Tang Hongzhi's research group of Shanghai Jiaotong University reviewed the theory of microbiome engineering and its application and prospect in the field of environment

The collaborative review "Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use" by Professor Tang Hongzhi of Shanghai Jiao Tong University and Associate Professor Nie Yong of Peking University was officially launched
on mLife on November 3, 2022 。 This review was jointly completed by young scholars from Shanghai Jiao Tong University, Peking University and ETH Zurich, and supported by Professor Wu Xiaolei of Peking University
.
This paper reviews the cutting-edge research in microbiome engineering theory in recent years, as well as the classical application in the field of environment, and looks forward
to future research ideas.
Hu Haiyang, assistant researcher at the School of Life Science and Technology of Shanghai Jiaotong University, and Miaoxiao Wang, postdoctoral fellow at ETH Zurich, are joint first authors, while Tang Hongzhi, tenured professor at the School of Life Science and Technology of Shanghai Jiaotong University, and Nie Yong, associate researcher at Peking University, are co-corresponding authors
.

This paper first reviews the recent important theoretical achievements in the field of microbiome engineering, namely the rational design of engineering microbiomes through "bottom-up" and "top-down" design strategies, and the "design-build-test-learn" (DBTL) cycle (see Figure 1).

。 Subsequently, based on the latest research results, the article summarizes in detail how to construct the engineering microbiome "bottom-up" based on natural or engineered strains, and build the engineering microbiome
"top-down" through three strategies: enrichment, artificial selection and directed evolution.
This paper also summarizes the application cases of various mathematical models in microbiome engineering, and analyzes the advantages, disadvantages and use of
various models.

Figure 1.
Two microbiome engineering strategies combining the DBTL cycle ("bottom-up" and "top-down")

Combined with the above theoretical research, this paper also summarizes the application results
of "bottom-up" and "top-down" strategies in the field of environment.
In the "bottom-up" strategy, the advantages, bottlenecks and development trends of metabolic division of labor theory in the construction of efficient degradation microbiome were discussed.
and the "top-down" strategy, artificial screening and directed evolution, which have great potential
in screening highly degrading flora.
Finally, based on the bottleneck problem in the current application in the environmental field, a set of research ideas that connect the two strategies of "top-down" and "bottom-up" is summarized (see Figure 2 for details
).
Aiming at the application of microbiome engineering in the environmental field, this paper proposes that the design of microbiome in pollutant degradation engineering must avoid the accumulation of toxic intermediates harmful to human health, and a number of new design strategies
are proposed based on this.

Figure 2.
" Top-down "+"bottom-up" series research idea schematic

In summary, through microbiome engineering research, an efficient, stable, safe and predictable microbiome
can be rationally designed.
In the future, we should further study how to regulate environmental factors, design microbial interactions and edit strain characteristics, and rationally design engineering microbiomes to make them perform more ideal functions
.
The feasibility of microbiome engineering theories should also be tested under more complex in situ environmental conditions, so as to promote the development of more quantitative theories and techniques and guide future research
on microbiome engineering.

Link to paper: https://onlinelibrary.
wiley.
com/doi/full/10.
1002/mlf2.
12043