Overproduction of microbial products--facts and ideas

Overproduction of microbial metabolites is related to developmental phases of microorganisms. Inducers, effectors, inhibitors and various signal molecules play a role in different types of overproduction. Primary and secondary metabolism are interconnected. Biosynthesis of enzymes catalyzing metabolic reactions in microbial cells is controlled by well-known positive and negative mechanisms, e.g. induction, repression, catabolite repression, mechanisms controlling enzyme activity include isosteric and allosteric interactions, e.g. competitive and non-competitive inhibition, allosteric effects, molecular conversion etc. Biosynthesis of secondary metabolites is catalyzed by unaltered enzymes of primary metabolism, by altered enzymes of primary metabolism and by specific enzymes of secondary metabolism. In addition to classical mutagenesis and selection of suitable microbial cells, methods of molecular genetics are used in the overproduction of microbial products.     

Fermentation trip: amazing microbes,amazing metabolisms

Fermentation has been applied to many areas of human life, including industrial production, sewage treatment, and environment management. By understanding the process and mechanism of fermentation, more comprehensive and profound cognition of the fermentation may be established to lay a foundation for our further research. In this review, we present a brief summary of recent research about fermentation and microorganisms in different territories, including foods, environment, and human health. According to the growth characteristics of different stages of microorganisms, we introduced a series of metabolic changes, fermentation mechanism, and regulation methods and how the enzymes were transported out of the cell. With further understanding and utilization of microorganisms, food can produce better flavor, nutrition, and functional metabolites through fermentation. Fermentation is also used in other industries, such as wastewater and garbage disposal, environment, and soil management. The human gut flora, in particular, has begun to receive more attention. The profound influence of microorganism on human health cannot to be underestimated. It has become a hot research area in recent years. We can get the metabolites we want by controlling the rate of fermentation and regulate the direction of fermentation. As one of the important components of modern biotechnology, fermentation engineering has been widely used in areas including food, pharmaceutical, energy, chemical industries, and environmental protection. The development of genetic engineering has brought new vitality to fermentation engineering. The application of modernization, automation and artificial intelligence technology also opens up new space for fermentation engineering. In addition, research on the understanding and regulation of metabolic mechanism has further developed the fermentation function of microorganisms.     

工业微生物：创新与突破专刊序言(2021)

工业微生物及其产品广泛用于工业、农业、医药等诸多领域,相关产业在国民经济中具有举足轻重的地位。高效的菌株是提高生产效率的核心,而先进发酵技术和仪器平台对充分开发菌株代谢潜能也很重要。近年来,工业微生物领域的研究取得了快速进展,人工智能、高效基因组编辑技术和合成生物学技术逐渐广泛使用,相关产业应用也在不断扩展。为进一步促进工业微生物在生物制造等领域的应用,《生物工程学报》特组织出版专刊,从微生物菌株的多样性和生理代谢、菌株改造技术、发酵过程优化和放大,高通量微液滴培养装备开发以及工业微生物应用等方面,分别阐述目前的研究进展,并展望未来的发展趋势,为促进工业微生物及生物制造等产业的发展奠定基础。     

A microbiological study of Hussuwa: a traditional Sudanese fermented food from germinated Sorghum bicolor c.v. feterita

Hussuwa is a traditional Sudanese fermented food. Hussuwa made from Sorghum bicolor variety feterita exists in northern, central and eastern Sudan. The microbiological study indicated that the fermentation was primarily a lactic acid fermentation. The changes in microbial population, acetic acid bacteria, lactic acid bacteria and yeasts during all stages of hussuwa preparation and ripening were studied. The identification of fermented hussuwa microorganisms revealed that the main microorganisms were Lactobacillus saccharolyticum, Gluconobacter oxydans, Acetobacter xylinum and Saccharomyces cerevisiae. The metabolic products were studied in all stages of preparation and the period of ripening of hussuwa. The values of pH decreased as fermentation proceeded, and titratable acidity and volatile fatty acids increased.     

