未来食品的低碳生物制造

受到人口增长过快、社会经济发展水平不平衡、人口老龄化和不健康饮食方式等影响,人类面临着食品和营养缺乏、部分人群中营养相关疾病高发等问题。同时,社会低碳发展的需求呼唤一种可持续的食物供给模式。因此,既能满足消费者口感和营养需求,又是绿色可持续食物供给模式的技术,例如功能糖、人造肉等未来食品技术,受到了广泛的关注。近年,新兴的生物制造技术及产品得到了迅猛发展,将会支撑形成绿色、低碳的未来食品产业,引发传统生产模式的深刻变革,是新兴生物经济的重大战略发展方向。本文聚焦于未来食品——功能糖、微生物蛋白及人造肉等关键辅配料的生物制造技术研究,追踪其在细胞工厂构建、工业环境下菌种测试与过程优化和衍生产品开发等研究的最新进展,展望未来的发展趋势,旨在为微生物制造未来食品的产业发展提供指导。     

Mass spectrometry methods in metabolomics

The review deals with metabolomics, a new and rapidly growing area directed to the comprehensive analysis of metabolites of biological objects. Metabolites are characterized by various physical and chemical properties, traditionally studied by methods of analytical chemistry focused on certain groups of chemical substances. However, current progress in mass spectrometry has led to formation of rather unified methods, such as metabolic fingerprinting and metabolomic profiling, which allow defining thousands of metabolites in one biological sample and therefore draw “a modern portrait of metabolomics.” This review describes basic characteristics of these methods, ways of metabolite separation, and analysis of metabolites by mass spectrometry. The examples shown in this review, allow to estimate these methods and to compare their advantages and disadvantages. Besides that, we consider the methods, which are of the most frequent use in metabolomics; these include the methods for data processing and the required resources, such as software for mass spectra processing and metabolite search database. In the conclusion, general suggestions for successful metabolomic experiments are given.     

Lipidomics and lipid profiling in metabolomics

PURPOSE OF REVIEW: The field of metabolomics is extending the principles of genomics into cellular and organism metabolism and driving a revolution in lipid biochemistry, physiology and nutrition. Lipids studied using metabolomic approaches - lipidomics - are an ideal subject for metabolomic measurements. RECENT FINDINGS: Lipids are small molecules that share common physical and chemical properties as a class, whose presence and abundance are key to much of metabolic regulation, from subcellular compartments to whole body energy control and signaling. Furthermore, by measuring changes in lipid concentrations, scientists are gaining a more detailed understanding of biochemistry and thus annotating genomes, but also understanding genetic polymorphisms and the postgenetic effects induced by drugs, foods and toxins. SUMMARY: Although in its infancy - there are fewer than 200 total articles on lipidomics and metabolomics focusing on lipids - the field of metabolomics is beginning to deliver on its promise to revolutionize lipid and metabolic disease research.     

Protective effects of bifidobacteria against enteropathogens

Recent major advances in metagenomics and metabolomics technologies have enabled us to collect more data on the gut microbiome and metabolome to evaluate its influence on host health. In this short opinion article, we have chosen to focus on summarizing the protective mechanisms of bifidobacteria, a highly regarded probiotic, and it's metabolite: acetate; against enteropathogens, specifically in the E. coli O157:H7 mice model. We advocate for using a novel approach metabologenomics, which is an integration of metagenomic and metabolomic information on a systems biology-wide approach to better understand this interplay between gut microbiome and host metabolism.     

Nanostructure Initiator Mass Spectrometry for tissue imaging in metabolomics: future prospects and perspectives

Mass spectrometry-based metabolomics provides a new approach to interrogate mechanistic biochemistry related to natural processes such as health and disease. Physiological and pathological conditions, however, are characterized not only by the identities and concentrations of metabolites present, but also by the location of metabolites within a tissue. Unfortunately, most relevant MS platforms in metabolomics can only measure samples in solution, therefore metabolites are typically extracted by tissue homogenization. Recent developments of imaging-MS technologies, however, have allowed particular metabolites to be spatially localized within biological tissues. In this context, Nanostructure-Initiator Mass Spectrometry (NIMS), a matrix-free technique for surface-based analysis, has proven an alternative approach for tissue imaging of metabolites. Here we review the basic principles of NIMS for tissue imaging and show applications that can complement LC/MS and GC/MS-based metabolomic studies investigating the mechanisms of fundamental biological processes. In addition, the new surface modifications and nanostructured materials herein presented demonstrate the versatility of NIMS surface to expand the range of detectable metabolites.     

