conditions , but weak growth was observed under anaerobic and microaerophilic conditions .
cells are gram - variable , endospore - forming rods with rounded ends ( fig .  2 ) and have a mean diameter of 0.6  m ( range , 0.50.7  m ) and a mean length of 2.8  m ( range , 2.13.5  m ) ( fig .  3 ) .
paenibacillus dakarensis is catalase positive and oxidase negative . using an api 50ch strip ( biomrieux ) , positive reactions were observed for d - ribose , d - glucose , d - mannose , n - acetyl - d - glucosamine , amygdaline , esculin , d - cellobiose , d - lactose , d - saccharose , d - trehalose , d- melezitose , gentiobiose and d - lyxose . using a api 20ne strip ( biomrieux ) ,
positive reactions were observed for esculin , -galactosidase , glucose and mannose . using a api zym strip ( biomrieux ) ,
negative reactions were observed for alkaline phosphatase , esterase , esterase - lipase , leucine arylamidase , acid phosphatase , naphthol - as - bi - phosphohydrolase , cystine arylamidase , valine arylamidase , trypsin , -glucosidase , -glucosidase , -galactosidase , -galactosidase , -glucuronidase , -mannosidase , -fucosidase and n - acetyl--glucosaminidase .
strain ff9 is susceptible to amoxicillin / clavulanic acid , ticarcillin , ceftriaxone , cefalotin , imipenem , gentamicin and doxycycline but is resistant to penicillin , metronidazole and trimethoprim / sulfamethoxazole .
the minimum inhibitory concentrations ( mics ) for some antibiotics tested by paenibacillus dakarensis strain ff9 sp . nov .
a comparison of phenotypic characteristics with paenibacillus polymyxa 
 , paenibacillus massiliensis and paenibacillus sanguinis 
  is summarized in table  3 .
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 2.000 with a species with a validly published name allows for identification at the species level ; a score 1.700 and < 2.000 allows for identification at the genus level ; and a score < 1.700 does not allow for any identification to be made .
two microlitres of matrix solution ( saturated solution of -cyano-4-hydroxycinnamic acid ) in 50% acetonitrile and 2.5% trifluoroacetic acid were distributed on each smear and subjected to air drying for 5 minutes .
the spectra from the 12 different colonies were then imported into the maldi biotyper 2.0 software ( bruker ) and analysed by standard pattern matching ( with default parameter settings ) against the main spectra of 6252 bacteria .
scores ranging from 1.225 to 1.456 were obtained for the ff9 , suggesting that this strain was not a member of any known species .
the reference mass spectrum from strain ff9 was incremented in our database ( fig .  4 ) .
the organism was selected for sequencing on the basis of its phylogenetic position , 16s rrna similarity and phenotypic differences with other members of the paenibacillaceae family .
there are more than 15 genomes for the paenibacillus genus available in public genomic collections . here
table  4 shows the project information and its association with minimum information about a genome sequence ( migs ) 2.0 compliance .
paenibacillus dakarensis strain ff9 (= csur p1429  =  dsm 29777 ) was grown on 5% sheep 's blood 
bacteria grown on four petri dishes were resuspended in 5    100  l of tris - edta ( te ) buffer ; 150  l of this suspension was diluted in 350  l te buffer 10 , 25  l proteinase k and 50  l sodium dodecyl sulfate for lysis treatment .
after centrifugation , dna was suspended in 65 l elution buffer ( eb ) buffer .
the genomic dna concentration was measured at 452.7  ng/l using the qubit assay with the high sensitivity kit ( life technologies , carlsbad , ca , usa ) .
the mate pair library was prepared with 1.5  g of genomic dna using the nextera mate pair illumina guide ( illumina , san diego , ca , usa ) .
the genomic dna sample was simultaneously fragmented and tagged with a mate pair junction adapter .
the pattern of fragmentation was validated on an agilent 2100 bioanalyzer ( agilent technologies , santa clara , ca , usa ) using a dna 7500 lab chip .
the dna fragments ranged in size from 1.5 to 11  kb , with an optimal size of 5.773  kb .
no size selection was performed , and 600  ng of tagmented fragments were circularized .
the circularized dna was mechanically sheared into small fragments with an optimal size of 932  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 19.07  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 in a 2    251  bp read length .
total information of 4.9  gb was obtained from a 506k / mm cluster density with a cluster passing quality control filters of 97% ( 9  954  000 clusters ) . within this run ,
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 trnascanse tool   was used to find trna genes , while ribosomal rnas were found using rnammer   and blastn against the genbank database .
lipoprotein signal peptides and the number of transmembrane helices were predicted using signalp   and tmhmm   respectively .
orfans were identified if their blastp e value was lower than 1e-03 for alignment length greater than 80 amino acids .
if alignment lengths were smaller than 80 amino acids , we used an e value of 1e-05 .
artemis   was used for data management and dna plotter   for visualization of genomic features .
the mauve alignment tool ( version 2.3.1 ) was used for multiple genomic sequence alignment . to estimate the mean level of nucleotide sequence similarity at the genome level
, we used the magi homemade software to calculate the average genomic identity of gene sequences ( agios ) among compared genomes .
