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:Enjoy the music based on this article at the end of the episode. 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/interspecies-ecoli-growth-microbiome 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 Aud... Chapters (00:00:13) - How the gut microbiome controls who gets to live there(00:05:47) - E. Coli SuperStands: Strains S3 and(00:09:41) - The Secret to E. Coli Fighting in M6(00:15:37) - The single microbe can profoundly alter the microbiome(00:21:32) - The master switch of the gut microbiome