TY  - JOUR
A1  - Li, Shuang
A1  - Abdulkadir, Nafi'u
A1  - Schattenberg, Florian
A1  - da Rocha, Ulisses Nunes
A1  - Grimm, Volker
A1  - Müller, Susann
A1  - Liu, Zishu
T1  - Stabilizing microbial communities by looped mass transfer
JF  - Proceedings of the National Academy of Sciences of the United States of America : PNAS
N2  - Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.
KW  - microbial ecology
KW  - metacommunity assembly
KW  - stability
KW  - microbial
KW  - community cytometry
KW  - single-cell analytics
Y1  - 2022
U6  - https://doi.org/10.1073/pnas.2117814119
SN  - 0027-8424
SN  - 1091-6490
VL  - 119
IS  - 17
PB  - National Acad. of Sciences
CY  - Washington
ER  -