With the VITA Single-Cell Transcriptome Platform, M20 Genomics has introduced a variety of high-throughput single-bacterial transcriptome kits offering new avenues and deeper insights in prokaryotic research. In this article, we will focus on practical tips for cDNA amplification to streamline workflows and improve experimental outcomes. We hope these guidelines help users achieve smoother and more efficient use of the VITA platform. Tip 1: Achieve complete cDNA recovery Incomplete mixture or not enough PFO during cDNA recovery can result in reduced cell yield. To address this, first invert the tube gently but thoroughly to mix the contents. Then, use a mini centrifuge to briefly spin down the mixture. This step helps separate the aqueous phase more effectively. Ensure that the aqueous phase is clearly separated before proceeding to avoid cross-contamination with oil residues. Tip 2: Minimize sample loss during cDNA recovery For maximum recovery of the aqueous phase after demulsification, carefully transfer the upper aqueous layer to a spin column without disturbing the oil layer and centrifuge for 30 seconds using a mini centrifuge to collect the filtrate. If residual liquid remains in the column, repeat centrifugation briefly to ensure complete recovery. Be sure to avoid excessive handling or delays during…

As we step into 2025, Nature has highlighted seven emerging technologies that are set to shape the future of science and innovation. Many of these innovations will have profound implications for the biotechnology sector, particularly in areas such as disease treatment, environmental sustainability, and cellular analysis1. Below is an overview of the most promising advancements: ‘Self-driving’ laboratories: The integration of AI and robotics heralds a new era in "chemical universe exploration." Big opportunities for CAR T cells: Revolutionizing cancer treatment with the potential to cure autoimmune diseases. Bioremediation: Utilizing microbes as "pollution digesters" for environmental cleanup. Foundation models for biology: AI-driven "virtual cells" that are poised to transform biology. Sustainable Urban Cooling: A "super-cold armor" to mitigate the effects of urban heat islands. Single-cell microbial analysis: Unlocking the "genetic black box" of microbiomes. Photonic computing for AI: AI’s "light-speed engine" advancing computational capabilities. Among these, single-cell sequencing stands out as a key technology driving forward the next frontier in microbial research. The Promise of Single-Cell Sequencing in Microbial Research Even within populations of bacteria with the same genetic background, phenotypic and functional heterogeneity can emerge. In more complex and diverse microbial communities, such heterogeneity is further amplified due to factors…

The high-throughput single-cell transcriptome products developed by M20 Genomics have gained widespread recognition for providing deeper insights into bacterial transcriptomes at the single-cell resolution. With these innovative products, researchers can explore microbial heterogeneity and gene expression with remarkable precision. In this article, we will introduce some practical tips to streamline workflows and improve experimental outcomes for the critical step of cell barcoding. We hope that these recommendations, drawing on valuable user feedback, can improve the user experience and experimental outcomes. Tip 1: Optimize cell concentration for barcoding Before loading the sample into the instrument, it is essential to perform cell counting under a microscope. To do this, prepare a small aliquot of bacterial suspension and stain with propidium iodide (PI). Next, transfer the stained suspension to a glass slide and count the cells under a microscope at 200x magnification. Then adjust the cell concentration to ensure there are 20–100 bacteria per field of view, which is crucial for the subsequent steps. Tip 2: Avoid bubbles during barcode bead collection When collecting barcode beads, align the pipette tip with the center bottom of the tube and aspirate slowly to avoid air bubbles. In addition, keep the pipette tip suspended approximately 2–3…

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…

Singapore, October 2024 - In life sciences research, complex diseases such as cancer, characterized by pronounced spatial heterogeneity within tissues, remain a central focus for spatial transcriptomics applications. Conventional spatial transcriptome platforms, however, typically require fresh-frozen samples and are constrained in their ability to analyze clinical samples like formalin-fixed paraffin embedded (FFPE) tissue. Furthermore, these platforms primarily capture only mRNA, thus omitting the abundant non-coding RNAs present in the transcriptome. Such limitations restrict our capacity to fully understand disease mechanisms. To overcome these technical challenges, in October 2023, we launched M20 Spatial, the world’s first random-priming-based comprehensive spatial transcriptome technology, compatible with all sample types, including FFPE (https://www.m20genomics.com/1085.html ). M20 Spatial captures both mRNA and non-coding RNA, ushering in a new era of multi-species, whole-sample, full-transcriptome, and full-length sequence coverage. Last week, we announced a major upgrade to M20 Spatial, with significant enhancements in sensitivity, resolution, and analytical depth (https://www.m20genomics.com/3818.html). We further evaluate the upgraded M20 Spatial on clinical FFPE tumor samples, confirming its exceptional performance in clinical research and its valuable contributions to understanding tumor heterogeneity. Below, we present the latest data from paired FFPE samples of human breast cancer tissue and peritumoral tissue: High-Sensitivity Detection of Gene Expression…

