Microbiome-Based Diagnostics: Ready for Applications in Laboratory Medicine?

Abstract

Laboratory medicine is ripe for a holistic approach to human disease that includes evaluation of human and microbial cells. Advancements in our understanding of the human microbiome are leading to new ideas regarding the diagnosis and management of human diseases. Nucleic acid sequencing, mass spectrometry, and immunoassays will facilitate the application of microbiome science to medical microbiology and clinical chemistry. Biomedical advances in the human microbiome will enlarge the scope of laboratory medicine and result in new diagnostic and disease monitoring strategies. Collaborative efforts within the International Human Microbiome Consortium and specific large-scale research initiatives such as Metagenomics of the Human Intestinal Tract and the Human Microbiome Project have documented differences in microbial composition and function in healthy and diseased states. Diagnostic applications of the microbiome can be divided into two categories: diagnosis of infectious diseases and monitoring of microbial components of noncommunicable chronic diseases. The diagnosis of human infections and selection of antimicrobial agents may be refined in the context of the microbiome. Rather than focusing solely on identification of the etiologic agent(s) of infection, clinical laboratories could evaluate the microbiome at a specific body site of interest. For example, rapid detection of Clostridium difficile in stool specimens in cases of recurrent C. difficile infection may be tested in parallel with stool-based 16S rRNA gene sequencing to evaluate the extent of dysbiosis or cooccurrence of other enteric pathogens. Microbial metabolites may provide useful microbial biomarkers to monitor effective treatment in chronic infections such as recurrent C. difficile associated disease. These parallel evaluations could aid medical decision-making regarding selection of antimicrobial agents or fecal microbiota transplantation (FMT).6 Advances in microbiome discovery are also altering the field of human microbiology for noncommunicable chronic diseases with a microbial component. For example, specific changes in microbial composition and patterns of intestinal dysbiosis …