Our Unique Microbiome: Does One’s Health and Environment Disrupt It?


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“Individuals with Type 2 diabetes exhibited a less stable and less diverse microbiome.”

The human microbiome is a community of microorganisms that populate various parts of our body, such as the gut, skin, mouth, and nose. These microorganisms play crucial roles in maintaining our health by aiding digestion, modulating our immune system, and protecting against harmful pathogens. The balance and composition of these microbial communities are affected by numerous factors, including diet, environment, and genetics. Understanding the stability and dynamics of the microbiome across different body sites can provide insights into its role in health and disease.

The study titled Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease by Dr. Xin Zhou et al. from Stanford University, published in Cell Host & Microbe in 2024, delves into the complex relationships between the human microbiome and its host across different body areas. This research aims to understand how the microbiome’s stability and individuality are influenced by host factors and how these microbial communities interact with host metabolic states, particularly insulin resistance.

The longitudinal study involved 86 participants who were monitored over six years. Microbiome samples were collected from four body sites: stool, skin, oral cavity, and nasal passages. Microbes were analyzed using 16S RNA gene sequencing to identify and differentiate bacterial taxa. A unique feature of this study cohort was the multi-omics phenotyping of participants at each time point. Multiomics phenotyping refers to multiple complementary analyses including untargeted proteomics (measuring 302 proteins), untargeted metabolomics (measuring 724 metabolic features), targeted lipidomics (measuring 846 annotated lipids), and 62 targeted cytokine and growth factor measurements. These analyses were accompanied by assessment of 51 clinical markers, including C-reactive protein (CRP), fasting glucose, hemoglobin A1C (HbA1C), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) from plasma samples.

“The personal microbiome is the most stable.”

The researchers found that the stability and individuality of the microbiome differed significantly across body sites. The stool and oral microbiomes were more stable over time than the skin and nasal microbiomes. This stability is thought to result from more consistent interaction between skin and nasal microbiomes and their environments, compared to stool microbiomes.

Interestingly, the study identified individual-specific and commonly shared bacterial taxa, with the individual-specific bacteria showing greater stability. This implies that while certain microbial taxa dominate individuals, personalized microbes exist and are sustained over time. One’s genetics, diet, and immune system create these highly individualized microbiomes.

“When people get sick, such as cold, their microbiome temporarily becomes dysregulated.”

The research also found several correlations between the microbiome and health. For instance, individuals with Type 2 diabetes exhibited a less stable and less diverse microbiome. When people get sick, such as cold, their microbiome temporarily becomes dysregulated. Meanwhile, the microbiome changes associated with diabetes are long-term rather than temporary.

Moreover, the microbiomes in different body areas were highly correlated. This means changes in one body area’s microbiome often correspond with changes in other areas. For instance, if nasal bacteria change when a respiratory infection begins, the gut, mouth, and skin microbes quickly change. Likewise, when gut bacteria change due to diabetes, the skin, mouth, and nose microbiomes also change.

“Microbes predictably shift with the seasons, likely due to changing humidity, sunlight levels, and the availability of fresh food.”

The study identified several environmental factors that influence the microbiome and these environmental influences were more pronounced for skin and nasal cavity. For example, microbial communities predictably shift with the seasons, likely due to changing humidity, sunlight levels, the availability of fresh food and outdoor activities. However, these environmental factors, including diet, did not fully explain individual variability.

This comprehensive and longitudinal study provides valuable insights into the stability and individuality of the human microbiome across different body areas and highlights the microbiome’s significant role in health and disease. Despite its limitations (limitations of the 16S RNA sequencing technique to assess gut microbial composition, and the inability to identify causal relationships) the studies provide a number of observations concerning the individuality and stability of the microbiome across multiple body sites during health and disease and in individuals with different insulin resistance and sensitivity status. According to the investigators, their observations have important implications in modulation human molecular health using personalized prebiotics and probiotics.

Richard Tirado is a recent graduate from UCLA, where he majored in Biology and minored in Anthropology.

This article was reviewed and approved by Emeran Mayer, MD