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

Gut microbiota and its roles in the pathogenesis and therapy of endocrine system diseases

A new field of microbial research is the relationship between microorganisms and multicellular hosts. It is known that gut microbes can cause various endocrine system diseases, such as diabetes and thyroid disease. Changes in the composition or structure and the metabolites of gut microbes may cause gastrointestinal disorders, including ulcers or intestinal perforation and other inflammatory and autoimmune diseases. In recent years, reports on the interactions between intestinal microorganisms and endocrine system diseases have been increasingly documented. In the meantime, the treatment based on gut microbiome has also been paid much attention. For example, fecal microbiota transplantation is found to have a therapeutic effect on many diseases. As such, understanding the gut microbiota-endocrine system interactions is of great significance for the theranostic of endocrine system diseases. Herein, we summarize the relations of gut microbiome with endocrine system diseases, and discuss the potentials of regulating gut microbiome in treating those diseases. In addition, the concerns and possible solutions regarding the gut microbiome-based therapy are discussed.

Biofilm ecology associated with dental caries: Understanding of microbial interactions in oral communities leads to development of therapeutic strategies targeting cariogenic biofilms

A biofilm is a sessile community characterized by cells attached to the surface and organized into a complex structural arrangement. Dental caries is a biofilm-dependent oral disease caused by infection with cariogenic pathogens, such as Streptococcus mutans, and associated with frequent exposure to a sugar-rich diet and poor oral hygiene. The virulence of cariogenic biofilms is often associated with the spatial organization of S. mutans enmeshed with exopolysaccharides on tooth surfaces. However, in the oral cavity, S. mutans does not act alone, and several other microbes contribute to cariogenic biofilm formation. Microbial communities in cariogenic biofilms are spatially organized into complex structural arrangements of various microbes and extracellular matrices. The balance of microbiota diversity with reduced diversity and a high proportion of acidogenic-aciduric microbiota within the biofilm is closely related to the disease state. Understanding the characteristics of polymicrobial biofilms and the association of microbial interactions within the biofilm (e.g., symbiosis, cooperation, and competition) in terms of their potential role in the pathogenesis of oral disease would help develop new strategies for interventions in virulent biofilm formation.

Paradigm shift in the pathogenesis and treatment of oral cancer and other cancers focused on the oralome and antimicrobial-based therapeutics

The oral microbiome is a community of microorganisms, comprised of bacteria, fungi, viruses, archaea, and protozoa, that form a complex ecosystem within the oral cavity. Although minor perturbations in the environment are frequent and compensable, major shifts in the oral microbiome can promote an unbalanced state, known as dysbiosis. Dysbiosis can promote oral diseases, including periodontitis. In addition, oral dysbiosis has been associated with other systemic diseases, including cancer. The objective of this review is to evaluate the epidemiologic evidence linking periodontitis to oral, gastrointestinal, lung, breast, prostate, and uterine cancers, as well as describe new evidence and insights into the role of oral dysbiosis in the etiology and pathogenesis of the cancer types discussed. Finally, we discuss how antimicrobials, antimicrobial peptides, and probiotics may be promising tools to prevent and treat these cancers, targeting both the microbes and associated carcinogenesis processes. These findings represent a novel paradigm in the pathogenesis and treatment of cancer focused on the oral microbiome and antimicrobial‐based therapies.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

The Potential Relevance of the Microbiome to Hair Physiology and Regeneration: The Emerging Role of Metagenomics

Human skin and hair follicles are recognized sites of microbial colonization. These microbiota help regulate host immune mechanisms via an interplay between microbes and immune cells, influencing homeostasis and inflammation. Bacteria affect immune responses by controlling the local inflammatory milieu, the breakdown of which can result in chronic inflammatory disorders. Follicular microbiome shifts described in some inflammatory cutaneous diseases suggest a link between their development or perpetuation and dysbiosis. Though the hair follicle infundibulum is an area of intense immunological interactions, bulb and bulge regions represent immune-privileged niches. Immune privilege maintenance seems essential for hair growth and regeneration, as collapse and inflammation characterize inflammatory hair disorders like alopecia areata and primary cicatricial alopecia. Current research largely focuses on immunological aberrations. However, studies suggest that external stimuli and interactions across the follicular epithelium can have profound effects on the local immune system, homeostasis, and cycling. Herein, we review hair follicle bacterial colonization, its possible effects on the underlying tissue, and links to the pathogenesis of alopecia, beyond the pure investigation of specific species abundance. As skin microbiology enters the metagenomics era, multi-dimensional approaches will enable a new level of investigations on the effects of microorganisms and metabolism on host tissue.

