Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics

Prediction of microbe-drug associations based on a modified graph attention variational autoencoder and random forest

Introduction

The identification of microbe-drug associations can greatly facilitate drug research and development. Traditional methods for screening microbe-drug associations are time-consuming, manpower-intensive, and costly to conduct, so computational methods are a good alternative. However, most of them ignore the combination of abundant sequence, structural information, and microbe-drug network topology.

Methods

In this study, we developed a computational framework based on a modified graph attention variational autoencoder (MGAVAEMDA) to infer potential microbedrug associations by combining biological information with the variational autoencoder. In MGAVAEMDA, we first used multiple databases, which include microbial sequences, drug structures, and microbe-drug association databases, to establish two comprehensive feature matrices of microbes and drugs after multiple similarity computations, fusion, smoothing, and thresholding. Then, we employed a combination of variational autoencoder and graph attention to extract low-dimensional feature representations of microbes and drugs. Finally, the lowdimensional feature representation and graphical adjacency matrix were input into the random forest classifier to obtain the microbe-drug association score to identify the potential microbe-drug association. Moreover, in order to correct the model complexity and redundant calculation to improve efficiency, we introduced a modified graph convolutional neural network embedded into the variational autoencoder for computing low dimensional features.

Results

The experiment results demonstrate that the prediction performance of MGAVAEMDA is better than the five state-of-the-art methods. For the major measurements (AUC =0.9357, AUPR =0.9378), the relative improvements of MGAVAEMDA compared to the suboptimal methods are 1.76 and 1.47%, respectively.

Discussion

We conducted case studies on two drugs and found that more than 85% of the predicted associations have been reported in PubMed. The comprehensive experimental results validated the reliability of our models in accurately inferring potential microbe-drug associations.

Oral Cardiac Drug-Gut Microbiota Interaction in Chronic Heart Failure Patients: An Emerging Association

Regardless of the currently proposed best medical treatment for heart failure patients, the morbidity and mortality rates remain high. This is due to several reasons, including the interaction between oral cardiac drug administration and gut microbiota. The relation between drugs (especially antibiotics) and gut microbiota is well established, but it is also known that more than 24% of non-antibiotic drugs affect gut microbiota, altering the microbe's environment and its metabolic products. Heart failure treatment lies mainly in the blockage of neuro-humoral hyper-activation. There is debate as to whether the administration of heart-failure-specific drugs can totally block this hyper-activation, or whether the so-called intestinal dysbiosis that is commonly observed in this group of patients can affect their action. Although there are several reports indicating a strong relation between drug-gut microbiota interplay, little is known about this relation to oral cardiac drugs in chronic heart failure. In this review, we review the contemporary data on a topic that is in its infancy. We aim to produce scientific thoughts and questions and provide reasoning for further clinical investigation.

The many faces of microbiota-gut-brain axis in autism spectrum disorder

The gut-brain axis is gaining more attention in neurodevelopmental disorders, especially autism spectrum disorder (ASD). Many factors can influence microbiota in early life, including host genetics and perinatal events (infections, mode of birth/delivery, medications, nutritional supply, and environmental stressors). The gut microbiome can influence blood-brain barrier (BBB) permeability, drug bioavailability, and social behaviors. Developing microbiota-based interventions such as probiotics, gastrointestinal (GI) microbiota transplantation, or metabolite supplementation may offer an exciting approach to treating ASD. This review highlights that RNA sequencing, metabolomics, and transcriptomics data are needed to understand how microbial modulators can influence ASD pathophysiology. Due to the substantial clinical heterogeneity of ASD, medical caretakers may be unlikely to develop a broad and effective general gut microbiota modulator. However, dietary modulation followed by administration of microbiota modulators is a promising option for treating ASD-related behavioral and gastrointestinal symptoms. Future work should focus on the accuracy of biomarker tests and developing specific psychobiotic agents tailored towards the gut microbiota seen in ASD patients, which may include developing individualized treatment options.

Drug-microbiota interactions: an emerging priority for precision medicine

Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.

The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health

Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.

Exploring the complex role of gut microbiome in the development of precision medicine strategies for targeting microbial imbalance-induced colon cancer

The gut microbiome has been increasingly recognized as a key player in the development and progression of colon cancer. Alterations in the gut microbiota, known as dysbiosis, can lead to a variety of medical issues. Microbial adaptation through signals and small molecules can enhance pathogen colonization and modulate host immunity, significantly impacting disease progression. Quorum sensing peptides and molecules have been linked to the progression of colon cancer. Various interventions, such as fecal microbiota transplantation, probiotics, prebiotics, synbiotics, and antibiotics, have been used to reverse dysbiosis with mixed results and potential side effects. Thus, a personalized approach to treatment selection based on patient characteristics, such as individual gut microbiota manipulation, is necessary to prevent and treat diseases like colon cancer. With advances in metagenomic sequencing and other omics technologies, there has been a growing interest in developing precision medicine strategies for microbial imbalance-induced colon cancer. This review serves as a comprehensive synthesis of current knowledge on the gut microbiome involvement in colon cancer. By exploring the potential of utilizing the gut microbiome as a target for precision medicine, this review underscores the exciting opportunities that lie ahead. Although challenges exist, the integration of microbiome data into precision medicine approaches has the potential to revolutionize the management of colon cancer, providing patients with more personalized and effective treatment options.

Can we manage gut microbiome imbalances in patients with bipolar disorder with pharmacotherapy?

INTRODUCTION

A novel new area of exploration in the treatment of bipolar disorder is the gut brain axis. Studies have shown significant differences between the gut microbiome in those with bipolar disorder and those without the illness, as well as documented microbiome changes associated with the effects of bipolar pharmacotherapy and targeted microbial interventions. Although we have evidence suggesting the bi-directional relationship between the gut microbiome and psychiatric disorders, we are still unable to utilize this understanding clinically.

AREAS COVERED

We need to better understand the factors that impact the microbiome in this illness and vice versa.

EXPERT OPINION

Additionally, changes in gut microbiome in bipolar disorder might be used for biomarker identification with a potential to help in diagnosis and monitoring of the condition. It is an important area for further research and may provide improved therapeutic outcomes.

