Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches

While lactic acid bacteria and bifidobacteria have been scientifically important for over a century, many of these are marketed today as probiotics and have become a valuable and rapidly expanding sector of the food market that is leading functional foods in many countries. The human gastro-intestinal tract with its various compartments and complex microbiota is the primary target of most of these functional foods containing lactic acid bacteria and bifidobacteria (LAB&B). In addition, their use as vectors for delivery of molecules with therapeutic value to the host via the intestinal tract is being studied. This review focuses on molecular approaches for the investigation of the diversity of lactic acid bacteria and bifidobacteria in the human intestine, as well as tracking of probiotic bacteria within this complex ecosystem. Moreover, methodologies to determine the viability of the lactic acid bacteria and bifidobacteria and molecular approaches to study the mechanisms by which they adapt, establish and interact with the human host via the digestive tract, are described.     

Post-genomics of lactic acid bacteria and other food-grade bacteria to discover gut functionality

Recent years have seen an explosion in the number of complete or almost complete genomic sequences of lactic acid bacteria and other food-grade bacteria that are used in functional foods to increase the health of the consumer. These have been instrumental in the development of functional, comparative and other post-genomics approaches that provide the possibility to detect, unravel and understand their functionality in the human intestinal tract. In conjunction with other high-throughput approaches, these advances can be exploited in the functional food innovation cycle for developing new or designed probiotic and other bacterial products that impact gut health.     

乳酸菌基因组学研究进展

乳酸菌广泛应用于食品发酵工业中,其中有些菌种是重要的益生菌。目前,对乳酸菌的研究已从最初的形态学研究进入到了分子水平的研究。乳酸菌全基因组测序研究已在全球展开。乳酸菌基因组研究有助于揭示乳酸菌的遗传和代谢机制,加速重要益生功能基因的挖掘,同时为乳酸菌的应用提供众多可能性。本文就乳酸菌基因组研究的概况、重要乳酸菌基因组、乳酸菌的功能基因组以及比较基因组进行了综述。     

Biotechnology of health-promoting bacteria

Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.     

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

Probiotic bacteria can modulate immune responses in the host gastrointestinal tract to promote health. The genomics era has provided novel opportunities for the discovery and characterization of bacterial probiotic effector molecules that elicit specific responses in the intestinal system. Furthermore, nutrigenomic analyses of the response to probiotics have unravelled the signalling and immune response pathways which are modulated by probiotic bacteria. Together, these genomic approaches and nutrigenomic analyses have identified several bacterial factors that are involved in modulation of the immune system and the mucosal barrier, and have revealed that a molecular 'bandwidth of human health' could represent a key determinant in an individual's physiological responsiveness to probiotics. These approaches may lead to improved stratification of consumers and to subpopulation-level probiotic supplementation to maintain or improve health, or to reduce the risk of disease.     

From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria

The lactic acid bacteria (LAB) are a functionally related group of low-GC Gram-positive bacteria known essentially for their roles in bioprocessing of foods and animal feeds. Due to extensive industrial use and enormous economical value, LAB have been intensively studied and a large body of comprehensive data on their metabolism and genetics was generated throughout the years. This knowledge has been instrumental in the implementation of successful applications in the food industry, such as the selection of robust starter cultures with desired phenotypic traits. The advent of genomics, functional genomics and high-throughput experimentation combined with powerful computational tools currently allows for a systems level understanding of these food industry workhorses. The technological developments in the last decade have provided the foundation for the use of LAB in applications beyond the classic food fermentations. Here we discuss recent metabolic engineering strategies to improve particular cellular traits of LAB and to design LAB cell factories for the bioproduction of added value chemicals.     

Current status and application of lactic acid bacteria in animal production systems with a focus on bacteria from honey bee colonies

Lactic acid bacteria (LAB) are widely distributed in nature and, due to their beneficial effects on the host, are used as probiotics. This review describes the applications of LAB in animal production systems such as beekeeping, poultry, swine and bovine production, particularly as probiotics used to improve health, enhance growth and reproductive performance. Given the importance of honeybees in nature and the beekeeping industry as a producer of healthy food worldwide, the focus of this review is on the coexistence of LAB with honeybees, their food and environment. The main LAB species isolated from the beehive and their potential technological use are described. Evidence is provided that 43 LAB bacteria species have been isolated from beehives, of which 20 showed inhibition against 28 species of human and animal pathogens, some of which are resistant to antibiotics. Additionally, the presence of LAB in the beehive and their relationship with antibacterial properties of honey and pollen is discussed. Finally, we describe the use of lactic bacteria from bee colonies and their antimicrobial effect against foodborne pathogens and human health . This review broadens knowledge by highlighting the importance of honeybee colonies as suppliers of LAB and functional food.     

Systems solutions by lactic acid bacteria: from paradigms to practice

Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.     

益生菌的安全性

益生菌是指一类活的,摄入足够量就能够对人体产生有益作用的微生物,目前广泛应用于食品发酵、工业乳酸发酵以及医疗保健领域.随着市场上商品化益生菌的不断出现,它所带来的安全性问题也更加引起人们的关注.目前益生菌主要存在四个方面的安全问题:致病性和感染能力;有害的代谢活动:过度的免疫反应和可能的基因转移.传统的益生菌安全性评价方法具有一定的局限性.我们需要针对目前益生菌安全性存在的问题建立一套包含基因组学,代谢组学,蛋白质组学等研究内容的评估方法,对益生菌的安全性进行系统全面的评估.本文总结了一些对于益生菌安全性的研究进展和研究方法,以提示我国应尽快完善益生菌及其制品的安全性评价方法指标并建立安全性评价体系,使益生菌更好的为人们的健康服务.     

