Journal: Journal of biotechnology

Article Title: An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

doi: 10.1016/j.jbiotec.2016.06.014

Figure Lengend Snippet: Figure 3: Annotation of three selected metagenomic contigs encoding proteins identified by

Article Snippet: Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.

Techniques:

Journal: Nature Communications

Article Title: Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery

doi: 10.1038/s41467-019-09285-9

Figure Lengend Snippet: Vaginal microbiota composition and structure and risk of sPTB. a Frequency of each CST in non-AA and AA pregnant women when considering samples collected at all three visits or visit 1 (16–20 weeks of gestation). b Frequency of each CST stratified by outcomes (sPTB vs term) in all subjects, non-AA and AA when considering samples collected at all three visits or visit 1 alone. n represents the number of samples included in the analysis. For ( a ) and ( b ) p -values were estimated using mixed effects Poisson regression models (all visits) or ordinary logistic regression models (single visit) ( c ) Volcano plot for seven bacterial taxa statistically significantly associated with increased risk of sPTB in all subjects (red) and AA (blue) showing the effect size on the x -axis and the strength of the association on the y -axis. The gray horizontal lines indicate q -value of 0.05. The median relative abundance of each phylotype is indicated by the size of the point. Dependence of the risk of sPTB (defined as <37 weeks of gestation) on the log 10 relative abundance of M. curtisii/mulieris and S. sanguinegens in all subjects and AA is shown on the right. Effect size is the difference between the lowest and highest probability of sPTB. Greyed area indicates 95% credible region. Dotted line corresponds to the significant risk of sPTB threshold values (taxa log 10 relative abundance above which the risk is significant different from baseline). n represents the number of samples in which the bacterial taxon was detected and included in the analysis. ( d ) is the same as ( c ) but with sPTB defined as birth at <34 weeks of gestation. N represents the number of subjects in each group. Statistically significant taxa were identified using a Bayesian logistic regression nonparametric adaptive spline models. e Kaplan–Meier survival plot for M. indolicus , M. curtisii/mulieris and S. sanguinegens in all and AA women who harbor these bacterial taxa at relative abundance (RA) below (blue) or above (orange) the threshold values above which the risk of sPTB is significant different from baseline. p -values estimated using Cox proportional hazard regression models using coxph() routine of the survival R package. Statistical significance is shown as * p -value < 0.01, ** p -value < 0.001, and *** p -value < 0.0001

Article Snippet: Cervicovaginal ESwabs were thawed on ice, and 300 μl of Amies transport medium containing vaginal secretion were processed using the MoBio PowerMag Microbiome DNA/RNA kit (now MagAttract PowerMicrobiome DNA/RNA kit, Qiagen) automated on a Hamilton Microlab STAR robotic platform after a bead-beating step on a Qiagen TissueLyser II (20 Hz for 20 min) in 96 deep well plate.

Techniques:

Journal: Nature Communications

Article Title: Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery

doi: 10.1038/s41467-019-09285-9

Figure Lengend Snippet: β-defensin-2 and microbiota modulate the risk of spontaneous preterm delivery. a Modulation of the risk of sPTB by relative abundance of M. curtisii/mulieris stratified by Lactobacillus spp. relative abundance tertiles within AA when all visits are considered. n represents the number of samples where M. curtisii/mulieris was detected. b log 10 β-defensin-2 abundances at visit 1 in AA women stratified by pregnancy outcomes and vaginal community state types. p -values estimated using a t -test. c At visit 1 in AA women, the risk of sPTB associated with the relative abundance of five bacterial taxa is modulated by the abundance of β-defensin-2. p -values were estimated using a Bayesian 2-proportions binomial model with uniform prior implemented in rstan R package. Statistical significance is shown as * p -value < 0.01, ** p -value < 0.001 and *** p -value < 0.0001

Article Snippet: Cervicovaginal ESwabs were thawed on ice, and 300 μl of Amies transport medium containing vaginal secretion were processed using the MoBio PowerMag Microbiome DNA/RNA kit (now MagAttract PowerMicrobiome DNA/RNA kit, Qiagen) automated on a Hamilton Microlab STAR robotic platform after a bead-beating step on a Qiagen TissueLyser II (20 Hz for 20 min) in 96 deep well plate.

Techniques: