barcoded pyrosequencing of 16s rrna amplicons  (Pyrosequencing Inc)

Journal: Marine Biotechnology (New York, N.y.)

Article Title: Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges

doi: 10.1007/s10126-017-9766-4

Figure Lengend Snippet: Hierarchical clustering using Bray-Curtis distance based on 16S rRNA gene amplicons generated from three sponge samples ( A. aerophoba , P . ficiformis and C. candelabrum ) and corresponding communities retrieved by scraping from agar media. Bacterial communities were investigated on marine agar ( squares ), marine agar 10-fold diluted ( open squares ), Mueller-Hinton agar ( circles ), Mueller-Hinton 10-fold diluted ( open circles ) and mucin agar ( open triangles ).Samples were either inoculated in direct contact with agar ( A ) or on top of a filter ( F ), and were harvested 15 and 30 days post inoculation. The sponge samples (inocula) are indicated with continuous colour bars. Hierarchical clustering was performed at the OTU level (97% identity clusters). The heatmap corresponds to relative abundance values of order-level phylogenetic groups (>0.01% relative abundance in at least one sample)

Article Snippet: Barcoded 16S rRNA gene amplicon 454-pyrosequencing was done (I) to analyse bacterial communities present in the sponge samples, (II) to identify bacterial colonies that were picked from media containing antibiotics and (III) to analyse bacterial communities retrieved by scraping from media without antibiotics.

Techniques: Generated

Journal: Marine Biotechnology (New York, N.y.)

Article Title: Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges

doi: 10.1007/s10126-017-9766-4

Figure Lengend Snippet: OTUs were derived from 16S rRNA gene sequences generated from bacterial communities retrieved from agar media inoculated with samples from three sponges ( A. aerophoba , P. ficiformis and C. candelabrum ) on different agar media

Article Snippet: Barcoded 16S rRNA gene amplicon 454-pyrosequencing was done (I) to analyse bacterial communities present in the sponge samples, (II) to identify bacterial colonies that were picked from media containing antibiotics and (III) to analyse bacterial communities retrieved by scraping from media without antibiotics.

Techniques: Derivative Assay, Generated

Journal: Marine Biotechnology (New York, N.y.)

Article Title: Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges

doi: 10.1007/s10126-017-9766-4

Figure Lengend Snippet: Phylogenetic tree based on 16S rRNA gene sequence similarity (>800-bp sequences) showing sponge bacteria cultured up to pure culture that were isolated agar media containing antibiotics ( green ), their closest type strain (based on blastn, blue ) and the nearest neighbour in the Silva guide tree ( black ). The tree was constructed in ARB by maximum likelihood analysis using 1000 iterations of RAxML rapid bootstrapping. For tree calculation, highly variable positions (1–9) were excluded using the bacterial positional variability by parsimony filter, and non-overlapping regions were excluded with a custom filter (window of inclusion, positions 5331 to 26,803). For each strain, the accession number, full species name and isolation source are indicated. Bootstrap values <50 are not shown. The horizontal bar corresponds to one substitution per site. After tree creation, representative pyrosequencing reads of OTUs for which unsuccessful attempts were made to obtain a representative in pure culture ( red ) were added using “add species to existing tree” with ARB_Parsimony, applying similar filtering settings as those used for creation of the base tree. For these OTUs, the OTU name is stated, thereafter followed by the isolation source

Article Snippet: Barcoded 16S rRNA gene amplicon 454-pyrosequencing was done (I) to analyse bacterial communities present in the sponge samples, (II) to identify bacterial colonies that were picked from media containing antibiotics and (III) to analyse bacterial communities retrieved by scraping from media without antibiotics.

Techniques: Sequencing, Bacteria, Cell Culture, Isolation, Construct