Replenishing our defensive microbes

Abstract

Large-scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of "Western diseases" may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices may deplete physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems.

Keywords: antibiotics; ecology; gut microbiota; human microbiome; hygiene hypothesis; pathogens.

Figure 1. 16S rRNA gene sequencing survey reveals major differences in community composition of ancient vs. present-day humans

Fecal samples were collected from four different sources; adults in present-day Malawi, adults in present-day Venezuela, adults in present-day United States, and a ∼1400 year old deposit in an ancient rock shelter in El Zape, Mexico. Briefly, the 16S rRNA gene was sequenced, taxonomy was assigned against a reference database, and the communities were compared using the unweighted UniFrac phylogenetic distance metric. Microbial communities that are more dissimilar are located further apart in principal coordinate space, while similar communities are found clustered together [28,30].

Figure 2. Diverting our microbial communities back towards ancestral states

Modern behaviors such as Cesarean sections and antibiotics may have the ability to push our microbial communities away from their natural, ancestral trajectories. However, microbiome manipulation may allow us to push our microbial communities back on track by replenishing the microbes that were affected by the disturbances. In this way, the impact on our microbial communities through events such as antibiotic use can be repaired such that our microbial communities maintain their protective benefits.