Systematic profiling of growth interactions in human gut microbiome species

Abstract

Microbial interactions shape the composition and stability of the human gut microbiome. Yet, few studies have systematically investigated species-species growth interactions and the mechanisms behind these. Here we show that among 36 representative gut bacterial strains, when two species interact, the interactions are mostly inhibitory. To provide biological insight into specific interactions, we further investigate the basis of a positive interaction, showing that Clostridium perfringens promotes the growth of Mediterraneibacter gnavus through extracellular vesicles. Additionally, we identify Veillonella parvula as a species capable of modulating environmental pH, thereby enabling the growth of Parabacteroides merdae, a strain highly sensitive to acidic conditions. This pH-increasing effect is enhanced by guanine supplementation and persists in multi-species communities containing different pH-lowering strains from diverse bacterial phyla. Although V. parvula is commonly present in human gut microbiomes, it is generally found at low levels. Given the spatial organization of bacteria in the gut, the local pH modulation by V. parvula might support the growth of acid-sensitive strains. Overall, the comprehensive dataset and mechanistic insights presented here provide a starting point to predict microbiome composition by integrating growth interactions.

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BibTeX RIS

BibTeX

@article{buyanbadrakh2026systematic,
  title = {{Systematic profiling of growth interactions in human gut microbiome species}},
  author = {Bolor Buyanbadrakh and Elisabeth Baland and Paula Lambeck and Lucía Pérez Jiménez and Sandra Holmberg and Fabiola Puértolas-Balint and Eric Toh and Sun Nyunt Wai and Bjoern Schroeder and Madeleine Ramstedt and Shaochun Zhu and André Mateus},
  journal = {Nature Communications},
  year = {2026},
  month = aug,
  doi = {10.1038/s41467-026-76526-z},
  url = {https://hal.science/hal-05771845v1},
  note = {CC BY},
}

RIS

TY  - JOUR
TI  - Systematic profiling of growth interactions in human gut microbiome species
AU  - Bolor Buyanbadrakh
AU  - Elisabeth Baland
AU  - Paula Lambeck
AU  - Lucía Pérez Jiménez
AU  - Sandra Holmberg
AU  - Fabiola Puértolas-Balint
AU  - Eric Toh
AU  - Sun Nyunt Wai
AU  - Bjoern Schroeder
AU  - Madeleine Ramstedt
AU  - Shaochun Zhu
AU  - André Mateus
PY  - 2026
DA  - 2026/08/07
JO  - Nature Communications
DO  - 10.1038/s41467-026-76526-z
UR  - https://hal.science/hal-05771845v1
AB  - Microbial interactions shape the composition and stability of the human gut microbiome. Yet, few studies have systematically investigated species-species growth interactions and the mechanisms behind these. Here we show that among 36 representative gut bacterial strains, when two species interact, the interactions are mostly inhibitory. To provide biological insight into specific interactions, we further investigate the basis of a positive interaction, showing that Clostridium perfringens promotes the growth of Mediterraneibacter gnavus through extracellular vesicles. Additionally, we identify Veillonella parvula as a species capable of modulating environmental pH, thereby enabling the growth of Parabacteroides merdae, a strain highly sensitive to acidic conditions. This pH-increasing effect is enhanced by guanine supplementation and persists in multi-species communities containing different pH-lowering strains from diverse bacterial phyla. Although V. parvula is commonly present in human gut microbiomes, it is generally found at low levels. Given the spatial organization of bacteria in the gut, the local pH modulation by V. parvula might support the growth of acid-sensitive strains. Overall, the comprehensive dataset and mechanistic insights presented here provide a starting point to predict microbiome composition by integrating growth interactions.
SN  - 2041-1723
SN  - 2041-1723
ER  -

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