The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations
Bibliographic record
Abstract
Abstract The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp ., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and showed that the porphyran PUL exists only in East Asia (Japan, China, Korea), but not anywhere else. Finally, we identified three major PUL haplotypes which frequency differ between countries. This geographic structure is likely the reflect of the rate of bacterial horizontal transmission between individuals. Background The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp ., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. Results We first demonstrated that both methylated and unmethylated fractions of porphyran are catabolized by the porphyran PUL without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and confirmed that the porphyran PUL exists only in East Asia (Japan, China, Korea). We identified three major porphyran PUL haplotypes which frequency differ between countries. Conclusion The encoded genes of the PUL porphyran can autonomously catabolized all the complex porphyran structure. The PUL is further encoded by a variety of bacterial species, and its genetic diversity is geographically structured, likely reflecting the rate of bacterial horizontal transmission between individuals.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".