BugBase Predicts Organism Level Microbiome Phenotypes

Key results

1. SuggestedOrganism-level pathway coverage gives smaller p-values than bag-of-genes profiling for HMP body-site contrasts, particularly at small sample sizes and between taxonomically similar sites.

   Mann-Whitney U tests on subsamples of 1 to 250 HMP samples per body site (30 repeats each) for 470 level-three KEGG modules and selected pathways such as starch metabolism: both approaches separate stool from tongue, bag-of-genes degrades faster as sample size falls, and only the organism-level approach separates supra- from subgingival plaque. No p-values or power estimates are printed in the text. · Organism-level predictions are more sensitive…; Organism-level and bag-of-genes prediction…

2. ShownOn held-out reference OTUs, 16S-based trait predictions are largely accurate, ranging from 76% for aerobes to 97% for pathogenicity-related genome content.

   Ten-fold cross-validation, each fold withholding 10% of the fully sequenced, labelled reference OTUs; for non-empirical traits the score is accuracy of predicted gene occurrence rather than of the phenotype. Per-trait values between these extremes are in a table not reproduced in this text. · Reference-based validation of BugBase…; Assessment of accuracy

3. ShownPredicted traits recover documented oxygen-tolerance differences across human body sites and a plaque biofilm difference consistent with earlier reports, and predict more potential pathogens in stool than in oral sites.

   HMP (stool n=394, tongue n=368, subgingival n=373, supragingival n=376): stool had more anaerobes, fewer biofilm formers, more potential pathogens (driven by Bacteroides) and fewer mobile-element carriers than oral sites; subgingival plaque had more anaerobes and supragingival plaque more biofilm formers (driven by Actinomyces); all p < 0.001. · Biological validation of predicted phenotypes in…; Phenotype Predictions for Published Datasets

4. SuggestedGram-stain and oxygen-tolerance predictions follow clinical Nugent scores in vaginal microbiome samples.

   Samples with high Nugent scores (bacterial vaginosis, n=97) were predicted to hold more anaerobes and Gram-negative bacteria than intermediate (n=49) or low (n=248) samples; the text prints the test result as 'p > 0.001' and gives no concordance statistic. · Biological validation of predicted phenotypes in…; Discussion; Phenotype Predictions for Published Datasets

5. ShownPredicted trait shifts also track lifestyle and environmental gradients, including water temperature and soil pH.

   Gut: USA (n=263) vs Malawi (n=54) and Venezuela (n=69) had fewer facultative anaerobes and pathogens and more Gram-positive bacteria (p < 0.001), with no aerobe difference (p > 0.620). Yellowstone hot-spring water (n=412): aerobes fell and facultative anaerobes rose with temperature (both p < 0.001). Soil: aerobes (p < 0.05) and oxidative-stress-tolerant taxa (p < 0.01) declined as pH rose. · Biological validation of predicted phenotypes in…; Phenotype Predictions for Published Datasets