[The association of aromatic microbial metabolites, inflammatory and autoimmune biomarkers with clinical dynamics in severe diseases of the central nervous system]

OBJECTIVE

To identify the association between the changes in the profile of microbial metabolites, inflammatory and autoimmune markers and the dynamics of neurological status in chronic critically ill patients with diseases of the central nervous system (CNS).

MATERIAL AND METHODS

Sixty serum samples from 37 patients, aged 19-77 years, with severe CNS diseases were studied. The changes in clinical condition were assessed with NIHSS, the Rankin scale, the Glasgow Coma Scale, the FOUR Coma Scale and the Rivermead Mobility Index. The levels of aromatic microbial metabolites (AMM) and several inflammatory and autoimmune biomarkers, including the contents of procalcitonin (PCT) and S100, the activity of leukocyte elastase (LE) and a1-proteinase inhibitor a1-PI, the levels of autoantibodies to S100b and MBP were measured. Serum from 60 age- and sex-matched healthy people with no signs of neurological and somatic pathology was used as a control.

RESULTS

All patients were divided into groups depending on the neurological dynamics: A - positive (n=16), B - without dynamics (n=15), C - negative (n=6). The study revealed a profile of AMM, as well as inflammatory and autoimmune biomarkers associated with the severity of neurological disorders. A significant increase in acute phase proteins, S-100 level and a decrease in the functional activity of neutrophils (via LE activity) were observed in the serum of patients. The different dynamics of neurological status was associated with the multidirectional changes in the microbial metabolites profile and biomarkers. The correlations between the clinical and biological parameters indicate that AMM might modulate immune reactions in patients with different dynamics of neurological status.

CONCLUSION

The results suggest the involvement of AMM and the level of immune activation via biomarkers in the pathogenesis of neurological dysfunction. Dynamic changes in the profile of microbial metabolites and the level of activation of the immune system may be a promising tool for prediction of neurological recovery.

Metabolic profiling of aromatic compounds in cerebrospinal fluid of neurosurgical patients using microextraction by packed sorbent and liquid-liquid extraction with gas chromatography-mass spectrometry analysis

A new approach to the quantitative analysis of aromatic metabolites in cerebrospinal fluid samples of neurosurgical patients based on microextraction by packed sorbent coupled with derivatization and GC-MS was developed. Analytical characteristics such as recoveries (40-90%), limit of detection (0.1-0.3 μm) and limit of quantitation (0.4-0.7 μm) values, accuracy (<±20%), precision (<20%) and linear correlations (R²  ≥ 0.99) over a 0.4-10 μm range of concentrations demonstrated that microextraction by packed sorbent provides results for the quantitative analysis of target compounds comparable with those for liquid-liquid extraction. Similar results were achieved using 40 μl of sample for microextraction by packed sorbent instead of 200 μl for liquid-liquid extraction. Benzoic, 3-phenylpropionic, 3-phenyllactic, 4-hydroxybenzoic, 2-(4-hydroxyphenyl)acetic, homovanillic and 3-(4-hydroxyphenyl)lactic acids were found in cerebrospinal fluid samples (n = 138) of neurosurgical patients in lower concentrations than in serum samples (n = 110) of critically ill patients. Analysis of the cerebrospinal fluid and serum samples taken at the same time from neurosurgical patients (n = 5) revealed similar results for patients without infection and multidirectional results for patients with central nervous system infection. Our preliminary results demonstrate the necessity of further evaluating the aromatic compound profile in cerebrospinal fluid for its subsequent verification for potential diagnostic markers.

Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches

The growing importance of astrocytes in the field of neuroscience has led to a greater number of computational models devoted to the study of astrocytic functions and their metabolic interactions with neurons. The modeling of these interactions demands a combined understanding of brain physiology and the development of computational frameworks based on genomic-scale reconstructions, system biology, and dynamic models. These computational approaches have helped to highlight the neuroprotective mechanisms triggered by astrocytes and other glial cells, both under normal conditions and during neurodegenerative processes. In the present review, we evaluate some of the most relevant models of astrocyte metabolism, including genome-scale reconstructions and astrocyte-neuron interactions developed in the last few years. Additionally, we discuss novel strategies from the multi-omics perspective and computational models of other glial cell types that will increase our knowledge in brain metabolism and its association with neurodegenerative diseases.

Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization

Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining the homeostatic balance. Bioactive compounds from the microbial community harboring the human gut are involved in a finely tuned network of interconnections with the host, orchestrating a wide variety of physiological processes. These includes the bi-directional crosstalk between the central nervous system, the enteric nervous system, and the gastrointestinal tract (i.e., gut-brain axis). The increasing accumulation of evidence suggest a pivotal role of the composition and activity of the gut microbiota in neurodegeneration. In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene expression, metaproteomics and metabolomics to identify and/or quantify microbial proteins and metabolites, respectively. The potential and limitations of each discipline were highlighted, as well as the advantages of an integrated approach (multi-omics) to predict microbial functions and molecular mechanisms related to human diseases. Particular emphasis is given to the latest results obtained with these approaches in an attempt to elucidate the link between the gut microbiota and the most common neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS).

The Microbiome and the Gut-Liver-Brain Axis for Central Nervous System Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models

The complexity of integrating microbiota into clinical pharmacology, environmental toxicology, and opioid studies arises from bidirectional and multiscale interactions between humans and their many microbiota, notably those of the gut. Hosts and each microbiota are governed by distinct central dogmas, with genetics influencing transcriptomics, proteomics, and metabolomics. Each microbiota's metabolome differentially modulates its own and the host's multi‐omics. Exogenous compounds (e.g., drugs and toxins), often affect host multi‐omics differently than microbiota multi‐omics, shifting the balance between drug efficacy and toxicity. The complexity of the host‐microbiota connection has been informed by current methods of in vitro bacterial cultures and in vivo mouse models, but they fail to elucidate mechanistic details. Together, in vitro organ‐on‐chip microphysiological models, multi‐omics, and in silico computational models have the potential to supplement the established methods to help clinical pharmacologists and environmental toxicologists unravel the myriad of connections between the gut microbiota and host health and disease.

Bibliometric and Visual Analysis of Research on the Links Between the Gut Microbiota and Depression From 1999 to 2019

Background: There is a crucial link between the gut microbiota and the host central nervous system, and the communication between them occurs via a bidirectional pathway termed the "microbiota-gut-brain axis." The gut microbiome in the modern environment has markedly changed in response to environmental factors. These changes may affect a broad range of host psychiatric disorders, such as depression, by interacting with the host through metabolic, immune, neural, and endocrine pathways. Nevertheless, the general aspects of the links between the gut microbiota and depression have not been systematically investigated through bibliometric analysis. Aim: This study aimed to analyze the current status and developing trends in gut microbiota research in the depression field through bibliometric and visual analysis. Methods: A total of 1,962 publications published between 1999 and 2019 were retrieved from the Web of Science Core Collection. CiteSpace (5.6 R5) was used to perform collaboration network analysis, co-citation analysis, co-occurrence analysis, and citation burst detection. Results: The number of publications has been rapidly growing since 2010. The collaboration network analysis revealed that the USA, University College Cork, and John F. Cryan were the most influential country, institute, and scholar, respectively. The most productive and co-cited journals were Brain Behavior and Immunity and Proceedings of the National Academy of Sciences of the United States of America, respectively. The co-citation analysis of references revealed that the most recent research focus was in the largest theme cluster, "cytokines," thus reflecting the important research foundation in this field. The co-occurrence analysis of keywords revealed that "fecal microbiota" and "microbiome" have become the top two research hotspots since 2013. The citation burst detection for keywords identified several keywords, including "Parkinson's disease," "microbiota-gut-brain axis," "microbiome," "dysbiosis," "bipolar disorder," "impact," "C reactive protein," and "immune system," as new research frontiers, which have currently ongoing bursts. Conclusions: These results provide an instructive perspective on the current research and future directions in the study of the links between the gut microbiota and depression, which may help researchers choose suitable cooperators or journals, and promote their research illustrating the underlying molecular mechanisms of depression, including its etiology, prevention, and treatment.

Nutritional interventions for autism spectrum disorder

Autism spectrum disorder (ASD) is an increasingly prevalent neurodevelopmental disorder with considerable clinical heterogeneity. With no cure for the disorder, treatments commonly center around speech and behavioral therapies to improve the characteristic social, behavioral, and communicative symptoms of ASD. Gastrointestinal disturbances are commonly encountered comorbidities that are thought to be not only another symptom of ASD but to also play an active role in modulating the expression of social and behavioral symptoms. Therefore, nutritional interventions are used by a majority of those with ASD both with and without clinical supervision to alleviate gastrointestinal and behavioral symptoms. Despite a considerable interest in dietary interventions, no consensus exists regarding optimal nutritional therapy. Thus, patients and physicians are left to choose from a myriad of dietary protocols. This review, summarizes the state of the current clinical and experimental literature on nutritional interventions for ASD, including gluten-free and casein-free, ketogenic, and specific carbohydrate diets, as well as probiotics, polyunsaturated fatty acids, and dietary supplements (vitamins A, C, B6, and B12; magnesium and folate).

Quantitative Systems Pharmacology for Neuroscience Drug Discovery and Development: Current Status, Opportunities, and Challenges

The substantial progress made in the basic sciences of the brain has yet to be adequately translated to successful clinical therapeutics to treat central nervous system (CNS) diseases. Possible explanations include the lack of quantitative and validated biomarkers, the subjective nature of many clinical endpoints, and complex pharmacokinetic/pharmacodynamic relationships, but also the possibility that highly selective drugs in the CNS do not reflect the complex interactions of different brain circuits. Although computational systems pharmacology modeling designed to capture essential components of complex biological systems has been increasingly accepted in pharmaceutical research and development for oncology, inflammation, and metabolic disorders, the uptake in the CNS field has been very modest. In this article, a cross-disciplinary group with representatives from academia, pharma, regulatory, and funding agencies make the case that the identification and exploitation of CNS therapeutic targets for drug discovery and development can benefit greatly from a system and network approach that can span the gap between molecular pathways and the neuronal circuits that ultimately regulate brain activity and behavior. The National Institute of Neurological Disorders and Stroke (NINDS), in collaboration with the National Institute on Aging (NIA), National Institute of Mental Health (NIMH), National Institute on Drug Abuse (NIDA), and National Center for Advancing Translational Sciences (NCATS), convened a workshop to explore and evaluate the potential of a quantitative systems pharmacology (QSP) approach to CNS drug discovery and development. The objective of the workshop was to identify the challenges and opportunities of QSP as an approach to accelerate drug discovery and development in the field of CNS disorders. In particular, the workshop examined the potential for computational neuroscience to perform QSP-based interrogation of the mechanism of action for CNS diseases, along with a more accurate and comprehensive method for evaluating drug effects and optimizing the design of clinical trials. Following up on an earlier white paper on the use of QSP in general disease mechanism of action and drug discovery, this report focuses on new applications, opportunities, and the accompanying limitations of QSP as an approach to drug development in the CNS therapeutic area based on the discussions in the workshop with various stakeholders.

Nutritional Supplements During Gestation and Autism Spectrum Disorder: What Do We Really Know and How Far Have We Gone?