Looking Back, Moving Forward in Pain Medicine

Pain is an ancient medical complaint and a clinical riddle that has never been entirely solved. Looking back into history was the springboard to a look into the future of pain medicine. This article was based on a series of presentations given in a recent congress (May 2023) and represents the research, views, and opinions of the authors. Opium has been used for millennia to treat pain, but when it gained broad use in the United States in the 1980s and 1990s, it was so vastly overprescribed and mis-prescribed that it led to a public health crisis. This, in turn, led to the reaction where opioids at times were under-prescribed, leaving out many patients who may have benefited from opioids while leaving many legacy pain patients to manage withdrawal on their own and with few analgesic options. Cannabinoids (CB) were likewise widely used for various conditions, including pain, but were outlawed in the 20th century, only to be brought back as a potential analgesic agent. Interventional pain medicine is a developing discipline and has reinforced the concept of the interdisciplinary pain clinic. It plays an increasingly important part in modern medicine overall, especially with the support of ultrasound, for both diagnosis and therapy. Today, the views about pain have changed. Anyone has accepted that pain is not purely a physical phenomenon but a biopsychosocial phenomenon that occurs within a cultural context. Pain management remains a small but vitally important medical subspecialty that is critical from a functional enablement and population health perspective, which is helping to navigate new therapeutic targets, new drugs and routes of administration, greater understanding of pain psychology, and new technologies. Pain control today means early intervention, functional enablement through pain alleviation, educating patients about pain management, and minimizing the transition from acute to chronic pain.

A New Paradigm in the Relationship between Gut Microbiota and Breast Cancer: β-glucuronidase Enzyme Identified as Potential Therapeutic Target

Breast cancer (BC) is the most frequently occurring malignancy and the second cancer-specific cause of mortality in women in developed countries. Over 70% of the total number of BCs are hormone receptor-positive (HR+), and elevated levels of circulating estrogen (E) in the blood have been shown to be a major risk factor for the development of HR+ BC. This is attributable to estrogen's contribution to increased cancer cell proliferation, stimulation of angiogenesis and metastasis, and resistance to therapy. The E metabolism-gut microbiome axis is functional, with subjacent individual variations in the levels of E. It is conceivable that the estrobolome (bacterial genes whose products metabolize E) may contribute to the risk of malignant neoplasms of hormonal origin, including BC, and may serve as a potential biomarker and target. It has been suggested that β-glucuronidase (GUS) enzymes of the intestinal microbiome participate in the strobolome. In addition, it has been proposed that bacterial GUS enzymes from the gastrointestinal tract participate in hormone BC. In this review, we discuss the latest knowledge about the role of the GUS enzyme in the pathogenesis of BC, focusing on (i) the microbiome and E metabolism; (ii) diet, estrobolome, and BC development; (iii) other activities of the bacterial GUS; and (iv) the new molecular targets for BC therapeutic application.

The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine

Trillions of diverse microbes reside in the gut and are deeply interwoven with the human physiological process, from food digestion, immune system maturation, and fighting invading pathogens, to drug metabolism. Microbial drug metabolism has a profound impact on drug absorption, bioavailability, stability, efficacy, and toxicity. However, our knowledge of specific gut microbial strains, and their genes that encode enzymes involved in the metabolism, is limited. The microbiome encodes over 3 million unique genes contributing to a huge enzymatic capacity, vastly expanding the traditional drug metabolic reactions that occur in the liver, manipulating their pharmacological effect, and, ultimately, leading to variation in drug response. For example, the microbial deactivation of anticancer drugs such as gemcitabine can lead to resistance to chemotherapeutics or the crucial role of microbes in modulating the efficacy of the anticancer drug, cyclophosphamide. On the other hand, recent findings show that many drugs can shape the composition, function, and gene expression of the gut microbial community, making it harder to predict the outcome of drug-microbiota interactions. In this review, we discuss the recent understanding of the multidirectional interaction between the host, oral medications, and gut microbiota, using traditional and machine-learning approaches. We analyze gaps, challenges, and future promises of personalized medicine that consider gut microbes as a crucial player in drug metabolism. This consideration will enable the development of personalized therapeutic regimes with an improved outcome, ultimately leading to precision medicine.

The Role of the Gut Microbiome in Bipolar Disorder and its Common Comorbidities

Bipolar disorder is a decidedly heterogeneous and multifactorial disease, with significant psychosocial and medical disease burden. Much difficulty has been encountered in developing novel therapeutics and objective biomarkers for clinical use in this population. In that regard, gut-microbial homeostasis appears to modulate several key pathways relevant to a variety of psychiatric, metabolic, and inflammatory disorders. Microbial impact on immune, endocrine, endocannabinoid, kynurenine, and other pathways are discussed throughout this review. Emphasis is placed on this system's relevance to current pharmacology, diet, and comorbid illness in bipolar disorder. Despite the high level of optimism promoted in many reviews on this topic, substantial obstacles exist before any microbiome-related findings can provide meaningful clinical utility. Beyond a comprehensive overview of pathophysiology, this review hopes to highlight several key areas where progress is needed. As well, novel microbiome-associated suggestions are presented for future research.

In Silico and In Vitro Investigation of the Distribution and Expression of Key Genes in the Fucose Operon of Escherichia coli

Many gut bacteria degrade polysaccharides, providing nutritional advantages to their hosts. Fucose, a mucin degradation product, was suggested as a communication molecule between the resident microbiota and external pathogens. However, the precise role and variants of the fucose utilization pathway remain to be elucidated. Here, we computationally and experimentally investigated the fucose utilization operon of E. coli. While the operon is conserved among E. coli genomes, a variant pathway, in which an ABC transporter system replaces the fucose permease gene (fucP), was computationally identified in 50 out of 1058 genomes. Comparative genomics and subsystems analysis results were confirmed by polymerase chain reaction-based screening of 40 human E. coli isolates, which indicated the conservation of fucP in 92.5% of the isolates (vs. 7.5% of its suggested alternative, yjfF). The in silico predictions were confirmed by in vitro experiments comparing the growth of E. coli strains K12, BL21, and isogenic fucose-utilization K12 mutants. Additionally, fucP and fucI transcripts were quantified in E. coli K12 and BL21, after in silico analysis of their expression in 483 public transcriptomes. In conclusion, E. coli utilizes fucose by two pathway variants, with measurable transcriptional differences. Future studies will explore this variation's impact on signaling and virulence.

Principles and Terminology for Host-Microbiome-Drug Interactions

Interactions between the microbiome and medical therapies are distinct and bidirectional. The existing term "pharmacomicrobiomics" describes the effects of the microbiome on drug distribution, metabolism, efficacy, and toxicity. We propose that the term "pharmacoecology" be used to describe the effects that drugs and other medical interventions such as probiotics have on microbiome composition and function. We suggest that the terms are complementary but distinct and that both are potentially important when assessing drug safety and efficacy as well as drug-microbiome interactions. As a proof of principle, we describe the ways in which these concepts apply to antimicrobial and non-antimicrobial medications.

