Exploring Microbial World: Advances and Innovations in Single-Cell Technologies
Microorganisms are deeply intertwined with human life and the Earth's ecosystem, playing roles both fundamental and extraordinary. Increasing attention has been given to their impact in various fields, from health to sustainability. Reflecting this, Cell's 50th-anniversary special issue, “A Microbial Future”1, and Nature Microbiology's annual review, “A Year of Microbiology”2, highlighted key research directions in microbiology. These include complex microbes through integration across scales, antimicrobial resistance, and bacteria-phage/host interactions, among others.
Over the past year, advances in symbiosis and microbiome research have revealed the dynamic interactions between microbes, their hosts, and the environment. Notable findings include the microbiome's role in diet and its interaction with mammalian immune systems. The need for innovative solutions in infectious disease treatment and prevention is critical.
Developing new antimicrobial drugs and therapies, such as combining bacteriophage therapy with antibiotics, is key to combating antimicrobial resistance. Understanding how hosts respond to infections is also essential for discovering new treatment strategies, some of which rely on insights into pathogen-host co-evolution.
Additionally, fundamental microbial biology has been a major focus. Studies have explored how some bacteria depend on others for cell wall formation and the mechanisms behind bacterial flagella movement.
The advancement of research in these areas owes much to the application of novel technologies. Single-microbe transcriptome sequencing has been introduced into microbiology research recently and provides researchers with precise tools and fresh perspectives for microbiological studies. To date, this innovative technology has enabled breakthroughs across multiple fields, offering transformative insights into microbial functions and interactions.
Microbiomes: Unraveling Functional Heterogeneity
Functional heterogeneity within microbiomes has long intrigued researchers, yet traditional approaches have been inadequate for linking species with their specific functions. In May 2024, a study titled "Single-Cell Transcriptomics across 2,534 Microbial Species Reveals Functional Heterogeneity in the Rumen Microbiome"3 was published in Nature Microbiology. Researchers created an extensive single-cell transcriptome atlas of the rumen microbiome, encompassing 174,531 cells and 2,534 species grouped into 12 functional clusters using VITA GutMicrobiome products (Figure 1).
Figure 1. Schematic of the biological processes/structures of the 12 functional groups in rumen microbiome.
Additionally, a focused investigation into carbohydrate metabolism uncovered functional heterogeneity and cellular metabolic trajectories driven by biofilm formation genes in Bacteroides succiniciproducens. This work not only underscores the complexity of microbial ecosystems but also exemplifies how single-cell technologies can decode these intricate dynamics.
Antimicrobial Resistance: Insights with Single-Cell Precision
Antimicrobial resistance (AMR) is one of the most pressing challenges facing modern medicine, with the heterogeneity within microbial communities being a key factor in the emergence of resistance. The article "Droplet-based high-throughput single-microbe RNA sequencing by smRandom-seq"4 published in Nature Communications, demonstrates how single-cell transcriptome can reveal antibiotic response heterogeneity within microbial populations (Figure 2). This approach paves the way for the development of novel therapeutic strategies to combat AMR.
The smRandom-seq (also known as M20-seq) offers a high-throughput solution for single-microbe transcriptome profiling, enabling detailed exploration of microbial resistance, persistence, microbe-host interactions, and microbiome research. This technology is a powerful tool in understanding the complexities of microbial resistance, providing new avenues for discovery.
Figure 2. A. Schematic illustration of experiment design of ampicillin treatment on E.coli. B and C. UMAP projection of all the cells collected at the different time points, based on their gene expression colored by time points (B) or sub-clusters (C).
In line with these advancements, M20 Genomics has initiated the Klebsiella Action Project (KAP) in September 2024, dedicated to accelerating research and innovation to combat Klebsiella pneumoniae resistance and further enhancing our understanding of microbial pathogenesis.
Bacteria-Phage Interactions: A Dynamic Relationship
The complex interactions between bacteria and phages remain a major frontier in microbiological research. A recent study published in Protein & Cell, titled "High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in the human gut microbiome" 5employed the VITA platform to explore the transcriptome landscapes of phage-infected bacterial populations. In this groundbreaking study, the transcriptome of 29,742 single bacteria were profiled, identifying 329 species. The study also identified hundreds of novel host-phage activity associations, showing that most phage species are linked to specific bacterial genera. This research highlights the unique capabilities of VITA GutMicrobiome in uncovering specific host-phage interactions within complex microbial communities, providing a deeper understanding of the gut microbiome's impact on human health and disease.