Solving the Differential Biochemical Jacobian from Metabolomics Covariance Data

High-throughput molecular analysis has become an integral part in organismal systems biology. In contrast, due to a missing systematic linkage of the data with functional and predictive theoretical models of the underlying metabolic network the understanding of the resulting complex data sets is lacking far behind. Here, we present a biomathematical method addressing this problem by using metabolomics data for the inverse calculation of a biochemical Jacobian matrix, thereby linking computer-based genome-scale metabolic reconstruction and in vivo metabolic dynamics. The incongruity of metabolome coverage by typical metabolite profiling approaches and genome-scale metabolic reconstruction was solved by the design of superpathways to define a metabolic interaction matrix. A differential biochemical Jacobian was calculated using an approach which links this metabolic interaction matrix and the covariance of metabolomics data satisfying a Lyapunov equation. The predictions of the differential Jacobian from real metabolomic data were found to be correct by testing the corresponding enzymatic activities. Moreover it is demonstrated that the predictions of the biochemical Jacobian matrix allow for the design of parameter optimization strategies for ODE-based kinetic models of the system. The presented concept combines dynamic modelling strategies with large-scale steady state profiling approaches without the explicit knowledge of individual kinetic parameters. In summary, the presented strategy allows for the identification of regulatory key processes in the biochemical network directly from metabolomics data and is a fundamental achievement for the functional interpretation of metabolomics data.     

Metabolomics in the fields of oncology: a review of recent research

The study of all endogenously produced metabolites, known as metabolomics, is the youngest of the "omics" sciences. It is becoming increasingly clear that, of all of the "omics" techniques, metabolomic approaches will become increasingly useful in disease diagnosis and have potential power to improve our understanding of the underlying mechanisms of cancer. The primary aim of the review is to discuss the relationship between metabolomics and tumors are elucidated in detail. Then the review is also to introduce the technologies of metabolomics, especially emphasizing the application of metabolomics in the fields of oncology.     

Plant metabolomics: from holistic hope, to hype, to hot topic

In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with newly designed, dedicated statistical, bioinformatics and data mining strategies, is beginning to broaden the horizons of our understanding of how plants are organized and how metabolism is both controlled but highly flexible. Metabolomics is predicted to play a significant, if not indispensable role in bridging the phenotype-genotype gap and thus in assisting us in our desire for full genome sequence annotation as part of the quest to link gene to function. Plants are a fabulously rich source of diverse functional biochemicals and metabolomics is also already proving valuable in an applied context. By creating unique opportunities for us to interrogate plant systems and characterize their biochemical composition, metabolomics will greatly assist in identifying and defining much of the still unexploited biodiversity available today.     

Plant nutrition research: Priorities to meet human needs for food in sustainable ways

The world population is expanding rapidly and will likely be 10 billion by the year 2050. Limited availability of additional arable land and water resources, and the declining trend in crop yields globally make food security a major challenge in the 21st century. According to the projections, food production on presently used land must be doubled in the next two decades to meet food demand of the growing world population. To achieve the required massive increase in food production, large enhancements in application of fertilizers and improvements of soil fertility are indispensable approaches. Presently, in many developing countries, poor soil fertility, low levels of available mineral nutrients in soil, improper nutrient management, along with the lack of plant genotypes having high tolerance to nutrient deficiencies or toxicities are major constraints contributing to food insecurity, malnutrition (i.e., micronutrient deficiencies) and ecosystem degradation. Plant nutrition research provides invaluable information highly useful in elimination of these constraints, and thus, sustaining food security and well-being of humans without harming the environment. The fact that at least 60% of cultivated soils have growth-limiting problems with mineral-nutrient deficiencies and toxicities, and about 50% of the world population suffers from micronutrient deficiencies make plant nutrition research a major promising area in meeting the global demand for sufficient food production with enhanced nutritional value in this millennium. Integration of plant nutrition research with plant genetics and molecular biology is indispensable in developing plant genotypes with high genetic ability to adapt to nutrient deficient and toxic soil conditions and to allocate more micronutrients into edible plant products such as cereal grains.     

代谢组学在乳酸菌研究中的应用

代谢组学是系统生物学的重要分支,因其高效、高通量等特点而广泛应用于食品科学、药物学等研究领域。本文概述了代谢组学的分离和检测技术,综述了代谢组学在乳酸菌鉴定、发酵调控、肠道菌群研究等方面中的应用,对代谢组学在乳酸菌研究中潜在的问题和未来发展趋势进行了讨论,期望为代谢组学在食品工业微生物中的应用提供参考。     

Biological features and regulatory mechanisms of salt tolerance in plants

Halophytes play a vital role in saline agriculture because these plants are necessary to increase the food supply to meet the demands of the growing world population. In addition, the transfer of salt-resistance genes from halophytes using genetic technologies has the potential to increase the salt tolerance of xerophytes. Characterization of some particularly promising halophyte model organisms has revealed the important new insights into the salt tolerance mechanisms used by plants. Numerous advances using these model systems have improved our understanding of salt tolerance regulation and salt tolerance-associated changes in gene expression, and these mechanisms have important implications for saline agriculture. Recent findings provide a basis for future studies of salt tolerance in plants, as well as the development of improved strategies for saline agriculture to increase yields of food, feed, and fuel crops.     

