World Digestive Health Day: Advancing Gut Microbiome Research with M20
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 particularly significant impacts on digestive health. It is prominently associated with inflammatory bowel disease (IBD) and colorectal cancer, highlighting its critical role in conditions directly affecting the gastrointestinal system. Dysbiosis also influences energy homeostasis, contributing to obesity, insulin resistance, and diabetes. Beyond digestive health, it affects cardiovascular health by altering lipid metabolism and promoting inflammation, which increases the risk of atherosclerosis. Additionally, certain microbial patterns are linked to neurological conditions.
Balancing Digesitive Health and Disease through the Gut Microbiome
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 (Figure 2), with particularly significant impacts on digestive health. It is prominently associated with inflammatory bowel disease (IBD) and colorectal cancer, highlighting its critical role in conditions directly affecting the gastrointestinal system. Dysbiosis also influences energy homeostasis, contributing to obesity, insulin resistance, and diabetes. Beyond digestive health, it affects cardiovascular health by altering lipid metabolism and promoting inflammation, which increases the risk of atherosclerosis. Additionally, certain microbial patterns are linked to neurological conditions.
Figure 2: Diseases associated with microbiome dysbiosis [1].
With the growing understanding of the microbiota’s impact on human health, the potential for treating diseases by manipulating the microbiome has garnered significant attention. Diet, along with a healthy lifestyle, is considered the main regulator of gut microbiota. However, various strategies targeting the gut microbiota are being increasingly explored, aiming to ultimately develop personalized treatment and prevention strategies (Figure 3).
Figure 3: Potential strategies to modify gut microbiota for disease prevention and treatment [1].
Despite significant advancements, considerable gaps remain in our understanding of the gut microbiome. Current research methodologies often lack the precision and sensitivity required to analyze the heterogeneity and dynamics of this complex community. This highlights the urgent need for more advanced technologies to achieve a comprehensive understanding of the gut microbiome and to develop effective prevention and treatment strategies that can contribute to maintaining and improving digestive health.
Advances in Gut Microbiota Analysis
Characterizing gut microbiota and their significant functions requires analysis at the strain level. However, current methods like metatranscriptomics and microarrays provide only averaged population data, obscuring individual strain dynamics and heterogeneity. While flow cytometry enables functional analysis at the cellular level, its limited scope to specific proteins fails to fully capture the microbiome's complexity.
Innovative technologies such as single-cell RNA sequencing (scRNA-seq) provide unmatched precision in analyzing functional heterogeneity at the single-cell level. However, applying scRNA-seq to dissect the complex microbial communities presents significant challenges. Although some platforms are established for bacterial samples, they require cultured bacteria and are only applicable to well-characterized taxa. This limitation has so far restricted the effectiveness in exploring the diverse communities of the human gut microbiome with scRNA-seq.
In November 2023, we introduced VITA GutMicrobiome, a pioneering single-bacterium transcriptome platform designed specifically for gut microbiome samples. This cutting-edge solution enables precise barcoding of individual bacteria, significantly enhancing the efficiency and accuracy of transcriptome analysis. By eliminating the need for cultivation and effectively analyzing a wide range of taxa, VITA GutMicrobiome offers a significant advantage in resolving functional heterogeneity and interactions among gut microbiota, making it a powerful analytical tool of unmatched resolution.
Figure 4: VITA GutMicrobiome product.
Revealing Heterogeneity within the Human Gut Microbiome with VITA GutMicrobiome
A research group at Zhejiang University has harnessed the groundbreaking capabilities of VITA GutMicrobiome (referred to as "smRandom-seq2" in the research article) to conduct an extensive study on human gut microbiome [2]. This research, recently published in the esteemed journal Protein & Cell, has highlighted VITA GutMicrobiome's unparalleled ability to uncover functional heterogeneity and intricate interactions within complex microbial communities.
This study investigated transcriptome profiles of single bacteria in a fecal sample from a healthy human donor, detecting a total of 8,478 cells and identifying 98 species. Among these, 15 genera exhibited abundances higher than 1%. Uniform Manifold Approximation and Projection (UMAP) analysis and taxonomic annotation revealed nine distinct clusters that were assigned to various genera (Figure 5A-B).
Figure 5: Analysis of bacterial genera, species, and gene expression in a human gut microbiome sample with VITA GutMicrobiome.
Within the genus Prevotella, 11 species were identified, with P. copri (79%) and P. sp900767615 (7.2%) being dominant. In the genus Roseburia, three species were identified: R. hominis (36%), R. intestinalis (18%), and R. sp900552665 (46%).
