Experimental Microbiomes: Models Not to Scale

Abstract

Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.

Keywords: interactions; microbial communities; microbiome; model systems.

FIG 1

Tradeoffs between experimental questions and complexity of microbiome systems. Each microbiome system is suited to address different types of questions based on the culturability of microbes, genetic tractability of microbes and host (where relevant), ability to maintain system in laboratory setting, and ability to make host/environment germfree. Three different systems are shown in this figure as examples. (A) Pairwise interactions between B. subtilis and Streptomyces spp. are well-suited for characterizing the functions of secondary metabolites in microbial interactions. (B) The symbiosis between bobtail squid and A. fischeri is fundamental to understanding host and microbial factors that influence colonization. (C) The use of gnotobiotic mice is crucial for making links between host diet and the effects on specific microbial taxa in a community (see the text for specific details). Specific original image credit from the Noun Project (https://thenounproject.com/): Fertile Soil by Ben Davis; Droplet by Focus; Mouse by Iconic; Cheese Wheel by Anniken & Andreas; Bacteria by Arthur Shlain; Squid by Artem Kovyazin; ant by Yugudesign; leaf by Saeful Muslim; all used and modified under the Creative Commons License, Attribution 3.0.

FIG 2

Secondary metabolites mediate interactions between B. subtilis and Streptomyces spp. (A) Summary schematic of interactions between B. subtilis and Streptomyces spp. The secondary metabolites produced by B. subtilis and Streptomyces spp. are represented by the purple and orange numbers, respectively, and the chemical structures are shown in panel B. SfhA refers to surfactin hydrolase produced by Streptomyces sp. strain Mg1 that specifically hydrolyzes the ester linkage in surfactin (compound 5). (C to E) Streptomyces spp. (vertical) and B. subtilis (horizontal) spotted in a perpendicular pattern on agar plates. (C) B. subtilis colonies proximal to Streptomyces sp. strain Mg1 colonies are lysed by linearmycins (compound 1). (Republished from Frontiers in Microbiology [3].) (D) Subinhibitory concentrations of chloramphenicol (compound 4) produced by Streptomyces venezuelae induce sliding motility of proximal B. subtilis colonies. (E) Production of the red pigment prodiginine (compound 2) is strongly induced in Streptomyces coelicolor colonies proximal to sliding B. subtilis colonies, which do not produce bacillaene (compound 3). (Images in panels D and E courtesy of Yongjin Liu and Paul Straight, reproduced with permission.)