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Feb 2, 2024

Unveiling the Microscopic World Within: Exploring the Urinary Microbiome of Healthy Individuals



Your urinary system might not be the first thing that comes to mind when you think of the human microbiome, but it's a fascinating and vital part of it. Imagine a world so small that it's invisible to the naked eye yet has a profound impact on our health. We're delving into the microbial world of the urinary system, exploring how it differs between healthy men and women, and what factors might shape its composition. In this blog, we'll present highlights from a study of 212 participants utilizing MicroGenDX NGS technologies and RTL Genomics bio-consulting.  

To study the urinary microbiome, researchers employed next-generation sequencing (NGS) to characterize the bacteria found by their DNA. The analysis involved careful data curation, removing reagent contaminants, and ensuring that the findings were reliable. Researchers focused on identifying what factors influence the composition of the urinary microbiome. Researchers examined variables like gender, age, diet, and medication history. Using statistical methods, they identified that gender and recent antibiotic use significantly affected the numbers of unique bacteria reported. 


The Microbiome: Alpha and Beta Diversity 

To better understand the urinary microbiome, researchers used two common approaches for summarizing and studying the differences in microbiome communities: alpha diversity and beta diversity. There are multiple ways of summarizing each type of diversity metric. Alpha diversity can measure the unique number of entities (e.g., species) within a sample, their evenness, their genetic distinction, or any combination of the three. For this analysis, Hill1, a preferred metric due to its accounting of evenness and linear scaling, was used. Additionally, the number of observed species per sample was considered.  

  • Alpha diversity can tell us when there are broad changes in the numbers of bacteria found, but not necessarily when the types of bacteria are different. Beta diversity explores the differences in the types of bacteria observed among samples. To quantify this, each unique patient in a study is compared against every other patient to determine their proportions of shared and unique species. This results in what is known as a Bray-Curtis Dissimilarity distance and is what was used in the present study, leading to interesting results. Gender and antibiotic use within the previous 3 months were the most correlated to differences in healthy urine alpha diversity. 
  • Conversely, gender and age were found to be the most influential factor for differences in beta diversity, meaning that different major types of bacteria were found relating to these factors. 
  • Taxonomic classification revealed a rich diversity within the urinary microbiome, comprising 643 species, 307 genera, 129 families, 66 orders, 30 classes, and 13 phyla. 
  • Age was another factor under the microscope. While age did not significantly affect alpha diversity, it was found to influence the composition of the urinary microbiome. This suggests that our microbial landscape changes in consistent ways over time. 

Community State Types: Microbial Neighborhoods

Researchers delved into the concept of Community State Types (CSTs), an innovative methodology that categorizes microbiomes according to their compositional similarities. This cutting-edge approach provides a nuanced understanding of how microbiomes assemble into distinctive communities within the urinary system. These different types may correspond to beneficial or harmful interactions with us – the hosts!

By analyzing the intricate interplay between microbial species, CSTs offer profound insights into the underlying mechanisms shaping the complex ecosystem of the urinary microbiome. Through this exploration, researchers uncovered fascinating patterns of microbial co-occurrence and interaction, shedding light on the dynamic relationships that govern the assembly and stability of microbial communities. This groundbreaking research not only enhances our comprehension of the urinary microbiome but also lays the foundation for novel approaches to studying and modulating microbial ecosystems in health and disease.


Conclusion - Unraveling the Microbial Tapestry 

In a world that's usually invisible to us, researchers continue to unravel the intricate tapestry of the urinary microbiome. This ecosystem, composed of hundreds of species, is influenced by various factors, from gender to medication use. These barely discernable differences can have great impact on our health, as was recently reported by our collaborators in Liss et al, which found that sex-linked differences in the urinary microbiome may translate to increased risk for infection after urological procedures and thus preventative treatment should be tailored to these differences. These findings shed light on the importance of understanding the microbial world within us and how it impacts our health. 


The urinary microbiome may not be something we often think about, but it plays a significant role in our overall well-being. Understanding how it varies between genders, ages, and other factors helps us appreciate the complexity of our own bodies. This research offers a glimpse into the microbial world within us and its potential impact on our health. 


Note: This is from unpublished data 


Nicholas Sanford
Nicholas Sanford