{"title":"Decoding Microbiome Research for Clinical Psychiatry","authors":"J. Foster","doi":"10.1177/0706743719890725","DOIUrl":null,"url":null,"abstract":"It is remarkable to see how fast and furious microbiome research over the past decade has advanced to the forefront of neuroscience and psychiatry. From an insider’s perspective, there are several reasons to consider the microbiome in clinical psychiatry: (1) to identify biomarkers related to biological differences that allow us to identify subgroups of clinical populations and improve the ability to match individuals to the best treatment, (2) to identify individuals at risk for early intervention, (3) to provide novel targets for drug development, and (4) to facilitate the expansion and new development of microbiome-targeted therapies including, but not limited to, diet, prebiotics, and probiotics. An individual’s microbiome is their own, and the colonization of all surfaces of our body that begins at birth continues through early life. The diversity, composition, and function of an individual’s microbiome are influenced early in life by mode of delivery, breast milk versus formula, exposure to antibiotics and nonantibiotic drugs, sex, diet, stress, housing conditions, and geography. Our own genetics influences our microbiome, and gene–environment interactions over life influence the microbe–host interactions that impact host physiological processes. Advances in our understanding of the microbiome in health and disease are promising. Media, public, academics, and health-care providers are challenged to understand this dynamic area of research and to implement best practices to improve treatment approaches in mental health. In a recent issue of The Canadian Journal of Psychiatry, Butler et al. provide an excellent overview of recent microbiome research and advice on best practices in clinical psychiatry related to the microbiome. For neuroscience and psychiatry, a few key studies using germ-free mice provided the spark for neuroscientists to consider how microbes may influence brain function. As additional neuroscientists considered the microbiome, new results demonstrated that the microbe–host interactions and signaling of the microbiota–gut–brain axis influence neurodevelopment, neuroplasticity, neurotransmitter systems, neurogenesis, many behavioral phenotypes, and more. Based on this preclinical work, interest in understanding a role for the microbiome in clinical psychiatry has recently emerged. As reviewed in the study of Butler et al., alterations in microbiota composition have been reported in major depressive disorder, bipolar affective disorder, anxiety disorders, schizophrenia and psychotic disorders, neurodegenerative disorders, and autism spectrum disorder. While differences between diagnostic groups and healthy volunteers have been observed, identifying key taxa and the functional microbial pathways that influence host physiology is an essential step to advance the translation of microbiome research to clinical applications. To date, many studies have relied on 16S rRNA gene sequencing and analytical tools that limit the specificity of taxa identified resulting in poor reproducibility of health-related bacterial taxa across studies. 16S rRNA sequencing only identifies taxa to the genus level and provides no direct insight into the functional changes of microbiota that may be driving effects on host physiology. Additional approaches include shotgun metagenomics and metabolomics. Shotgun metagenomics sequencing provides not only who is there but gives functional readouts of bacterial metabolism. Metabolomics examines the metabolites of the bacteria and/or the host. As noted in the study of Butler et al., short chain fatty acids (SCFAs) are important bacterial metabolites produced by gut bacteria that influence other commensals and are important to gut physiology as well as part of microbiota–host signaling systems that extend beyond the gut. Beyond SCFAs, microbially derived molecules include neurotransmitters, indoles, bile acids, choline metabolites, lactate, and vitamins, and evidence is accumulating that the microbial metabolites may","PeriodicalId":309115,"journal":{"name":"The Canadian Journal of Psychiatry","volume":"57 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2019-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Canadian Journal of Psychiatry","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1177/0706743719890725","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 3
Abstract
It is remarkable to see how fast and furious microbiome research over the past decade has advanced to the forefront of neuroscience and psychiatry. From an insider’s perspective, there are several reasons to consider the microbiome in clinical psychiatry: (1) to identify biomarkers related to biological differences that allow us to identify subgroups of clinical populations and improve the ability to match individuals to the best treatment, (2) to identify individuals at risk for early intervention, (3) to provide novel targets for drug development, and (4) to facilitate the expansion and new development of microbiome-targeted therapies including, but not limited to, diet, prebiotics, and probiotics. An individual’s microbiome is their own, and the colonization of all surfaces of our body that begins at birth continues through early life. The diversity, composition, and function of an individual’s microbiome are influenced early in life by mode of delivery, breast milk versus formula, exposure to antibiotics and nonantibiotic drugs, sex, diet, stress, housing conditions, and geography. Our own genetics influences our microbiome, and gene–environment interactions over life influence the microbe–host interactions that impact host physiological processes. Advances in our understanding of the microbiome in health and disease are promising. Media, public, academics, and health-care providers are challenged to understand this dynamic area of research and to implement best practices to improve treatment approaches in mental health. In a recent issue of The Canadian Journal of Psychiatry, Butler et al. provide an excellent overview of recent microbiome research and advice on best practices in clinical psychiatry related to the microbiome. For neuroscience and psychiatry, a few key studies using germ-free mice provided the spark for neuroscientists to consider how microbes may influence brain function. As additional neuroscientists considered the microbiome, new results demonstrated that the microbe–host interactions and signaling of the microbiota–gut–brain axis influence neurodevelopment, neuroplasticity, neurotransmitter systems, neurogenesis, many behavioral phenotypes, and more. Based on this preclinical work, interest in understanding a role for the microbiome in clinical psychiatry has recently emerged. As reviewed in the study of Butler et al., alterations in microbiota composition have been reported in major depressive disorder, bipolar affective disorder, anxiety disorders, schizophrenia and psychotic disorders, neurodegenerative disorders, and autism spectrum disorder. While differences between diagnostic groups and healthy volunteers have been observed, identifying key taxa and the functional microbial pathways that influence host physiology is an essential step to advance the translation of microbiome research to clinical applications. To date, many studies have relied on 16S rRNA gene sequencing and analytical tools that limit the specificity of taxa identified resulting in poor reproducibility of health-related bacterial taxa across studies. 16S rRNA sequencing only identifies taxa to the genus level and provides no direct insight into the functional changes of microbiota that may be driving effects on host physiology. Additional approaches include shotgun metagenomics and metabolomics. Shotgun metagenomics sequencing provides not only who is there but gives functional readouts of bacterial metabolism. Metabolomics examines the metabolites of the bacteria and/or the host. As noted in the study of Butler et al., short chain fatty acids (SCFAs) are important bacterial metabolites produced by gut bacteria that influence other commensals and are important to gut physiology as well as part of microbiota–host signaling systems that extend beyond the gut. Beyond SCFAs, microbially derived molecules include neurotransmitters, indoles, bile acids, choline metabolites, lactate, and vitamins, and evidence is accumulating that the microbial metabolites may