Interaction of lactic acid bacteria with metal ions: opportunities for improving food safety and quality

Certain species of lactic acid bacteria (LAB), as well as other microorganisms, can bind metal ions to their cells surface or transport and store them inside the cell. Due to this fact, over the past few years interactions of metal ions with LAB have been intensively investigated in order to develop the usage of these bacteria in new biotechnology processes in addition to their health and probiotic aspects. Preliminary studies in model aqueous solutions yielded LAB with high absorption potential for toxic and essential metal ions, which can be used for improving food safety and quality. This paper provides an overview of results obtained by LAB application in toxic metal ions removing from drinking water, food and human body, as well as production of functional foods and nutraceutics. The biosorption abilities of LAB towards metal ions are emphasized. The binding mechanisms, as well as the parameters influencing the passive and active uptake are analyzed.     

Genomic features of lactic acid bacteria effecting bioprocessing and health

The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems.     

Next-generation sequencing and its potential impact on food microbial genomics

Recent efforts of researchers to elucidate the molecular mechanisms of biological systems have been revolutionized greatly with the use of high throughput and cost-effective techniques such as next generation sequencing (NGS). Application of NGS to microbial genomics is not just limited to predict the prevalence of microorganisms in food samples but also to elucidate the molecular basis of how microorganisms respond to different food-associated conditions, which in turn offers tremendous opportunities to predict and control the growth and survival of desirable or undesirable microorganisms in food. Concurrently, NGS has facilitated the development of new genome-assisted approaches for correlating genotype and phenotype. The aim of this review is to provide a snapshot of the various possibilities that these new technologies are opening up in area of food microbiology, focusing the discussion mainly on lactic acid bacteria and yeasts associated with fermented food. The contribution of NGS to a system level understanding of food microorganisms is also discussed.     

乳酸菌对真菌毒素的脱毒作用研究进展

真菌毒素广泛存在于农业产品中,对人和动物的健康构成巨大威胁。乳酸菌作为一种公认安全的微生物,在食品生物减毒方面具有巨大的应用潜力,成本低廉且不会对食品品质及生态环境造成不良影响。文章主要根据近年来国内外研究进展,阐述乳酸菌对食品和饲料中几种常见真菌毒素的脱毒作用(抑制真菌生长、毒素的吸附和降解),关注乳酸菌在生物脱毒方面的实际应用,为乳酸菌在食品保鲜领域的应用提供理论指导。     

Metagenomics in animal gastrointestinal ecosystem: a microbiological and biotechnological perspective

Metagenomics- the application of the genomics technologies to nonculturable microbial communities, is coming of age. These approaches can be used for the screening and selection of nonculturable rumen microbiota for assessing their role in gastrointestinal (GI) nutrition, plant material fermentation and the health of the host. The technologies designed to access this wealth of genetic information through environmental nucleic acid extraction have provided a means of overcoming the limitations of culture-dependent microbial genetic exploitation. The molecular procedures and techniques will result in reliable insights into the GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Future developments and applications of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural habitats with their genetic potential and in situ activities.     

乳酸菌对重金属吸附作用的研究进展

重金属污染是人们关注的食品安全问题热点之一,使用食品安全级乳酸菌吸附重金属成为了新的研究方向。本文在分析环境和食品中汞、镉、铅污染的来源及对人类危害的基础上,对微生物与重金属的相互作用进行介绍,重点归纳了乳酸菌作为重金属吸附剂的潜能,以及吸附重金属的作用机制和研究现状,为研发高效吸附重金属的乳酸菌吸附剂提供了可行性的思路。     

Metagenomics in animal gastrointestinal ecosystem: Potential biotechnological prospects

Microbial metagenomics---the applications of the genomics suit of technologies to nonculturable microorganisms, is coming of age. These approaches can be used for the screening and identification of nonculturable gastrointestinal (GI) microflora for assessing and exploiting them in nutrition and the health of the host. Advances in technologies designed to access this wealth of genetic information through environmental nucleic acids extraction and analysis have provided the means of overcoming the limitations of conventional culture-dependent microbial genetic exploitation. The molecular techniques and bioinformatics tools will result in reliable insights into the animals' GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Further developments and applications of these methods promise to provide the opportunity to link distribution and identity of various GI microbes in their natural habitats, and explore their use for promoting livestock health and industrial development.     

乳酸菌治疗乳糖不耐受症的研究进展

乳糖不耐受与人体健康尤其是婴儿期的营养密切相关,该病症主要影响人体对乳糖的消化吸收。乳酸菌作为有效的微生态制剂,已被广泛应用于医药卫生、营养保健、食品工业等领域。近年研究发现,含乳酸菌的微生态制剂在治疗乳糖不耐受症方面具有明显疗效。本文综述了乳糖不耐受症的发病机制及分型、乳酸菌治疗乳糖不耐受症的研究进展。     

Bacteriophage defence systems in lactic acid bacteria

The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.     

Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

Bifidobacteria and lactobacilli are widely exploited as health-promoting bacteria in many functional foods. However, the molecular mechanisms as to how these bacteria positively impact on host health are far from completely understood. For this reason these microorganisms represent a growing area of interest with respect to their genomics, molecular biology and genetics. Recent genome sequencing of a large number of strains of bifidobacteria and lactobacilli has allowed access to the complete genetic makeup of representative members of these bacteria. Here, we will discuss how the analysis of genomic data has helped us to understand the mechanisms by which these bacteria adapt to the specific environment of the gastrointestinal tract, while also revealing genetic functions that mediate specific host-microbe interactions.