Plots of the number of sequences [log (x + 1) scale] from bacterial OTUs in both PCR replicates (PCR1 and PCR2) of the 348 wild rodents analyzed in the.

Slides:

Advertisements

Similar presentations

The Build-up of the Red Sequence at z

Advertisements

Supplementary Fig. 1. Transcriptome analysis of MENX-associated pituitary adenomas and and comparison with human studies. Control samples from wild-type.

May 12-15, 2011 (red) May 6-11, 2011 (light red) Permanent Water (blue)

Strategy for F1 mutation carrier screening and identification of their mutations. Strategy for F1 mutation carrier screening and identification of their.

Sensitivity of RNA‐seq.

Taxonomic composition of subway microbial communities.

Microbial community dissimilarity.

HIS-24 regulates expression of infection-inducible genes.

Fig. 4 Bacterial taxonomic groups that discriminate among RYGB-, SHAM-, and WMS-derived samples. Bacterial taxonomic groups that discriminate among RYGB-,

Heatmap displaying consistent similarity-based OTU results based on SIMPER intragroup similarity analyses for the tissue, mucus, holobiont, and seawater.

Relative abundances of the top 10 most abundant OTUs across all fish samples are shown along with the data from the probiotic B. pumilus RI06-95 (OTU 3673)

Number of flowering plants 1999 (log-scale) Compatibility (%)

Benchmarks of OTU picking tools on natural communities.

Q-Q plot of observed P values against theoretical P values for factor analysis (red dots) and single gene–based methods (in blue). Q-Q plot of observed.

Analysis of changes in the host metabolome during M

Differential abundance of bacterial families.

NGS on SOP-generated HRV-16-specific sequence from pure and mixed samples is slightly less sensitive than quantitative real-time RT-PCR (qrRT-PCR). NGS.

Venn diagram of blaKPC-containing plasmids detected in the environment and patients. Venn diagram of blaKPC-containing plasmids detected in the environment.

A small number of bacteria showed high levels of growth in the storage studies. A small number of bacteria showed high levels of growth in the storage.

Taxonomic composition of the baboon and human gut microbiota.

(a) Correspondence analysis of 88 soil samples.

Lack of phylogenetic conservatism of Bacillus anthracis plasmid copy number. Lack of phylogenetic conservatism of Bacillus anthracis plasmid copy number.

Correlation of mouse gene expression with bacterial gene expression.

Performance of FDR methods on filtered microbiome data.

Distribution of the bacterial taxa that exhibit the greatest log fold changes in mean relative abundance. Distribution of the bacterial taxa that exhibit.

Comparing read recruitment, de novo, and insertion tree strategies for phylogenetic diversity computation. Comparing read recruitment, de novo, and insertion.

Enrichment of members of KEGG Orthology (KOs) families across MBTA surfaces before and after P. acnes removal. Enrichment of members of KEGG Orthology.

Phylogenetic tree of genome-sequenced bacterial strains from the Populus microbiome. Phylogenetic tree of genome-sequenced bacterial strains from the Populus.

OTU and beta-diversity novelty.

Distributions of pairwise correlation coefficients from cooccurrence models computed from temporal data (fecal) and spatial data (biopsy samples; means.

miRNA target pathways correlated with CRC-associated bacteria.

Box plots of quality scores over positions in sequenced reads.

Gene-wise Tajima’s D values and gene lengths.

Bacteria significantly correlated with DE miRNAs.

Differential relative abundance of major taxa for successive pairwise comparisons. Differential relative abundance of major taxa for successive pairwise.

The similar shifts of gut microbiota in IBD across cohorts.

Stability of fecal microbiomes in different preservatives and under different temperature treatments. Stability of fecal microbiomes in different preservatives.

Example of amplicon performance in our presented workflow.

Workflow of the wet laboratory, bioinformatics, and data filtering procedures in the process of data filtering for 16S rRNA amplicon sequencing. Workflow.

Outgrowth of passaged strains.

