The healthy human microbiome

Abstract

Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human microbiome—the total DNA content of microbes inhabiting our bodies—is quite a bit more variable, with only a third of its constituent genes found in a majority of healthy individuals. Understanding this variability in the “healthy microbiome” has thus been a major challenge in microbiome research, dating back at least to the 1960s, continuing through the Human Microbiome Project and beyond. Cataloguing the necessary and sufficient sets of microbiome features that support health, and the normal ranges of these features in healthy populations, is an essential first step to identifying and correcting microbial configurations that are implicated in disease. Toward this goal, several population-scale studies have documented the ranges and diversity of both taxonomic compositions and functional potentials normally observed in the microbiomes of healthy populations, along with possible driving factors such as geography, diet, and lifestyle. Here, we review several definitions of a ‘healthy microbiome’ that have emerged, the current understanding of the ranges of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies to be addressed in the future.

Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome

“…An essential capability of the gut microbiome is adaptation to widely varying nutritional environments while avoiding community instability that results in dysbiosis [65]. We performed biofilm simulations with the essential cross-feeding relationships for changes in the biofilm thickness and nutrient levels to ensure that species coexistence was not an artifact of the specific conditions chosen (see Table 1) but rather was a robust property of the cross-fed community.…”

Investigation of Oligosaccharides for Prebitoic Action on Vaginal Lactobacilli

“…FOS group (Group II) revealed mild focal hyperplasia of squamous epithelium and multifocal mild lymphocytic infiltration at lamina propria (1). GOS group (Group III) revealed mild diffuse lymphocytic infiltration at lamina propria (1).…”

“…Microbiota generally resides on skin, mouth, gut and vagina. 1 Female genital tract is one of the major sites occupied by microbiota, commonly dominated by Doderlen's bacilli (Lactobacillus species). 2 Presence of Lactobacilli is important sign of healthy vagina which inhibits the growth of pathogenic microorganism.…”

On the Importance of the Microbiome and Pathobiome in Coral Health and Disease

“…This new term has been used to describe the complex interactions of pathogenic microbes which may influence or drive disease processes and their relationship to the "normal" microbiome of the organism in question (Chow et al, 2011;Vayssier-Taussat et al, 2014). Both terms are now widely used throughout the literature, particularly in the medical domain, for example with respect to the human gut (Huttenhower and Human Microbiome Project Consortium, 2012;Krezalek et al, 2015;Lloyd-Price et al, 2016). However, these terms are less widely used in the environmental sciences, and studies focused on Scleractinian corals for example have more commonly utilized the terms "microbiota" or "microbial associates" to describe the microbial communities associated with these hosts.…”