Metabolic regulation of fermentation processes

To compete in nature against other forms of life, microorganisms possess regulatory mechanisms which control production of their metabolites, thus, protecting against overproduction and excretion of these primary and secondary metabolites into the environment. To effect such an economical form of life, they possess regulatory mechanisms which control production of these metabolites and protect against overproduction and excretion into the environment of excess concentrations. In the field of industrial fermentation, the opposite concept prevails. Fermentation microbiologists search for a rare overproducing strain in nature, then further deregulate the microorganism so that it overproduces huge quantities of a desired commercially important product such as a metabolite or an enzyme. Deregulation is brought about by nutritional as well as classical and molecular genetic manipulations to bypass and/or remove negative regulatory mechanisms and to enhance positive regulatory mechanisms. These mechanisms include induction, nutritional regulation by sources of carbon, nitrogen and phosphorus, and feedback control. The controls and their modification by biotechnologists are the subjects of this review.     

Some aspects of overproduction of secondary metabolites

Different approaches used to increase production of secondary metabolites and construct overproducing strains of microorganisms are reviewed. Overproduction of secondary metabolites incuudes the physiological control,e.g. feed-back inhibition, carbon and energy source regulation, nitrogen source regulation, phosphate regulation and the effect of autoregulatory compounds. The genetic control of overproduction of secondary metabolites includes mechanisms similar to those controlling the expression of primary metabolism coding genes, although the genes specifying biosynthesis of secondary metabolites and their expression have some particular features. Possible future trends in the study of overproduction of secondary metabolites are discussed. Dedicated to the 70th birthday of Dr. Z. Vanêk     

微生物法生产1,3-二羟基丙酮代谢工程研究进展

1,3-二羟基丙酮是一种重要的化工原料和医药中间体,广泛应用于化妆品、医药、食品等领域。以下综述了微生物法生产1,3-二羟基丙酮的代谢途径和关键酶,以及微生物法生产1,3-二羟基丙酮所涉及的代谢工程技术的研究进展。指出利用基因工程的方法对菌株进行改造,提高甘油脱氢酶催化活性,同时根据菌株的代谢特性,对发酵过程进行调控,提高1,3-二羟基丙酮的得率,是今后的研究方向。     

Influence of dietary fat on intestinal microbes,inflammation, barrier function and metabolic outcomes

Recent studies using germ-free, gnotobiotic microbial transplantation/conventionalization or antibiotic treatment in rodent models have highlighted the critical role of intestinal microbes on gut health and metabolic functions of the host. Genetic and environmental factors influence the abundance and type of mutualistic vs. pathogenic bacteria, each of which has preferred substrates for growth and unique products of fermentation. Whereas some fermentation products or metabolites promote gut function and health, others impair gut function, leading to compromised nutrient digestion and barrier function that adversely impact the host. Such products may also influence food intake, energy harvest and expenditure, and insulin action, thereby influencing adiposity and related metabolic outcomes. Diet composition influences gut microbiota and subsequent fermentation products that impact the host, as demonstrated by prebiotic studies using oligosaccharides or other types of indigestible fiber. Recent studies also show that dietary lipids affect specific populations of gut microbes and their metabolic end products. This review will focus on studies examining the influence of dietary fat amount and type on the gut microbiome, intestinal health and positive and negative metabolic consequences. The protective role of omega-3-rich fatty acids on intestinal inflammation will also be examined.     

Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of ''intelligent'' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.     

萜烯生物合成中关键酶的研究进展*

萜烯类化合物是一类高度多样化的天然产物,具有抗肿瘤、抗氧化及免疫调节等生理活性,因此被广泛应用于医药健康、食品、化妆品领域。然而,直接从自然资源中获取萜烯类化合物效率低、成本高,且往往对生态环境产生不利影响,不能实现绿色可持续生产。微生物合成萜烯类化合物近年来备受关注,研究人员从合成途径的构建与调控、关键酶的理性及半理性改造、发酵工艺优化等多个方面进行了探究,取得了丰硕的成果。其中,合成途径中关键酶的催化效率是影响微生物生产萜烯类化合物的重要因素。针对关键酶的研究对于提高微生物合成萜烯类化合物的能力,推动该类天然产物微生物生产的大规模应用具有重要意义。对萜烯类化合物合成途径中的3-羟基-3-甲基戊二酰辅酶A还原酶(HMGR)、1-脱氧-D-木酮糖-5-磷酸合酶(DXS)、异戊二烯基二磷酸合成酶(IDS)和萜烯合酶(TPS)4种关键酶的研究进行了综述,并总结讨论了如何通过代谢工程和蛋白质工程手段以及合成生物学技术调节关键酶的催化活性,提高微生物合成萜烯类化合物的效率,对未来利用微生物合成萜烯类化合物的发展进行了展望。     

