Host-microbiota interactions: from holobiont theory to analysis

Abstract

In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of hostassociated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration

“…The goal of systems biology studies is to develop and validate models that accurately reflect, and predict, the behaviors of complex biological systems (i.e., a cell, an organism, or a community), which may then be used to predict microbiome behavior in similar systems. For host-microbe interactions, this goal -the precise interpretation and prediction of phenotypic (e.g., health status or the composition of the microbiome) outcomes from currently available measures -is one of the greatest challenges in human microbiome analysis [82][83][84][85]. Nevertheless, systems biology approaches offer a promising direction in understanding the dynamics and pathophysiology of airway microbiomes in CF [25].…”

Interaction networks and trait evolution

“…However, most of the studies focused on pairwise interactions (one microbial species and one host). Consequently, the role of microbial communities in shaping plant evolution deserves further investigation (Simon et al , 2019). Overall, species interactions within networks are complex and dynamic over space and time.…”

MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities

“…In particular, it is now well acknowledged that most metazoans are associated with microbes, forming complex entities named as holobionts. In these systems, microbes are interacting together as well as with their host, and host-microbe interactions can have significant effects on the host phenotype (1). Many animals have microbial associations with one ore a few specific symbionts.…”