Nutritional interventions are gaining remarkable attention as complementary management options for autism. Our aim is to provide literature data about the impact of the administration of dietary supplements during pregnancy on the risk of autism spectrum disorder in the offspring. A comprehensive search was undertaken by 2 reviewers independently using PubMed as the medical database source. Prospective clinical and experimental studies were considered and no year-of-publication restriction was placed. We were able to identify 4 basic (conducted in rodents) and 3 clinical research papers fulfilling our selection criteria. Supplements studied included folic acid, iron, multivitamins, choline, vitamin D, and docosahexaenoic acid. Choline and folic acid had a significant impact on the expression of autism-related genes. However, from a clinical point of view, prenatal folate administration did not reduce the risk of autism. Similarly, iron had no significant impact, while the use of multivitamins in moderate frequency had a protective effect. The use of vitamin D and docosahexaenoic acid during gestation decreased the incidence of autism in animal models. In conclusion, available data are controversial and cannot change current routine practice. More large-scale prospective studies are needed to identify the real effect of nutritional supplements and also optimize their administration.Key teaching pointsMultivitamins use during pregnancy can exert a protective effect on the risk of autism, although depending on the frequency of use. Nevertheless, prenatal iron and folate were not shown to have any significant impact.Research based on animal models showed that choline and folic acid can have a significant impact on the expression of autism-related genes in a sex-specific manner.Furthermore, the use of vitamin D and docosahexaenoic acid during gestation seem to decrease the incidence of autism in animal offspring.In the future, more clinical, large-scale prospective and methodologically homogenous clinical studies are needed to further investigate the effect of the periconceptional use of nutritional supplements on autism risk.

Systems biology in inflammatory bowel diseases: on the way to precision medicine

Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.

Gut Microbiome in Critical Illness (Review)

Radical changes in the composition, diversity and metabolic activity of gut microbiome in critically ill patients most probably affect adversely the outcome of treatment. Microbiota dysfunction may be a predictor and presumably the main cause of infectious complications and sepsis. Clinicists use objective scales for evaluation of patient condition severity including specific parameters of disorders of organs and systems; however, microbiota function is not considered specific and, hence, not evaluated. Technical capabilities of the recent decade have allowed characterizing the intestinal microbiota and that helped understanding the ongoing processes. The authors have analyzed data about the role of intestinal microbiota as a metabolic 'reactor' during critical states, possible complications related to misbalance of 'harmful' and 'beneficial' bacteria, and examined potential of a targeted therapy aimed directly at correction of intestinal microbiota. Search for papers was carried out using Scopus and Web of Science databases 2001 to 2018 years: (Gut Microbiota) AND (Critically ill OR Intensive care unit), key words taken for the search were: intestinal microbiota, metabolism, sepsis, antibiotics, critically ill patients, multiple organ failure. A number of questions in understanding of the interaction between gut microbiome and host remain open. It is necessary to take into account interference of microbial metabolism while assessing metabolome of patients with sepsis. Among low-molecular compounds found in blood of sepsis patients, special attention should be paid to molecules that can be classified as ‘common metabolites’ of humans and bacteria, for example, degradation products of aromatic compounds, which many-fold rise in blood of septic patients. It is necessary to take into consideration and experimentally model changes in the human internal environment, which occur during radical transformation of microbiome in critically ill patients. Such approach brings in new prospects for objective monitoring of diseases by evaluating metabolic profile at a particular moment of time based on integral indices reflecting the status of microbiome/metabolome system, which will supply new targets for therapeutic intervention in future.

Are therapeutic diets an emerging additional choice in autism spectrum disorder management?

BACKGROUND

A nutritional background has been recognized in the pathophysiology of autism and a series of nutritional interventions have been considered as complementary therapeutic options. As available treatments and interventions are not effective in all individuals, new therapies could broaden management options for these patients. Our aim is to provide current literature data about the effect of therapeutic diets on autism spectrum disorder.

DATA SOURCE

A systematic review was conducted by two reviewers independently. Prospective clinical and preclinical studies were considered.

RESULT

Therapeutic diets that have been used in children with autism include ketogenic and gluten/casein-free diet. We were able to identify 8 studies conducted in animal models of autism demonstrating a beneficial effect on neurophysiological and clinical parameters. Only 1 clinical study was found showing improvement in childhood autism rating scale after implementation of ketogenic diet. With regard to gluten/casein-free diet, 4 clinical studies were totally found with 2 of them showing a favorable outcome in children with autism. Furthermore, a combination of gluten-free and modified ketogenic diet in a study had a positive effect on social affect scores. No serious adverse events have been reported.

CONCLUSION

Despite encouraging laboratory data, there is controversy about the real clinical effect of therapeutic diets in patients with autism. More research is needed to provide sounder scientific evidence.