Journal: The ISME Journal

Article Title: Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype

doi: 10.1038/s41396-021-00955-5

Figure Lengend Snippet: This figure was generated using the 16S rRNA gene amplicon sequencing data from the biogeography dataset, and the 16S rRNA gene amplicon sequencing data from the plant development dataset (Montcalm growing location). DESeq2 was used to identify differentially abundant taxa by compartment ( p -value < 0.05 after false discovery rate correction). Log2 fold change values were used to determine shading; taxa shaded in green were enriched in the rhizoplane and taxa shaded in brown were enriched in the rhizosphere. Sloan neutral models were fit to both datasets to understand which core taxa were above (blue) or below (red) the model expectation. All taxa that are not highlighted follow the neutral prediction. The sample sizes are provided in brackets. Core taxa are arranged and color-coded by taxonomic classification at the phylum level.

Article Snippet: This figure was generated using the 16S rRNA gene amplicon sequencing data from the biogeography dataset, and the 16S rRNA gene amplicon sequencing data from the plant development dataset (Montcalm growing location).

Techniques: Generated, Amplification, Sequencing

Journal: NPJ Biofilms and Microbiomes

Article Title: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

doi: 10.1038/s41522-017-0040-3

Figure Lengend Snippet: Meta-analysis of biofilm prevalence in CRC. a Microbial biofilms in Carnoy’s-fixed tissue were detected by FISH with the universal 16S rRNA gene probe Eub338 (stained in red) and the nucleic acid stain DAPI (blue). White brackets denote the mucus layer, visible via autofluorescence of the tissue. Left panel: a biofilm-positive paired normal tissue from the right colon of a CRC patient with abundant bacteria adjacent to the epithelium (arrow). Right panel: a biofilm-negative paired normal tissue from the left colon of a CRC patient with minimal bacteria (arrow) present only in the outer edge of the mucus. Scale bars represent 100 μm. b The locations of tumors from USA, MAL1, and MAL2 are overlaid on a diagram of the colon. c Percentage of biofilm-positive right and left tumors for the three cohorts. All statistics shown are Fisher’s exact tests. d Total percentage of biofilm-positive right- and left-sided tumors from all three cohorts is depicted with a Fisher’s exact test p -value. e Left-sided and right-sided tumors separated according to tumor stage and biofilm status. Multivariate logistic regression analysis was performed after controlling for tumor side. f , g Biofilm-positive samples were stained with DAPI (blue) and probes against four bacterial membership groups: Fusobacterium (yellow), Bacteroidetes (green), Lachnospiraceae (red), and Proteobacteria (magenta). Scale bars in large images represent 100 μm; scale bars in smaller, inset images represent 5 μm. f Representative polymicrobial biofilm from a tumor (left panel) and its paired normal tissue (right panel), with blooms of Fusobacterium in yellow visible only in the tumor. g Representative Proteobacteria-dominant tumor (left panel) and its paired normal tissue (right panel)

Article Snippet: To enhance our taxonomic resolution, 16S rRNA amplicon sequence data sets from USA, MAL1, and MAL2 cohorts were analyzed using Resphera Insight, a high-resolution methodology for species-level characterization (see Methods).

Techniques: Staining, Bacteria

Journal: NPJ Biofilms and Microbiomes

Article Title: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

doi: 10.1038/s41522-017-0040-3

Figure Lengend Snippet: Microbial associations with biofilm status. Frozen tissue from USA, MAL1, and MAL2 cohorts were characterized by 16S rRNA amplicon sequencing. a Top panel: biofilm positive CRC and normal flanking tissues demonstrated several functional shifts in the bacterial composition, including increases in gene content associated with cytoskeletal proteins, peptidoglycan biosynthesis, sporulation, and flagellar assembly based on PICRUSt analysis. Bottom panel: the bacterial families Veillonellaceae, Coriobacteriaceae, and Lachnospiraceae were enriched in biofilm-positive samples, while Sphingomonadaceae was enriched in biofilm-negative samples. Random-effects models with 95% CI above or below 0 (red diamonds) were considered statistically significant. Hedge’s g difference statistic is shown on the X axes. The fixed effects model assumes there exists a single effect size shared by all included studies, while the random effects model allows for variation in the effect size from study to study. Heterogeneity analysis includes estimates of I 2 (percentage of variation reflecting true heterogeneity), τ 2 (random-effects between study variance), and p -value from Cochran’s Q test for heterogeneity. b The functional alterations due to biofilm status were linked to multiple, differentially abundant families (f) and genera (g) in the biofilms

Article Snippet: To enhance our taxonomic resolution, 16S rRNA amplicon sequence data sets from USA, MAL1, and MAL2 cohorts were analyzed using Resphera Insight, a high-resolution methodology for species-level characterization (see Methods).

Techniques: Amplification, Sequencing, Functional Assay

Journal: NPJ Biofilms and Microbiomes

Article Title: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

doi: 10.1038/s41522-017-0040-3

Figure Lengend Snippet: Associations of B. fragilis and human oral microbiota with CRC status for USA, MAL1, and MAL2 cohorts. Microbiome profiling with 16S rRNA gene sequencing was applied to tumor (CRC) and paired normal tissues (Normal) from CRC patients for all three cohorts, as well as healthy biopsies (Healthy Bx) for USA and MAL1. a Bar charts of microbial sequence relative abundance for B. fragilis and bacteria from the Human Oral Microbiome Database (HOMD) from the three 16S rRNA amplicon data sets: USA (top panel), MAL1 (middle panel), and MAL2 (bottom panel). Each vertical bar represents an individual patient. b B. fragilis as well as the oral pathogens F. nucleatum , P. micra , P. stomatis, G. morbillorum , and the overall consortia associated with the Human Oral Microbiome Database (HOMD) were all found to be significantly enriched in tumor specimens compared to biopsies from healthy patients without cancer (top panel), and compared to normal flanking tissue (bottom panel). Random-effects models with 95% CI above or below 0 (red diamonds) were considered statistically significant. Hedge’s g difference statistic is shown on the X axes. The fixed effects model assumes there exists a single effect size shared by all included studies, while the random effects model allows for variation in the effect size from study to study. Heterogeneity analysis includes estimates of I 2 (percentage of variation reflecting true heterogeneity), τ 2 (random-effects between study variance), and p -value from Cochran’s Q test for heterogeneity

Article Snippet: To enhance our taxonomic resolution, 16S rRNA amplicon sequence data sets from USA, MAL1, and MAL2 cohorts were analyzed using Resphera Insight, a high-resolution methodology for species-level characterization (see Methods).

Techniques: Sequencing, Bacteria, Amplification

Journal: NPJ Biofilms and Microbiomes

Article Title: High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

doi: 10.1038/s41522-017-0040-3

Figure Lengend Snippet: Combined prevalence of CRC-associated microbial features in USA, MAL1, and MAL2 cohorts. Positive status for B. fragilis and the human oral microbes from the HOMD database were defined as a relative abundance >2 and >10% of all 16S rRNA gene sequences, respectively. a Percentage of healthy biopsies, paired normal, and tumor tissues that were positive for each microbial feature (biofilms, HOMD, and B. fragilis ). Statistics shown are Fisher’s exact test. * p < 0.01, *** p < 0.001. b Percentage and overlap of healthy biopsies, paired normal, and tumor tissues harboring one, two, three or no microbial features

Article Snippet: To enhance our taxonomic resolution, 16S rRNA amplicon sequence data sets from USA, MAL1, and MAL2 cohorts were analyzed using Resphera Insight, a high-resolution methodology for species-level characterization (see Methods).

Techniques: