Additional file 9 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Additional file 9: Table S7. Metagenomic analysis of the TM7 genomes. (a) Detection of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (b) Non-outlier mean coverage of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (c) Occurrence statistics for our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier including normalized coverage. (d) Accession and reference information for the 12 previously published TM7 genomes used in the pangenomic and metagenomic analyses. (e) Metadata, including accession numbers, for the 150 TM7 genomes from NCBI used for the phylogenomic analysis in Fig. 3. (f) Average nucleotide identity (ANI) pairwise coverage values for the 55 TM7 genomes (our 43 in addition to the previously published 12). (g) ANI percent identity values. (h) ANI summary information for pairs of TM7 genomes with alignment coverage greater than 0.25. (i) Clade affiliation (as defined in this study) and group affiliation (as defined by Camanocha & Dewhirst [34]) for the 52 oral TM7 genomes. (j) Summary of mapping results of short reads from 481 oral metagenomes from the Human Microbiome Projects (HMP) to the 55 TM7 genomes, including the total number of reads that mapped from each sample, the total number of reads in each sample, and the percentage of reads that mapped, as well as the oral site affiliation of each metagenomic sample. (k) Metadata for HMP samples used in this study, including accession numbers. (l) Detection and (m) non-outlier mean coverage of the 55 TM7 genomes in the HMP samples as computed by anvi-mcg-classifier. (n) Summary of occurrence of the 55 TM7 genomes in the HMP samples including the mean value of the non-outlier mean coverage for each genome, number of samples in which a genome was detected above threshold of 0.5 with breakdown for plaque and tongue samples, the percent of HMP samples in which the genome was above detection threshold, and the results from a chi-squared test to compare occurrence of each genome between tongue and plaque samples. (o) Percent detection (above 0.5 threshold) for each TM7 genome broken down by the 9 HMP sample types. (p) Detection values as computed by anvi-mcg-classifier in subgingival plaque metagenomes from the HMP and from [84]. (q) Non-outlier mean coverage and (r) detection summary statistics for TM7 genomes in subgingival plaque metagenomes. (s) Percent of reads from each subgingival plaque sample that mapped to each TM7 genome. (t) Variability information as computed by anvi-gen-variability-profile for the “cosmopolitan” TM7 MAG (T_C_M_Bin_00022).