Understanding the factors regulating host–microbiome interactions using Caenorhabditis elegans

Abstract

The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host–microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host–microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host–microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue ‘Sculpting the microbiome: how host factors determine and respond to microbial colonization’.

Sculpting the microbiome

“…Interactions between hosts and bacterial metabolites are appreciated across organisms. Singh & Luallen [ 14 ] review factors shaping interactions between the roundworm Caenorhabditis elegans and its microbiome, including behaviour, immunity, diet and the gut niche. They underscore the use of this in vivo model in exploring the genetic basis and heritability of microbiome interactions with host health and disease, insights which may be broadly applicable to understanding host-microbiome interactions in animals including humans.…”

“…Singh & Luallen [ 14 ] are authors from the same institution as C.S. Schrankel (San Diego State University).…”

Caenorhabditis elegans as a Convenient Animal Model for Microbiome Studies

“…The development of simpler models is necessary, as it is challenging to interrogate the causal role of the microbiome shaped by human genetics. This is less known within the HMP due to humans’ varying ethnicities and limited genetic diversity [ 3 ].…”

“…C. elegans interacts with a wide range of microorganisms, comprising bacteria, fungi, and other microbes. Various factors, including soil type, geographic location, and environmental conditions, influence the composition of its microbiome [ 3 ]. As a result, the microbiome of C. elegans may exhibit considerable variation.…”