Additional file 1: of Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls

Supplementary Methods (Appendix 1) and eTables 1 to 3.2 [23, 29, 30]. (DOCX 38 kb

A Metagenomic Framework for the Study of Airborne Microbial Communities

<div><p>Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.</p></div

Abundances of KEGG functional categories.

<p>Abundances of KEGG functional categories.</p

Ordination of the six metagenomic samples by principal component analysis based on KO abundance profiles.

<p>The first three principal components (PC1, PC2, and PC3) account for 83.1% of the total variation. The dashed lines in the 3D plot shows the height (PC3) of the sample points when projected on to the PC1-PC2 plane.</p

Taxonomic classification and diversity of the NYC 16S data.

<p>In the stacked barcharts, only those taxonomic groups that have ≥2% abundance in at least one of the samples is reported. The rarefaction curves along with the richness and diversity estimates were calculated using mothur and were based on averages of 25 random samples of 10,000 sequences from each dataset.</p

DNA yields after amplification.

<p> The MDA products for the NYC samples were quantified by UV spectroscopy and the linker amplification products for the SD samples were quantified by fluorescence spectroscopy.</p

Taxonomic classification of metagenomic reads.

<p>Taxonomic classification of metagenomic reads.</p

Taxonomic classification of metagenomic reads.

<p><i>Mixed</i> refers to a read that had matches to multiple kingdoms and could not be definitively assigned to one kingdom. <i>Other</i> refers to sequences that could not be identified (NCBI taxonomy ID 32644), mostly synthetic constructs. <i>Unclassified</i> refers to a read that could not be assigned to any kingdom (i.e. had no match in the reference databases). Kingdom taxonomy: </p