454 GS FLX+ sequencing; qiita_ptid_557:232.M2Thmr217
samples of sebum from human fingers matched to key surfaces on keyboard
16S rRNA gene sequences were processed according to the methods described in our previous publications (Fierer et al., 2008; Hamady et al., 2008). Briefly, sequences &lt;200 or &gt;300gnt or with average quality scores of &lt;25 were removed from the dataset, as were those with uncorrectable barcodes, ambiguous bases, or if the bacterial 16S rRNA gene-specific primer was absent. Sequences were then assigned to the specific subsamples based on their unique 12nt barcode and then grouped into phylotypes at the 97% level of sequence identity using cd-hit (Li &amp; Godzik, 2006) with a minimum coverage of 97%. We chose to group the phylotypes at 97% identity because this matches the limits of resolution of pyrosequencing (Kunin et al., 2010) and because the branch length so omitted contributes little to the tree and therefore to phylogenetic estimates of diversity (Hamady et al., 2009). A representative for each phylotype was chosen by selecting the most abundant sequence in the phylotype, with ties being broken by choosing the longest sequence. A phylogenetic tree of the representative sequences was constructed using the Kimura 2-parameter model in Fast Tree (Price et al., 2009) after sequences were aligned with NAST (minimum 150nt at 75% minimum identity) (DeSantis et al., 2006a) against the GreenGenes database (DeSantis et al., 2006b). Hypervariable regions were screened out of the alignment using PH Lane mask (http://greengenes.lbl.gov/). Differences in the community composition for each pair of samples were determined from the phylogenetic tree using the weighted and unweighted UniFrac algorithms (Lozupone &amp; Knight, 2005; Lozupone et al., 2006). UniFrac is a tree-based metric that measures the distance between two communities as the fraction of branch length in a phylogenetic tree that is unique to one of the communities (as opposed to being shared by both). This method of community comparison accounts for the relative similarities and differences among phylotypes (or higher taxa) rather than treating all taxa at a given level of divergence as equal (Lozupone &amp; Knight, 2008). Although UniFrac depends on a phylogenetic tree, it is relatively robust to differences in the tree reconstruction method or to the approximation of using phylotypes to represent groups of very similar sequences (Hamady et al., 2009).
barcode
AATCAGTCTCGT
center_name
CCME
center_project_name
Forensic identification using skin bacterial communities
key_seq
TCAG
linker
CA
primer
CATGCTGCCTCCCGTAGGAGT
region
0
run_center
CCME
run_date
8/14/08
run_prefix
FFCKVMW
samp_size
1, swab
sample_center
CCME
sequencing_meth
pyrosequencing
target_gene
16S rRNA
target_subfragment
V2