Beneficial microbes going underground of root immunity

Plant roots interact with an enormous diversity of commensal, mutualistic, and pathogenic microbes, which poses a big challenge to roots to distinguish beneficial microbes from harmful ones. Plants can effectively ward off pathogens following immune recognition of conserved microbe‐associated molecular patterns (MAMPs). However, such immune elicitors are essentially not different from those of neutral and beneficial microbes that are abundantly present in the root microbiome. Recent studies indicate that the plant immune system plays an active role in influencing rhizosphere microbiome composition. Moreover, it has become increasingly clear that root‐invading beneficial microbes, including rhizobia and arbuscular mycorrhiza, evade or suppress host immunity to establish a mutualistic relationship with their host. Evidence is accumulating that many free‐living rhizosphere microbiota members can suppress root immune responses, highlighting root immune suppression as an important function of the root microbiome. Thus, the gate keeping functions of the plant immune system are not restricted to warding off root‐invading pathogens but also extend to rhizosphere microbiota, likely to promote colonization by beneficial microbes and prevent growth‐defense tradeoffs triggered by the MAMP‐rich rhizosphere environment.     

Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms

For thousands of years, humans have safely consumed microorganisms through fermented foods. Many of these bacteria are considered probiotics, which act through diverse mechanisms to confer a health benefit to the host. However, it was not until the availability of whole-genome sequencing and the era of genomics that mechanisms of probiotic efficacy could be discovered. In this review, we explore the history of the probiotic concept and the current standard of integrated genomic techniques to discern the complex, beneficial relationships between probiotic microbes and their hosts.     

The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota

The human gut is home to trillions of microbes that form a symbiotic relationship with the human host. During health, the intestinal microbiota provides many benefits to the host and is generally resistant to colonization by new species; however, disruption of this complex community can lead to pathogen invasion, inflammation, and disease. Restoration and maintenance of a healthy gut microbiota composition requires effective therapies to reduce and prevent colonization of harmful bacteria (pathogens) while simultaneously promoting growth of beneficial bacteria (probiotics). Here we review the mechanisms by which the host modulates the gut community composition during health and disease, and we discuss prospects for antibiotic and probiotic therapy for restoration of a healthy intestinal community following disruption.     

基于代谢组学的植物多酚及其肠道健康效应研究进展

综述了植物多酚的分类和来源、在代谢组学技术的驱动下,新型多酚物质的鉴定、控制植物多酚合成途径的关键因子以及多酚的功能特性的研究进展,阐述了植物多酚在肠道中的代谢以及其作为“益生元”调节肠道微生态并影响机体健康的重要功能。目前的研究表明不同植物多酚在调节肠道微生态方面存在差异,多数有促进肠道有益菌作用,并通过与肠道微生物“互作”发挥促进健康效应。总之,植物多酚作为“益生元”影响人体健康可能离不开肠道微生物的介导。各个植物多酚的益生功能也需要进一步阐析,在此过程中需要考虑宿主,膳食等混杂因素的综合影响,且需要拓展临床应用方面的研究。     

Wired to the roots: Impact of root-beneficial microbe interactions on aboveground plant physiology and protection

Often, plant-pathogenic microbe interactions are discussed in a host-microbe two-component system, however very little is known about how the diversity of rhizospheric microbes that associate with plants affect host performance against pathogens. There are various studies, which specially direct the importance of induced systemic defense (ISR) response in plants interacting with beneficial rhizobacteria, yet we don’t know how rhizobacterial associations modulate plant physiology. In here, we highlight the many dimensions within which plant roots associate with beneficial microbes by regulating aboveground physiology. We review approaches to study the causes and consequences of plant root association with beneficial microbes on aboveground plant-pathogen interactions. The review provides the foundations for future investigations into the impact of the root beneficial microbial associations on plant performance and innate defense responses.     

Towards understanding molecular modes of probiotic action

The possibility that certain microorganisms might be beneficial to human health is highlighted by the numerous consumer products containing probiotic bacteria. Probiotics are typically administered in food that, following entry into the gastro-intestinal tract, results in measurable health-promoting effects. Although there is a growing list of health benefits provided by the consumption of probiotics, their precise mechanisms of action remain largely unknown. Recent molecular- and genomics-based studies are starting to provide insight into the ways probiotic bacteria sense and adapt to the gastro-intestinal tract environment. Complementary approaches using host cell in vitro systems together with animal models and human volunteers are revealing specific intestinal cell responses to probiotics. These studies should ultimately disclose the molecular mechanisms and pinpoint the bacterial and host effector molecules and pathways by which probiotics are able to modulate human health.     

