M20 Genomics has introduced VITA Single-Cell Transcriptome Platform for both cultured bacteria and gut microbiome samples, opening new avenues and providing deep insights into prokaryotic research. Drawing from valuable user feedback and experiences, we’ve complied practical insights to help streamline the preprocessing of bacteria samples and formal experimental workflows. We hope these tips will enhance both efficiency and reliability when using VITA products. Tips for Sample Processing Tip 1: Use the same method for sample fixation. There are several effective methods for fixing bacterial samples, each suitable for different experimental conditions and sample characteristics. When selecting a fixation method, it is important to consider these factors. To ensure consistency and comparability of result, it is recommended to use the same fixation method for all samples within a single project. Tip 2: Minimize the sample loss for single bacterium samples. If the sample size is small in cultured single-bacterium samples, it is recommended to increase the centrifugation time during fixation to reduce sample loss. Tip 3: Remove impurities in gut microbiome samples. For gut microbiome samples like feces, impurities can be removed by centrifugation after fixation. The precipitate represents the impurities, which should be discarded, while the supernatant should be retained…

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…

Since its launch in 2023, the VITA single-cell transcriptome solution for formalin-fixed paraffin-embedded (FFPE) samples has helped numerous research teams overcome significant challenges previously associated with single-cell transcriptome studies using FFPE samples. Drawing from invaluable user feedback, we have continuously refined our protocols to enhance user experience and optimize outcomes. In this article, we summarize key tips and insights for users of the VITA single-cell transcriptome solution for FFPE samples. These essential practical insights and tips aim to streamline FFPE sample preparation and processing on the VITA platform, helping researchers achieve smoother and more efficient workflows, and high-quality single-cell transcriptome data. I. Tips for FFPE Sample Preparation Tip 1: Refine FFPE Tissue Roll Thickness. For optimal results, use FFPE tissue rolls with a thickness between 10 and 20 μm. Rolls thinner than 10 μm can lead to increased nuclear fragmentation, while rolls thicker than 20 μm may hinder reagent penetration due to the density of the tissue. Tip 2: Avoid Using FFPE Block Edges. Avoid selecting FFPE rolls from the edges of the block, as prolonged air exposure and reduced tissue content in these areas can compromise sample quality and integrity. Tip 3: Adjust Sample Volume. Ensure that the tissue…

Bacterial infections are on the rise, presenting increasingly complex challenges to human health. The mechanisms of infection often involve complex interactions between various species. The synergistic interactions within and between bacterial populations can enhance pathogenicity, antibiotic resistance, and evasion of host immune responses. Understanding how different bacterial species interact within these mixed populations is crucial for developing preventive stategies and treatments for infections and to combat cirtical phenomena such as antibiotic resitance. In 2022, M20 Genomics introduced VITApilote MscRNA-seq, a revolutionary technology in high-throughput single-species single-bacterium transcriptome analysis. By leveraging random primers for RNA capture, this innovative platform not only enables precise single-cell transcriptome profiling across a wide spectrum of bacterial species—such as Escherichia coli, Acinetobacter baumannii, Streptococcus pneumoniae, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Lactobacillus, and Clostridium difficile—but also extends its application to mixed bacterial samples. Unlike traditional methods such as bulk RNA-seq, which provide averaged data across samples, VITApilote MscRNA-seq offers single-cell resolution. This capability reveals the functional and phenotypic heterogeneity within mixed bacterial populations. By uncovering the intricate functional states and interations, researchers can unravel mechanisms of pathogenicity, identify cooperative or competitive behaviors, and understand how antibiotic resistance develops across different cells. Figure 1: VITA MscRNA-seq product…

Cardiovascular diseases (CVDs) are the leading cause of death globally, claiming 17.9 million lives annually according to the WHO[1]. CVDs include coronary heart disease, cerebrovascular disease, rheumatic heart disease, and other heart and blood vessel disorders. Major risk factors include hypertension, high cholesterol, smoking, diabetes, and obesity. In the past decade, the gut microbiome—the complex environment of our intestines—has emerged as another significant factor in CVD pathogenesis. This microbial environment both responds to and influences cardiovascular risk factors, producing components that can impact the host's cardiovascular health in diverse ways  (Figure 1). Figure 1: Gut dysbiosis is linked to endogenous and exogenous risk factors, the latter related to several systemic inflammatory and metabolic conditions [2]. The Association of the Gut Microbiota Composition and CVDs The pivotal connection between the gut microbiome and cardiovascular disease (CVD) has been a focus of extensive research efforts. A recent study demonstrated that an elevated abundance of Streptococcus spp and other species typically found in the oral cavity is associated with coronary atherosclerosis and systemic inflammation markers (Figure 2)[3]. Figure 2: Associations between coronary artery calcium score–associated gut species and alternate measurements of atherosclerosis and markers of inflammation and infection [3]. Another study reported decreased…

World Digestive Health Day (WDHD), established by the World Gastroenterology Organisation (WGO), aims to raise awareness about the prevention, diagnosis, management, and treatment of digestive diseases. Each year, May 29th marks the beginning of a global campaign addressing a critical issue related to digestive health. This year's theme, "Your Digestive Health: Make It A Priority," underscores the vital importance of maintaining digestive wellness. Figure 1: WDHD 2024’ theme "Your Digestive Health: Make it A Priority". Digestive health is fundamental to overall well-being, encompassing nutrient absorption, hormone regulation, detoxification, and mental health. Fundamental to these vital functions is the digestive system, a network of various organs. In recent years, the gut microbiome has emerged as a critical component of this system. Often referred to as the "hidden organ," it plays a significant role in shaping digestive health.   The Gut Microbiome: A Central Player in Digestive Health A balanced gut microbiome, or symbiosis, is characterized by a diverse and stable microbial community. Conversely, an imbalanced gut microbiome, or dysbiosis, occurs when this microbial equilibrium is disrupted, often characterized by reduced microbial diversity and the overgrowth of harmful microbes. Dysbiosis of the gut microbiota is linked to a wide range of diseases, with…