Analysis of differentially expressed genes between species within the same genera revealed insights into functional heterogeneity. In Prevotella sp900767615, genes related to adaptive cellular responses were upregulated. In Roseburia, the flagellated species R. hominis showed high expression of motility-related genes, while R. intestinalis exhibited upregulation of genes associated with adaptive-response sensory mechanisms and multidrug resistance.
These findings underscore the capability of VITA GutMicrobiome to identify bacterial species and uncover functional heterogeneity in complex microbial communities.
Deciphering Functional Heterogeneity on the Subspecies Level
Another highly abundant genus identified was Phascolarctobacterium, with all bacteria in this genus found in this sample being classified as the species P. succinatutens. Unsupervised clustering of bacteria in this species revealed three distinct subpopulations (Figure 6A).
Figure 6: Analysis of functional heterogeneity in supopulations of Phascolarctobacterium succinatutens in a human gut microbiome with VITA Gut Microbiome.
Subpopulation 1 exhibited elevated expression of genes related to mobile genetic elements (MGE) (Figure 6B), which are known to promote antibiotic resistance. Gene expression co-occurrence analysis of MGE genes and multidrug resistance genes revealed a significant correlation between their expression levels (Figure 6C). Subpopulation 2 showed elevated expression of genes involved in the succinate pathway (Figure 6B), indicating a greater capacity for chemical energy conversion via this pathway (Figure 6D).
These insights into intra-species adaptive strategy heterogeneity within P. succinatutens, highlighting the capability of VITA GutMicrobiome to provide unprecedented insights at the subspecies level.
Host-Phage Activity Associations in the Human Gut Microbiome
Bacteriophages play crucial roles in the human gut microbiome. Leveraging the advanced capabilities of VITA GutMicrobiome, the study obtained data on bacteria and their associated phages simultaneously. This capability facilitated the detection of 15 to 25 phages per bacterium across various genera (Figure 7A).
Figure 7: Analysis of bacterial host-phage transcriptional activity associations in different genus in the human gut microbiome with VITA Gut Microbiome.
Clustering bacterial cells based on both phage and bacterial data revealed distinct clusters highly corresponding to the nine major genera. Remarkably, all 180 phage genomes could be reliably mapped to their corresponding bacterial reference genomes, demonstrating accurate relationship prediction.
In total, the study identified 373 host-phage relationships, with 325 newly discovered and 48 previously predicted relationships. The significant differences in phage-related gene expression levels among genera highlighted the unique characteristics and capabilities of phage-specific infections.
Using phage sequences at the species level, cell clustering and taxonomic annotation maintained excellent consistency, underscoring the capability of VITA GutMicrobiome to deliver in-depth insights at the species level and the robustness of our analytical methods.
Figure 8: Host-phage transcriptional relationship at the species level.
This study showcases the exceptional capabilities of VITA GutMicrobiome in providing unprecedented insights into the gut microbiota. By revealing the functional heterogeneity and complex interactions in the gut microbiome, researchers are now equipped to precisely understand their roles in digestive health.
Enhancing Gut Health Research with VITA GutMicrobiome
Digestive health is a crucial aspect of overall well-being. This year's World Digestive Health Day motto, "Your Digestive Health: Make It A Priority," underscores the importance of maintaining individual digestive health and advancing research to uncover the complex mechanisms and connections within our systems. At M20 Genomics, we are dedicated to supporting these efforts with our cutting-edge single-cell technologies, such as the VITA GutMicrobiome product.
VITA GutMicrobiome provides unparalleled insights into the functional and phenotypic heterogeneity of complex microbial communities at the single-cell level. These insights are crucial for revealing the detailed interactions and mechanisms among bacteria, their hosts, and associated phages. This advanced knowledge is vital for developing innovative prevention and treatment strategies that enhance digestive health.
Join us in revolutionizing gut health research with the power of VITA GutMicrobiome. Together, we can harness next-generation single-cell technologies to explore the gut microbiome, advancing our understanding and paving the way for a healthier future. Let’s make digestive health a priority, starting today.
*For further inquiries or to learn more about our VITA GutMicrobiome, please feel free to contact us at info@m20genomics.com. We welcome the opportunity to collaborate and contribute to the collective efforts in comprehensively understanding the gut microbiome.
References
[1] Hou, K., Wu, Z.X., Chen, X.Y., et al. (2022). Microbiota in health and diseases. Signal Transduction and Targeted Therapy, 7, 135.
[2] Shen, Y., Qian, Q., Ding, L., Qu, W., Zhang, T., Song, M., Huang, Y., Wang, M., Xu, Z., Chen, J., Dong, L., Chen, H., Shen, E., Zheng, S., Chen, Y., Liu, J., Fan, L., Wang, Y. (2024). High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome. Protein & Cell. pwae027.
