We talk a lot about gut health these days. Probiotics, fiber, fermented foods. There’s a whole wellness industry dedicated to the ecosystem inside us. But here’s something most people don’t realize: even scientists are still figuring out how consistent our gut microbes really are. Do they change wildly day to day? Or do they stay mostly the same over time?
That’s the question Drs. Darya Moosavi and Meredith Hullar and their colleagues at Fred Hutch Cancer Center set out to answer. In a newly published study, the team followed 25 older adults from different ethnic backgrounds for two years. Every six months, participants collected stool samples and mailed them in. The goal was to understand whether a single gut microbiome sample can provide reliable information about long-term health, especially when studying complex diseases like cancer. If we want to use the microbiome as a tool in prevention, diagnosis or treatment, we first need to know how consistent those measurements really are.
To determine the stability of the microbiome, the team first needed a method to measure it. For this, they used a technique called metagenomic sequencing. Now, that might sound intimidating, but the concept is fairly straightforward. Metagenomics is a powerful technique that goes far beyond simply identifying which general types of bacteria are present in a sample. It uses the sequence of each microbe’s genetic sequence to identify it and its abundance. Metagenomics reads the entire genetic material of all the microbes in a sample—this means researchers can see not just who’s there, but what they’re capable of doing.
Overall, the gut microbiome turned out to be pretty stable. The mix of microbes—in terms of how many different kinds were there and how balanced they were—didn’t change all that much over time (within the same person). Some metrics, like “species richness”, stayed remarkably consistent from year to year. So, if someone had a diverse gut microbiome when the study started, they likely still did two years later. But when the team looked more closely at specific microbes, things got a little more nuanced. Some bacterial species were solid and predictable, showing up at steady levels in sample after sample. Others, however, were more variable Take a specific bug called Faecalibacterium prausnitzii, for example — this species showed up in almost every sample, but its abundance bounced all over the place. Thus, even a well-known gut resident can be a bit inconsistent.
And then there’s what the bacteria were genetically equipped to do. The team looked at the functional potential of the microbiome — the genes and metabolic pathways present in the DNA — involved in processes including breaking down carbohydrates or producing vitamins. While many core genes (those shared across most microbes) were pretty stable, the relative abundance of genes contributing to specific functions varied more. For example, the pathway for biotin production was relatively stable, while those involved in amino acid metabolism fluctuated more between time points.
One reason the gut microbiome manages to stay so stable is that many microbes can carry out the same functions —a concept known as functional redundancy. If one species dips in number, others with similar metabolic capabilities can pick up the slack, often because they access the same nutrients or produce overlapping metabolites. It’s like having several players who all know the same tune—even if one takes a break, the music doesn’t stop.
These findings have real implications for science and medicine. If a researcher wants to know whether someone has bacteria that can help fight inflammation, for example, one stool sample might give them a decent answer, but only for the most abundant or consistent bacteria. However, for detecting more subtle, variable microbial processes or transient taxa, sampling over time may be necessary to capture the full functional potential of the microbiome.
Fred Hutch/UW/Seattle Children’s Cancer Consortium member Dr. Johanna Lampe contributed to this work.
This work was supported by the National Institutes of Health and Fred Hutchinson Cancer Center.
Moosavi, D., Curtis, K. R., Randolph, T. W., Kahsai, O. J., Ammar, H., Lim, U., Cheng, I., Wilkens, L. R., Le Marchand, L., Lampe, J. W., & Hullar, M. A. J. (2025). Stability and Variability of the Human Fecal Microbiome Over Two Years in the Multiethnic Cohort Study: A Metagenomic Analysis. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 10.1158/1055-9965.EPI-24-1770. Advance online publication. https://doi.org/10.1158/1055-9965.EPI-24-1770
Science Spotlight writer Darya Moosavi is a postdoctoral research fellow within Johanna Lampe's research group at Fred Hutch. Darya studies the nuanced connections between diet, gut epithelium, and gut microbiome in relation to colorectal cancer using high-dimensional approaches.
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