Beneficial effects of probiotics in upper respiratory tract infections and their mechanical actions to antagonize pathogens

Probiotics are live micro‐organisms with beneficial effects on human health, which have the ability to counteract infections at different locations of the body. Clinical trials have shown that probiotics can be used as preventive and therapeutic agents in upper respiratory tract infections (URTIs) and otitis. Their mechanical properties allow them to aggregate and to compete with pathogens for nutrients, space and attachment to host cells. Consequently, they can directly antagonize pathogens and thus exert beneficial effects without directly affecting the metabolism of the host. An overview of the probiotics with such traits, tested up to date in clinical trials for the prevention or treatment of URTIs and otitis, is presented in this review. Their mechanical properties in the respiratory tract as well as at other locations are also cited. Species with interesting in vitro properties towards pharyngeal cells or against common respiratory pathogens have also been included. The potential safety risks of the cited species are then discussed. This review could be of help in the screening of probiotic strains with specific mechanical properties susceptible to have positive effects in clinical trials against URTIs.     

Hazard Group 3 agent decontamination using hydrogen peroxide vapour in a class III microbiological safety cabinet

Probiotics administration in aquafeed is known to increase feed consumption and absorption due to their capacity to release a wide range of digestive enzymes and nutrients which can participate in digestion process and feed utilization, along with the absorption of diet components led to an increase in host’s health and well-being. Furthermore, probiotics improve gut maturation, prevention of intestinal disorders, predigestion of antinutrient factors found in the feed ingredients, gut microbiota, disease resistance against pathogens and metabolism. The beneficial immune effects of probiotics are well established in finfish. However, in comparison, similar studies are less abundant in the shellfish. In this review, the discussions will mainly focus on studies reported the last 2 years. In recent studies, native probiotic bacteria were isolated and fed back to their hosts. Although beneficial effects were demonstrated, some studies showed adverse effects when treated with a high concentration. This adverse effect may be due to the imbalance of the gut microbiota caused by the replenished commensal probiotics. Probiotics revealed greatest effect on the shrimp digestive system particularly in the larval and early post-larval stages, and stimulate the production of endogenous enzymes in shrimp and contribute with improved the enzyme activities in the gut, as well as disease resistance.     

Programmed cell death in host-symbiont associations,viewed through the Gene Ontology

Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms.     

Evolving Roles of Probiotics in Cancer Prophylaxis and Therapy

In nutraceutical science, the ingestible live microbes ‘probiotics’ are regarded for their ability to confer multiplicity of health benefits on the consumers. Wide spectrum impact of these friendly microbes on the host health has been proved very frequently. They have been confirmed to boost immunity, aid in digestion, eliminate pathogens, curb inflammatory bowel diseases, moderate side effects of antibiotic therapy, lower cholesterol and blood glycemic index and produce vitamins. This review, however, focuses on the incipient, but promising area of probiotic diet-based prevention and remedy of cancer. Researchers are in universal agreement with the critical role of probiotics in getting rid of mutagens, delaying the onset of tumors, alleviating the side effects, pepping up chemotherapy, easing the postoperative complications, foiling remission and lifting the spirit of survivors. The key findings in the emerging roles of probiotics in onco-care have been summarized; the biological pathways discussed and anticipated developments in coming times are presented.     

Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus

Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics.     

Organic fertilizers alter the composition of pathogens and arbuscular mycorrhizal fungi in maize roots

Roots of agricultural crops, including maize, are hosts of different microorganisms, many beneficial, like plant growth and health‐promoting arbuscular mycorrhizal fungi (AMF), as well as pathogens including Pythium, Polymyxa and Microdochium. To improve crop nutrition and health, profound knowledge is required regarding how agricultural practices affect field populations of root‐associated microorganisms. Hence, the objective of this work was to evaluate the effect of crop genotype and organic fertilizers on the plant growth performance of maize and their root‐associated microorganisms. The experiment was conducted as a fully factorial greenhouse pot experiment with maize cultivars (two land races and two hybrids) and organic fertilizers (green manure, cow manure and compost) as the two main factors. Plants were harvested 8 weeks after sowing. In general, the different maize cultivars responded similarly to the applications of the organic fertilizers. Cow manure and compost increased plant growth, whereas green manure had limited effect on plant growth. Root colonization with AMF was reduced by green manure with rape. Infection with the root pathogens Pythium and Polymyxa was reduced by all organic fertilizers, whereas in contrast, infection with Microdochium increased with the majority of the organic fertilizers applied. In conclusion, both maize genotype and organic fertilizers affect the abundance of AMF and root pathogens in maize, which should be considered when developing management strategies of these root‐inhabiting microorganisms.     

