Abstract
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.
Highlights
ID Sex P1 Female P2 Male P3 Female P4 Female P5 Male P6 Male P7 Female
Based on these considerations and the results of 16S-based taxonomic and functional analyses, we successfully developed a scoring system that had favorable correlations with 16S-based reports and offered mechanistic insights into how Clostridium butyricum Miyairi 588 (CBM588) drives the evolution of fecal bacteria communities in small bowel transplantation (SBT) recipients
Taxonomic shifts of fecal microbiota associated with CBM588 ingestion
Summary
ID Sex P1 Female P2 Male P3 Female P4 Female P5 Male P6 Male P7 Female. Intestinal failure due to chronic intestinal pseudo-obstruction syndrome individuals without specialized knowledge such as patients. We conducted a pilot study examining Clostridium butyricum Miyairi 588 (CBM588) in patients undergoing small bowel transplantation (SBT). Probiotics could be a promising option in suitable candidates Based on these considerations and the results of 16S-based taxonomic and functional analyses, we successfully developed a scoring system that had favorable correlations with 16S-based reports and offered mechanistic insights into how CBM588 drives the evolution of fecal bacteria communities in SBT recipients. The scores were based on integrated counts of carbohydrate-active protein domains after probability analyses were conducted using hidden Markov models. This system indicates the potential of protein domain–based scoring of focused metabolisms as readouts for understanding probiotic characteristics and their effects on fecal metagenomes
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