Journal: Microbiome

Article Title: HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

doi: 10.1186/2049-2618-1-26

Figure Lengend Snippet: Schematic of sampling and bioinformatic methodology. Rectal mucosa secretions were collected from 60 human subjects as shown and subjected to high-throughput deep V4 16S sequencing. Alpha and beta diversity analyses were then performed, which suggested microbial composition was altered in HIV-infected subjects who were not receiving combination anti-retroviral therapy (cART). Microbial differences in these subjects were identified and compared with HIV-infected subjects receiving cART. In addition, the different classes of cART were analyzed to determine whether any class was significantly associated with differences in microbial composition. Imputed metagenomic differences between HIV-infected subjects not receiving cART and healthy control subjects were then identified and compared between the three patient cohorts. PICRUSt, phylotypic investigation of communities by reconstruction of unobserved states; HUMAnN, HMP unified metabolic analysis network.

Article Snippet: Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing).

Techniques: Sampling, High Throughput Screening Assay, Sequencing, Infection, Retroviral, Control

Journal: PLoS ONE

Article Title: Insights from Characterizing Extinct Human Gut Microbiomes

doi: 10.1371/journal.pone.0051146

Figure Lengend Snippet: These data resulted from comparison of the 16S rRNA V3. Taxon distribution and cluster dendrogram were limited to phyla with a frequency of 5% or more.

Article Snippet: After removing primer sequences, barcoded data from pyrosequencing of 16S rRNA amplicons averaged 150 bases in length.

Techniques: Comparison

Journal: PLoS ONE

Article Title: Insights from Characterizing Extinct Human Gut Microbiomes

doi: 10.1371/journal.pone.0051146

Figure Lengend Snippet: Both Rio Zape samples assign partially to the rural African children source, with sample ZA04 also containing a predicted partial match to the modern non-human primate gut source. Caserones sample CA18 assigns almost entirely to the compost source with relatively high confidence; sample CA10 is predicted with low confidence to contain a small proportion of compost (See for variability in proportion estimates). The sources for the Hinds Cave samples were unrecognized given our training data, resulting in nearly complete assignments to the “Unknown” source. When extraction blanks were subjected to 60 cycles of 16S PCR, the amplified microbial community signature assigns to either a skin community or unknown community.

Article Snippet: After removing primer sequences, barcoded data from pyrosequencing of 16S rRNA amplicons averaged 150 bases in length.

Techniques: Extraction, Amplification