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Bowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic  Clostridium butyricum  MIYAIRI 588 ( CBM588 ) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9,  p  < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97,  p  < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes,  CBM588  had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores ( p  < 5 × 10 −4 ). The distributions of the scored protein domains indicated that  CBM588  had a considerably higher ( p  < 10 −5 ) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of  CBM588  to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes