A reader asked why different models to generate suggestions for their microbiome disagreed for a probiotic.

Two primary data sources exist regarding the effects of Bifidobacterium longum subsp. infantis: clinical studies and computational modeling data. I pulled some statistics from my databases.

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Two primary data sources exist regarding the effects of Bifidobacterium longum subsp. infantis: clinical studies and computational modeling data.

1. Clinical studies (PubMed):

• A total of 34 clinical studies were identified, many of which involved participants with existing medical conditions.
• Across these studies, an impact was reported on only 24 bacterial taxa.
  • Among these, six taxa showed consistent results (replication)
• The remaining 18 taxa were each reported as impacted in only a single study, indicating a lack of replication.
• Statistical significance in these studies was typically defined as (P < 0.05).
• Moreover, each study employed distinct microbiome testing methodologies, contributing to substantial variability—a phenomenon sometimes referred to as the “taxonomy nightmare.”

2. Computational model (R2 Model):

• Analysis using the R2 Model (link) identified statistically strong associations between B. longum subsp. infantis and 73 bacterial taxa among healthy individuals.
• The statistical significance threshold in this dataset was generally (P < 0.00001),
• All samples were processed using a standardized microbiome testing pipeline, eliminating cross-platform variability.

Interpretation:
Medical professionals predominantly rely on clinical trial data when evaluating probiotic efficacy, often without critically assessing methodological consistency or statistical robustness. Consequently, computational models such as R2—despite their reproducibility and rigor—are often perceived as opaque or “black box” approaches.

Example: Bacteroides 

The following probiotics report different results (i.e. one study report increases, a different study report decreases)

• bacillus subtilis {B.Subtilis }
• Bifidobacterium animalis {B. animalis}
• bifidobacterium longum {B.Longum }
• Lacticaseibacillus casei {L. casei}
• Lacticaseibacillus paracasei {L.paracasei}
• Lacticaseibacillus rhamnosus {l. rhamnosus}
• lactobacillus acidophilus {L. acidophilus}
• Lactobacillus plantarum {L. plantarum}
• Limosilactobacillus fermentum {L. fermentum}
• Limosilactobacillus reuteri {L. Reuteri}

Example: Clostridium

The following probiotics report different results (i.e. one study report increases, a different study report decreases)

• bacillus subtilis {B.Subtilis }
• Bifidobacterium animalis {B. animalis}
• bifidobacterium longum {B.Longum }
• Heyndrickxia coagulans {B. coagulans}
• Lactobacillus plantarum {L. plantarum}
• Limosilactobacillus reuteri {L. Reuteri}

Example: Lachnospiraceae

The following probiotics report different results (i.e. one study report increases, a different study report decreases)

• bacillus subtilis {B.Subtilis }
• bifidobacterium longum {B.Longum }
• Lacticaseibacillus paracasei {L.paracasei}
• lactobacillus acidophilus {L. acidophilus}