Host-Microbiome Interactions in the Era of Single-Cell Biology

Abstract

Microbes are the most prevalent form of life yet also the least well-understood in terms of their diversity. Due to a greater appreciation of their role in modulating host physiology, microbes have come to the forefront of biological investigation of human health and disease. Despite this, capturing the heterogeneity of microbes, and that of the host responses they induce, has been challenging due to the bulk methods of nucleic acid and cellular analysis. One of the greatest recent advancements in our understanding of complex organisms has happened in the field of single-cell analysis through genomics, transcriptomics, and spatial resolution. While significantly advancing our understanding of host biology, these techniques have only recently been applied to microbial systems to shed light on their diversity as well as interactions with host cells in both commensal and pathogenic contexts. In this review, we highlight emerging technologies that are poised to provide key insights into understanding how microbe heterogeneity can be studied. We then take a detailed look into how host single-cell analysis has uncovered the impact of microbes on host heterogeneity and the effect of host biology on microorganisms. Most of these insights would have been challenging, and in some cases impossible, without the advent of single-cell analysis, suggesting the importance of the single-cell paradigm for progressing the microbiology field forward through a host-microbiome perspective and applying these insights to better understand and treat human disease.

Keywords: genomics; host-microbiome interaction; microbial heterogeneity; microbiome; single-cell sequencing; technology.

Figure 1

Single-cell characterization techniques for microbes and host cells involved in microbial interactions. Microbes can be studied through a variety of single-cell genomics, spatial characterization, and combined spatial genomic techniques. (A) Microbial split-pool ligation transcriptomics (microSPLiT) leverages multiple rounds of cell pooling and random splitting to uniquely barcode cDNA by cell of origin, leading to unbiased capture of RNA expression profiles and bypassing a requirement for single cell isolation (Kuchina et al., 2019). (B) Single amplified genome (SAG) gel sequencing involves single bacterial cell isolation via microfluidic droplets, two rounds of parallel multiple displacement amplification (MDA), and multiplex single-cell genome sequencing (Chijiiwa et al., 2020). (C) The combination of spatial and genomic resolution is leveraged in metagenomic plot sampling by sequencing (MaPS-seq) (Sheth et al., 2019). Input microbiome samples are fixed in a gel matrix and cryofractured to yield spatial clusters, which can be encapsulated by barcoded beads and subjected to 16S rRNA amplification and deep sequencing. (D) The tunable promoter technology allows for generation of promoters with expression levels across a broad range. This can be applied to create species-specific fluorescence signatures to visualize strain-level distinction of bacterial cells in vivo (Whitaker et al., 2017). (E) Highly phylogenetic resolution fluorescence in-situ hybridization (HiPR-FISH) relies on a binary system of taxa barcoding based on hybridization of up to 10 distinct fluorophores (Shi et al., 2019). The barcode spectra are decoded via a machine-learning classifier to allow for taxa identification and visualization. Host cells can be studied through in vivo and ex vivo mechanism to understand cell heterogeneity in the context of microbial influences. (F) A variety of host cells can be studied through single-cell RNA-seq (scRNA-seq) of cells from model organisms with varying degrees of microbiota alteration (Gury-BenAri et al., ; Kang et al., 2020). (G) Host immune cells subjected to pathogens can be sorted by cell outcomes and characterized by scRNA-seq to understand host heterogeneity in the context of pathogenic microbes (Avraham et al., ; Saliba et al., 2016). (H) Human peripheral blood mononuclear cells (PBMC) can be studied in response to pathogenic microbes to generate predictive models of disease outcomes for patients (Bossel Ben-Moshe et al., 2019). (I) The intestinal epithelium is a classic example of a host-microbiota interface. Single-cell analysis of microbial and host cells offers insight into their biological heterogeneity as well as the influence of each organism on adaptive cellular responses by the other.