An introduction to microbiome analysis for human biology applications

Abstract

Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health. However, much remains to be learned about the broader ecological and evolutionary contexts within which gut microbes and humans are affecting each other. Here, I outline the procedures for generating data describing the gut microbiota with the goal of facilitating the wider integration of microbiome analyses into studies of human biology. I describe the steps involved in sample collection, DNA extraction, PCR amplification, high-throughput sequencing, and bioinformatics. While this review serves only as an introduction to these topics, it provides sufficient resources for researchers interested in launching new microbiome initiatives. As knowledge of these methods spreads, microbiome analysis should become a standard tool in the arsenal of human biology research.

The crosstalk between microbiome and asthma: Exploring associations and challenges

“…Various sequencing platforms are available which differ based on the read length, sequencing depth and error rates . The most frequently used platforms in the literature are Illumina platforms (eg, MiSeq and HiSeq) and 454 pyrosequencing.…”

“…Other platforms are also available such as Ion Torrent, PacBio and SOLiD. It is important to note that different sequencing platforms may produce variable results for the same samples . For a clear comparison between sequencing approaches and platforms, see recent articles written by Liu et al and Tessler et al …”

Cannabinoids and the Microbiota–Gut–Brain Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders

“…The GBA consists of bidirectional communication between the CNS, GI tract, and endocrine, autonomic, enteric, and immune systems (Zhu et al, ). The quantity and composition of gut microbial species inhabiting the GI tract (known as the “gut microbiome”) has a bidirectional influence on GBA interactions, and this relationship is referred to as the “MGBA” (Amato, ; Mayer et al, ). The immune system is fundamental to gut–brain communication and comprises a critical piece of the MGBA (Cryan and Dinan, ; Petra et al, ), as accumulating evidence suggests important bidirectional communication between the gut microbiota, brain, and immune systems.…”

Biological Systems Are a Common Link Between Alcohol Use Disorder and Co‐Occurring Psychiatric and Medical Conditions

“…Over 100 trillion microbial species inhabiting the gastrointestinal tract, known as gut microbiota , play a fundamental role in the gut–brain axis. Gut microbiota are characterized (e.g., diversity, abundance) by the genomes of the microbiota in a host, known as the gut metagenome or microbiome (Amato, ). Importantly, the microbiome differentiates healthy controls from those with psychiatric conditions and psychiatric conditions, such as AUD (Leclercq et al., ; Malaguarnera et al., ; Mutlu et al., ).…”