Gut microbiota dependant trimethylamine N-oxide and hypertension

The human gut microbiota environment is constantly changing and some specific changes influence the host's metabolic, immune, and neuroendocrine functions. Emerging evidence of the gut microbiota's role in the development of cardiovascular disease (CVD) including hypertension is remarkable. There is evidence showing that alterations in the gut microbiota and especially the gut-dependant metabolite trimethylamine N-oxide is associated with hypertension. However, there is a scarcity of literature addressing the role of trimethylamine N-oxide in hypertension pathogenesis. In this review, we discuss the impact of the gut microbiota and gut microbiota dependant trimethylamine N-oxide in the pathogenesis of hypertension. We present evidence from both human and animal studies and further discuss new insights relating to potential therapies for managing hypertension by altering the gut microbiota.

Sex differences in gastrointestinal dysfunction among patients with Parkinson's disease

BACKGROUND AND OBJECTIVE

Sex differences in gastrointestinal dysfunction have not been systematically analyzed in patients with Parkinson's disease (PD). This study was aimed to investigate the sex differences in gastrointestinal dysfunctions among the patients with PD using a multicenter trial dataset.

METHODS

We analyzed the baseline data of prospectively enrolled set of patients with gastrointestinal dysfunctions. Possible sex differences in gastrointestinal symptoms assessed on the Nepean Dyspepsia Index-Korean Version (NDI-K), gastrointestinal symptom diary, and Bristol stool scale were analyzed in association with clinical PD severity and antiparkinsonian drug dosages by multiple linear regression models. We also performed post hoc analysis of the dyspepsia symptom sub-items, adjusting for multiple comparisons.

RESULTS

Sixty-six of the 144 participants were female (45.8%). There were no differences in age, PD duration, Hoehn and Yahr stage, and daily dopaminergic medication dosages between sexes. NDI-K symptom and dyspepsia scores were correlated with the activity of daily living in females but not in males. In the multiple regression analysis controlling for all possible variables, female patients were shown to have worse gastrointestinal symptoms than males. When we performed post hoc analysis of the dyspepsia symptoms, inability to finish a regular meal and nausea were significantly worse in female patients. Gastrointestinal symptom diary supported that female patients more frequently complained of early fullness and bloating in the upper abdomen after meals than males, and burning pain in upper abdomen was more severe in female patients.

CONCLUSION

Gastrointestinal dysfunctions may differentially affect female and male PD patients.

Bioaccumulation and biotransformation of simvastatin in probiotic bacteria: A step towards better understanding of drug-bile acids-microbiome interactions

Introduction: Although pharmacogenetics and pharmacogenomics have been at the forefront of research aimed at finding novel personalized therapies, the focus of research has recently extended to the potential of intestinal microbiota to affect drug efficacy. Complex interplay of gut microbiota with bile acids may have significant repercussions on drug pharmacokinetics. However, far too little attention has been paid to the potential implication of gut microbiota and bile acids in simvastatin response which is characterized by large interindividual variations. The Aim: In order to gain more insight into the underlying mechanism and its contribution in assessing the clinical outcome, the aim of our study was to examine simvastatin bioaccumulation and biotransformation in probiotic bacteria and the effect of bile acids on simvastatin bioaccumulation in in vitro conditions. Materials and methods: Samples with simvastatin, probiotic bacteria and three different bile acids were incubated at anaerobic conditions at 37°C for 24 h. Extracellular and intracellular medium samples were collected and prepared for the LC-MS analysis at predetermined time points (0 min, 15 min, 1 h, 2 h, 4 h, 6 h, 24 h). The concentrations of simvastatin were analyzed by LC-MS/MS. Potential biotransformation pathways were analyzed using a bioinformatics approach in correlation with experimental assay. Results: During the incubation, simvastatin was transported into bacteria cells leading to a drug bioaccumulation over the time, which was augmented upon addition of bile acids after 24 h. A decrease of total drug level during the incubation indicates that the drug is partly biotransformed by bacterial enzymes. According to the results of bioinformatics analysis, the lactone ring is the most susceptible to metabolic changes and the most likely reactions include ester hydrolysis followed by hydroxylation. Conclusion: Results of our study reveal that bioaccumulation and biotransformation of simvastatin by intestinal bacteria might be the underlying mechanisms of altered simvastatin bioavailability and therapeutic effect. Since this study is based only on selected bacterial strains in vitro, further more in-depth research is needed in order to elicit completely the contribution of complex drug-microbiota-bile acids interactions to overall clinical response of simvastatin which could ultimately lead to novel approaches for the personalized lipid-lowering therapy.

Effects of intestinal microbiota on pharmacokinetics of cyclosporine a in rats

BACKGROUND

Intestinal microbiota has been confirmed to influencing the pharmacokinetic processes of a variety of oral drugs. However, the pharmacokinetic effects of the gut microbiota on cyclosporine A, a drug with a narrow therapeutic window, remain to be studied.

METHOD

Twenty-one rats were randomly divided into three groups: (a) control group (CON), (b) antibiotic treatment group (ABT) and (c) fecal microbe transplantation group (FMT). The ABT group was administrated with water containing multiple antibiotics to deplete microorganisms. FMT was with the same treatment, followed by oral administration of conventional rat fecal microorganisms for normalization.

RESULT

The bioavailability of CSA increased by 155.6% after intestinal microbes were consumed by antibiotics. After intestinal microbiota reconstruction by fecal transplantation, the increased bioavailability was significantly reduced and basically returned to the control group level. Changes in gut microbiota alter the protein expression of CYP3A1, UGT1A1 and P-gp in liver. The expressions of these three proteins in ABT group were significantly lower than those in CON and FMT groups. The relative abundance of Alloprevolleta and Oscillospiraceae UCG 005 was negatively correlated with CSA bioavailability while the relative abundance of Parasutterella and Eubacterium xylanophilum group was negatively correlated with CSA bioavailability.

CONCLUSION

Intestinal microbiota affects the pharmacokinetics of CSA by regulating the expression of CYP3A1, UGT1A1 and P-GP.

GSAMDA: a computational model for predicting potential microbe-drug associations based on graph attention network and sparse autoencoder

BACKGROUND

Clinical studies show that microorganisms are closely related to human health, and the discovery of potential associations between microbes and drugs will facilitate drug research and development. However, at present, few computational methods for predicting microbe-drug associations have been proposed.

RESULTS

In this work, we proposed a novel computational model named GSAMDA based on the graph attention network and sparse autoencoder to infer latent microbe-drug associations. In GSAMDA, we first built a heterogeneous network through integrating known microbe-drug associations, microbe similarities and drug similarities. And then, we adopted a GAT-based autoencoder and a sparse autoencoder module respectively to learn topological representations and attribute representations for nodes in the newly constructed heterogeneous network. Finally, based on these two kinds of node representations, we constructed two kinds of feature matrices for microbes and drugs separately, and then, utilized them to calculate possible association scores for microbe-drug pairs.

