Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: ( A ) Stacked bar plot depicting mean relative abundance of top nine abundant phyla in the fecal samples of HIV negative and HIV positive children. Dot Plots representing relative abundance of phyla ( B ) Bacteroidetes ( C ) Firmicutes, ( D ) Actinobacteria, and ( E ) Spirochaetes in HIV negative and HIV positive children. ( F ) Stacked bar plot showing mean relative abundance of top twelve abundant families in the fecal samples of HIV negative and HIV positive children. Dot Plots representing relative abundance of families ( G ) Prevotellaceae, ( H ) Bacteroidaceae ( I ) Ruminococcaceae ( J ) Lachnospiraceae and ( K ) Rikenellaceae in HIV negative and HIV positive children. ( L ) Stacked bar plot showing mean relative abundance of top twelve abundant genera in the fecal samples of HIV negative and HIV positive children. Dot Plots representing relative abundance of genera ( M ) Prevotella ( N ) Bacteroides ( O ) Faecalibacterium ( P ) Megasphaera ( Q ) Ruminococcus and ( R ) Haemophilus in HIV negative and HIV positive children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney-U-test was performed for statistical analysis. p < 0.05 was considered to be significant. Significant differences in the overall relative abundance of fecal microbiota at phylum, family and genus level between HIV negative and HIV positive children were estimated using adonis function of vegan R package.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: MANN-WHITNEY

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Comparison of Plasma IP-10 levels in ( A ) HIV positive and HIV negative children and ( B ) HIV negative, on ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. p < 0.05 was considered to be significant. ( C ) Heatmap representing the associations of relative abundance of significantly distinct genera with CD4 count, viral load, IL-1β, TNF-α, IP-10, GRO, MCD, sCDl40L and microbial translocation marker, sCD14. Blue and red shading represents positive and negative association respectively. Clustering was carried out based on the association of genera with clinical and immune parameters. ( D ) Heatmap representing the associations of absolute abundance of significantly distinct genera with IP-10. Blue shading indicates positive association and red shading indicates negative association. Clustering was carried out based on the association of genera with IP-10. Statistical analysis was carried out using Spearman t -test. p < 0.05 was considered to be significant. *p < 0.05.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Comparison, Clinical Proteomics, Infection, MANN-WHITNEY, Translocation Assay, Marker

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Dot plots representing relative abundance of Prevotella copri in the fecal sample of ( A ) HIV positive and HIV negative children and ( B ) HIV negative, On ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. The p < 0.05 was considered to be significant. Correlation between relative abundance of Prevotella copri and CD4 count in ( C ) HIV positive children (overall), ( D ) treatment naïve. ( E ) On ART perinatally HIV infected children. Statistical analysis was carried out using Spearman t -test. A linear regression line is included in each plot. p < 0.05 was considered to be significant.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Infection, MANN-WHITNEY, Comparison

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Association between absolute abundance of Prevotella and plasma IP-10 level (pg/ml) in ( A ) HIV positive children, ( B ) on ART and ( C ) treatment naïve perinatally HIV infected children. Statistical analysis was performed using Spearman t -test. A linear regression line is included in each plot. p < 0.05 was considered to be significant. Comparison of Plasma sCD14 levels in ( D ) HIV positive and HIV negative children and ( E ) HIV negative, on ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. p < 0.05 was considered to be significant. Association between ( F ) relative abundance of Prevotella and plasma sCD14 level (ng/ml) ( G ) relative abundance of Prevotella copri and plasma sCD14 level (ng/ml) in ART-suppressed perinatally HIV infected children. Statistical analysis was performed using Spearman t -test. A linear regression line is included in each plot. The p < 0.05 was considered to be significant.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Clinical Proteomics, Infection, Comparison, MANN-WHITNEY

