Exploring and evaluating microbiome resilience in the gut

Abstract

The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.

Keywords: host–microbe interactions; microbe–microbe interplays; microbiome resilience; microbiome structure and keystone species.

Figure 1.

Factors influence gut microbiome homeostasis. Environmental factors and host factors are considered external factors that affect the microbial community balance, while microbiome resilience is considered an internal factor that maintains microbiome stability.

Figure 2.

Host–microbe interactions in association with microbiome resilience: immune facilitating microbial preservation, colonization, construction, protection, and suppression via mucins, Treg, M_Ø, RegIIIγ, sIgA, AMPs, and microbial immunomodulation via LPSs, SCFs, and MAMPs.