CONCLUSION

A novel computational model is proposed for predicting potential microbe-drug associations based on graph attention network and sparse autoencoder. Compared with other five state-of-the-art competitive methods, the experimental results illustrated that our model can achieve better performance. Moreover, case studies on two categories of representative drugs and microbes further demonstrated the effectiveness of our model as well.

Microbiome dysbiosis and epigenetic modulations in lung cancer: From pathogenesis to therapy

The lung microbiome plays an essential role in maintaining healthy lung function, including host immune homeostasis. Lung microbial dysbiosis or disruption of the gut-lung axis can contribute to lung carcinogenesis by causing DNA damage, inducing genomic instability, or altering the host's susceptibility to carcinogenic insults. Thus far, most studies have reported the association of microbial composition in lung cancer. Mechanistic studies describing host-microbe interactions in promoting lung carcinogenesis are limited. Considering cancer as a multifaceted disease where epigenetic dysregulation plays a critical role, epigenetic modifying potentials of microbial metabolites and toxins and their roles in lung tumorigenesis are not well studied. The current review explains microbial dysbiosis and epigenetic aberrations in lung cancer and potential therapeutic opportunities.

Role of the Gut Microbiome in Diabetes and Cardiovascular Diseases Including Restoration and Targeting Approaches- A Review

Metabolic diseases, including cardiovascular diseases (CVD) and diabetes, have become the leading cause of morbidity and mortality worldwide. Gut microbiota appears to play a vital role in human disease and health, according to recent scientific reports. The gut microbiota plays an important role in sustaining host physiology and homeostasis by creating a cross-talk between the host and microbiome via metabolites obtained from the host's diet. Drug developers and clinicians rely heavily on therapies that target the microbiota in the management of metabolic diseases, and the gut microbiota is considered the biggest immune organ in the human body. They are highly associated with intestinal immunity and systemic metabolic disorders like CVD and diabetes and are reflected as potential therapeutic targets for the management of metabolic diseases. This review discusses the mechanism and interrelation between the gut microbiome and metabolic disorders. It also highlights the role of the gut microbiome and microbially derived metabolites in the pathophysiological effects related to CVD and diabetes. It also spotlights the reasons that lead to alterations of microbiota composition and the prominence of gut microbiota restoration and targeting approaches as effective treatment strategies in diabetes and CVD. Future research should focus onunderstanding the functional level of some specific microbial pathways that help maintain physiological homeostasis, multi-omics, and develop novel therapeutic strategies that intervene with the gut microbiome for the prevention of CVD and diabetes that contribute to a patient's well-being.

Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction

Background

Efficient identification of microbe-drug associations is critical for drug development and solving problem of antimicrobial resistance. Traditional wet-lab method requires a lot of money and labor in identifying potential microbe-drug associations. With development of machine learning and publication of large amounts of biological data, computational methods become feasible.

Methods

In this article, we proposed a computational model of neighborhood-based inference (NI) and restricted Boltzmann machine (RBM) to predict potential microbe-drug association (NIRBMMDA) by using integrated microbe similarity, integrated drug similarity and known microbe-drug associations. First, NI was used to obtain a score matrix of potential microbe-drug associations by using different thresholds to find similar neighbors for drug or microbe. Second, RBM was employed to obtain another score matrix of potential microbe-drug associations based on contrastive divergence algorithm and sigmoid function. Because generalization ability of individual method is poor, we used an ensemble learning to integrate two score matrices for predicting potential microbe-drug associations more accurately. In particular, NI can fully utilize similar (neighbor) information of drug or microbe and RBM can learn potential probability distribution hid in known microbe-drug associations. Moreover, ensemble learning was used to integrate individual predictor for obtaining a stronger predictor.

Results

In global leave-one-out cross validation (LOOCV), NIRBMMDA gained the area under the receiver operating characteristics curve (AUC) of 0.8666, 0.9413 and 0.9557 for datasets of DrugVirus, MDAD and aBiofilm, respectively. In local LOOCV, AUCs of 0.8512, 0.9204 and 0.9414 were obtained for NIRBMMDA based on datasets of DrugVirus, MDAD and aBiofilm, respectively. For five-fold cross validation, NIRBMMDA acquired AUC and standard deviation of 0.8569 ± -0.0027, 0.9248 ± -0.0014 and 0.9369 ± -0.0020 on the basis of datasets of DrugVirus, MDAD and aBiofilm, respectively. Moreover, case study for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed that 13 out of the top 20 predicted drugs were verified by searching literature. The other two case studies indicated that 17 and 17 out of the top 20 predicted microbes for the drug of ciprofloxacin and minocycline were confirmed by identifying published literature, respectively.

The Gut Microbiota (Microbiome) in Cardiovascular Disease and Its Therapeutic Regulation

In the last two decades, considerable interest has been shown in understanding the development of the gut microbiota and its internal and external effects on the intestine, as well as the risk factors for cardiovascular diseases (CVDs) such as metabolic syndrome. The intestinal microbiota plays a pivotal role in human health and disease. Recent studies revealed that the gut microbiota can affect the host body. CVDs are a leading cause of morbidity and mortality, and patients favor death over chronic kidney disease. For the function of gut microbiota in the host, molecules have to penetrate the intestinal epithelium or the surface cells of the host. Gut microbiota can utilize trimethylamine, N-oxide, short-chain fatty acids, and primary and secondary bile acid pathways. By affecting these living cells, the gut microbiota can cause heart failure, atherosclerosis, hypertension, myocardial fibrosis, myocardial infarction, and coronary artery disease. Previous studies of the gut microbiota and its relation to stroke pathogenesis and its consequences can provide new therapeutic prospects. This review highlights the interplay between the microbiota and its metabolites and addresses related interventions for the treatment of CVDs.

Pharmacomicrobiomics: Influence of gut microbiota on drug and xenobiotic metabolism

Gut microbiota is the most diverse and complex biological ecosystem, which is estimated to consist of greater than 5 million distinct genes and 100 trillion cells which are in constant communication with the host environment. The interaction between the gut microbiota and drugs and other xenobiotic compounds is bidirectional, quite complicated, and not fully understood yet. The impact of xenobiotics from pollution, manufacturing processes or from the environment is harmful to human health at varying degrees and this needs to be recognized and addressed. The gut microbiota is capable of biotransforming/metabolizing of various drugs and xenobiotic compounds as well as altering the activity and toxicity of these substances, thereby influencing how a host responds to drugs and xenobiotics and this emerging field is known as pharmacomicrobiomics. In this review, we discussed different mechanisms of drug-gut microbiota interaction and highlighted the influence of drug-gut microbiome interactions on the clinical response in humans.