Environmental metabolomics: a critical review and future perspectives

Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.     

Plant genetics, sustainable agriculture and global food security

The United States and the world face serious societal challenges in the areas of food, environment, energy, and health. Historically, advances in plant genetics have provided new knowledge and technologies needed to address these challenges. Plant genetics remains a key component of global food security, peace, and prosperity for the foreseeable future. Millions of lives depend upon the extent to which crop genetic improvement can keep pace with the growing global population, changing climate, and shrinking environmental resources. While there is still much to be learned about the biology of plant-environment interactions, the fundamental technologies of plant genetic improvement, including crop genetic engineering, are in place, and are expected to play crucial roles in meeting the chronic demands of global food security. However, genetically improved seed is only part of the solution. Such seed must be integrated into ecologically based farming systems and evaluated in light of their environmental, economic, and social impacts-the three pillars of sustainable agriculture. In this review, I describe some lessons learned, over the last decade, of how genetically engineered crops have been integrated into agricultural practices around the world and discuss their current and future contribution to sustainable agricultural systems.     

Exploratory analysis of high-throughput metabolomic data

In order to make sense of the sheer volume of metabolomic data that can be generated using current technology, robust data analysis tools are essential. We propose the use of the growing self-organizing map (GSOM) algorithm and by doing so demonstrate that a deeper analysis of metabolomics data is possible in comparison to the widely used batch-learning self-organizing map, hierarchical cluster analysis and partitioning around medoids algorithms on simulated and real-world time-course metabolomic datasets. We then applied GSOM to a recently published dataset representing metabolome response patterns of three wheat cultivars subject to a field simulated cyclic drought stress. This novel and information rich analysis provided by the proposed GSOM framework can be easily extended to other high-throughput metabolomics studies.     

Liver tumors in wild flatfish: a histopathological, proteomic, and metabolomic study

Fish play host to viral, bacterial, and parasitic diseases in addition to non-infectious conditions such as cancer. The National Marine Monitoring Programme (NMMP) provides information to the U.K. Government on the health status of marine fish stocks. An aspect of this work relates to the presence of tumors and other pathologies in the liver of the offshore sentinel flatfish species, dab (Limanda limanda). Using internationally agreed quality assurance criteria, tumors and pre-tumors are diagnosed using histopathology. The current study has expanded upon this work by integrating these traditional diagnostic approaches with ones utilizing modern technologies for analysis of proteomic and metabolomic profiles of selected lesions. We have applied SELDI and FT-ICR technologies (for proteomic and metabolomic analyses, respectively) to tumor and non-tumor samples resected from the liver of dab. This combined approach has demonstrated how these technologies are able to identify protein and metabolite profiles that are specific to liver tumors. Using histopathology to classify "analysis groups" is key to the success of such an approach since it allows for elimination of spurious samples (e.g., those containing parasite infections) that may confuse interpretation of "omic" data. As such, the pathology laboratory plays a central role in collating information relating to particular specimens and in establishing sampling groups relative to specific diagnostic questions. In this study, we present pilot data, which illustrates that proteomics and metabolomics can be used to discriminate fish liver tumors and suggest future directions for work of this type.     

A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties

Using a novel approach combining four complementary metabolomic and mineral platforms with genome-wide genotyping at 1536 single nucleotide polymorphism (SNP) loci, we have investigated the extent of biochemical and genetic diversity in three commercially-relevant waxy rice cultivars important to food production in the Lao People??s Democratic Republic (PDR). Following cultivation with different nitrogen fertiliser regimes, multiple metabolomic data sets, including minerals, were produced and analysed using multivariate statistical methods to reveal the degree of similarity between the genotypes and to identify discriminatory compounds supported by multiple technology platforms. Results revealed little effect of nitrogen supply on metabolites related to quality, despite known yield differences. All platforms revealed unique metabolic signatures for each variety and many discriminatory compounds could be identified as being relevant to consumers in terms of nutritional value and taste or flavour. For each platform, metabolomic diversity was highly associated with genetic distance between the varieties. This study demonstrates that multiple metabolomic platforms have potential as phenotyping tools to assist breeders in their quest to combine key yield and quality characteristics. This better enables rice improvement programs to meet different consumer and farmer needs, and to address food security in rice-consuming countries.