MOESM1 of Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity

Additional file 1: Table S1. Collection details of the samples studie

Additional file 1: Table S1. of Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India

Metadata and numbered of analysed reads for each sample. Table S2. Additional metadata of Swedish study participants. Table S3. Average abundance of amino acid substitutions detected in >1 % of all reads. (DOC 91 kb

Secretor Status Is Strongly Associated with Microbial Alterations Observed during Pregnancy

<div><p>During pregnancy there are significant changes in gut microbiota composition and activity. The impact of secretor status as determined by genotyping <i>FUT2</i> (fucosyltransferase 2) gene was taken as one of the confounding factors associated with faecal microbiota changes during pregnancy. In this prospective study, we followed women during pregnancy (total = 123 of which secretors = 108, non-secretors = 15) and characterised their gut microbiota by quantitative polymerase chain reaction (qPCR), Fluorescence In situ Hybridisation (FISH), Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing. qPCR revealed that <i>C</i>. <i>coccoides group</i> counts decreased significantly in non-secretors in comparison to secretors (p = 0.02). Similar tendency was found by FISH analysis in <i>Clostridium histolyticum</i> and <i>Lactobacillus-Enterococcus</i> groups between the secretor and the non-secretor pregnant women. DGGE analysis showed significant decrease in richness of <i>Clostridium</i> sp. between secretor and non-secretor mothers during pregnancy. Pyrosequencing based analysis at phyla level showed that there is greater increase in Actinobacteria in secretors in comparison to non-secretors, whereas Proteobacteria showed more increase in non-secretors. Change in relative abundance of <i>Clostridiaceae</i> family from first to third trimester were significantly associated with secretor status of pregnant women (p = 0.05). Polyphasic approach for microbiota analysis points out that the host secretor status (FUT2 genotype) affects the gut microbiota during pregnancy. This may lead to altered infant gut microbiota colonization.</p></div

Quantitative PCR analysis for bacterial counts in faecal samples of pregnant women at first trimester and third trimester.

<p>a = Baseline differences at first trimester</p><p>b = test for secretor status as fixed effect</p><p>c = interaction between secretor and time as factors</p><p>d = P for time effect <0.002, SD = Standard deviation</p><p>Quantitative PCR analysis for bacterial counts in faecal samples of pregnant women at first trimester and third trimester.</p

Pie chart of percent mean relative abundance of microbial composition as determined by pyrosequencing A) Phylum B) Family level (with percent relative abundance of more than 1%), at First trimester (T1) and at Second trimester (T2) compared between Secretors and Non-secretors.

<p>Pie chart of percent mean relative abundance of microbial composition as determined by pyrosequencing A) Phylum B) Family level (with percent relative abundance of more than 1%), at First trimester (T1) and at Second trimester (T2) compared between Secretors and Non-secretors.</p

RDA plots for pyrosequencing based microbiota analysis: Family level (A&B) microbial composition was significantly different at third trimester when compared A) Secretors (blue circles) vs Non Secretors (red circles) (p = 0.04); B) and genotypes (AA = red, GA = green, GG = blue) (p = 0.01).

<p><b>Phyla level</b> (C&D) difference was found to be different at first trimester when C) Secretor status D) Genotypes are compared (p = 0.005). Triangles indicate centroids of study groups.</p

Fluorescent in situ hybridization analysis for bacterial counts in faecal samples of pregnant women at first trimester and third trimester.

<p>a = Baseline differences at first trimester</p><p>b = test for secretor status as fixed effect</p><p>c = interaction between secretor and time as factors</p><p>d = P for time effect <0.0007, SD = Standard deviation</p><p>Fluorescent in situ hybridization analysis for bacterial counts in faecal samples of pregnant women at first trimester and third trimester.</p

Fluoroquinolones and <i>qnr</i> Genes in Sediment, Water, Soil, and Human Fecal Flora in an Environment Polluted by Manufacturing Discharges

There is increasing concern that environmental antibiotic pollution promotes transfer of resistance genes to the human microbiota. Here, fluoroquinolone-polluted river sediment, well water, irrigated farmland, and human fecal flora of local villagers within a pharmaceutical industrial region in India were analyzed for quinolone resistance (<i>qnr)</i> genes by quantitative PCR. Similar samples from Indian villages farther away from industrial areas, as well as fecal samples from Swedish study participants and river sediment from Sweden, were included for comparison. Fluoroquinolones were detected by MS/MS in well water and soil from all villages located within three km from industrially polluted waterways. Quinolone resistance genes were detected in 42% of well water, 7% of soil samples and in 100% and 18% of Indian and Swedish river sediments, respectively. High antibiotic concentrations in Indian sediment coincided with high abundances of <i>qnr</i>, whereas lower fluoroquinolone levels in well water and soil did not. We could not find support for an enrichment of <i>qnr</i> in fecal samples from people living in the fluoroquinolone-contaminated villages. However, as <i>qnr</i> was detected in 91% of all Indian fecal samples (24% of the Swedish) it suggests that the spread of <i>qnr</i> between people is currently a dominating transmission route

Various life history stages of <i>Frankixalus jerdonii</i>.

<p>(A) lateral, (B) dorsal, (C) ventral views of a preserved stage 36 tadpole, (D) unfertilised “nutritive” eggs found inside the dissected larval gut (mean diameter = 1.0 mm), (E) oral disc with papillae demarcating its margins, shown in frontal view of a stage 36 tadpole, (F) dextral vent tube, in ventral view of a stage 26 tadpole, (G) sinistral spiracular tube, in ventral view of a stage 36 tadpole, (H) gel-encapsulated eggs (mean diameter = 2.0 mm) found on the inside wall of a tree hole, (I) dorsolateral view of a stage 44 tadpole, (J) oral disc of a live stage 36 tadpole having a bifurcated muscular tongue, shown in frontal view, (K) dorsal, (L) ventral views of a live stage 35 tadpole, (M) serrated, inverted upper jaw of a stage 37 tadpole in ventral view, (N) serrated, V-shaped lower jaw of a stage 37 tadpole in ventral view.</p

A–C, <i>Frankixalus jerdonii</i> in life.

<p>(A) dorsolateral view of an adult male (BNHS 5976), (B) an adult male (SDBDU 2009.271) emerging from a tree hole, (C) frontal view of an adult male (BNHS 5977). D–H, A composite showing the breeding habitat of <i>Frankixalus jerdonii</i>. (D) Evergreen forest at Mawphlang in East Khasi Hills district of Meghalaya state, (E) close-up of a tree hole opening located 3.4 meters above the ground, (F) oviposition site with eggs adhered to the inner vertical walls of the tree hole above the water level, and arrow pointing towards an adult female found submerged about 1 cm below the water surface, (G) unpigmented gel-encapsulated eggs, (H) premetamorphic larva inside the water-filled tree hole.</p