Microbiomics: The Next Pillar of Precision Medicine and Its Role in African Healthcare

Limited access to technologies that support early monitoring of disease risk and a poor understanding of the geographically unique biological and environmental factors underlying disease, represent significant barriers to improved health outcomes and precision medicine efforts in low to middle income countries. These challenges are further compounded by the rich genetic diversity harboured within Southern Africa thus necessitating alternative strategies for the prediction of disease risk and clinical outcomes in regions where accessibility to personalized healthcare remains limited. The human microbiome refers to the community of microorganisms (bacteria, archaea, fungi and viruses) that co-inhabit the human body. Perturbation of the natural balance of the gut microbiome has been associated with a number of human pathologies, and the microbiome has recently emerged as a critical determinant of drug pharmacokinetics and immunomodulation. The human microbiome should therefore not be omitted from any comprehensive effort towards stratified healthcare and would provide an invaluable and orthogonal approach to existing precision medicine strategies. Recent studies have highlighted the overarching effect of geography on gut microbial diversity as it relates to human health. Health insights from international microbiome datasets are however not yet verified in context of the vast geographical diversity that exists throughout the African continent. In this commentary we discuss microbiome research in Africa and its role in future precision medicine initiatives across the African continent.

The microbiome and precision oncology: an emerging paradigm in anticancer therapy

Understanding the host-microbiome interactions has emerged as an essential factor in improving human health and disease. Recent advances in understanding the intimate relationship of microbes with the host have uncovered various previously unknown underlying causes of disease development, progression, and treatment failure. The dynamic behaviour of the microbiome confers the heterogeneity in treatment response by modulating the immune response and inflammation in various diseases, including cancer. The growing insights into the microbial modulation of cancer through immunoregulation, xenometabolism, and increase in toxicity open a new era of personalised medicine. In the current review, we discuss the essential roles played by the microbiome in modulating the efficacy and toxicity of anticancer therapies (immunotherapy, chemotherapy, and radiotherapy). We also outline the current state of personalised medicine in the context of cancer and microbiome modulation. The knowledge about the role of cancer-microbiome communication will lead to designing other precise microbial modulation strategies for cancer treatment through enhanced efficacy and decreased toxicity.

Human Microbiota and Immunotherapy in Breast Cancer - A Review of Recent Developments

Breast cancer (BC) is the most common malignancy and the second cause of cancer-specific death in women from high-income countries. Infectious agents are the third most important risk factor for cancer incidence after tobacco and obesity. Dysbiosis emerged as a key player that may influence cancer development, treatment, and prognosis through diverse biological processes. Metastatic BC has a highly variable clinical course, and more recently, immune checkpoint inhibitors (ICIs) have become an emerging therapy in BC. Even with standardised treatment protocols, patients do not respond similarly, reflecting each individual´s heterogeneity, unique BC features, and tumour microenvironment. However, there is insufficient data regarding predictive factors of response to available treatments for BC. The microbiota could be a crucial piece of the puzzle to anticipate better individual BC risk and prognosis, pharmacokinetics, pharmacodynamics, and clinical efficacy. In recent years, it has been shown that gut microbiota may modulate cancer treatments' efficacy and adverse effects, and it is also apparent that both cancer itself and anticancer therapies interact with gut microbiota bidirectionally. Moreover, it has been proposed that certain gut microbes may protect the host against inappropriate inflammation and modulate the immune response. Future clinical research will determine if microbiota may be a prognostic and predictive factor of response to ICI and/or its side effects. Also, modulation of microbiota can be used to improve outcomes in BC patients. In this review, we discuss the potential implications of metabolomics and pharmacomicrobiomics that might impact BC immunotherapy treatment.

Pharmacomicrobiomics: Exploiting the Drug-Microbiota Interactions in Antihypertensive Treatment

Hypertension is a leading risk factor for cardiovascular diseases and can reduce life expectancy. Owing to the widespread use of antihypertensive drugs, patients with hypertension have improved blood pressure control over the past few decades. However, for a considerable part of the population, these drugs still cannot significantly improve their symptoms. In order to explore the reasons behind, pharmacomicrobiomics provide unique insights into the drug treatment of hypertension by investigating the effect of bidirectional interaction between gut microbiota and antihypertensive drugs. This review discusses the relationship between antihypertensive drugs and the gut microbiome, including changes in drug pharmacokinetics and gut microbiota composition. In addition, we highlight how our current knowledge of antihypertensive drug-microbiota interactions to develop gut microbiota-based personalized ways for disease management, including antihypertensive response biomarker, microbial-targeted therapies, probiotics therapy. Ultimately, a better understanding of the impact of pharmacomicrobiomics in the treatment of hypertension will provide important information for guiding rational clinical use and individualized use.

Gut Microbiota Metabolites in Major Depressive Disorder-Deep Insights into Their Pathophysiological Role and Potential Translational Applications

The gut microbiota is a complex and dynamic ecosystem essential for the proper functioning of the organism, affecting the health and disease status of the individuals. There is continuous and bidirectional communication between gut microbiota and the host, conforming to a unique entity known as "holobiont". Among these crosstalk mechanisms, the gut microbiota synthesizes a broad spectrum of bioactive compounds or metabolites which exert pleiotropic effects on the human organism. Many of these microbial metabolites can cross the blood-brain barrier (BBB) or have significant effects on the brain, playing a key role in the so-called microbiota-gut-brain axis. An altered microbiota-gut-brain (MGB) axis is a major characteristic of many neuropsychiatric disorders, including major depressive disorder (MDD). Significative differences between gut eubiosis and dysbiosis in mental disorders like MDD with their different metabolite composition and concentrations are being discussed. In the present review, the main microbial metabolites (short-chain fatty acids -SCFAs-, bile acids, amino acids, tryptophan -trp- derivatives, and more), their signaling pathways and functions will be summarized to explain part of MDD pathophysiology. Conclusions from promising translational approaches related to microbial metabolome will be addressed in more depth to discuss their possible clinical value in the management of MDD patients.

Gut microbiome in allogeneic hematopoietic stem cell transplantation and specific changes associated with acute graft vs host disease

Allogeneic hematopoietic stem cell transplantation (aHSCT) is a standard validated therapy for patients suffering from malignant and nonmalignant hematological diseases. However, aHSCT procedures are limited by potentially life-threatening complications, and one of the most serious complications is acute graft-versus-host disease (GVHD). During the last decades, DNA sequencing technologies were used to investigate relationship between composition or function of the gut microbiome and disease states. Even if it remains unclear whether these microbiome alterations are causative or secondary to the presence of the disease, they may be useful for diagnosis, prevention and therapy in aHSCT recipients. Here, we summarized the most recent findings of the association between human gut microbiome changes and acute GVHD in patients receiving aHSCT.

