Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

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The molecular mechanism involved in tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to inhibitors (such as furfural, acetic acid, and phenol) represented in lignocellulosic hydrolysate is still unclear. Here, 18 O-labeling-aided shotgun comparative proteome analysis was applied to study the global protein expression profiles of S. cerevisiae under conditions of treatment of furfural compared with furfural-free fermentation profiles. Proteins involved in glucose fermentation and/or the tricarboxylic acid cycle were upregulated in cells treated with furfural compared with the control cells, while proteins involved in glycerol biosynthesis were downregulated. Differential levels of expression of alcohol dehydrogenases were observed. On the other hand, the levels of NADH, NAD ؉ , and NADH/NAD ؉ were reduced whereas the levels of ATP and ADP were increased. These observations indicate that central carbon metabolism, levels of alcohol dehydrogenases, and the redox balance may be related to tolerance of ethanologenic yeast for and adaptation to furfural. Furthermore, proteins involved in stress response, including the unfolded protein response, oxidative stress, osmotic and salt stress, DNA damage and nutrient starvation, were differentially expressed, a finding that was validated by quantitative real-time reverse transcription-PCR to further confirm that the general stress responses are essential for cellular defense against furfural. These insights into the response of yeast to the presence of furfural will benefit the design and development of inhibitor-tolerant ethanologenic yeast by metabolic engineering or synthetic biology.

Four isonitrogenous and isolipidic diets containing fresh fish oil (peroxide value, POV: 11.5 meq kg−1, diet FR) and three degrees of oxidized fish oil (POV: 132, 277 and 555 meq kg−1, diet OX132, OX277 and OX555, respectively) were formulated to investigate the effects of dietary oxidized fish oil on growth performance, body composition, antioxidant defence mechanism and liver histology of juvenile largemouth bass. After a 12‐week feeding trail, a proportion of approximately 9% of Micropterus salmoides showed inflammation and haemorrhage at the base of dorsal, pectoral and tail fin in both groups OX277 and OX555. Fish fed oxidized oil diets obtained significantly higher (P < 0.05) weight gain and specific growth rate because of their remarkable higher feed intakes, compared with the fresh oil receiving group. The analysis of biometric parameters and body composition indicated significant differences (P < 0.05) in various test diets. The activities of hepatic catalase and superoxide dismutase were significantly stimulated (P < 0.05) by oxidized oil ingestion. Hepatic glutathione peroxidase, glutathione reductase and glutathione‐S‐transferase activities were significantly higher (P < 0.05), and liver glutathione content was markedly lower (P < 0.05) in group OX555 than the other treatments. Oxidized oil consumption resulted in marked depletion (P < 0.05) of vitamin E concentration in plasma, liver and muscle tissue, increased plasma and muscle malondialdehyde content along with decreased haematocrit value. Histological examinations indicated that hepatocytes with lipid vacuoles and nuclear migration were shown in groups OX277 and OX555. The overall results in this study suggested that an increased oxidative stress in M. salmoides fed oxidized lipid may account for their stimulated hepatic antioxidant defences, vitamin E depletion in plasma and certain tissues, and pathological changes. The detrimental effect of oxidation products on fish health and the unexpectedly enhanced feed intake of oxidized feeds in M. salmoides underline the importance that cares should be taken to minimize dietary oxidation products to the greatest extent possible.