In the last few years, high-throughput (or 'next-generation') sequencing technologies have delivered a step change in our ability to sequence genomes, whether human or bacterial. Further comparative genome analysis enables us to reveal detailed knowledge of genetics or physiology of industrial important strains obtained in laboratory, to analyze genotype-phenotype correlations of mutants with improved performance. Based on identified key mutations or mutation combinations, Inverse Metabolic Engineering (IME) can be performed by using accurate genetic modification system. Recently, IME has been successfully used for strain improvement and has become a research hotspot, including improving substrate utilization, engineering the robustness of industrial microbes and enhancing production of bio-based products. Here, we describe recent advances in research methods of IME, with an emphasis on characterization of genotype-phenotype and the latest advances and application of IME. Possible directions and challenges for further development of IME are also discussed.
Industrial Microbiology ; trends ; Metabolic Engineering ; trends ; Mutation

Industrial biotechnology, which employs microorganisms or enzymes to produce industrial useful products, has been considered as a promising solution for the sustainable development of society and economy. This special issue collects some recent research progresses on industrial biotechnology in China, including research articles in the field of genetic engineering, metabolic engineering and synthetic biology, physiological engineering, fermentation engineering and biochemical engineering, biocatalysis and biotransformation, as well as new biotechniques and methods.
Biotechnology ; trends ; Genetic Engineering ; trends ; Industrial Microbiology ; trends ; Metabolic Engineering ; trends ; Synthetic Biology

The use of microbial cell factories to achieve efficient conversion of raw materials and synthesis of target substances is one of the important research directions of synthetic biology. Traditional industrial microorganisms have mainly used sugar-based raw materials as fermentation substrates. How to adopt cheaper carbon resources and realize their efficient use has been widely concerned. Formic acid is an important organic one-carbon source and widely used in industrial manufacturing of pesticides, leather, dyes, medicine and rubber. In recent years, due to the demand fluctuation in downstream industries, formic acid production is facing the dilemma of overcapacity, and therefore, requiring new conversion paths for expansion and extension of the related industrial chain. Biological route is one of the important options. However, natural formate-utilizing microorganisms generally grow slowly when metabolizing formic acid, and moreover, are difficult to be artificially modified by the absence of effective genetic tools. Construction of non-natural formate-utilizing microorganisms is another alternative strategy, but still in its infancy and has a huge space for further improvements. Here, we briefly summarize the recent research progress of biological utilization of formic acid, and also propose the future research focus and direction.
Fermentation ; Formates ; metabolism ; Industrial Microbiology ; trends ; Synthetic Biology ; trends

The fermentation processing of traditional Chinese medicines (TCMs), as an important processing method for TCM, originated from the ancient brewing technology. It has a long history in China. Fermented TCMs (FTCMs) are widely applied among folks for preventing and treating many diseases. There are many kinds of TCM processed by spontaneous fermentation, including Massa Medicata Fermentata, Rhizoma Pinelliae Fermentata, Red fermented rice, Semen Sojae Praepaaratum, Mass Galla chinesis et camelliae Fermentata and Pien Tze Huang. This essay summarizes historical origin, main varieties, the effect of microbial strains, current processing techniques and existing problems of FTCM, and look into the prospect of modern development of FTCMs.
China ; Drug Compounding ; methods ; trends ; Drug Industry ; methods ; trends ; Fermentation ; Industrial Microbiology ; methods ; trends ; Medicine, Chinese Traditional ; methods ; trends

Dwindling supplies of conventional energy sources and the demand to increase the share of renewable energy for sustainability have increased the significance of biogas, the product of synergistic fermentation of biodegrable organic wastes from municipal, agricultural and industrial activities by microbial populations under anaerobic conditions. With extensive research and engineering practice, many technologies and modes have been developed for biogas production and application. Currently, the most widely used mode is the complete-mixing mesophilic fermentation. Europe, especially Germany, is leading the world in the combined heat and power production (CHP) from biogas. In this paper, updated progress in biogas technologies is reviewed, with focuses on anaerobic microorganisms, bioreactor configurations and process development, biogas production and applications, in which perspectives of biogas as a clean and renewable energy are projected.
Bacteria, Anaerobic ; metabolism ; physiology ; Biodegradation, Environmental ; Bioelectric Energy Sources ; microbiology ; trends ; Biofuels ; microbiology ; Fermentation ; Industrial Microbiology ; trends ; Refuse Disposal ; methods