Exploiting the Metabolism of the Gut Microbiome as a Vehicle for Targeted Drug Delivery to the Colon

The prevalence of colon-associated diseases has increased significantly over the past several decades, as evidenced by accumulated literature on conditions such as Crohn’s disease, irritable bowel syndrome, colorectal cancer, and ulcerative colitis. Developing therapeutics for these diseases is challenging due to physiological barriers of the colon, systemic side effects, and the intestinal environment. Therefore, in a search for novel methods to overcome some of these problems, researchers discovered that microbial metabolism by gut microbiotia offers a potential method for targeted drug delivery This overview highlights several drug delivery systems used to modulate the microbiota and improve colon-targeted drug delivery. This technology will be important in developing a new generation of therapies which harness the metabolism of the human gut microflora.

Can manipulation of gut microbiota really be transformed into an intervention strategy for cardiovascular disease management?

Recent advancement in manipulation techniques of gut microbiota either ex vivo or in situ has broadened its plausible applicability for treating various diseases including cardiovascular disease. Several reports suggested that altering gut microbiota composition is an effective way to deal with issues associated with managing cardiovascular diseases. However, actual translation of gut microbiota manipulation-based techniques into cardiovascular-therapeutic approach is still questionable. This review summarized the evidence on challenges, opportunities, recent development, and future prospects of gut microbiota manipulation for targeting cardiovascular diseases. Initially, issues associated with current cardiovascular diseases treatment strategy, association of gut microbiota with cardiovascular disease, and its influence on cardiovascular drugs were discussed, followed by applicability of gut microbiota manipulation as a cardiovascular disease intervention strategy along with its challenges and future prospects. Despite the fact that the gut microbiota is rugged, interventions like probiotics, prebiotics, synbiotics, fecal microbiota transplantation, fecal virome transplantation, antibiotics, diet changes, and exercises could manipulate it. Advanced techniques like administration of engineered bacteriophages and bacteria could also be employed. Intensive exploration revealed that if sufficiently controlled approach and proper monitoring were applied, gut microbiota could provide a compelling answer for cardiovascular therapy.

Cardiovascular Diseases and Pharmacomicrobiomics: A Perspective on Possible Treatment Relevance

Cardiovascular diseases (CVDs), the most common cause of mortality in rich countries, include a wide variety of pathologies of the heart muscle and vascular system that compromise the proper functioning of the heart. Most of the risk factors for cardiovascular diseases are well-known: lipid disorders, high serum LDL cholesterol, hypertension, smoking, obesity, diabetes, male sex and physical inactivity. Currently, much evidence shows that: (i) the human microbiota plays a crucial role in maintaining the organism’s healthy status; and (ii) a link exists between microbiota and cardiovascular function that, if dysregulated, could potentially correlate with CVDs. This scenario led the scientific community to carefully analyze the role of the microbiota in response to drugs, considering this the right path to improve the effectiveness of disease treatment. In this review, we examine heart diseases and highlight how the microbiota actually plays a preponderant role in their development. Finally, we investigate pharmacomicrobiomics—a new interesting field—and the microbiota’s role in modulating the response to drugs, to improve their effectiveness by making their action targeted, focusing particular attention on cardiovascular diseases and on innovative potential treatments.

Bipolar disorder and the gut microbiome: A systematic review

OBJECTIVES

The microbiome is a rapidly advancing biomedical frontier with relevance for psychiatric illness. The gut microbiota interact with the central nervous system bidirectionally through the gut-brain axis and generate substances that may influence host metabolism, including short-chain fatty acids such as butyrate. Understanding gut microbiota in bipolar disorder (BD) may suggest new disease markers and treatment approaches.

METHODS

A PubMed search was performed on January 7, 2020 using terms "bipolar AND (microbiome OR microbiota)", for articles in English in which the study population included a distinct BD group and the gut microbiota/microbiome was assessed.

RESULTS

Thirteen articles met the inclusion criteria. In four of five studies that reported on group comparisons with respect to diversity, lower α-diversity was observed in BD relative to healthy controls (HC). The most convergent taxonomic finding was that in four studies, one particular clade distinguished gut microbiota between BD and HC: family Ruminococcaceae, genus Faecalibacterium, and species Faecalibacterium prausnitzii. Members of this clade, known for butyrate production, were reduced in BD relative to HC in three studies but elevated in a fourth. Additionally, genera Bacteroides or Bacteroides-Prevotella group species were elevated in BD in two studies but lower in a third.

CONCLUSIONS

Despite few studies and modest sample sizes, salient findings suggest that low α-diversity and dysbiosis with respect to abundance of Faecalibacterium and Bacteroides may characterize BD in both a trait and state-dependent fashion. Decreased richness and butyrate production also foster inflammation, which may be a hitherto unrecognized part of the pathophysiology underlying BD.

Drug discovery oncology in a mouse: concepts, models and limitations

The utilization of suitable mouse models is a critical step in the drug discovery oncology workflow as their generation and use are important for target identification and validation as well as toxicity and efficacy assessments. Current murine models have been instrumental in furthering insights into the mode of action of drugs before transitioning into the clinic. Recent advancements in genome editing with the development of the CRISPR/Cas9 system and the possibility of applying such technology directly in vivo have expanded the toolkit of preclinical models available. In this review, a brief presentation of the current models used in drug discovery will be provided with a particular emphasis on the novel CRISPR/Cas9 models.

Gynecology Meets Big Data in the Disruptive Innovation Medical Era: State-of-Art and Future Prospects

Tremendous scientific and technological achievements have been revolutionizing the current medical era, changing the way in which physicians practice their profession and deliver healthcare provisions. This is due to the convergence of various advancements related to digitalization and the use of information and communication technologies (ICTs)—ranging from the internet of things (IoT) and the internet of medical things (IoMT) to the fields of robotics, virtual and augmented reality, and massively parallel and cloud computing. Further progress has been made in the fields of addictive manufacturing and three-dimensional (3D) printing, sophisticated statistical tools such as big data visualization and analytics (BDVA) and artificial intelligence (AI), the use of mobile and smartphone applications (apps), remote monitoring and wearable sensors, and e-learning, among others. Within this new conceptual framework, big data represents a massive set of data characterized by different properties and features. These can be categorized both from a quantitative and qualitative standpoint, and include data generated from wet-lab and microarrays (molecular big data), databases and registries (clinical/computational big data), imaging techniques (such as radiomics, imaging big data) and web searches (the so-called infodemiology, digital big data). The present review aims to show how big and smart data can revolutionize gynecology by shedding light on female reproductive health, both in terms of physiology and pathophysiology. More specifically, they appear to have potential uses in the field of gynecology to increase its accuracy and precision, stratify patients, provide opportunities for personalized treatment options rather than delivering a package of “one-size-fits-it-all” healthcare management provisions, and enhance its effectiveness at each stage (health promotion, prevention, diagnosis, prognosis, and therapeutics).