In 1957, Francis Crick introduced the central dogma of molecular biology, stating that information flows from DNA to RNA to proteins [1-2]. This concept laid the foundation for understanding gene expression and regulation. Initially, the discovery that less than 2% of the human genome codes for proteins led to the rest being labeled as "junk DNA." However, much of this DNA is transcribed into non-coding RNAs. Among these, long non-coding RNAs (lncRNAs) are crucial regulators of gene expression.   LncRNAs: Crucial Regulators of Gene Expression LncRNAs, non-coding transcripts of more than 200 nucleotides, regulate gene expression by organizing chromatin, modifying histones, recruiting transcription factors, and stabilizing mRNA. Additionally, lncRNAs can influence gene expression in neighboring cells via extracellular vesicles (Figure 1). Figure 1: Mechanisms of lncRNAs in gene expression regulation [3]. LncRNAs influence various physiological processes, including development and immune responses. For instance, lncRNA TUNA is essential for neural differentiation in embryonic stem cells [4]. In the immune system, lncRNAs like lincRNA-Cox2 modulate immune cell differentiation, activation, and function [5]. Moreover, lncRNAs play crucial roles in disease development, such as cancer progression. HOTAIR, an oncogenic lncRNA, is overexpressed in various cancers, promoting metastasis, proliferation, invasion, and resistance to apoptosis [6].   The Current State and Frontiers of lncRNA Analysis Given…

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…

Single-cell RNA sequencing (scRNA-seq) is transforming our comprehension of cellular mechanisms, and has become indispensable in clinical studies over the past decades [1-4]. However, the procurement of fresh samples, a commonly held requirement for most scRNA-Seq technologies, comes with significant challenges for clinical studies. Formalin-fixed and paraffin-embedded (FFPE) samples, commonly used in clinical settings for long-term storage, have been largely incompatible with conventional single-cell transcriptome methods due to the extensive RNA cross-linking and fragmentation caused by the fixation process. As a result, the majority of single-cell technologies have been unable to effectively analyze FFPE samples, limiting researchers' ability to leverage the wealth of clinical specimens available for study. The recent development of the novel single-cell transcriptome technology M20 Seq, alongside the VITA single-cell transcriptome product series, which are compatible with FFPE samples, provides a groundbreaking solution. This significant advancement allows researchers to leverage existing clinical archives for biomedical research, expanding the scope of clinical studies and enhancing our understanding of disease mechanisms.   FFPE Samples: The Hidden Treasure FFPE samples have long served as a critical resource in clinical studies and diagnostics, widely collected and stored in clinical settings. Their long-term preservation capacity and widespread availability make them indispensable for retrospective and longitudinal studies…

The environment is essential for our health and well-being, providing essential resources such as clean air, water, and fertile soil, while sustaining the ecological balance. Since its inception in 1970, Earth Day has served as an annual reminder of our obligation to protect our planet and has mobilized global efforts to address environmental issues. This year's theme, 'Planet vs. Plastic,' casts a spotlight on one of the most pressing environmental challenges of our century. The forecast surge in plastic production, from 9.2 billion tons between 1950 and 2017 to 34 billion tons by 2050, underscores the magnitude of the challenge[1]. Plastic poses a significant environmental threat throughout its lifecycle, with its production alone accounting for 3.4% of global greenhouse gas emissions in 2019[2]. Additionally, the release of harmful additives from plastics, such as bisphenol A (BPA) and phthalates, contaminates ecosystems and poses health risks. Once discarded, plastic waste persists for hundreds or thousands of years, accumulating in landfills and infiltrating ecosystems worldwide. The widespread use of plastics has led to a staggering increase in global annual plastic waste, doubling from 156 million tons in 2000 to 353 million tons in 2019. Projections indicate that this figure could triple by 2060…

