Microbial underdogs: exploring the significance of low-abundance commensals in host-microbe interactions

Abstract

Our understanding of host-microbe interactions has broadened through numerous studies over the past decades. However, most investigations primarily focus on the dominant members within ecosystems while neglecting low-abundance microorganisms. Moreover, laboratory animals usually do not have microorganisms beyond bacteria. The phenotypes observed in laboratory animals, including the immune system, have displayed notable discrepancies when compared to real-world observations due to the diverse microbial community in natural environments. Interestingly, recent studies have unveiled the beneficial roles played by low-abundance microorganisms. Despite their rarity, these keystone taxa play a pivotal role in shaping the microbial composition and fulfilling specific functions in the host. Consequently, understanding low-abundance microorganisms has become imperative to unravel true commensalism. In this review, we provide a comprehensive overview of important findings on how low-abundance commensal microorganisms, including low-abundance bacteria, fungi, archaea, and protozoa, interact with the host and contribute to host phenotypes, with emphasis on the immune system. Indeed, low-abundance microorganisms play vital roles in the development of the host's immune system, influence disease status, and play a key role in shaping microbial communities in specific niches. Understanding the roles of low-abundance microbes is important and will lead to a better understanding of the true host-microbe relationships.

Fig. 1. Overview of the significance of low-abundance commensals in host physiology.

Low-abundance commensals, including bacteria, fungi, archaea, and protozoa, play pivotal roles in various aspects of host physiology. These microorganisms establish mutualistic relationships with the host, exerting profound effects on the host. Notably, they influence diverse phenotypes, including immune activation (e.g., Th17 cells, tuft cells, dendritic cells, MHC class II expression), the occurrence of several diseases (e.g., inflammatory bowel disease, obesity, asthma, cystic fibrosis, Alzheimer’s disease, multiple sclerosis, rheumatoid arthritis, periodontal disease, cancer), social behavior, and protection against pathogenic infections. Moreover, interactions occur among these microorganisms themselves or with other commensal bacteria in their niche. Created with BioRender.com.