10 Things You Didn’t Know About the Gut Microbiome

1. Your microbiome may weigh around 2 kilograms 

That gut microbe community isn't just vast—it has substance. There are approximately 100 trillion microbes in your gut, across as many as 5,000 species, collectively weighing about 2 kg—roughly the weight of a large paperback novel on your system!  

2. Your microbiome may act like a fingerprint 

Just as no two fingerprints are identical, your gut microbiome is uniquely yours. While humans share many of the same microbial species, the exact combination, abundance, and strain variations differ from person to person. This individuality can persist for years, making your microbiome a kind of biological ID card. It also explains why certain diets, probiotics, or treatments work well for some people but not others. 

3. Modern sequencing unlocked hidden microbial worlds 

Before the mid-2000s, microbiome research was limited to culturing microbes in the lab—a method that could only capture a fraction of gut species, since most can’t survive outside the anaerobic environment of the intestines. That meant we were effectively blind to the majority of our microbial partners. The arrival of next-generation sequencing (NGS), and later metagenomics, changed everything. Now, scientists can identify microbes directly from DNA in stool samples, including rare and previously unknown species. This has opened the door to discovering new health associations, tracking microbiome shifts over time, and developing precision tools—like the GutID test—that can detect and classify microbes down to the strain level. 

4. Microbes help train your immune system 

From infancy, gut microbes act as instructors for your immune system, teaching it to distinguish between harmless substances and real threats. This training helps prevent overreactions that can lead to allergies or autoimmune conditions. A diverse microbiome is especially important—reduced microbial exposure in early life has been linked to higher rates of asthma, eczema, and other immune-related disorders. 

5. Your microbiome influences your mood and behavior 

Emerging research shows a strong connection between gut microbes and the brain, known as the gut-brain axis. Gut bacteria produce neurotransmitters like serotonin and GABA, which can affect mood, anxiety, and cognitive function. This means your gut health may play a bigger role in mental wellness than previously thought. 

6. Your microbiome starts before birth—maybe 

Once thought sterile before birth, the gut may begin colonizing in utero, as suggested by the presence of microbes in meconium. After birth, factors like delivery method and feeding (breast vs. formula) shape your microbiome’s development until it stabilizes around ages 2–3.  

7. Antibiotics early in life can have long-term effects 

When used during infancy or childhood, antibiotics can shift your gut's bacterial profile toward one linked to obesity, metabolic dysfunction, or autoimmune issues—similar to how low-dose antibiotics promote growth in livestock.  

8. Even “normal” microbiomes include potentially harmful bacteria 

Microbiome is not synonymous with “good.” It commonly includes species like E. coli and Enterococci, blurring the line between beneficial and pathogenic.  

9. Gut microbes are biochemical powerhouses 

They harvest energy from food, produce vital nutrients like vitamin K, manufacture neurotransmitters such as serotonin, and help balance your immune system and metabolism.