Microbiome

The Nobel Laureate, Dr. Joshua Lederberg, used the term "microbiome" to describe an ecological system of commensal, symbiotic, and perhaps pathogenic microorganisms that reside in the human body [1]. Interestingly, the microbiome is not exclusive to humans, as it has also been found and studied in other animals and even in plants. Today, the term microbiome typically refers to a collection of genomes of the microorganisms living in a specific niche and the group of microorganisms themselves, such as bacteria, fungi, or archaea, is called the microbiota.

Over the past 15 years, the microbiome has been gaining increased interest in the research community. Scientists have begun to uncover the heterogeneity and complexity of the microbiome and how these microorganisms that share our body space could impact our health in various ways. For example, a microbiome exists in multiple locations of the human body including the GI system, hair, nostrils, skin, vagina, and oral cavity and has been shown to be associated with conditions such as gastric ulcers, eczema, dental cavities, and even cancer [2]. Some of these conditions result from a disturbance to the natural microbiome whereas others may benefit from such a community of microbes and their ability to directly cause disease or to create a pathogenic environment [3]. In fact, in 2008, the National Institute of Health (NIH) initiated the Human Microbiome Project (HMP) in an effort to gain a more complete and thorough understanding of human microbiomes at different body locations and their associations with diseases [4]. The HMP leveraged high-throughput sequencing technology to address these questions. In this September issue of the Yale Journal of Biology and Medicine (YJBM), we are presenting a list of articles that all focus on the microbiome but from various perspectives.

Among all the sites in the human body, the gut microbiome has been studied the most extensively. The Jones study delves into the mechanistic events that maintain and/or alter the intestinal microbiome at the molecular level. For instance, the author discusses how symbiotic bacteria trigger redox-dependent cell signaling by generating reactive oxygen species (ROS) in the gut epithelia and how that could contribute to mucosal wound recovery after injury. Next, the review article by Enright et al. discusses how gut microbiota can affect drug pharmacokinetics and the recent advances that take advantage of a particular microbiota to improve clinical responses to therapeutics. Similarly, Marotz and Zarrinpar also examine the therapeutic potential of the gut microbiome. In this article, the authors review Fecal Matter Transplant (FMT) and the recent animal and clinical studies using FMT to treat obesity. Interestingly, the Schnorr and Bachner study discusses how the gut microbiome may regulate the neuroendocrine pathways that partly modulate anxiety. They also include a case study of an anxiolytic targeting the gut-brain-axis. Next, Cong et al. examine how various factors such as the birth delivery and feeding methods and medication use may affect gut microbiota in infants. Furthermore, the study sheds light on the parallel development between infant gut microbiome and the neuronal system and how the brain-gut-microbiota axis may regulate early life experiences.

Moving away from gut microbiome, the Adami and Bracken study investigates the association between asthma and the host microbiome, in particular the lung microbiome. In this article, the authors discuss whether exposure to microorganisms could prevent asthma and how the microbiome may have an impact on asthma by interacting with the immune system. In the study by Lu and Liu, the authors examine a very different site from the gut, the ocular surface. In this article, the authors provide an overview of the microbiota colonizing the ocular surface and the role of human microbiota in ophthalmic diseases. We then present a study from Smith et al., which investigates the oral, anal, and cervical microbiomes from sexually active adolescent females. The study suggests that the same individual could carry distinct microbial communities across different body sites. Similarly, the study by Nunn and Forney discusses the vaginal microbiome but the authors take on a unique perspective and choose to examine how glycogen-derived resources and competition might determine the composition of human vaginal bacterial communities.

The Parker study then moves on to study the viral microbiome. In this study, the author describes a framework for human virome classification that will benefit future research that aims to identify novel virus-host interactions. With a focus on the technological aspect of microbiome research, Ghurye et al., highlight the opportunities and challenges of developing new algorithms that account for the specific characteristics of metagenomic data in the context of sequence assembly. Finally, in the review article by Bik, the author identifies and summarizes the current challenges in conducting microbiome-related experiments as well as the recent pseudoscientific commercialization of microbiome research as a result of data misinterpretation.

This issue of the YJBM covers a variety of microbiome-related topics, ranging from microbiomes at various body sites and virus-focused microbiome to the technological and ethical challenges that microbiome research faces in general. Some of the articles also shed light on the therapeutic potential of leveraging the human microbiome in treating different conditions such as obesity and anxiety. Overall, this issue aims to provide you an overview of the recent advances in microbiome research as well as exciting translational opportunities in this field.

Abbreviations

NIH

National Institute of Health

HMP

Human Microbiome Project

ROS

reactive oxygen species

FMT

Fecal Matter Transplant