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. 2022 May 21;16(9):2065–2075. doi: 10.1038/s41396-022-01252-5

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — All consitunents of the model are represented in illustrating basic assumptions and interactions. Fermenters (θ_f) metabolize (S_G) as a carbon source, which produce acid (F) leading to an increase in hydrons (H⁺) (i.e. lowering the pH) under anaerobic conditions. This pH decrease inhibitis the growth of pathogens. Pathogens (θ_P) in the presence of oxygen (S_O) (i.e., aerobic conditions) use amino acids (S_A) as their primary carbon source. The byproduct of this metabolism is ammonium (P), which produces hydroxide (OH^-) leading to an increase in pH, inhibiting fermenter growth. Under anaerobic conditions pathogens use nitrate (S_N) as an electron acceptor. In addition to this pathogens produce a chemical inhibitor of fermenters (I).