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Filtered taxonomy tables

Relative abundance taxonomy tables with low-abundant OTUs and low-depth samples removed:

  • All Levels (tab-delimited format, BIOM format)
  • Species Level (tab-delimited)
  • Phylum Level (tab-delimited)

    Methods. DNA sequences were aligned to a curated database containing all representative genomes in RefSeq for bacteria with additional manually curated strains. Alignments were made at 97% identity against all reference genomes. Every input sequence was compared to every reference sequence in the CoreBiome Venti database using fully gapped alignment with BURST. Ties were broken by minimizing the overall number of unique Operational Taxonomic Units (OTUs). For taxonomy assignment, each input sequence was assigned the lowest common ancestor that was consistent across at least 80% of all reference sequences tied for best hit. The number of counts for each OTU was normalized to the OTU's genome length. OTUs accounting for less than one millionth of all species-level markers and those with less than 0.01% of their unique genome regions covered (and < 1% of the whole genome) were discarded. Samples with fewer than 10,000 sequences were also discarded. Count data was converted to relative abundance for each sample. The normalized and filtered table was used for all downstream analyses.

Raw taxonomy tables

Non-filtered taxonomy tables of count data:

  • tab-delimited
  • BIOM

    Methods. These tables are the full set of database hits without filtering, normalizing or coverage-based analysis. These tables including counts at all taxonomic levels from species to phylum measured as absolute (count) abundance. The count for a given genus reflects only those sequences that matched multiple species in that genus.

Strain coverage tables

  • Unique Genomic Region Coverage table
  • Overall Genomic Coverage Table
  • Taxonomy Table

    Methods. These tables provide strain-level coverage information in terms of the fraction of unique regions covered and the fraction of the overall genome covered for each strain in each sample. This data is used to filter OTUs from the raw OTU table. The first table gives the fraction of the genomic regions unique to a given strain that was covered by at least one sequence in the raw sequencing data from a given sample; the second table gives the fraction of the overall genome of a given strain that was covered by at least one sequence in the raw sequencing data from a given sample. Each row is labeled with the accession number or strain ID of a strain. Each column is a samples. The third table contains the taxonomy mapping for the provided strain IDs. These tables were used to apply the coverage filters described above to determine true OTUs.

Function tables

  • KEGG Orthology Groups
  • KEGG Modules
  • KEGG Level 2 Pathways
  • KEGG Level 3 Pathways
  • KEGG Enzymes

    Methods. Kyoto Encyclopedia of Genes and Genomes Orthology groups (KEGG KOs) were observed directly using alignment at 97% identity against a gene database derived from the strain database used above. The KO table and downstream tables contain the directly observed KO counts converted to relative abundance within a sample. KOs were collapsed to level-2 and -3 KEGG pathways and KEGG Modules.

Beta diversity

Alpha diversity

  • Alpha Diversity Table

    Methods. The Chao1 index, Shannon Index and observed OTU count (taxonomic group) were calculated using a rarefied OTU table set to the minimum depth allowed for a sample (10,000) using QIIME 1.9.1.


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