Figure 3. Number of phages identified (up) and the proportion of reads aligned to the gut phage reference genomes in Gut Phage Database (down) in the cells from nine bacterial genera.
Bacteria-Host Interactions: Decoding Intracellular Dynamics
Understanding intracellular bacteria-host interactions is critical for studying infectious diseases. In the article “Hosts manipulate lifestyle switch and pathogenicity heterogeneity of opportunistic pathogens in the single-cell resolution”6 featured in eLife, scientists discovered that co-culturing Drosophila larvae with Serratia marcescens can trigger a lifestyle switch in the bacteria, transforming them from pathogenic to symbiotic.
Figure 4. A. mRNA gene counts per cell for S. marcescens alone, with force and with larvae. Each dot represents a bacterial cell of S. marcescens. B and C. Bacterial cell population (B) or subpopulations (C) based on differential gene expression. D. Mean expression levels of genes involved in ABC transporter, quorum sensing, secretion system, two-component system, LPS and peptidoglycan biosynthesis, and virulence-related genes in different subclusters. The shape of each dot indicates the proportion of cells in the cluster, while the color indicates the average activity normalized from 0% to 100% across all clusters.
Another article “High-Throughput Host–Microbe Single-Cell RNA Sequencing Reveals Ferroptosis-Associated Heterogeneity during Acinetobacter baumannii Infection” 7published Angewandte Chemie (International ed.) also highlights the power of VITA platform in exploring the intricate mechanisms behind microbial interactions and pathogenicity, offering new perspectives on the dynamic interplay between hosts and their microbiomes. Exploring the effects of Acinetobacter baumannii infection revealed ferroptosis-associated heterogeneity in THP-1 derived macrophages. Moreover, modulating ferroptosis with ferrostatin has been shown to enhance infection resistance, indicating its potential as a clinical target.
Figure 5. A. Schematic illustration of THP-1 cells infected by A. baumannii at different time points. B. THP-1 cells collected at different infection time points are clustered based on differential gene expression.
By leveraging VITA single-microbe transcriptome sequencing, the research delved deeply into the transcriptome heterogeneity regulated by the host, shedding new light on the mutualistic symbiotic relationships between hosts and pathogens.
The knowledge gained from fundamental microbiology research forms the cornerstone for translational approaches and applications. Despite their microscopic size, microbes make substantial contributions to science, and the progress made by researchers in this field is often both significant and surprising. For years, M20 Genomics has partnered with scientists to advance microbiological research. Since the launch of our VITA products, we have conducted single-cell transcriptome sequencing on over 5,000 microbial samples worldwide, driving meaningful progress across various fields.
In June 2024, our team had the honor of presenting the cutting-edge VITA platform for single-cell transcriptome profiling of microbial samples at ASM Microbe 2024, one of the most influential international conferences in microbiology. During the event, we engaged with numerous dedicated professionals, forging collaborations that promise to shape the future of microbial research.
Microorganisms play a crucial role in human health, influencing disease resistance and metabolism. By leveraging state-of-the-art technologies, we aim to deepen our understanding of microbial ecosystems and their impact on the human body. This knowledge will pave the way for new treatment strategies, preventative measures, and the full potential of the microbiome in improving human health.
Looking ahead, we are excited to continue collaborating with scientists to explore the vast microbial world, uncover its secrets, and drive even greater breakthroughs. We eagerly anticipate the discoveries that the coming year will bring.
Reference:
1. Cell, T. A microbial future. Cell 187, 5119–5120 (2024).
2. Communications, B. A year of microbiology. Nat. Microbiol. 9, 3079–3080 (2024).
3. Jia, M. et al. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat. Microbiol. 9, 1884–1898 (2024).
4. Xu, Z. et al. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq. Nat. Commun. 14, 1–12 (2023).
5. Shen, Y. et al. High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome. Protein Cell 1–16 (2024). doi:10.1093/procel/pwae027
6. Wang, Z. et al. Hosts manipulate lifestyle switch and pathogenicity heterogeneity of opportunistic pathogens in the single- cell resolution. 1–25 (2024).
7. Meng, H. et al. High-Throughput Host–Microbe Single-Cell RNA Sequencing Reveals Ferroptosis-Associated Heterogeneity during Acinetobacter baumannii Infection. Angew. Chemie - Int. Ed. 63, (2024).