The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices

Monitoring of the human microbiome is an emerging area of diagnostics for personalized medicine. Here, the potential of different nanomaterials and nanobiosensing technologies is reviewed for the development of novel diagnostic devices for the detection and measurement of microbiome-related biomarkers. Moreover, the current and future landscape of microbiome-based diagnostics is defined by exploring the advantages and disadvantages of current nanotechnology-based approaches, especially in the context of developing point-of-care (PoC) devices that would meet the international guidelines known as REASSURED (Real-time connectivity; Ease of specimen collection; Affordability; Sensitivity; Specificity; User-friendliness; Rapid & robust operation; Equipment-free; and Deliverability). Finally, the strategies of the latest international scientific consortia working in this field are analyzed, the current microbiome diagnostics market are reported and the principal ethical, legal, and societal issues related to microbiome R&D and innovation are discussed.

The gut microbiome influences the bioavailability of olanzapine in rats

Background

The role of the gut microbiome in the biotransformation of drugs has recently come under scrutiny. It remains unclear whether the gut microbiome directly influences the extent of drug absorbed after oral administration and thus potentially alters clinical pharmacokinetics.

Methods

In this study, we evaluated whether changes in the gut microbiota of male Sprague Dawley rats, as a result of either antibiotic or probiotic administration, influenced the oral bioavailability of two commonly prescribed antipsychotics, olanzapine and risperidone.

Findings

The bioavailability of olanzapine, was significantly increased (1.8-fold) in rats that had undergone antibiotic-induced depletion of gut microbiota, whereas the bioavailability of risperidone was unchanged. There was no direct effect of microbiota depletion on the expression of major CYP450 enzymes involved in the metabolism of either drug. However, the expression of UGT1A3 in the duodenum was significantly downregulated. The reduction in faecal enzymatic activity, observed during and after antibiotic administration, did not alter the ex vivo metabolism of olanzapine or risperidone. The relative abundance of Alistipes significantly correlated with the AUC of olanzapine but not risperidone.

Interpretation

Alistipes may play a role in the observed alterations in olanzapine pharmacokinetics. The gut microbiome might be an important variable determining the systemic bioavailability of orally administered olanzapine. Additional research exploring the potential implication of the gut microbiota on the clinical pharmacokinetics of olanzapine in humans is warranted.

Funding

This research is supported by APC Microbiome Ireland, a research centre funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (grant no. 12/RC/2273 P2) and by Nature Research-Yakult (The Global Grants for Gut Health; Ref No. 626891).

Human Microbiota and Breast Cancer-Is There Any Relevant Link?-A Literature Review and New Horizons Toward Personalised Medicine

Breast cancer (BC) is the most common malignancy and the second cause of cancer-specific death in women from high-income countries. Recently, gut microbiota dysbiosis emerged as a key player that may directly and/or indirectly influence development, treatment, and prognosis of BC through diverse biological processes: host cell proliferation and death, immune system function, chronic inflammation, oncogenic signalling, hormonal and detoxification pathways. Gut colonisation occurs during the prenatal period and is later diversified over distinct phases throughout life. In newly diagnosed postmenopausal BC patients, an altered faecal microbiota composition has been observed compared with healthy controls. Particularly, β-glucuronidase bacteria seem to modulate the enterohepatic circulation of oestrogens and their resorption, increasing the risk of hormone-dependent BC. Moreover, active phytoestrogens, short-chain fatty acids, lithocholic acid, and cadaverine have been identified as bacterial metabolites influencing the risk and prognosis of BC. As in gut, links are also being made with local microbiota of tumoural and healthy breast tissues. In breast microbiota, different microbial signatures have been reported, with distinct patterns per stage and biological subtype. Total bacterial DNA load was lower in tumour tissue and advanced-stage BC when compared with healthy tissue and early stage BC, respectively. Hypothetically, these findings reflect local dysbiosis, potentially creating an environment that favours breast tumour carcinogenesis (oncogenic trigger), or the natural selection of microorganisms adapted to a specific microenvironment. In this review, we discuss the origin, composition, and dynamic evolution of human microbiota, the links between gut/breast microbiota and BC, and explore the potential implications of metabolomics and pharmacomicrobiomics that might impact BC development and treatment choices toward a more personalised medicine. Finally, we put in perspective the potential limitations and biases regarding the current microbiota research and provide new horizons for stronger accurate translational and clinical studies that are needed to better elucidate the complex network of interactions between host, microorganisms, and drugs in the field of BC.

Radiotherapy and the gut microbiome: facts and fiction

An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating “hot” versus “cold” tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple ‘-omic’ approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi “-omic” approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.

Association Mining to Identify Microbe Drug Interactions Based on Heterogeneous Network Embedding Representation

Accurately identifying microbe-drug associations plays a critical role in drug development and precision medicine. Considering that the conventional wet-lab method is time-consuming, labor-intensive and expensive, computational approach is an alternative choice. The increasing availability of numerous biological data provides a great opportunity to systematically understand complex interaction mechanisms between microbes and drugs. However, few computational methods have been developed for microbe drug prediction. In this work, we leverage multiple sources of biomedical data to construct a heterogeneous network for microbes and drugs, including drug-drug interactions, microbe-microbe interactions and microbe-drug associations. And then we propose a novel Heterogeneous Network Embedding Representation framework for Microbe-Drug Association prediction, named (HNERMDA), by combining metapath2vec with bipartite network recommendation. In this framework, we introduce metapath2vec, a heterogeneous network representation learning method, to learn low-dimensional embedding representations for microbes and drugs. Following that, we further design a bias bipartite network projection recommendation algorithm to improve prediction accuracy. Comprehensive experiments on two datasets, named MDAD and aBiofilm, demonstrated that our model consistently outperformed five baseline methods in three types of cross-validations. Case study on two popular drugs (i.e., Ciprofloxacin and Pefloxacin) further validated the effectiveness of our HNERMDA model in inferring potential target microbes for drugs.