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 .
genomes from the paenibacillus genus and closely related genera were used for the calculation of agios values .
the script created to calculate agios values was named magi ( marseille average genomic identity ) and is written in perl and bioperl modules .
genome - to - genome distance calculator ( ggdc ) analysis was also performed using the ggdc web server ( http://ggdc.dsmz.de ) as previously reported , . here , we compared the genome sequences of p.  dakarensis strain ff9 ( genbank accession no .
cdse01000001 ) with those of paenibacillus lactis strain 154 ( agip00000000 ) , paenibacillus polymyxa strain atcc 842 ( afox00000000 ) , paenibacillus massiliensis strain 2301065 ( aril00000000 ) , paenibacillus sabinae strain t27 ( cp004078 ) , paenibacillus borealis strain dsm 13188 ( cp009285 ) and paenibacillus forsythiae strain t98 ( assc00000000 ) .
the genome of the p.  dakarensis strain ff9 is 4  569  428  bp long with a 45.7% g+c content ( fig . 
of the 4427 predicted genes , 4352 were protein - coding genes and 75 were rna genes .
six rrna genes ( two 16s rrna , two 23s rrna and two 5s rrna ) and 69 predicted trna genes were identified in the genome .
the draft genome of p.  dakarensis is smaller than that of p.  lactis , p. polymyxa , p. massiliensis , p. sabinae , p. borealis and p.  forsythiae ( 4.56 , 6.81 , 5.9 , 6.39 , 5.27 , 8.16 and 5.08 mb , respectively ) .
the g+c content of p.  dakarensis is higher than those of p.  polymyxa ( 45.7 and 44.9% , respectively ) but lower than those of p.  lactis , p. massiliensis , p. sabinae , p. borealis and p.  forsythiae ( 49.1 , 48.5 , 52.6 , 51.4 and 52.9 respectively ) .
the gene content of p.  dakarensis is lower than those of p.  lactis , p. massiliensis , p. sabinae , p. borealis and p.  forsythiae ( 4427 , 6234 , 5206 , 5193 , 4896 , 6382 and 5103 respectively ) .
however , the distribution of genes into cogs categories was similar in all compared genomes ( fig .  7 ) .
in addition , p.  dakarensis shared 4352 , 6149 , 5068 , 5055 , 4788 , 6213 and 5011 orthologous genes with p.  lactis , p. polymyxa , p. massiliensis , p. sabinae , p. borealis and p.  forsythiae respectively ( table  7 ) . among species with standing in nomenclature , agios values ranged from 69.19% between p. 
polymyxa and p.  forsythiae to 84.00% between p.  forsythiae and p.  sabinae . on the basis of phenotypic , phylogenetic and genomic analyses
the strain was isolated from a blood sample taken from a 16-month - old senegalese child presenting at the hpital principal de dakar .
n. dakarensis , or originating from dakar , the capital of senegal ,  where the type strain was isolated ) .
the strain ff9 is  a facultative anaerobic , gram variable bacterium , with small , white  colonies on 5% sheep 's blood 
cells have a mean diameter of  0.6  m ( range , 0.50.7  m ) and a mean length of 2.8  m ( range , 2.13.5  m ) .
positive reactions were observed for d - ribose , d - glucose , d - mannose , n - acetyl - d - glucosamine , amygdaline , esculin , d - cellobiose , d - lactose , d - saccharose , d - trehalose , d - melezitose , gentiobiose , d - lyxose and -galactosidase .
paenibacillus dakarensis strain ff9 is susceptible to amoxicillin / clavulanic acid , ticarcillin , ceftriaxone , cefalotin , imipenem , gentamicin and doxycycline but resistant to metronidazole , penicillin and trimethoprim / sulfamethoxazole .
the 16s rrna and genome sequences are deposited in genbank under accession numbers lm652718 and cdse01000001 , respectively .
the type strain ff9 (= csur p1429  =  dsm 29777 ) was isolated from a blood sample taken from a 16-month - old child presenting at the hpital principal de dakar , senegal .
 strain ff9 t was isolated in dakar ( senegal ) from a blood - culture taken from a 16-month - old child . 
 maldi - tof analysis did not allow for identification . 
 after sequencing , strain ff9 t exhibited 98.18% similarity with the 16srrna sequence of paenibacillus uliginis . 
 a polyphasic study of phenotypic and genomic analyses showed that strain ff9 t is gram variable , catalase - positive , and presents a genome of 4,569,428 bp ( one chromosome but no plasmid ) with 4,427genes ( 4,352 protein - coding and 75 rna genes ( including 3 rrna operons ) . 
 the g+c content is 45.7% . on the basis of these genomic and phenotypic data analyses 
 , we propose the creation of paenibacillus dakarensis strain ff9 t . 
Introduction
Classification and features
Genome sequencing information
Insights from genome sequence
Taxonomic and nomenclatural proposals
Conflict of interest