Emerging Technologies for Gut Microbiome Research

Compositional and functional analyses of the gut microbiome by next-generation sequencing methods have completely transformed research approaches to determine microbial species and their role in human health and disease. New culturing technologies facilitate mechanistic studies of difficult-to-culture gut microbes. A number of previously uncultivable microbes are now cultivable as a result of these advancements, providing insight into community dynamics and network interactions. Stem cell technologies and tissue engineering allow for construction of organoids capable of facilitating cost-effective, high-throughput microbiome studies. Modulation of the gut microbiota is emerging as an effective method to delineate composition and function of microbial communities, providing new methods to prevent and treat disease. Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies. Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies. universally conserved bacterial ribosomal RNA gene. 16S rDNA is regularly the target for sequencing microbial metagenomes. able to be grown conventionally by traditional microbiology approaches. method that utilizes a polyacrylamide gel with increasing concentration of denaturing chemicals (SDS, urea, etc.) at constant temperature. PCR products run through the gel separately based on nucleotide composition, and different sequences appear as different bands on the gel. compositional or functional shift within host-associated microbial communities that has the potential to facilitate growth of pathogens and/or onset diseases. profile of existing intermediate and end products of metabolic pathways within a system under a given set of conditions. all RNA molecules, including mRNA, rRNA, tRNA, and other noncoding RNA transcribed in a population. all nucleic acids composing a complex microbial community. any compound, microbe, or environmental factor that results in a compositional or functional modification of the microbiome. ecological community of commensal, symbiotic, and pathogenic microorganisms in a particular site, habitat, or geological period. multidisciplinary field intersecting engineering, physics, chemistry, and biology. Microfluidics systems are designed such that low volumes of fluids can be processed to achieve high-throughput screening, multiplexing, and/or automation. a selectively fermented compound that results in specific changes in the composition and/or activity of the gastrointestinal (GI) microbiota, thus conferring benefit(s) upon host health. live microorganisms which, when administered in adequate amounts, confer a health benefit on the host. similar to DGGE but uses variable temperature and a constant detergent concentration. PCR amplification with labeled primers generally targeting the 16S rRNA gene followed by restriction digest of products and detection of fluorescent-labeled fragments. Since different sequences yield different sized fragments, profiles of microbial communities based on sequence dissimilarities can be generated through this procedure.