A cross-talk between gut microbiome, salt and hypertension

Cardiac disorders contribute to one of the major causes of fatality across the world. Hypertensive patients, even well maintained on drugs, possess a high risk to cardiovascular diseases. It is, therefore, highly important to identify different factors and pathways that lead to risk and progression of cardiovascular disorders. Several animals and human studies suggest that taxonomical alterations in the gut are involved in the cardiovascular physiology. In this article, with the help of various experimental evidences, we suggest that the host gut-microbiota plays an important in this pathway. Short chain fatty acids (SCFAs) and Trimethyl Amine -n-Oxide (TMAO) are the two major products of gut microbiome. SCFAs present a crucial role in regulating the blood pressure, while TMAO is involved in pathogenesis of atherosclerosis and other coronary artery diseases, including hypertension. We prove that there exists a triangular bridge connecting the gap between dietary salt, hypertension and gut microbiome. We also present some of the dietary interventions which can regulate and control microbiota that can prevent cardiovascular complications.We strongly believe that this article would improve the understanding the role of gut microbiota in hypertension, and will be helpful in the development of novel therapeutic strategies for prevention of hypertension through restoring gut microbiome homeostasis in the near future.

Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine

Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.

The Gut Microbiome in Bipolar Disorder and Pharmacotherapy Management

The gut microbiome is a complex and dynamic community of commensal, symbiotic, and pathogenic microorganisms that exist in a bidirectional relationship with the host. Bacterial functions in the gut play a critical role in healthy host functioning, and its disruption can contribute to many medical conditions. The relationship between gut microbiota and the brain has gained attention in mental health due to the mounting evidence supporting the association of gut bacteria with mood and behavior. Patients with bipolar disorder exhibit an increased frequency of gastrointestinal illnesses such as inflammatory bowel disease, which mechanistically has been linked to microbial community function. While the heterogeneity in microbial communities between individuals might be associated with disease risk, it may also moderate the efficacy or adverse effects associated with the use of medication. The following review highlights published evidence linking the function of gut microbiota both to bipolar disorder risk and to the effect of medications that influence microbiota, inflammation, and mood symptoms.

Live Biotherapeutic Products, A Road Map for Safety Assessment

Recent developments in the understanding of the relationship between the microbiota and its host have provided evidence regarding the therapeutic potential of selected microorganisms to prevent or treat disease. According to Directive 2001/83/EC, in the European Union (EU), any product intended to prevent or treat disease is defined as a medicinal product and requires a marketing authorization by competent authorities prior to commercialization. Even if the pharmaceutical regulatory framework is harmonized at the EU level, obtaining marketing authorisations for medicinal products remains very challenging for Live Biotherapeutic Products (LBPs). Compared to other medicinal products currently on the market, safety assessment of LBPs represents a real challenge because of their specific characteristics and mode of action. Indeed, LBPs are not intended to reach the systemic circulation targeting distant organs, tissues, or receptors, but rather exert their effect through direct interactions with the complex native microbiota and/or the modulation of complex host-microbiota relation, indirectly leading to distant biological effects within the host. Hence, developers must rely on a thorough risk analysis, and pharmaceutical guidelines for other biological products should be taken into account in order to design relevant non-clinical and clinical development programmes. Here we aim at providing a roadmap for a risk analysis that takes into account the specificities of LBPs. We describe the different risks associated with these products and their interactions with the patient. Then, from that risk assessment, we propose solutions to design non-clinical programmes and First in Human (FIH) early clinical trials appropriate to assess LBP safety.

Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics

The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.

Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders

Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.

Digging Deeper into Precision/Personalized Medicine: Cracking the Sugar Code, the Third Alphabet of Life, and Sociomateriality of the Cell

Precision/personalized medicine is a hot topic in health care. Often presented with the motto "the right drug, for the right patient, at the right dose, and the right time," precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise programs) using biomarkers. Yet, an alien visitor to planet Earth reading the contemporary textbooks on diagnostics might think precision medicine requires only two biomolecules omnipresent in the literature: nucleic acids (e.g., DNA) and proteins, known as the first and second alphabet of biology, respectively. However, the precision/personalized medicine community has tended to underappreciate the third alphabet of life, the "sugar code" (i.e., the information stored in glycans, glycoproteins, and glycolipids). This article brings together experts in precision/personalized medicine science, pharmacoglycomics, emerging technology governance, cultural studies, contemporary art, and responsible innovation to critically comment on the sociomateriality of the three alphabets of life together. First, the current transformation of targeted therapies with personalized glycomedicine and glycan biomarkers is examined. Next, we discuss the reasons as to why unraveling of the sugar code might have lagged behind the DNA and protein codes. While social scientists have historically noted the importance of constructivism (e.g., how people interpret technology and build their values, hopes, and expectations into emerging technologies), life scientists relied on the material properties of technologies in explaining why some innovations emerge rapidly and are more popular than others. The concept of sociomateriality integrates these two explanations by highlighting the inherent entanglement of the social and the material contributions to knowledge and what is presented to us as reality from everyday laboratory life. Hence, we present a hypothesis based on a sociomaterial conceptual lens: because materiality and synthesis of glycans are not directly driven by a template, and thus more complex and open ended than sequencing of a finite length genome, social construction of expectations from unraveling of the sugar code versus the DNA code might have evolved differently, as being future-uncertain versus future-proof, respectively, thus potentially explaining the "sugar lag" in precision/personalized medicine diagnostics over the past decades. We conclude by introducing systems scientists, physicians, and biotechnology industry to the concept, practice, and value of responsible innovation, while glycomedicine and other emerging biomarker technologies (e.g., metagenomics and pharmacomicrobiomics) transition to applications in health care, ecology, pharmaceutical/diagnostic industries, agriculture, food, and bioengineering, among others.

Metabolomics in pharmacology - a delve into the novel field of pharmacometabolomics

Introduction: Pharmacometabolomics is an emerging science pursuing the application of precision medicine. Combining both genetic and environmental factors, the so-called pharmacometabolomic approach guides patient selection and stratification in clinical trials and optimizes personalized drug dosage, improving efficacy and safety.Areas covered: This review illustrates the progressive introduction of pharmacometabolomics as an innovative solution for enhancing the discovery of novel drugs and improving research and development (R&D) productivity of the pharmaceutical industry. An extended analysis on published pharmacometabolomics studies both in animal models and humans includes results obtained in several areas such as hepatology, gastroenterology, nephrology, neuropsychiatry, oncology, drug addiction, embryonic cells, neonatology, and microbiomics.Expert opinion: a tailored, individualized therapy based on the optimization of pharmacokinetics and pharmacodynamics, the improvement of drug efficacy, and the abolition of drug toxicity and adverse drug reactions is a key issue in precision medicine. Genetics alone has become insufficient for deciphring intra- and inter-individual variations in drug-response, since they originate both from genetic and environmental factors, including human microbiota composition. The association between pharmacogenomics and pharmacometabolomics may be considered the new strategy for an in-deep knowledge on changes and alterations in human and microbial metabolic pathways due to the action of a drug.