We’re learning every day about how our bodies work—and it turns out; it’s not just our DNA that matters. While our DNA provides the foundation for how we interact with the world, tiny organisms living in our gut, called microbes, play an important role in shaping our health. Together with our genes and other biological factors, they help determine how diseases like asthma develop and affect us.
Maggie Stanislawski, PhD, assistant professor of biomedical informatics at the University of Colorado Anschutz School of Medicine is exploring how our genes, gut bacteria and other biological signals interact to influence our health. “I am an epidemiologist by training, so I use these large epidemiological cohorts to understand how genetic, microbe, and multi-omic relationships vary across diverse populations,” explained Stanislawski. “Integrating these biological layers to advance personalized medicine and enhance treatment efficacy is extremely important.”
After we’re born, our genetics remain largely stable throughout life. This means our genetic predisposition to disease is consistent at the DNA level, however, a range of other factors influence how that risk manifests over time. Stanislawski's recent paper, Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults, published in Nature Communications, looked at how genetic and other risk factors interact in relation to asthma.
Stanislawski focused on subgroups of Hispanic and Latino individuals in the United States, each of whom immigrated within the past two generations. These subgroups experience asthma in strikingly different ways, with Puerto Ricans exhibiting notably higher prevalence, while individuals of Mexican origin show significantly lower rates.
She also emphasized the importance of looking beyond broad disease labels. Asthma, for example, isn’t just one condition; it is a set of symptoms that include different types, or “endotypes,” that may have different pathophysiology. Along these lines, she and her team found differences in the gut microbial signatures of childhood-onset asthma versus adult-onset asthma.
Humans and microbes have a long history of co-evolution. “There are many foods that we eat that cannot be digested without the help of microbes,” explained Stanislawski. “They help synthesize vitamins and neurotransmitters, resist pathogen colonization, and modulate our immune system.”
Prebiotics are foods, such as dietary fibers and resistant starch, that feed and support microbial growth. Context makes a big difference when it comes to the utilization of prebiotic compounds. Potatoes hot out of the oven have fewer prebiotic components. As they are cooled, the resistant starch forms, which is beneficial to gut microbes.
Probiotic sources, such as fermented foods, contain live cultures that enhance and help restore microbial diversity in the gut; a measure often referred to as alpha diversity. Lactobacillus and Bifidobacterium are among the most studied probiotic bacterial genera, known for supporting a balanced intestinal ecosystem. These bacteria help to create bioactive compounds that contribute to digestive health and immune function. Much like how a healthy natural environment depends on a balanced ratio of predators and prey, probiotic species help maintain equilibrium within the microbiome.
Stanislawski’s research found that numerous strains of anti-inflammatory bacteria, such as Lactobacillus and Enterococcus, were reduced in asthmatics. The Lactobacillus genus is commonly found in yogurt and contains many beneficial species, such as Lactobacillus reuteri. This species was shown to “alleviate airway inflammation, promote the proliferation of regulatory T-cells and modulate gut microbiota composition overall, enriching the generation of butyrate, which is a strong anti-inflammatory short chain fatty acid (SCFA)”.
Measuring metabolites produced by the microbiome provides insight into microbial activity and the corresponding host systemic functions. For instance, SCFAs are metabolites produced when gut microbes ferment dietary fiber. Along with building a protective intestinal gut barrier, they help regulate inflammation and immune function. Dysregulated SCFA production can lead to increased intestinal permeability or “leaky gut”. Subsequently, chronic inflammation is triggered from microbial products entering circulation.
Combining microbiome data with other molecular layers in a multi-omics framework provides a comprehensive perspective on contributors to disease progression. Insights into the many molecular mechanisms of inflammation may inform personalized interventions, such as dietary changes, instead of defaulting to conventional broad-spectrum treatments for chronic inflammatory conditions like asthma.
To get the full picture, Stanislawski uses a “multi-omics” approach. That means looking at many layers of biology at once—like genes, microbes, proteins, and chemical signals in the body.
“Studying different markers gives us a better idea of what’s causing disease and how it works,” added Stanislawski. Rather than viewing disease as an isolated pathway, multi-omics models the interconnectedness of physiology as an integrated system.
Incorporating additional biological layers into a patient’s profile—such as understanding how genes influence protein dynamics, metabolic activity, and drug metabolism—enables treatment strategies to achieve unprecedented precision. These integrative approaches are captured through multi-omic techniques, including the microbiome, transcriptomics, proteomics, metabolomics, and pharmacogenomics.
This multi-omics approach also helps explain why some diseases often occur together. For example, looking at obesity alongside asthma shows unique biological patterns that aren’t seen when each condition is studied alone. Multi-omics helps tease apart these overlaps, revealing the different root causes behind conditions that may look similar on the surface.
Researchers like Stanislawski are transforming how individual patients are characterized and treated. Examining a person as a whole brings a more detailed understanding. As this research evolves, it reinforces that our everyday choices, from what we eat to how we live, play a vital role in shaping our health. Understanding and nurturing our microbiome may one day be a cornerstone of managing disease and improving quality of life for millions.