Habitat impacts the distribution of arsenic-related genes in <i>Burkholderiales</i>.

<p>The scatter distribution of the number of arsenic-related genes per genome grouped by the isolation sources. The isolation sources included human (H), plant (P), animal (Z), rhizosphere or root nodules (R), soil (S), sediment (D) and wastewater or sludge (W) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092236#pone.0092236.s003" target="_blank">Table S1</a>).</p

Four major metabolic strategies for arsenic resistance and transformation were found in microbes.

<p>a) cytoplasmic AsV reduction by ArsC and As III extrusion by ArsB or ACR3; b) periplasmic AsV reduction under anaerobic conditions by ArrAB; c) As III oxidation by AioAB and AsV extrusion through a phosphate transporter system; d) As III methylation to the gaseous compound As(CH)3 by ArsM. The gene organizations representative of these four processes are shown in the pale blue box, and the corresponding functions of the genes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092236#pone-0092236-t001" target="_blank">Table 1</a>.</p

Diversity of organizations of the arsenate-resistance operon (<i>ars</i>) cluster in the 161 <i>Burkholderiales</i> genomes.

<p>Diversity of organizations of the arsenate-resistance operon (<i>ars</i>) cluster in the 161 <i>Burkholderiales</i> genomes.</p

Comparisons of the organization of the <i>aio</i> cluster and flanking sequence in 39 arsenite oxidizers genomes.

<p><i>H. arsenicoxydans</i> ULPAs1 is used as the reference genome. From outside to inside, first two rings donated ORF encoded from forward/reverse strand of the partial region of the <i>H. arsenicoxydans</i> ULPAs1 genome; rings 3 to 41 represent the 39 arsenite oxidizers at this order, which are shown under the cycle (from up to down and left to right).</p

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in <i>Burkholderiales</i>

<div><p>So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as “arsenic-related genes”). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 <i>Burkholderiales</i> genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for <i>aio</i> (arsenite oxidase) (12 strains), <i>arr</i> (arsenate respiratory reductase) (1 strain) and <i>arsM</i> (arsenite methytransferase)-like genes (4 strains), the <i>ars</i> (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 <i>ars</i>-like genes were clustered as <i>ars</i> operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for <i>ars-</i>like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in <i>Burkholderiales</i>; d) only a few numbers of <i>arsM</i> and <i>arrAB</i> are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in <i>Burkholderiales</i> members; (e) the <i>aio-like</i> gene is mostly flanked with <i>ars-like</i> genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.</p></div

Arsenic-related genes involved in bacterial arsenic resistance and transformation.

<p>Note: <i>ars</i>, cytoplasmic AsV reduction; <i>arr</i>, periplasmic AsV reduction; <i>aio</i>, arsenite oxidation; <i>arsM</i>, arsenite methylation.</p

Multiple organizations of the <i>aio</i> gene cluster and flanking sequences were detected in arsenite-oxidizing bacteria in <i>Burkholderiales</i>.

<p>Multiple organizations of the <i>aio</i> gene cluster and flanking sequences were detected in arsenite-oxidizing bacteria in <i>Burkholderiales</i>.</p

Distribution of arsenic-related genes in 188 <i>Burkholderiales</i> genomes.

<p>From upstream to downstream in the 10 core genes-based tree, the 188 strains' names and their detailed distribution of the arsenic-related genes is listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092236#pone.0092236.s005" target="_blank">Table S3</a>. The color of the bar indicates the gene numbers. One asterisk and double asterisks represent two times or four times as many as the average number of arsenic-related genes per genome, respectively.</p

Phylogenetic information on the 188 <i>Burkholderiales</i> bacterial genomes.

<p>Phylogenetic information on the 188 <i>Burkholderiales</i> bacterial genomes.</p

Additional file 1: of Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Table S1. Phenotype information of AS patient individuals and health controls in discovery stage (156 samples) and validation stage (55 samples). Table S2. Data production and quality control of 156 samples in discovery stage and 55 samples in validation stage. Table S3. The 8743 reference genomes from NCBI and HMP (downloaded on 15 Dec 2013). Table S4. The differentially abundant genus in AS patients (n = 73) and healthy controls (n = 83). Table S5. Assembly result of 156 samples in discovery stage. Table S6. The improvement with the repeatedly assembly. Table S7. Gene prediction of 156 samples in discovery stage. Table S8. Genes with abundance which belong to proteasome modules. All the differentially abundant genes identified in this study only belong to bacterial proteasome. Table S9. The taxonomic annotation of MGSs. Table S10. The phenotypic correlation analysis (p value) of 12 MGSs according to different clinical groups. Table S11. Comparison of the MGS in different diseases. Table S12. The taxonomic annotation of CAGs (Gene number ≥ 100). Table S13. The details of the best markers selected for five monitoring and classification models based on five kinds of bio-markers. Table S14. The 210 differentially abundant sequenced reference genome markers used for classification training. (XLSX 870 kb