Stabilizing microbial communities by looped mass transfer

Abstract

Significance The population ecology of microbial communities is still poorly understood and their notorious instability makes them impossible to control. Much of the instability is caused by the stochastic assembly of microorganisms, especially in highly diverse microbiomes where structural and hence functional changes occur rapidly due to the short generation time of their members. Usually, to maintain organismic proportions in communities, their niches are deterministically reinforced, but stochasticity strongly counteracts this. Based on metacommunity theory, a looped mass transfer was developed that uses the rescue effect to stabilize communities. This study fills a long-standing gap and enables continuous and proportionally equal growth of community members using an unprecedented operational design that addresses an acute need in the healthcare and biotechnology industries.

Development of an Automated Online Flow Cytometry Method to Quantify Cell Density and Fingerprint Bacterial Communities

“…A higher resolution allows the partitioning of communities into more subgroups to obtain the fingerprints of current states of bacterial consortia, which enables the calculation of the ecological parameters of these communities [ 49 ]. DAPI as a stain for generating community fingerprints has never been used in conjunction with online flow cytometry thus far.…”

“…DAPI as a stain for generating community fingerprints has never been used in conjunction with online flow cytometry thus far. DAPI was chosen over SYBR Green due to its better resolution of microbial communities into cell subsets and, thus, its higher discriminative power when dealing with complex microbial communities [ 38 , 49 ]. Given that we wanted to use online flow cytometry to assess the community dynamics using a fingerprinting approach based on DAPI staining, on the one hand, and fast bioinformatic evaluation tools based on it, such as flowCyBar [ 43 ] and flowEMMi v2 [ 37 ], on the other hand, a completely new online script for cell handling was developed.…”

Designs and methodologies to recreate in vitro human gut microbiota models

“…This model has been found to maintain a stable microbial community for 38 days [134]. Another approach in guaranteeing a stable microbial profile, even where cells are suspended, is described by Li and colleagues [135]. In fact, they demonstrated that unlike a continuous reactor system, a looped mass transfer can stabilize microbial communities over a long period of time.…”