Regulation of immune response at intestinal and peripheral sites by probiotics

The gut associated lymphoid tissue (GALT) should protect intestinal mucosa against pathogens, but also avoid hypersensitivity reactions to food proteins, normal bacterial flora and other environmental macromolecules. The interaction between epithelial cells and microflora is fundamental to establish gut mucosal barrier and GALT development. The normal colonization of intestine by commensal bacteria is thus crucial for a correct development of mucosal immune system. Probiotic bacteria are normal inhabitants of microflora and may confer health benefits to the host. The modification of the intestinal microflora towards a healthier probiotics enriched microflora may generate beneficial mucosal immunomodulatory effects and may represent a new strategy to cure intestinal and allergic diseases. The health benefits may be specific for different probiotic strains. Ongoing research is providing new insights into the probiotic beneficial effects and related mechanisms. This review represents an update of immunomodulatory activity of different probiotics and of the more accredited mechanisms underlying such activities. Presented at the Second Probiotic Conference, Košice, 15–19 September 2004, Slovakia.     

miRNA介导植物-微生物互作中的调控作用及其研究进展北大核心CSCD

微生物与植物之间存在错综复杂的双向交流和串扰,植物与病原微生物互作直接影响寄主植物的生存状况,而植物和益生微生物互作则有利于宿主的生长和健康,共生微生物也会从中受益。不管是病原微生物还是有益微生物进入植物体内,植物miRNA都会迅速做出响应,同时微生物也可以产生miRNA样RNA(miRNA-likeRNA,milRNA)影响植物健康,可见miRNA(或milRNA)是植物与微生物互作过程中迅速响应的重要媒介分子,其内在机制研究近年来取得了许多进展。文中概述了植物-病原微生物、植物-益生微生物互作中miRNA的调控作用,重点阐述了植物miRNA在植物-病原微生物互作过程中对寄主植物抗病性的调控作用和植物-益生微生物互作过程中对宿主植物生长发育及代谢的调控,以及真菌milRNA对寄主植物的跨界调控作用。     

Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.     

Evidence-based review of probiotics for antibiotic-associated diarrhea and Clostridium difficile infections

Probiotics are living microbes taken to confer a health benefit on the host. Although probiotics have a long history of use in Europe and Asia and have been on the U.S. market for over 14 years, there is still confusion about how to effectively use them. The use of probiotics for the prevention of antibiotic-associated diarrhea (AAD) and the treatment of Clostridium difficile infections (CDI) has been tested in randomized controlled clinical trials.This paper will review the evidence supporting probiotic therapy for these two diseases and also review the advantages and disadvantages of probiotics. The advantages of probiotic therapy include multiple mechanisms of action against pathogens, the ability to interact with the host's natural defense systems, survival to the target organ and a good risk to benefit ratio. Disadvantages of probiotics include lack of standardization for clinical trial designs, variations in regulatory standards, poor quality control for some products and infrequent serious adverse reactions. Overall, probiotics offer a promising strategy for the prevention and treatment for AAD and CDI     

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant–microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant‐associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant–microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil‐borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere‐related traits, (c) the role of root exudation in microbe‐mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.     

Bacillus probiotics: an alternative to antibiotics for livestock production

The use of probiotics as feed supplements in animal production has increased considerably over the last decade, particularly since the ban on antibiotic growth promoters in the livestock sector. Several Bacillus sp. are attractive for use as probiotic supplements in animal feed due to their ability to produce spores. Their heat stability and ability to survive the low pH of the gastric barrier represent an advantage over other probiotic micro‐organisms. This review discusses important characteristics required for selection of Bacillus probiotic strains and summarizes the beneficial effect of Bacillus‐based feed additives on animal production. Although the mechanism of action of Bacillus probiotics has not been fully elucidated, they are effective in improving the growth, survival and health status of terrestrial and aquatic livestock. Bacillus strains also have utility in bioremediation and can reduce nitrogenous waste, thereby improving environmental conditions and water quality. Finally, recent innovative approaches for using Bacillus spores in various applications are discussed.