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: ( A ) Stacked bar plot depicting mean relative abundance of top nine abundant phyla n the fecal samples of HIV negative, on ART and treatment naïve perinatally HIV-infected children. Comparison of relative abundance of phyla ( B ) Bacteroidetes ( C ) Firmicutes, ( D ) Actinobacteria and ( E ) Spirochaetes across HIV negative, on ART and treatment naïve perinatally HIV-infected children. ( F ) Stacked bar plot showing mean relative abundance of top twelve abundant families in the fecal samples of HIV negative, on ART and treatment naïve perinatally HIV-infected children. Comparison of relative abundance of families ( G ) Prevotellaceae, ( H ) Bacteroidaceae ( I ) Ruminococcaceae ( J ) Lachnospiraceae and ( K ) Rikenellaceae across HIV negative, on ART and treatment naïve perinatally HIV-infected children. ( L ) Stacked bar plot showing mean relative abundance of top twelve abundant genera in the fecal samples of HIV negative, on ART and treatment naïve perinatally HIV-infected children. Comparison of relative abundance of genera ( M ) Prevotella ( N ) Bacteroides ( O ) Faecalibacterium ( P ) Megasphaera ( Q ) Ruminococcus and ( R ) Haemophilus across HIV negative, on ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison was performed for statistical analysis. p < 0.05 was considered to be significant. Significant differences in the overall relative abundance of fecal microbiota at phylum, family and genus level between HIV negative controls, On ART and treatment naïve HIV-infected children were estimated using adonis function of vegan R package. *p < 0.05, **p < 0.005, p < 0.0005.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Infection, Comparison

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Comparison of Plasma IP-10 levels in ( A ) HIV positive and HIV negative children and ( B ) HIV negative, on ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. p < 0.05 was considered to be significant. ( C ) Heatmap representing the associations of relative abundance of significantly distinct genera with CD4 count, viral load, IL-1β, TNF-α, IP-10, GRO, MCD, sCDl40L and microbial translocation marker, sCD14. Blue and red shading represents positive and negative association respectively. Clustering was carried out based on the association of genera with clinical and immune parameters. ( D ) Heatmap representing the associations of absolute abundance of significantly distinct genera with IP-10. Blue shading indicates positive association and red shading indicates negative association. Clustering was carried out based on the association of genera with IP-10. Statistical analysis was carried out using Spearman t -test. p < 0.05 was considered to be significant. *p < 0.05.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Comparison, Clinical Proteomics, Infection, MANN-WHITNEY, Translocation Assay, Marker

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Dot plots representing relative abundance of Prevotella copri in the fecal sample of ( A ) HIV positive and HIV negative children and ( B ) HIV negative, On ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. The p < 0.05 was considered to be significant. Correlation between relative abundance of Prevotella copri and CD4 count in ( C ) HIV positive children (overall), ( D ) treatment naïve. ( E ) On ART perinatally HIV infected children. Statistical analysis was carried out using Spearman t -test. A linear regression line is included in each plot. p < 0.05 was considered to be significant.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Infection, MANN-WHITNEY, Comparison

Journal: Scientific Reports

Article Title: High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy

doi: 10.1038/s41598-018-35877-4

Figure Lengend Snippet: Association between absolute abundance of Prevotella and plasma IP-10 level (pg/ml) in ( A ) HIV positive children, ( B ) on ART and ( C ) treatment naïve perinatally HIV infected children. Statistical analysis was performed using Spearman t -test. A linear regression line is included in each plot. p < 0.05 was considered to be significant. Comparison of Plasma sCD14 levels in ( D ) HIV positive and HIV negative children and ( E ) HIV negative, on ART and treatment naïve perinatally HIV-infected children. The horizontal line and deviation in the dot plot represents median and interquartile range (IQR), respectively. Mann-Whitney U- test and Kruskal-Wallis one-way ANOVA with Dunn’s multiple comparison were performed for statistical analysis. p < 0.05 was considered to be significant. Association between ( F ) relative abundance of Prevotella and plasma sCD14 level (ng/ml) ( G ) relative abundance of Prevotella copri and plasma sCD14 level (ng/ml) in ART-suppressed perinatally HIV infected children. Statistical analysis was performed using Spearman t -test. A linear regression line is included in each plot. The p < 0.05 was considered to be significant.

Article Snippet: Statistical analysis of alpha diversity indices, the relative abundance of taxa, plasma cytokines, and soluble sCD14 levels between two and three groups was performed using non-parametric Mann Whitney U test and Kruskal-Wallis 1-way ANOVA with Dunn’s multiple comparison respectively in GraphPad Prism v. 6.

Techniques: Clinical Proteomics, Infection, Comparison, MANN-WHITNEY