Trends in Microbiology
Volume 24, Issue 11, November 2016, Pages 887-901
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Review
Emerging Technologies for Gut Microbiome Research

https://doi.org/10.1016/j.tim.2016.06.008Get rights and content

Trends

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.

Section snippets

The Gut Microbiome

Humans are associated in a symbiotic relationship with up to 1014 microorganisms [1]. The majority of these host-associated microbes reside within the gastrointestinal tract and have extraordinary metabolic potential, playing a pivotal role in human health [2]. The gut microbiota enhances the host's response to pathogen invasion [3], modulates host gene expression and immune response, and ultimately impacts overall health 4, 5, 6. Normal inhabitants of the gastrointestinal tract facilitate the

The Study of the Gut Microbiome Before Next-Generation Sequencing (NGS)

Prior to the advent of NGS, the accurate identification of most members of a complex microbial community was challenging. This was especially true for the gut microbiome, a highly diverse community and one of the densest microbial communities on the planet, with a small percentage of culturable microbes [18]. Early gut microbiome studies involved cultivation of individual bacteria [19], and studies of interactions by co-culture of microbial consortia [20]. While these methods allowed

NGS Technologies and Metabolomics in Gut Microbiome Research

Connections between microbes and host health were postulated before the advent of high-throughput sequencing technology [27]. However, prior to technological advancements, these studies lacked the ability to take entire community dynamics into consideration. The identification and relative quantification of microbial taxa via high-throughput sequencing drastically improved the ability to study the gut microbiome. While initially focused on compositional studies (who is there?), microbiome

Advancements in Culturing Technologies

The information provided by compositional and functional studies of the gut microbiome have permitted inference of microbial interactions within complex communities. After determining the composition of the gut microbiome, and the microbial genes and pathways impacted by health or disease condition, the next logical step is to address the mechanistic networks involved in microbiome–host interactions. In order to explore the mechanisms by which individual microorganisms modulate the microbiota

In vitro Simulation of the Host-Specific Gut Microenvironment

Most microbiota studies have been carried out on animal models; however, this method is costly, both from financial and temporal standpoints. A review outlining the study of the microbiota in animal models has discussed the importance of animal models in microbiome studies [69]. While animal models hold great importance for understanding host–microbe interactions, advancements in engineering of biomaterials have recently provided an optional approach to study the complex interactions occurring

Advancements in Gut Microbiome Modulation and Host Health

Advancement of microbiome research technology converges at one point: the identification and study of microbiome modulators and their impact on host health. As technology and research advance, an iterative process is established where well characterized modulators can be applied in the discovery of other parameters that impact the gut microbiota. Any compound, microbe, or environmental factor that results in a compositional or functional modification of the microbiome can be considered a

Concluding Remarks and Future Directions

There is a wealth of untapped information within the gut microbiome. Information about the countless biological processes occurring in this complex microbial community, which are not entirely understood, provides valuable insight into microbial impact on host health. The data obtained by high-throughput sequencing contain more information than can be analyzed effectively using existing bioinformatics platforms and microbiology techniques. However, as technology advances, it becomes easier to

Acknowledgments

The Microbiome Core Facility is supported in part by the NIH/National Institute of Diabetes and Digestive and Kidney Diseases grant P30 DK34987. We thank Drs N. Butz, J. Kwintkiewicz, and S. Fabela for critical reading of this manuscript.

Glossary

16S rRNA
universally conserved bacterial ribosomal RNA gene. 16S rDNA is regularly the target for sequencing microbial metagenomes.
Cultivable
able to be grown conventionally by traditional microbiology approaches.
Denaturing gradient gel electrophoresis (DGGE)
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

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      Citation Excerpt :

      Thanks to these opportunities, there have been developments in emerging technologies used in the studies of human microbiome along with consumer behaviors and human capital development. The main technologies with that are used for microbiome studies are high-throughput (HTP) culturing, HTP metabolomics, HTP sequencing, bioinformatics, metatranscriptomics, microfluidics assays, engineered organoids derived from human stem cells and fecal microbiota transplantation [14,15]. Besides novel approaches in human microbiome, machine learning methods (Algorithms can change according to their learning approaches and analysis purposes.)

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