高通量测序技术在食品微生物研究中的应用

高通量测序技术的快速发展对食品微生物发酵过程和机制研究产生了深刻的影响,主要体现在食品微生物生理功能、代谢能力和进化的研究以及食品微生物群落结构、动态变化及其对环境的响应机制等方面。另外,通过对食品微生物基因组和元基因组进行数据分析,也对食品发酵过程优化、微生物功能改造、食源性微生物疾病预防和控制等提供了重要的依据。本文总结了近年来利用高通量测序技术对食品微生物基因组和元基因组进行测序的研究,并探讨了测序技术的发展对食品微生物研究的影响及发展趋势。     

哺乳动物肠道微生物与碳水化合物的互作及其影响

肠道微生物具有调节宿主营养、免疫以及能量代谢等生理功能。饮食是影响哺乳动物的肠道微生物的一个重要因素。碳水化合物是哺乳动物食物能量的主要来源,因此研究肠道微生物与碳水化合物的代谢之间的关系及其影响具有重要意义。基于近年相关研究,本文从碳水化合物对肠道微生物组成的影响、肠道微生物对碳水化合物的代谢机制以及碳水化合物发酵产物短链脂肪酸对宿主的影响3个方面进行了综述。研究表明,肠道微生物可用于发酵的碳水化合物类型主要是抗性淀粉和非淀粉多糖;不同类型的碳水化合物会导致肠道菌群发生适应性变化;复杂多糖发酵产生的短链脂肪酸在调节宿主能量平衡和免疫应答方面发挥了重要作用。总结近年来相关研究,可加深对肠道菌群对宿主碳水化合物代谢贡献的理解,为哺乳动物机体健康状况的营养调控策略提供参考。     

The interplay between host cellular and gut microbial metabolism in NAFLD development and prevention

Metabolism regulation centred on insulin resistance is increasingly important in nonalcoholic fatty liver disease (NAFLD). This review focuses on the interactions between the host cellular and gut microbial metabolism during the development of NAFLD. The cellular metabolism of essential nutrients, such as glucose, lipids and amino acids, is reconstructed with inflammation, immune mechanisms and oxidative stress, and these alterations modify the intestinal, hepatic and systemic environments, and regulate the composition and activity of gut microbes. Microbial metabolites, such as short-chain fatty acids, secondary bile acids, protein fermentation products, choline and ethanol and bacterial toxicants, such as lipopolysaccharides, peptidoglycans and bacterial DNA, play vital roles in NAFLD. The microbe–metabolite relationship is crucial for the modulation of intestinal microbial composition and metabolic activity. The intestinal microbiota and their metabolites participate in epithelial cell metabolism via a series of cell receptors and signalling pathways and remodel the metabolism of various cells in the liver via the gut–liver axis. Microbial metabolic manipulation is a promising strategy for NAFLD prevention, but larger-sampled clinical trials are required for future application.     

Genetic improvement of processes yielding microbial products

Although microorganisms are extremely good in presenting us with an amazing array of valuable products, they usually produce them only in amounts that they need for their own benefit; thus, they tend not to overproduce their metabolites. In strain improvement programs, a strain producing a high titer is usually the desired goal. Genetics has had a long history of contributing to the production of microbial products. The tremendous increases in fermentation productivity and the resulting decreases in costs have come about mainly by mutagenesis and screening/selection for higher producing microbial strains and the application of recombinant DNA technology.     

