Human health and disease in a microbial world

Gut Lactobacillus and Probiotics Lactobacillus lactis/rhamnosis Ameliorate Liver Fibrosis in Prevention and Treatment

The progression and exacerbation of liver fibrosis are closely related to the gut microbiome. It is hypothesized that some probiotics may slow the progression of liver fibrosis. In human stool analysis [healthy group (n = 44) and cirrhosis group (n = 18)], difference in Lactobacillus genus between healthy group and cirrhosis group was observed. Based on human data, preventive and therapeutic effect of probiotics Lactobacillus lactis and L. rhamnosus was evaluated by using four mice fibrosis models. L. lactis and L. rhamnosus were supplied to 3,5-diethoxycarbonyl-1,4-dihydrocollidine or carbon tetrachloride-induced liver fibrosis C57BL/6 mouse model. Serum biochemical measurements, tissue staining, and mRNA expression in the liver were evaluated. The microbiome was analyzed in mouse cecal contents. In the mouse model, the effects of Lactobacillus in preventing and treating liver fibrosis were different for each microbe species. In case of L. lactis, all models showed preventive and therapeutic effects against liver fibrosis. In microbiome analysis in mouse models administered Lactobacillus, migration and changes in the ratio and composition of the gut microbial community were confirmed. L. lactis and L. rhamnosus showed preventive and therapeutic effects on the progression of liver fibrosis, suggesting that Lactobacillus intake may be a useful strategy for prevention and treatment.

Contact lens-related corneal infection: Intrinsic resistance and its compromise

Contact lenses represent a widely utilized form of vision correction with more than 140 million wearers worldwide. Although generally well-tolerated, contact lenses can cause corneal infection (microbial keratitis), with an approximate annualized incidence ranging from ~2 to ~20 cases per 10,000 wearers, and sometimes resulting in permanent vision loss. Research suggests that the pathogenesis of contact lens-associated microbial keratitis is complex and multifactorial, likely requiring multiple conspiring factors that compromise the intrinsic resistance of a healthy cornea to infection. Here, we outline our perspective of the mechanisms by which contact lens wear sometimes renders the cornea susceptible to infection, focusing primarily on our own research efforts during the past three decades. This has included studies of host factors underlying the constitutive barrier function of the healthy cornea, its response to bacterial challenge when intrinsic resistance is not compromised, pathogen virulence mechanisms, and the effects of contact lens wear that alter the outcome of host-microbe interactions. For almost all of this work, we have utilized the bacterium Pseudomonas aeruginosa because it is the leading cause of lens-related microbial keratitis. While not yet common among corneal isolates, clinical isolates of P. aeruginosa have emerged that are resistant to virtually all currently available antibiotics, leading the United States CDC (Centers for Disease Control) to add P. aeruginosa to its list of most serious threats. Compounding this concern, the development of advanced contact lenses for biosensing and augmented reality, together with the escalating incidence of myopia, could portent an epidemic of vision-threatening corneal infections in the future. Thankfully, technological advances in genomics, proteomics, metabolomics and imaging combined with emerging models of contact lens-associated P. aeruginosa infection hold promise for solving the problem - and possibly life-threatening infections impacting other tissues.

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

Modeling the Role of the Microbiome in Evolution

There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.

Probiotic and synbiotic therapy in the critically ill: State of the art

Recent medical history has largely viewed our bacterial symbionts as pathogens to be eradicated rather than as essential partners in optimal health. However, one of the most exciting scientific advances in recent years has been the realization that commensal microorganisms (our microbiome) play vital roles in human physiology in nutrition, vitamin synthesis, drug metabolism, protection against infection, and recovery from illness. Recent data show that loss of "health-promoting" microbes and overgrowth of pathogenic bacteria (dysbiosis) in patients in the intensive care unit (ICU) appears to contribute to nosocomial infections, sepsis, and poor outcomes. Dysbiosis results from many factors, including ubiquitous antibiotic use and altered nutrition delivery in illness. Despite modern antibiotic therapy, infections and mortality from often multidrug-resistant organisms are increasing. This raises the question of whether restoration of a healthy microbiome via probiotics or synbiotics (probiotic and prebiotic combinations) to intervene on ubiquitous ICU dysbiosis would be an optimal intervention in critical illness to prevent infection and to improve recovery. This review will discuss recent innovative experimental data illuminating mechanistic pathways by which probiotics and synbiotics may provide clinical benefit. Furthermore, a review of recent clinical data demonstrating that probiotics and synbiotics can reduce complications in ICU and other populations will be undertaken. Overall, growing data for probiotic and symbiotic therapy reveal a need for definitive clinical trials of these therapies, as recently performed in healthy neonates. Future studies should target administration of probiotics and synbiotics with known mechanistic benefits to improve patient outcomes. Optimally, future probiotic and symbiotic studies will be conducted using microbiome signatures to characterize actual ICU dysbiosis and determine, and perhaps even personalize, ideal probiotic and symbiotic therapies.

Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events

Asian dust events transport the airborne bacteria in Chinese desert regions as well as mineral particles and influence downwind area varying biological ecosystems and climate changes. However, the airborne bacterial dynamics were rarely investigated in the Gobi desert area, where dust events are highly frequent. In this study, air samplings were sequentially performed at a 2-m high above the ground at the sampling site located in desert area (Tsogt-Ovoo of Gobi desert; Mongolia 44.2304°N, 105.1700°E). During the dust event days, the bacterial cells and mineral particles increased to more than tenfold of concentrations. MiSeq sequencing targeting 16S ribosomal DNA revealed that the airborne bacteria in desert area mainly belonged to the classes Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Bacilli, Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. The bacterial community structures were different between dust events and non-dust events. The air samples collected at the dust events indicated high abundance rates of Alpha-proteobacteria, which were reported to dominate on the leaf surfaces of plants or in the saline lake environments. After the dust events, the members of Firmicutes (Bacilli) and Bacteroidetes, which are known to form endospore and attach with coarse particles, respectively, increased their relative abundances in the air samples. Presumably, the bacterial compositions and diversities in atmosphere significantly vary during dust events, which carry some particles from grassland (phyllo-sphere), dry lake, and sand surfaces, as well as some bacterial populations such as Firmicutes and Bacteroidetes maintain in the atmosphere for longer time.