With the widely application of the metagenomics, the relationship between microbiota and disease has become a hot research topic. Understanding the potential association between upper gastrointestinal cancer or precancerous lesions and microbiota may play an important role in the early detection, clinical diagnosis and treatment, and prognostic evaluation of upper gastrointestinal cancer. Therefore, a literature retrieval was conducted by using PubMed, Embase and wanfang databases to summarize the latest research progress in the microbiota of upper gastrointestinal cancer, including oral, esophageal, gastric cancer and precancerous lesions. Lower microbial diversity or richness in esophageal cancer and precancerous lesions and specific prognostic biomarkers for esophageal cancer were found. Lactobacillus richness showed an increase trend during the process from gastritis to gastric cancer. This paper summarizes the progress in the research of potential biological etiology of upper gastrointestinal cancer from the perspective of metagenomics in order to provide evidence on the, prevention and control of upper gastrointestinal cancer.
Esophageal Neoplasms/microbiology* ; Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/microbiology* ; Gastrointestinal Tract/microbiology* ; Humans ; Lactobacillus ; Metagenomics/trends* ; Microbiota ; Precancerous Conditions/microbiology* ; Prognosis ; Research/trends* ; Risk Factors ; Stomach Neoplasms/microbiology*

Industrial biocatalysis is currently attracting much attention to rebuild or substitute traditional producing process of chemicals and drugs. One of key focuses in industrial biocatalysis is biocatalyst, which is usually one kind of microbial enzyme. In the recent, new technologies of bioinformatics have played and will continue to play more and more significant roles in researches of industrial biocatalysis in response to the waves of genomic revolution. One of the key applications of bioinformatics in biocatalysis is the discovery and identification of the new biocatalyst through advanced DNA and protein sequence search, comparison and analyses in Internet database using different algorithm and software. The unknown genes of microbial enzymes can also be simply harvested by primer design on the basis of bioinformatics analyses. The other key applications of bioinformatics in biocatalysis are the modification and improvement of existing industrial biocatalyst. In this aspect, bioinformatics is of great importance in both rational design and directed evolution of microbial enzymes. Based on the successful prediction of tertiary structures of enzymes using the tool of bioinformatics, the undermentioned experiments, i.e. site-directed mutagenesis, fusion protein construction, DNA family shuffling and saturation mutagenesis, etc, are usually of very high efficiency. On all accounts, bioinformatics will be an essential tool for either biologist or biological engineer in the future researches of industrial biocatalysis, due to its significant function in guiding and quickening the step of discovery and/or improvement of novel biocatalysts.
Biocatalysis ; Computational Biology ; trends ; Enzymes ; chemistry ; metabolism ; Industrial Microbiology

Microbial fuel cell (MFC) is a new technology that can recover energy from biomass with simultaneous waste treatment. This technique has been developed fast in recent years in combining with environmental techniques such as wastewater treatment, degradation of toxic pollutants and desalination. With the increase of solid waste, applying MFC in composting is promising due to its property of waste disposal with simultaneous energy generation. In this paper, the microbial community of MFCs during composting was summarized. Four major influencing factors including electrodes, separators, oxygen supplement and configurations on the performance of composting MFCs were discussed. The characteristics of composting MFC as a new technique for reducing solid waste were as follows: high microbial biomass resulted in the high current density; adaptable to different environmental conditions; self-adjustable temperature with high energy efficiency; the transportation of proton from anode to cathode were limited by different solid substrates.
Bioelectric Energy Sources ; microbiology ; trends ; Electricity ; Electrodes ; Refuse Disposal ; methods

In the last few decades, with the development of recombinant DNA technology, metabolic engineering has made tremendous advances. Synthetic biology is a newly and rapidly emerging discipline. It has great potential in assisting and simplifying the study of metabolic engineering. This review focuses on the recent development of synthetic biology and its application in optimizing metabolic pathway and engineering cellular chassis.
Genetic Engineering ; methods ; Industrial Microbiology ; methods ; Metabolism ; Synthetic Biology ; trends

The background for developing metabolic engineering was reviewed, followed by a discussion on analyzing the driving force for developing metabolic engineering. Twelve papers published in this special section were briefly introduced with the aim to stimulate further developments in this fast evolving field.
Biotechnology ; trends ; Genetic Engineering ; methods ; Industrial Microbiology ; methods ; Metabolism