Occurrence and distribution of the 34 PCR-TTGE bands observed among the <i>Aeromonas</i> population.

a<p>Bold type indicates bands which were successfully sequenced (GenBank accession numbers JX014439-JX014453 and JX453432-JX453445).</p>b<p>Bold type indicates that all patterns with the corresponding band showed heterogeneity.</p>c<p>Bold and italics, bands only found in one taxon; bold and underlined, bands found in all representatives of a taxon for taxa including more than one strain (bold, italics and underlined combined for band 38 in <i>A. sobria</i>).</p

Schematic representation of I-<i>Ceu</i>I-restricted DNA fragment sizes for <i>Aeromonas</i> spp. strains with 10 <i>rrn</i> operons.

<p>Data were given for the 142 <i>A. veronii</i>, <i>A. hydrophila</i>, <i>A. aquariorum</i>, <i>A. caviae</i> and <i>A. salmonicida</i> strains with 10 <i>rrn</i> operons with the aim to illustrate interspecific variability between the 5 taxa and the intraspecific variability for the 3 main species. I-<i>Ceu</i>I-restricted DNA fragments were numbered in size descending order; the size of the largest fragment 1 was not measured (as discussed in the text). A to F, size distribution for fragments 2 to 7, respectively. Fragment mean sizes (in kilobases) were indicated in the corresponding tables according to the species and by a blue line in the corresponding scheme A to F. Standard deviation values (SD) and coefficient of variation (CV) were indicated in kb and %, respectively, in the corresponding tables according to the species except for species with less than 10 representatives; +/−1 SD were represented by black dotted lines and +/−2 SD by red dotted lines in the corresponding scheme A to F. Schematic representations for the 3 smallest fragments with mean size lower than 97 kb (mean size and SD of 93.7±23 kb, 66.7±9.1 kb and 40.5±7.5 kb, respectively) were not presented here because they were not informative.</p

Number of <i>rrn</i> operons and PCR-TTGE patterns for the 195 <i>Aeromonas</i> strains of the study.

<p>Results are presented according to the structure of the population observed in multilocus phylogenetic analysis (MLPA). Unrooted maximum-likelihood tree was based on concatenated sequences of five housekeeping genes (<i>gltA</i>, <i>gyrB</i>, <i>rpoB</i>, <i>tsf</i> and <i>zipA</i> genes), as described in Roger <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046268#pone.0046268-Roger1" target="_blank">[13]</a>. Only type and references strains are indicated within clades on the tree. The horizontal lines show genetic distance, the scale bar indicating the number of substitutions per nucleotide position. The numbers at the nodes are support values estimated with 100 bootstrap replicates. Only bootstrap values >70 are indicated on the tree. When all members of a clade shared identical features, the common <i>rrn</i> operon number and/or PCR-TTGE pattern was indicated. * The <i>A. caviae</i> clade included the type strain <i>A. caviae</i> CECT 838^T displaying an external position to other members of the <i>A. caviae</i> clade in the tree.</p

Effect of three sub-inhibitory concentrations of NaCl against <i>P. aeruginosa</i> CF isolate biofilm biomass formation.

<p>Tested for 55 adherent CF isolates of <i>P. aeruginosa</i> with MIC values > 3% distributed as follows: strongly adherent (n = 13, violet bars), moderately adherent (n = 15, green bars), weakly adherent phenotype (n = 27, blue bars). Prevention of biofilm biomass formation is presented as percentage of strains for which ability to form biofilm biomass was decreased by at least 25% compared to controls (not exposed).</p

Rate of motile isolates according to NaCl concentration.

<p>Green bars show the number of motile isolates among isolates with non-inhibited growth (full bars).</p

Time-kill kinetics of different NaCl concentrations against <i>P. aeruginosa</i> isolate Pa71.

<p>3% NaCl solution (orange line, filled triangles), 5% NaCl solution - corresponding to the MBC value (violet line, dash), 7% NaCl solution (red line, filled circles), and 10% NaCl solution (green line, filled squares). Control (blue line, filled lozenges) was not exposed to NaCl. Time-kill curves of 15% (not shown) and 10% NaCl solution were similar.</p

Comparison of NaCl Minimal Inhibitory Concentration (MIC), Minimal Bactericidal Concentration (MBC) and Killing quotient (KQ) distributions for subgroups of <i>P. aeruginosa</i> CF isolates according to mucoid characteristic, antimicrobial susceptibility pattern, ability to form biofilm and patient under HTS treatment.