Human gut microbiota plays a role in the metabolism of drugs

BACKGROUND AND AIMS

The gut microbiome, an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract, is now known to play a critical role in human health and predisposition to disease. It is also involved in the biotransformation of xenobiotics and several recent studies have shown that the gut microbiota can affect the pharmacokinetics of orally taken drugs with implications for their oral bioavailability.

METHODS

Review of Pubmed, Web of Science and Science Direct databases for the years 1957-2016.

RESULTS AND CONCLUSIONS

Recent studies make it clear that the human gut microbiota can play a major role in the metabolism of xenobiotics and, the stability and oral bioavailability of drugs. Over the past 50 years, more than 30 drugs have been identified as a substrate for intestinal bacteria. Questions concerning the impact of the gut microbiota on drug metabolism, remain unanswered or only partially answered, namely (i) what are the molecular mechanisms and which bacterial species are involved? (ii) What is the impact of host genotype and environmental factors on the composition and function of the gut microbiota, (iii) To what extent is the composition of the intestinal microbiome stable, transmissible, and resilient to perturbation? (iv) Has past exposure to a given drug any impact on future microbial response, and, if so, for how long? Answering such questions should be an integral part of pharmaceutical research and personalised health care.

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model

BACKGROUND

This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administered at doses comparable to human exposure to Sprague-Dawley rats from birth through adulthood. Fecal samples were collected at two time points: postnatal day (PND) 62 (adolescence) and PND 181 (adulthood). The gut microbiome was profiled by 16S ribosomal RNA gene sequencing, taxonomically assigned and assessed for diversity.

RESULTS

Metagenomic profiling revealed that the low-dose chemical exposure resulted in significant changes in the overall bacterial composition, but in adolescent rats only. Specifically, the individual taxon relative abundance for Bacteroidetes (Prevotella) was increased while the relative abundance of Firmicutes (Bacilli) was reduced in all treated rats compared to controls. Increased abundance was observed for Elusimicrobia in DEP and MPB groups, Betaproteobacteria in MPB and MIX groups, and Deltaproteobacteria in TCS group. Surprisingly, these differences diminished by adulthood (PND 181) despite continuous exposure, suggesting that exposure to the environmental chemicals produced a more profound effect on the gut microbiome in adolescents. We also observed a small but consistent reduction in the bodyweight of exposed rats in adolescence, especially with DEP and MPB treatment (p < 0.05), which is consistent with our findings of a reduced Firmicutes/Bacteroidetes ratio at PND 62 in exposed rats.

CONCLUSIONS

This study provides initial evidence that postnatal exposure to commonly used environmental chemicals at doses comparable to human exposure is capable of modifying the gut microbiota in adolescent rats; whether these changes lead to downstream health effects requires further investigation.

'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics

BACKGROUND

Although many probiotic products are currently available in yogurt or pill form in the United States (US), there is uncertainty surrounding the structure of regulation of these products. As more therapeutic probiotics are developed, changes to existing regulatory process in the United States may be required to meet the needs of patients and users in the population.

OBJECTIVE

This study examined how patients with chronic gastrointestinal (GI) diseases view the regulation of probiotics.

DESIGN

We conducted a multi-site qualitative study consisting of focus groups of patients with chronic gastrointestinal diseases at three tertiary hospitals: at [institutions removed for blinded review].

RESULTS

We conducted 22 focus groups with 136 patients with major gastrointestinal (GI) diseases between March and August 2009. Participants were not familiar with the existing regulation of probiotic products but wanted assurances of accurate labelling of strain as well as safety. Participants raised concerns that regulation of probiotics might be accompanied by greater costs, reduced access and increased involvement of pharmaceutical companies. Although participants voiced significant doubt of government regulators, they felt that products containing genetically modified probiotic strains should have oversight comparable to that of pharmaceutical drugs.

DISCUSSION AND CONCLUSION

If GI patient perspectives are indicative of public perceptions of therapeutic probiotics in the United States, consumers may expect more rigorous regulation in the future while simultaneously wanting low costs, easy access and low involvement of pharmaceutical companies. Manufacturers, translational scientists, clinicians and regulators should be sensitive to consumer attitudes when designing, testing and regulating new therapeutic probiotics.

Developing a metagenomic view of xenobiotic metabolism

The microbes residing in and on the human body influence human physiology in many ways, particularly through their impact on the metabolism of xenobiotic compounds, including therapeutic drugs, antibiotics, and diet-derived bioactive compounds. Despite the importance of these interactions and the many possibilities for intervention, microbial xenobiotic metabolism remains a largely underexplored component of pharmacology. Here, we discuss the emerging evidence for both direct and indirect effects of the human gut microbiota on xenobiotic metabolism, and the initial links that have been made between specific compounds, diverse members of this complex community, and the microbial genes responsible. Furthermore, we highlight the many parallels to the now well-established field of environmental bioremediation, and the vast potential to leverage emerging metagenomic tools to shed new light on these important microbial biotransformations.