Comparison of 16S sequencing and shallow shotgun recovery of species-level taxa. Comparison of 16S sequencing and shallow shotgun recovery of species-level.

Slides:

Advertisements

Similar presentations

Nonmetric multidimensional scaling (NMDS) ordination of variation in bacterial community structure of tree phyllosphere along a gradient of urban intensity.

Advertisements

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome Ohad Manor, Elhanan Borenstein Cell Host.

16S rRNA gene abundance and total gene expression of Tannerella species in healthy patient and periodontitis patient samples. 16S rRNA gene abundance and.

Boxplots displaying relative percent abundance of consistent abundance-based microbiome members present in the tissue, mucus, and holobiont (Holo) fractions.

Exploration of the data set with age as a continuous variable.

Validation of the CCE associations by mass spectrometry.

Histograms of grades in two classes, each of 200 students

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)

Fig. 2. Associations between bacterial taxa abundance ascertained by fecal shotgun metagenomic sequencing and the fecal metabolome in healthy pediatric.

Transdomain taxonomic profiles from subway shotgun metagenomes.

A1 A2 B1 B2 C1 C2 C3 C4 Figure S1. Comparison of percentage relative abundances of polyamines taking country (A1) and mode of delivery (A2) as factors.

Bacterial biomarkers associated with disease severity.

Differential abundance of bacterial families.

Fluoride affects stool-derived taxa found in the oral cavity.

Hierarchical cluster analysis of reproducible parent masses (MS) representative of produced SMs from oral in vitro-grown biofilm representing >100 bacterial.

Transcription levels of metabolic pathways and genes in mother and infant pair 4 at time point 2. Transcription levels of metabolic pathways and genes.

Bacteroidetes bacteria are the main contributors to LPS biosynthesis in the human gut microbiome. Bacteroidetes bacteria are the main contributors to LPS.

Differences in microbiome between control and BPA-exposed rabbit offspring and dams according to linear discriminant analysis effect size (LEfSe). Differences.

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.

OTU and beta-diversity novelty.

Ortholog identification and summaries.

Structure of benthic microbial communities of residential and industrial land use types before and after two rain events in urban waterways are shown.

Volume 88, Issue 4, Pages (November 2015)

Comparison of distal gut metabolite profiles between Egyptian and U. S

Bacteria significantly correlated with DE miRNAs.

Example usage of mockrobiota MC resource for marker gene and metagenome sequencing pipelines. Example usage of mockrobiota MC resource for marker gene.

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

Enterotypes of the distal gut microbial profiles.

Distribution of microbial functions in urban waterways.

Comparison of the original ITS primer pair and the new, modified ITS primer pair. Comparison of the original ITS primer pair and the new, modified ITS.

Comparison of the modified 515f/806rB V4 primer pair and the 515f (modified)/926r primer pair. Comparison of the modified 515f/806rB V4 primer pair and.

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

Comparison of observed and predicted coverage patterns.

Volume 22, Issue 3, Pages e4 (September 2017)

Canonical correspondence analysis (CCA) showing the correlations among soil edaphic factors and microbial communities from each sample type. Canonical.

Field community comparisons via 16S and between sequencing runs.

(a, b) Hypothetical scenario where 2 samples of 2 proportions may explain two different scenarios in the environment. (a, b) Hypothetical scenario where.

Relative ITS2 abundance of Saccharomyces in stool over time as a Saccharomyces cerevisiae-free diet was consumed. Relative ITS2 abundance of Saccharomyces.

Spearman correlation of normalized relative abundances between MAGs from TBE6 and taxa in the epilimnion of the environment of origin (Trout Bog Lake).

T7 transcripts increase relative to E. coli transcripts over time.

Label frequency and average enrichment of taxa.

Framework for integrating taxonomic and metabolomic data.

RNA abundance correlates with fitness.

Exploration of gut and skin microbiome of the habitat switching experiment with Calour. Exploration of gut and skin microbiome of the habitat switching.

Altered mycobiota and bacterial-fungal correlation in AS patients receiving different therapeutic regimens. Altered mycobiota and bacterial-fungal correlation.

Taxonomy assessment of metagenes with differential abundance as a result of the AXOS intervention. Taxonomy assessment of metagenes with differential abundance.

Benchmarks of OTU picking tools on artificial communities.

Comparison of Nonpareil Nd sequence diversity and 16S rRNA gene OTU Shannon H′ taxonomic diversity indices on 90 metagenomes. Comparison of Nonpareil Nd.

Microbial differences found between TPC- and PBS-treated mice with lupus. Microbial differences found between TPC- and PBS-treated mice with lupus. (A)

Diversity of whale blow and seawater samples from minimum entropy decomposition (MED) node groupings (17), including observed number of MEDs, a relative.

Cyanophage-host interactions from metatranscriptomic data.

A principal-coordinate analysis plot of UniFrac distances from Deblur as visualized by Emperor. A principal-coordinate analysis plot of UniFrac distances.

Comparison of species and function profiles with ultradeep sequencing data. Comparison of species and function profiles with ultradeep sequencing data.

Pairwise UniFrac distances for each consecutive-time pair from the same sample, aggregated and smoothed to distribution functions before and while taking.

Fig. 1 A phylogenetically cohesive core rumen microbiome was found across farms with highly conserved hierarchical structure and tight association to overall.

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

A principal-coordinate analysis plot of UniFrac distances from UNOISE2 as visualized by Emperor. A principal-coordinate analysis plot of UniFrac distances.

OTU and family-level changes in murine gut as a result of acarbose feeding on a high-starch diet. OTU and family-level changes in murine gut as a result.

Comparison of the original 515f/806r primer pair and the new, modified 515f/806rB primer pair. Comparison of the original 515f/806r primer pair and the.

PCoA plots of subgingival samples with disease classification overlaid

K-means clusters of T. elongatus and M

Relationships between antimicrobial chemicals, features of the built environment, and microbial communities. Relationships between antimicrobial chemicals,

Hierarchically clustered heat map showing correlations between the relative abundances of microbial species and the levels of volatile compounds in kefir.

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.

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.

Relative abundance and expression of the 10 most abundant MAGs in the bioreactor at day 96. Relative abundance and expression of the 10 most abundant MAGs.

Fig. 3 Postnatal assembly of the humanized gut microbiota.

Infant skin and oral mycobiomes by birth mode.

Presentation transcript:

Comparison of 16S sequencing and shallow shotgun recovery of species-level taxa. Comparison of 16S sequencing and shallow shotgun recovery of species-level taxa. (A) Histogram of average Pearson correlation (R-squared) of species profiles between 16S sequencing and shallow shotgun sequencing from the same HMP sample (R-squared = 0.918), compared to the permutation-based null distribution of R-squared values for random pairings (P < 0.001). (B) Scatterplot of relative abundances of species in shallow shotgun sequencing versus 16S sequencing from the same HMP samples. Species found in only one data type are shown in a different color. (C) Fractions of all observed species, with relative abundance accounted for by species found by 16S sequencing only, shallow shotgun sequencing only, or both. Benjamin Hillmann et al. mSystems 2018; doi:10.1128/mSystems.00069-18