红树林样品不经分离的微生物群体培养物生物活性研究

从海南、广西与广东三省的红树林区采集了181个样品,不进行微生物分离而直接作发酵剂接种到发酵培养基进行发酵,取发酵上清液进行抗细菌、抗真菌与肿瘤细胞毒活性的测定。同时对样品进行可培养微生物的分离与生物活性测定。结果显示:不同样品类型的生物活性差异较大。在15个具有强抗活性的样品中,有5个样品分离到的单株菌均无任何生物活性,说明这5个样品的生物活性可能是由微生物的群体作用产生的,也可能是某种没有培养出的微生物产生的。初步表明了探索微生物混合培养获得生物活性代谢产物的可能性。     

Improvement of microbial strains and fermentation processes

Improvement of microbial strains for the over-production of industrial products has been the hallmark of all commercial fermentation processes. Conventionally, strain improvement has been achieved through mutation, selection, or genetic recombination. Over-production of primary or secondary metabolites is a complex process, and successful development of improved strains requires a knowledge of physiology, pathway regulation and control, and the design of creative screening procedures. In addition, it requires mastery of the fermentation process for each new strain, as well as sound engineering know-how for media-optimization and the fine-tuning of process conditions. This review focuses on the various options that may be employed to improve microbial strains and addresses the complex problems of screening, the tools and technology behind the selection of targeted organisms, and the importance of process optimization. Furthermore, this review discusses new and emerging technologies and designing optimized media for tracking mutants with enhanced productivity or other desired attributes. Received: 7 February 2000 / Received revision: 2 May 2000 / Accepted: 2 May 2000     

Zur biotechnologischen Relevanz von Regulationsvorgängen des mikrobiellen Sekundärstoffwechsels

Although the regulation of microbial secondary metabolism belongs to the important objects of actual investigations the results and knowledges are used rather poorly in industrial fermentations. This situation arises from the discrepancy between the economically driven development of the know how as soon as possible contrary to the more slow progress of profound examination of the complicated network of secondary metabolism. Nevertheless some well known principles of metabolic regulation, e.g. catabolite repression or resistance against products or metabolites are considered in fermentation processes by means of suitable substrate application as well as improvement of high yield strains. Both aspects are discussed with respect to examples of fermentations of β-lactams, polyketides and glycopeptides.     

Recent advances in microbial production of mannitol: utilization of low-cost substrates,strain development and regulation strategies

Mannitol has been widely used in fine chemicals, pharmaceutical industries, as well as functional foods due to its excellent characteristics, such as antioxidant protecting, regulation of osmotic pressure and non-metabolizable feature. Mannitol can be naturally produced by microorganisms. Compared with chemical manufacturing, microbial production of mannitol provides high yield and convenience in products separation; however the fermentative process has not been widely adopted yet. A major obstacle to microbial production of mannitol under industrial-scale lies in the low economical efficiency, owing to the high cost of fermentation medium, leakage of fructose, low mannitol productivity. In this review, recent advances in improving the economical efficiency of microbial production of mannitol were reviewed, including utilization of low-cost substrates, strain development for high mannitol yield and process regulation strategies for high productivity.     

用自身次生代谢产物抗性筛选宁南霉素高产菌株

宁南霉素是诺尔斯链霉菌西昌变种产生的一种胞嘧啶核苷肽型新抗生素,它对多种病毒、细菌和真菌引起的作物病害都有较好的防治效果,毒性低、残留量小,无蓄积作用,具有良好的应用前景.然而它的原始菌株 16A—6发酵单位仅 700U/ml~1000U/ml,严重阻碍了它的推广应用.     

ATP调控策略及其在微生物代谢产物合成中的应用

辅因子工程是代谢工程的一个新兴分支领域,主要通过直接调控细胞内关键酶的辅因子,如ATP/ADP、NADH/NAD+、NADPH/NADP+等的浓度和形式来实现代谢流的最大化,快速地将物质流导向目标代谢物。ATP作为一种重要辅因子参与微生物细胞内大量的酶催化反应,将物质代谢途径串联或并联成复杂的网络体系,最终使得物质代谢流的分配受到牵制。因此ATP调控策略有望成为微生物菌株改造的有利工具,用于提高目标代谢物的浓度和生产能力,强化微生物对于环境的耐受以及促进底物利用等。文中将重点论述目前常用的有效ATP调控策略以及ATP调控对于细胞代谢的影响,以期为微生物细胞工厂的高效构建提供参考。