Stable-Isotope Probing of Human and Animal Microbiome Function

Abstract

Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.

Keywords: NanoSIMS; RNA-SIP; Raman microspectroscopy; gut microbiota; single-cell imaging.

Figure 1

In Vivo Stable-Isotope Probing (SIP). Options for mode of administration of stable-isotope-labeled substrate as well as sampling for molecular and chemical analysis.

Figure 2

Mass Flows in the Host-Associated Microbiota. (A) Schematic of general mass flows in the gut ecosystem, from diet to and between host and microbiota. (B) Conceptual example of how stable-isotope probing (SIP) can be used to specifically track isotopically labeled microbes involved in ¹³C-starch degradation or downstream in the trophic cascade, and to follow the fate of starch degradation metabolism and products in the microbiota and host (red indicates ¹³C in compounds and biomass). Intestinal metabolites are absorbed and metabolized by the epithelium and/or further distributed to peripheral host tissues and organs (e.g., liver, kidney, brain) by the circulation. SCFA, short-chain fatty acid.

Figure 3

Outline of a Holistic Stable-Isotope Probing (SIP) Experiment. SIP technologies are integrated with multi-omics, microscopic and chemical imaging to provide a comprehensive picture of the microbiome dynamics and activities, and specific identities and physiological interactions of isotope-labelled microorganisms. Thick black arrow with clock indicates the timeline of an experiment. Thick and thin blue arrows indicate sampling time-points during the experiment for different analyses. IRMS, isotope ratio mass spectrometry. FISH, fluorescence in situ hybridization.