Beyond Commensals — Interactions Between the Gut Microbiome and Metazoan Host Metabolic Performance

Ongoing advances in next-generation sequencing technologies and bioinformatics have sparked a growing interest in characterizing the taxonomic and functional diversity of microbial communities. Indeed, the number of articles describing microbial communities (i.e., using ‘microbiome’ as a search term in Web of Knowledge) from diverse habitats including the digestive tracts of animals has increased from single digits in 2001 to more than 18,000 in 2020. Evidence also continues to emerge that resident microbial communities, including the bacteria, fungi, protozoa, archaea, and viruses that comprise the ‘gut microbiome’, can play integral roles in animal behavior, immunity, and metabolism (Moran et al. 2019). However, such experimental evidence is limited to few host taxa, and to bacterial members of the microbiome. There is therefore a growing need for additional functional studies, and the subsequent integration of results across diverse host species, to understand the impacts of the gut microbiome on animal fitness and evolution.

Most animal-associated microorganisms (e.g., 99% in humans) are in fact harbored in the digestive tract (Sender et al. 2016). This ‘gut microbiome’ is often deemed a main player in host metabolism through effects on diverse fitness-related host traits like growth, survival, and performance. However, recent empirical evidence also indicates that animal hosts can vary greatly in their dependence upon the gut microbiome. Some animals harbor low abundance and transient gut microbial communities that are dispensable for their growth and survival (Hammer et al. 2019), while others cannot live in the absence of a gut microbiome under natural conditions. Building on an exciting decade in this new field and the rapid accumulation of a tremendous amount of amplicon and metagenomic sequencing data, this Research Topic aims to synthesize our current understanding of the role of the gut microbiome in shaping metazoan growth and metabolism and vice versa (i.e., host metabolism as a driver of gut microbial diversity) and to promote future work to integrate functional studies of microbial impacts on host physiology, ecology, and life-history with microbiome sequence data.

We invite submissions of Original Research, Review Articles, Methodological and Conceptual Essays, and Perspectives in the following areas:


• Developing a holistic understanding of host-microbiome metabolic interactions, to include articles that step beyond descriptive studies to (i) employ inference-based, hypothesis-driven approaches, (ii) seek to disentangle direct and indirect effects of the gut microbiome on host metabolism, (iii) integrate data across multiple levels of organization (growth, digestion, metabolic rate, expression of specific genes), and/or (iv) include a comprehensive analysis of the microbiome, including bacteria, fungi, protozoa, archaea, viruses, and eukaryotic parasites.

• Characterizing the functional basis of host-microbiome interactions, to include articles that involve the experimental manipulation of microbiomes (e.g., microbiome removal, microbial transplantation) and/or the integration of quantitative and qualitative microbial measures and methods of microbial detection in order to (i) determine the dependency of animal hosts upon gut microbes, (ii) differentiate between transient and resident microbes, and/or (iii) mechanistically link diverse host measures with each other and to the microbiome.

• Defining novel approaches for host-microbiome data analysis, interpretation and presentation, to include articles that establish novel or build on existing methods to (i) differentiate between quantitative and qualitative microbiome data, and between the structure, function and diversity of microbiomes, and/or (ii) elucidate interactions among members of microbial communities and host traits (beyond compositional abundance data).