352: Interspecies control of E. coli growth in human gut microbiomes

Boumasmoud M et al., PNAS - Reciprocal transplant experiments in anaerobic microcosms show that resident human gut microbiome context alters growth of introduced Escherichia coli strains and that microbially mediated acidification, driven by a Clostridium butyricum strain, can reproducibly suppress E. coli and reshape community fermentation profiles. Key terms: gut microbiome, Escherichia coli, interspecies interaction, acidification, Clostridium butyricum.

Study Highlights:
Using six human stool-derived microbiome samples and six resident E. coli isolates in replicated anaerobic microcosms, the authors measured strain-level and species-level growth across 36 strain-by-microbiome combinations. Growth performance of E. coli strains varied with microbiome context and was constrained by intraspecific competition setting a finite E. coli abundance per microbiome. One microbiome (M6) acidified during cultivation, inhibiting E. coli growth; a Clostridium butyricum isolate from M6 reproduced this acidification when transplanted into other samples. Addition of C. butyricum lowered pH, increased butyrate and decreased acetate/lactate, suppressed E. coli and altered overall community composition.

Conclusion:
Interindividual gut-microbiome variation causes variable ecological interactions that affect colonization by incoming strains, and a single transferable taxon (C. butyricum) can act as an ecological control point by driving acidification and reshaping community growth and metabolites.

Music:
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Article title:
Interspecies interaction controls Escherichia coli growth in human gut microbiome samples

First author:
Boumasmoud M

Journal:
PNAS

DOI:
10.1073/pnas.2527793123

Reference:
Boumasmoud M., León-Sampedro R., Beusch V., Benza F., Arnoldini M., Hall A.R. Interspecies interaction controls Escherichia coli growth in human gut microbiome samples. PNAS. 2026;123(17):e2527793123. doi:10.1073/pnas.2527793123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-04-27.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript's discussion of experimental design, key results (strain performance variation, acidification, keystone C. butyricum), and ecological implications; compared to the original article's reported methods, results, and interpretations.
- transcript topics: Experimental design: reciprocal transplant in anaerobic microcosms (M2–M7) with six E. coli strains; Strain-level and species-level growth variation across microbiome samples; Intraspecific competition and microbiome-specific finite E. coli abundance; Acidification as a driver of growth suppression; pH measurements; Clostridium butyricum as a keystone species driving acidification and community shifts; Transplantation of C. butyricum into other microbiomes; effects on butyrate, acetate, lactate

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Six donor microbiome samples (M2–M7) and six focal E. coli strains (S2–S7) tested in 36 strain–microbiome combinations; growth varied by microbiome context
- No average home-field adaptation detected; rank order of strains largely consistent across microbiomes with S3 and S7 often most abundant
- Microbiome sample M6 acidified during incubation (pH ~5.4) and suppressed E. coli growth; neutralization restored growth
- A Clostridium butyricum strain isolated from M6 acidified medium and, when transplanted into other microbiomes, reduced pH and altered fermentation products (increased butyrate, de
- Butyricum transplantation reduced E. coli and total bacterial growth and reshaped community composition
- Butyrate production increased by 14.8 mM on average after C. butyricum inoculation; acetate decreased by ~8.08 mM and lactate by ~6.45 mM

QC result: Pass.