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.
Highlights
Microbial organisms are the predominant life form inhabiting our planet, with approximately 1030 cells of bacteria and archaea estimated to exist on Earth
One study in particular performed single-cell RNA sequencing on colon macrophages of germfree (GF) and specific pathogen-free (SPF) mice (Kang et al, 2020)
Single microbial cells can be analyzed with high resolution through a variety of modalities (Figures 1A–E), many of which have been adapted from eukaryotic applications and optimized for microbial use
Summary
Microbial organisms are the predominant life form inhabiting our planet, with approximately 1030 cells of bacteria and archaea estimated to exist on Earth. One such technique, termed SPLiT-Seq, involves combinatorial barcoding of RNA and has yielded novel insights into bacterial transcriptomics at the single-cell level. Another technique that has recently been applied to microbial analysis is Single Amplified Genome (SAG) sequencing (Chijiiwa et al, 2020; Figure 1B).
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