Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes

Abstract

Summary The community of microorganisms in the mammalian gastrointestinal tract, referred to as the gut microbiota, influences host physiology and immunity. The last decade of microbiome research has provided significant advancements for the field and highlighted the importance of gut microbes to states of both health and disease. Novel molecular techniques have unraveled the tremendous diversity of intestinal symbionts that potentially influence the host, many proof-of-concept studies have demonstrated causative roles of gut microbial communities in various pathologies, and microbiome-based approaches are beginning to be implemented in the clinic for diagnostic purposes or for personalized treatments. However, several challenges for the field remain: purely descriptive reports outnumbering mechanistic studies and slow translation of experimental results obtained in animal models into the clinics. Moreover, there is a dearth of knowledge regarding how gut microbes, including novel species that have yet to be identified, impact host immune responses. The sheer complexity of the gut microbial ecosystem makes it difficult, in part, to fully understand the microbiota-host networks that regulate immunity. In the present manuscript, we review key findings on the interactions between gut microbiota members and the immune system. Because culturing microbes allows performing functional studies, we have emphasized the impact of specific taxa or communities thereof. We also highlight underlying molecular mechanisms and discuss opportunities to implement minimal microbiome-based strategies.

The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

“…An advantage of the latter method is the known composition of the microbiota, as emphasized above. A drawback, however, is formed by the risk that the desired phenotype (in this case a normalized host) cannot be entirely recapitulated (100).…”

“…Nevertheless, due to the complexity of the immune system, it is difficult to quantify and compare the model hosts used with respect to immunological parameters. The key findings on the interactions of gut microbiota members and their products with the immune system have recently been reviewed elsewhere (100). Those authors emphasized the value of minimal microbiomes and subsequent standardized (animal) models.…”

Development of selected bacterial groups of the rectal microbiota of healthy calves during the first week postpartum

“…Salmonella enterica, Escherichia coli, rotavirus, coronavirus Cryposporidium parvum) that can endanger the newborn (Cho and Yoon, 2014;Gomez and Weese 2017). However, there is increasing evidence that the colonization of the mammalian gastrointestinal tract plays a crucial role in the development of the mucosal immune system and influences the growth and performance of the individual (Schwarzer et al 2016;Clavel et al 2017). In summary, the evolution of the microbiota has great significance for the health of the newborn.…”

Induction of gut Lactobacillus reuteri in normal ICR mice by oral administration of L. plantarum AN1

“…Recent culture‐independent next‐generation DNA sequencing (NGS) analysis of 16S rRNA genes has revealed that the guts of humans and other mammals contain trillions of bacterial cells, comprising 500–1000 different bacterial species. The importance of the gut microbiota to host health has been suggested in numerous studies (Clavel, Gomes‐Neto, Lagkouvardos, & Ramer‐Tait, ; Clavel, Lagkouvardos, & Steacher, ). In addition, the relationship between aging and the gut microbiota, which was proposed by Metchnikoff over a century ago (Cavaillon & Legout, ), and has been supported by the results of NGS analyses (Sánchez et al, ).…”