Influence of Cultivation pH on Composition, Diversity, and Metabolic Production in an In Vitro Human Intestinal Microbiota

Abstract

Fecal microbiota transplantation, an alternative treatment method for gastrointestinal diseases, has a high recovery rate, but comes with disadvantages, such as high donor requirements and the low storability of stool. A solution to overcome these problems is the cultivation of an in vitro microbiota. However, the influence of cultivation conditions on the pH are yet unknown. In this study, the influence of the cultivation pH (6.0–7.0) on the system’s behavior and characteristics, including cell count, metabolism, and microbial composition, was investigated. With an increasing cultivation pH, an increase in cell count, total amount of SCFAs, acetate, propionate, and the abundance of Bacteroidetes and Verrucomicrobia were observed. For the concentration of butyrate and the abundance of Actinobacteria and Firmicutes, a decrease with increasing pH was determined. For the concentration of isovalerate, the abundance of Proteobacteria and diversity (richness and Shannon effective), no effect of the pH was observed. Health-promoting genera were more abundant at lower pH levels. When cultivating an in vitro microbiota, all investigated pH values created a diverse and stable system. Ultimately, therefore, the choice of pH creates significant differences in the established in vitro microbiota, but no clear recommendations for a special value can be made.

Preservation by lyophilization of a human intestinal microbiota: influence of the cultivation pH on the drying outcome and re‐establishment ability

“…While the abundance of Bacteroidetes increased with the pH value, the abundance of Firmicutes, in contrast, decreased. This effect was already shown during cultivation before drying (Haindl et al ., 2021b ), but did not explain the peak in butyrate production after drying during re‐cultivation. On genera level, Faecalibacterium, Clostridium Cluster XIVa, Blautia and Roseburia are the main butyrate‐producing bacteria in the microbiota (Bircher et al ., 2018 ).…”

“…The diversity, measured by the Shannon effective index was also comparable at 29 (donor stool), 24 ± 1 before and 24 ± 6 after drying. Akkermansia and Roseburia were able to establish in the cultivation step prior to drying in small abundances (Haindl et al ., 2021b ). In the re‐cultivation step after drying they were hardly detectable (<0.01% abundance).…”

“…For the drying of probiotic single cell cultures, the influence of the cultivation pH was already investigated and shown to have a major impact (Bauer et al ., 2012 ). Further, the impact during the establishment of an in vitro microbiota was shown in former studies (Haindl et al ., 2021b ). In this study, the in vitro microbiota was cultivated prior to and after the drying process at three different physiological pH values (pH 6.0, 6.5, 7.0).…”

“…Further, the influence of the donor itself was found to be small, with only some factors from the stool as, e.g., high abundances of single genera and metabolic characteristics sustain in the individual cultivated system (Haindl et al ., 2021a ). The choice of the cultivation pH had a major impact on the established in vitro system (Haindl et al ., 2021b ). The choice of a physiological cultivation pH during growth in a bioreactor system was found to depend on different criteria: a pH of 7.0 created a higher number of cells, whereas a lower pH of 6.0 resulted in a system with a phyla distribution more comparable with the donor stool and an higher abundance of health indicating microorganisms (Haindl et al ., 2021b ).…”

“…The choice of the cultivation pH had a major impact on the established in vitro system (Haindl et al ., 2021b ). The choice of a physiological cultivation pH during growth in a bioreactor system was found to depend on different criteria: a pH of 7.0 created a higher number of cells, whereas a lower pH of 6.0 resulted in a system with a phyla distribution more comparable with the donor stool and an higher abundance of health indicating microorganisms (Haindl et al ., 2021b ). The purpose in this study compared with previous studies was to determine whether the pH value may also have an influence not only during cultivation but also on the resistance of the in vitro cultured microbiota during freeze–drying and its ability to re‐establish.…”