Pathological research assays, including histological, IHC, and in situ genomics analyses, frequently utilize formalin-fixed paraffin-embedded (FFPE) samples. Biorepositories and pathology departments worldwide house millions of these samples, offering an extensive collection of readily available specimens for in-depth analysis. However, despite their prevalence, FFPE samples pose challenges due to molecular cross-linking and nucleic acid degradation during preservation. Single-cell RNA Sequencing (scRNA-seq) on clinical FFPE specimens promises breakthroughs in precision diagnostics, treatment strategies, and prognostic insights for human diseases. However, challenges persist in isolating intact cells or nuclei and capturing RNA from FFPE tissues. Until today, few commercial platforms are available that enable scRNA-seq in these precious but challenging samples. With the introduction of M20 VITA technology in August 2022, alongside our VITA product series, we've provided a solution to access the valuable information stored in these samples. Using random primers, M20 VITA overcomes the boundaries of  other scRNA-seq technologies that mostly rely on poly(A) tails for RNA capture. As these structures are prone to chemical modification and degradation, the capabilities to obtain quality data from FFPE samples using technologies based on poly(A) capture are limited. In parallel, 10x Genomics introduced the Chromium Single Cell Gene Expression Flex  (from here on called 10x…

In 1946, a historic gathering of 61 nations convened heralding to establish the World Health Organization (WHO), marking a pivotal moment in global health governance. Just two years later, the WHO officially came into existence on April 7th, 1948, marking a monumental leap in international efforts to combat global health challenges. Since 1950, April 7th has been recognized as World Health Day, serving as an annual reminder of our collective commitment to prioritize global health and tackling the most urgent health issues of our time. The theme for World Health Day 2024, "My Health, My Right," emphasizes the urgent need to ensure equitable access to healthcare for all individuals, irrespective of socio-economic background or geographic location. This powerful call to action urges us all to uphold and defense the right to health for every individual. As we strive to extend healthcare access to everyone, we're faced with the daunting challenge of Antimicrobial Resistance (AMR)—one of the foremost threats to public health in the 21st century. A study published in The Lancet highlighted the devastating impact of AMR, with approximately 1.27 million deaths directly attributed to antimicrobial resistant infections in 2019, and an additional 4.95 million deaths indirectly linked to this phenomenon[1]. The WHO's predictive models suggest a worrisome scenario, forecasting that, fatalities…

In the rapidly evolving landscape of single-cell transcriptome analysis, precision and accuracy are paramount. Researchers worldwide are increasingly turning to innovative technologies to dissect the complex cellular landscape with unprecedented resolution. Among these advancements, M20 Genomics distinguishes itself with its pioneering VITA Single-Cell Full-Length Transcriptome Sequencing Platform. In August 2022, M20 Genomics unveiled M20 Seq along with the VITA Single-Cell Full-Length Transcriptome Sequencing Platform, redefining the boundaries of single-cell transcriptomics. The VITA platform offers unparalleled features, including comprehensive compatibility across various species and sample types, coupled with full transcriptome capture, thereby greatly expanding the scope of single-cell technology and enabling researchers to explore uncharted territories of cellular heterogeneity. Diverging from poly(A)-based single-cell transcriptome technologies, the VITA platform operates on the principle of random primers. While this unique approach enhances single-cell transcriptome analysis, it poses potential challenges in cell type annotation. The divergence from traditional poly(A)-based single-cell transcriptome necessitates optimized annotation tools tailored to the distinct characteristics of random primer-based single-cell transcriptome data.    Navigating Complexity: Equipped with VITA CytBase and VITA Biscuit To address this challenge, we have developed VITA CytBase, a database meticulously designed for precise annotation of cell types using data derived from the VITA platform. VITA CytBase offers a comprehensive suite of annotation capabilities…

Over the last two decades, the gut microbiome has emerged as a prominent research field, revealing its pivotal role in human physiology and its significant association with various diseases [1-3]. However, our understanding of the intricate functional mechanisms within the gut microbiome remains incomplete and current applied methodologies often rely on bulked analyses, offering only insights based on averaged data and lack sensitivity to detect nuanced dynamics and diverse functions present within complex microbial communities. In November 2023, we launched VITA GutMicrobiome, our pioneering single-bacterial transcriptome product designed for the gut microbiome. Our cutting-edge  solution enables accurate barcoding of each individual bacterium in gut microbiome samples, improving the efficiency and accuracy of  of bacterial transcriptome analysis by clearly identifying the cellular origin of each sequenced fragment and eliminating the need for culture processes. Moreover, the high-resolution data for single bacterial transcriptomes offer an advantage in resolving functional heterogeneity even within homogeneous populations, serving as a powerful analytical tool at the single-cell level. Here, we showcase the exceptional performance of our VITA GutMicrobiome product through single-bacteria transcriptome analysis on a fecal sample from a healthy human individual. Practical Application and Performance Assessment of VITA GutMicrobiome The workflow commenced with the preparation…