<p>MIC₅₀ and MIC₉₀ values were defined as the lowest concentration of NaCl at which 50% and 90% of the isolates were inhibited, respectively.</p>a<p>Only isolates exhibiting MBC values within tested range were considered.</p>b<p>5 isolates recovered in one patient.</p>c<p>isolates were randomly selected.</p>d<p>Comparison of MIC, MBC and KQ distribution between subgroups was performed with Mann-Whitney’s test, with the exception of the evaluation depending on biofilm producer groups, assessed by the Kruskal-Wallis’ test, and Spearman correlation coefficient (Rs) when Kruskal-Wallis’ test was positive. A <i>P</i> value ≤0.05 was considered to reflect significance and was indicated in bold type.</p><p>ND, not determined either because only one isolate or one patient was included in the sub-population, or because one isolate exhibiting a MBC value within the tested range.</p

Bacterial Diversity Associated with Wild Caught <i>Anopheles</i> Mosquitoes from Dak Nong Province, Vietnam Using Culture and DNA Fingerprint

<div><p>Background</p><p>Microbiota of <i>Anopheles</i> midgut can modulate vector immunity and block <i>Plasmodium</i> development. Investigation on the bacterial biodiversity in <i>Anopheles</i>, and specifically on the identification of bacteria that might be used in malaria transmission blocking approaches, has been mainly conducted on malaria vectors of Africa. Vietnam is an endemic country for both malaria and Bancroftian filariasis whose parasitic agents can be transmitted by the same <i>Anopheles</i> species. No information on the microbiota of <i>Anopheles</i> mosquitoes in Vietnam was available previous to this study.</p><p>Method</p><p>The culture dependent approach, using different mediums, and culture independent (16S rRNA PCR – TTGE) method were used to investigate the bacterial biodiversity in the abdomen of 5 <i>Anopheles</i> species collected from Dak Nong Province, central-south Vietnam. Molecular methods, sequencing and phylogenetic analysis were used to characterize the microbiota.</p><p>Results and Discussion</p><p>The microbiota in wild-caught <i>Anopheles</i> was diverse with the presence of 47 bacterial OTUs belonging to 30 genera, including bacterial genera impacting <i>Plasmodium</i> development. The bacteria were affiliated with 4 phyla, <i>Actinobacteria</i>, <i>Bacteroidetes</i>, <i>Firmicutes</i> and <i>Proteobacteria</i>, the latter being the dominant phylum. Four bacterial genera are newly described in <i>Anopheles</i> mosquitoes including <i>Coxiella</i>, <i>Yersinia</i>, <i>Xanthomonas</i>, and <i>Knoellia</i>. The bacterial diversity per specimen was low ranging from 1 to 4. The results show the importance of pairing culture and fingerprint methods to better screen the bacterial community in <i>Anopheles</i> mosquitoes.</p><p>Conclusion</p><p>Sampled <i>Anopheles</i> species from central-south Vietnam contained a diverse bacterial microbiota that needs to be investigated further in order to develop new malaria control approaches. The combination of both culture and DNA fingerprint methods allowed a thorough and complementary screening of the bacterial community in <i>Anopheles</i> mosquitoes.</p></div

Distribution of the 171 strains (n = 148) and clones (n = 23) of <i>O. intermedium</i>/<i>O. ciceri</i> identified from the litterature and databases according to the habitat.

<p>The figure has been constructed from data presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376.s003" target="_blank">Tables S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376.s004" target="_blank">S2</a>.</p

Characteristics of the 15 <i>O. intermedium</i> strains and <i>O. ciceri</i> type strain of environmental origin presented according to MLST results.

<p>CC, clonal complex; ST, sequence type; Fr, France.</p><p>^a Strains noted RT were isolated from systematic searching of <i>O. intermedium</i> in 200 soil and water samples randomly collected worldwide.</p><p>^b For each locus, each different allele was assigned an arbitrary number.</p><p>^c 46-bp atypical insertion in <i>rrs</i> described by Teyssier et al., 2003 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376-Teyssier1" target="_blank">[9]</a>.</p