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).

附加文件9：表S7。TM7基因组的宏基因组学分析。(a) 经anvi-mcg-classifier计算，在本研究的71个样本中检测到43个非冗余TM7宏基因组组装基因组（Metagenome-Assembled Genome，MAG）。(b) 经anvi-mcg-classifier计算，本研究71个样本中43个非冗余TM7 MAG的非异常值平均覆盖度。(c) 经anvi-mcg-classifier计算的71个样本中43个非冗余TM7 MAG的出现统计信息，包含归一化覆盖度。(d) 用于泛基因组与宏基因组分析的12个已发表TM7基因组的登录号及参考信息。(e) 用于图3系统发育基因组学分析的、来自NCBI的150个TM7基因组的元数据，包含登录号。(f) 55个TM7基因组（含本研究的43个与已发表的12个）的平均核苷酸一致性（Average Nucleotide Identity，ANI）成对覆盖度值。(g) ANI百分比一致性值。(h) 比对覆盖度大于0.25的TM7基因组对的ANI汇总信息。(i) 52个口腔TM7基因组的进化枝归属（本研究定义）与类群归属（Camanocha与Dewhirst[34]定义）。(j) 人类微生物组计划（Human Microbiome Project，HMP）的481个口腔宏基因组的短读长序列比对至55个TM7基因组的结果汇总，包含每个样本的比对读长总数、单个样本总读长数、比对读长占比，以及每个宏基因组样本的口腔位点归属。(k) 本研究使用的HMP样本元数据，包含登录号。(l) 经anvi-mcg-classifier计算的HMP样本中55个TM7基因组的检测情况；(m) 其非异常值平均覆盖度。(n) HMP样本中55个TM7基因组的出现情况汇总，包含每个基因组的非异常值平均覆盖度均值、在0.5阈值以上被检测到的样本数（按牙菌斑与舌部样本拆分）、该基因组在HMP样本中超过检测阈值的占比，以及用于比较舌部与牙菌斑样本中各基因组出现情况的卡方检验结果。(o) 按9种HMP样本类型拆分的、每个TM7基因组的检出百分比（超过0.5阈值）。(p) 经anvi-mcg-classifier计算的HMP与文献[84]中龈下菌斑宏基因组的检测值。(q) 龈下菌斑宏基因组中TM7基因组的非异常值平均覆盖度；(r) 其检测汇总统计信息。(s) 每个龈下菌斑样本中比对至每个TM7基因组的读长占比。(t) 经anvi-gen-variability-profile计算的“泛分布型”TM7 MAG（T_C_M_Bin_00022）的变异信息。