Relative proportions of taxa and UPGMA hierarchical clustering of the mock communities. Relative proportions of taxa and UPGMA hierarchical clustering.

Slides:



Advertisements
Similar presentations
Distance methods. UPGMA: similar to hierarchical clustering but not additive Neighbor-joining: more sophisticated and additive What is additivity?
Advertisements

Taxonomic composition of subway microbial communities.
Microbial community dissimilarity.
Changes in archaeal diversity during great ape diversification.
Microbial diversity was broadly compared across three unique built-environment study sites for 16S rRNA amplicon and shotgun metagenome sequencing. Microbial.
Metagenomics and development of the gut microbiota in infants
Microbial diversity of the 10 body locations sampled.
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.
5-ALA increased porphyrin production, which was further enhanced by vitamin B12 supplementation in acne-associated type IA-2 strains. 5-ALA increased porphyrin.
Positions of LSUCC isolates relative to matching OTUs within the top 60 ranks for the most successful experiment, CJ2, which is enlarged to allow for OTU.
Bacterial community dissimilarity, as measured by weighted UniFrac, a quantitative measurement (a), and unweighted UniFrac, a qualitative measurement (b),
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.
Growth of L. monocytogenes strains AL4E, AT3E, and 10403S, derivative cured strain AT3Epc, and conjugation strains 10403SpclpL and 10403SpPL2 displayed.
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.
(A and B) Relative (A) and mean (B) abundances of reference viral genomes across the continuum summarized by host type. (A and B) Relative (A) and mean.
The Inuit microbiome has a community composition similar to that of the Western microbiome. The Inuit microbiome has a community composition similar to.
Binding competition between B2′B3 and B3 fragments of TcdB.
Cecal metabolome during C. difficile colonization and infection.
KEGG pathway analysis of the C
Microbial community structure analysis.
Relative ITS2 abundance of Saccharomyces in stool over time as a Saccharomyces cerevisiae-free diet was consumed. Relative ITS2 abundance of Saccharomyces.
Aboveground and belowground samples showed differences in their bacterial community structures and compositions, while bulk soil and root communities differed.
Spearman correlation of normalized relative abundances between MAGs from TBE6 and taxa in the epilimnion of the environment of origin (Trout Bog Lake).
Co-occurrence network in tongue microbiota of 506 elderly adults built from SparCC correlation coefficients between sequence abundances. Co-occurrence.
Belowground microbiome community responses.
(A) Taxonomic identity at the phylum level of raw leachate (RL) and enrichment microcosms (E) as determined via Ion Torrent 16S rRNA gene amplicon sequencing.
Relative abundances of microeukaryotic taxa detected by ITS2 analysis of DNA or cDNA from stool. Relative abundances of microeukaryotic taxa detected by.
Microbial communities of the differently treated mice with lupus cluster separately after treatment. Microbial communities of the differently treated mice.
Benchmarks of OTU picking tools on artificial communities.
Shifts in the microbial community compositions of the control and antibiotic groups. Shifts in the microbial community compositions of the control and.
Bray-Curtis beta diversity analysis of Kaneohe Bay (KB) ANG and JC bacterial communities. Bray-Curtis beta diversity analysis of Kaneohe Bay (KB) ANG and.
Nonmetric multidimensional scaling (NMDS) (A) and dendrogram and heat map (B) of the relative abundances of the data in the custom database across the.
Cyanophage-host interactions from metatranscriptomic data.
Comparison of taxonomic differences between stool microbiota from healthy patients and stool microbiota from ICU patients and stool from healthy patients.
Dynamic light scattering (DLS) analysis of S
Change in fluorescence of C. neoformans upon addition of DM262.
The ND6P25L mtDNA mutation reduces gut microbiota diversity in C57BL/6J mice. The ND6P25L mtDNA mutation reduces gut microbiota diversity in C57BL/6J mice.
The Amazon viral scaffolds and viral genomes most important for river and plume segregation. The Amazon viral scaffolds and viral genomes most important.
Fig. 1 A phylogenetically cohesive core rumen microbiome was found across farms with highly conserved hierarchical structure and tight association to overall.
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.
Spearman’s correlation analysis of microbiota and NMR spectra of the control and ciprofloxacin groups (A, C) or the vancomycin-imipenem group (B, D) after.
Bacterial composition of olive fermentations is affected by microbial inoculation. Bacterial composition of olive fermentations is affected by microbial.
Taxonomic composition over time was determined by (A) metagenomic sequencing and (B) qualitative culturomics. Taxonomic composition over time was determined.
ITS rRNA gene locus. ITS rRNA gene locus. Schematic of the eukaryotic ribosomal gene cluster. The SILVA database contains sequences of the 18S gene, while.
KEGG cluster of DEGs of S
by Peter J. Turnbaugh, Vanessa K. Ridaura, Jeremiah J
PCoA plots of subgingival samples with disease classification overlaid
Wolbachia bacterial infection does not affect the expression of Imd pathway components and ROS-producing oxidases. Wolbachia bacterial infection does not.
Integrated mRNA and microRNA expression and DNA methylation clusters.
Procrustes analysis comparing the spatial fit of unweighted UniFrac principal-coordinate matrices of bacterial communities (yellow spheres) and Bray-Curtis.
ICU stays result in drastic community changes.
LEfSe comparison analysis between the control and ciprofloxacin or vancomycin-imipenem groups at the end of antibiotic treatment (A or B, respectively)
Beta-diversity analyses of microbial taxa recovered from ATM keypads.
Bipartite co-occurrence networks were generated in CoNet and visualized in Cytoscape to display significant strong positive and negative co-occurring relationships.
Small-molecule inhibitor reduced porphyrin production in P
After the addition of fluconazole, there were bands that were higher in molecular weight than the starting library, N40 (lane N), and the original sequences.
In silico taxon coverage.
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.
Acarbose reversibly changes the structure of the murine gut community.
Variations in beta and alpha diversity of gut microbiome bacterial communities in relation to presence of Blastocystis. Variations in beta and alpha diversity.
General overview of the bioinformatic pipelines for the 16S rRNA gene microbial profiling and shotgun metagenomics. General overview of the bioinformatic.
Alpha diversity analysis of Kaneohe Bay ANG and JC bacterial communities. Alpha diversity analysis of Kaneohe Bay ANG and JC bacterial communities. Two-way.
Northern shovelers may have unique microbiome differences with respect to IAV infection, relative to the other duck species. Northern shovelers may have.
GBM 112 and GBM 144 cells infected in vitro with HCMV resist growth inhibition by temozolomide. GBM 112 and GBM 144 cells infected in vitro with HCMV resist.
Relative abundances of bacterial/archaeal groups in 16S rRNA data set.
Identification of bacterial species producing the anti-Candida molecules. Identification of bacterial species producing the anti-Candida molecules. (A)
Presentation transcript:

Relative proportions of taxa and UPGMA hierarchical clustering of the mock communities. Relative proportions of taxa and UPGMA hierarchical clustering of the mock communities. UPGMA hierarchical clustering was based on the (A) Bray-Curtis dissimilarity matrix and (B) weighted Unifrac distance matrix. Expected taxa (9 bacterial species) are labeled with the corresponding taxonomic level from the DNA sequencing results. Each bar contains the results from each of the three mock community replicates tested using different DNA sequencing methods. The results shown were analyzed following the DADA2 pipeline with the Greengenes database. Zhengyao Xue et al. mSphere 2018; doi:10.1128/mSphere.00410-18