Field community comparisons via 16S and between sequencing runs.

The mass spectrum of heterocyst glycolipid and the corresponding structures are shown on the right. The mass spectrum of heterocyst glycolipid and the.

Trends in metabolite predictability in terms of key gene contributors.

Gut microbiota components influenced by AXOS intake.

Benchmarks of OTU picking tools on artificial communities.

(a) A band table where the y axis data represent individual OTUs and the x axis data represent samples. (a) A band table where the y axis data represent.

Box plots displaying the median, minimum, maximum, and first and third quartiles of the percentage of the 25 members of the core microbiome detected in.

Statistical chart of significantly differentially expressed genes

Daily percentages of probiotic oligotype reads found in the dolphin rectum samples. Daily percentages of probiotic oligotype reads found in the dolphin.

Relative growth of transcription factor knockout mutants on different sulfur sources. Relative growth of transcription factor knockout mutants on different.

Comparison of biological replicates for Ery-treated samples.

MiRNA expression profiling in adipocytes from wild-type (WT) and leptin-deficient ob/ob mice. miRNA expression profiling in adipocytes from wild-type (WT)

Chd5-deficient NSCs generate excessive astrocytes at the expense of neurons. Chd5-deficient NSCs generate excessive astrocytes at the expense of neurons.

Heatmap showing Spearman’s rho values for significant correlations between weed abundances and bacterial classes (i.e., OTU data pooled at the class level;

Template application to detect KC-like activity.

Principal-coordinate analysis (PCoA) (Hellinger distance metric) of plant community (A), soil chemistry (B), 16S rRNA gene (prokaryotic) (C), and ITS (fungal)

Bacterial composition of olive fermentations is affected by microbial inoculation. Bacterial composition of olive fermentations is affected by microbial.

Enrichment of KEGG pathways in microbial genes in different samples.

Transcriptomic changes in strains PAK and PAKpmrB6 in response to polymyxin B (PMB). Transcriptomic changes in strains PAK and PAKpmrB6 in response to.

PCoA plots of subgingival samples with disease classification overlaid

Identification of a ufo1 Candidate Gene from the Mapping Region.

Change in FES uptake in the tumor during fulvestrant treatment.

Relative abundance of taxa in the 16S rRNA PCR amplicon and gDNA mock communities. Relative abundance of taxa in the 16S rRNA PCR amplicon and gDNA mock.

Comparison of PQ-CSF and IQ-CSF RT-QuIC analyses of individual sCJD and negative-control CSF samples. Comparison of PQ-CSF and IQ-CSF RT-QuIC analyses.

Variations in beta and alpha diversity of gut microbiome bacterial communities in relation to presence of Blastocystis. Variations in beta and alpha diversity.

Variations in beta and alpha diversity of gut microbiome eukaryotic communities explained by presence of Blastocystis. Variations in beta and alpha diversity.

ChIP-chip analysis of wild-type (WT) and RpoZ-defective mutant RNAP

The slope of a displacement-time graph represents the velocity.

Fig. 3 Genome editing of the MSTN gene.

Small RNA sequencing data quality.

Presentation transcript:

Plots of the number of sequences [log (x + 1) scale] from bacterial OTUs in both PCR replicates (PCR1 and PCR2) of the 348 wild rodents analyzed in the first MiSeq run. Plots of the number of sequences [log (x + 1) scale] from bacterial OTUs in both PCR replicates (PCR1 and PCR2) of the 348 wild rodents analyzed in the first MiSeq run. Note that each rodent was tested with two replicate PCRs. Green points correspond to rodents with two positive results after filtering; red points correspond to rodents with one positive result and one negative result; and blue points correspond to rodents with two negative results. The light blue area and lines correspond to threshold values used for the data filtering: samples below the lines were filtered out. See Fig. S3 for plots corresponding to the second MiSeq run. Maxime Galan et al. mSystems 2016; doi:10.1128/mSystems.00032-16