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SLC39A8, Your Gut Barrier, and the Microbiome: What Your Genotype May Mean

The gut microbiome is a community of trillions of microorganisms that help with digestion, immunity, and overall well-being. A healthy gut depends on a strong intestinal barrier and a balanced population of beneficial bacteria. The SLC39A8 gene helps move essential metals such as manganese and zinc into cells. These metals are important for maintaining the structure and function of the gut lining. Variations in SLC39A8 can change metal transport, which may affect the mucus layer, glycocalyx, immune signaling, and the composition of the microbiome.

How SLC39A8 variants can influence gut health

  • Metal transport: SLC39A8 controls uptake of manganese and zinc into cells. Reduced transport can lower local availability of these cofactors needed for enzymes and barrier maintenance.
  • Barrier integrity: Lower manganese or zinc at the epithelial surface can weaken the mucus layer and glycocalyx, making it easier for microbes to interact with immune cells.
  • Microbiome composition: Changes in the intestinal environment may reduce populations of beneficial bacteria such as Anaerostipes, Coprococcus, Roseburia, Lachnospira, and SMB53, which are linked to healthy short-chain fatty acid production and gut homeostasis.
  • Inflammation risk: A weakened barrier and altered microbiome can increase exposure of the immune system to bacterial products, contributing to low-grade inflammation and dysbiosis.

Practical steps to support your gut and barrier function

Genetic variants are one piece of the puzzle. Diet and lifestyle strongly influence microbiome composition and intestinal barrier health. The following strategies are broadly useful and may be especially helpful if your SLC39A8 genotype suggests reduced metal transport.

Diet

  • Eat a diverse, plant-rich diet: Include a variety of vegetables, fruits, legumes, nuts, seeds, and whole grains to feed a broad range of beneficial microbes.
  • Prioritize fermentable fiber: Foods high in resistant starch and soluble fiber—oats, barley, legumes, green bananas, cooked and cooled potatoes—support bacteria that make short-chain fatty acids like butyrate.
  • Include fermented foods: Yogurt, kefir, sauerkraut, kimchi, and other fermented foods can introduce beneficial microbes and support microbial diversity.
  • Choose manganese-rich foods: Whole grains, nuts (especially pecans and hazelnuts), leafy greens (spinach, kale), legumes, and dark chocolate can help supply manganese through diet.
  • Maintain adequate zinc intake: Include meat, shellfish, legumes, pumpkin seeds, and dairy to support zinc status.
  • Limit processed and high-sugar foods: These can promote growth of less beneficial microbes and impair barrier function.

Supplements to consider

  • Probiotic supplements: Strains that support butyrate producers or general diversity may be useful. Choose high-quality products and discuss strains and dose with your clinician.
  • Zinc: If dietary intake or labs show low zinc, targeted supplementation can support mucosal integrity and immune function. Avoid excessive zinc without medical supervision.
  • Manganese: Dietary sources are preferred. Supplementation should be considered only when indicated and monitored, since excess manganese can be harmful.
  • L-glutamine: An amino acid that supports intestinal epithelial cells and may help repair the barrier in some individuals.
  • Prebiotic fibers: Inulin, FOS, and other fermentable fibers can feed beneficial bacteria, but start slowly to avoid gas and bloating.

Lifestyle habits

  • Manage stress: Chronic stress can alter the microbiome and increase intestinal permeability. Practices such as breathing exercises, mindfulness, and therapy can help.
  • Sleep well: Aim for consistent quality sleep. Sleep disruption is linked to microbiome changes and inflammation.
  • Exercise regularly: Moderate physical activity supports microbial diversity and gut motility.
  • Avoid unnecessary antibiotics: Use antibiotics only when prescribed and follow clinician guidance to minimize long-term microbiome disruption.

Blood tests and monitoring

  • Consider checking serum zinc and manganese if symptoms or clinical context suggest deficiency or if you plan to supplement.
  • Inflammatory markers: CRP or fecal calprotectin may be helpful if there are signs of gut inflammation.
  • Stool tests: Comprehensive microbiome or targeted stool testing can provide additional context about microbial composition and function.
  • Work with a clinician to interpret labs and tailor interventions to your health history and current medications.
Two effect alleles (TT) — what this means

If you have the TT genotype for rs13107325, you carry two copies of the effect allele. This variant is associated with altered gut microbiota and lower levels of beneficial bacteria such as Anaerostipes, Coprococcus, Roseburia, Lachnospira, and SMB53. Metal transport into cells may be affected, potentially leading to lower local manganese and zinc availability. Reduced manganese can weaken the intestinal barrier, including the mucus layer and glycocalyx, making it easier for bacteria and immune cells to interact and possibly increasing inflammation and dysbiosis.

Actionable considerations: emphasize a diverse, fiber-rich, plant-forward diet; include manganese- and zinc-rich foods; consider targeted supplements such as probiotics, zinc, and L-glutamine after discussing with your healthcare provider; focus on stress management, sleep, and regular exercise; and monitor nutrient levels and gut-related symptoms with clinical testing as advised by a provider.

One effect allele (CT) — what this means

If you have the CT genotype for rs13107325, you carry one copy of the effect allele. This genotype may influence how effectively your body transports manganese and zinc into cells. Research links this genotype to altered gut microbiota, potentially including lower levels of beneficial bacteria like Anaerostipes, Coprococcus, Roseburia, Lachnospira, and SMB53, and to subtle changes in gut barrier function.

Actionable considerations: follow the general recommendations above—diverse plant-based foods, fermentable fiber, fermented foods, and manganese- and zinc-containing foods. Probiotics, zinc, and L-glutamine may be considered if needed. Maintain healthy lifestyle habits and discuss testing for nutrient levels and gut health with your healthcare provider to guide any supplementation.

No effect alleles (CC) — what this means

If you have the CC genotype for rs13107325, you carry two copies of the non-effect allele. This common genotype is associated with typical SLC39A8 function and normal transport of manganese and zinc into cells. With this genotype, the gut barrier and microbiome are more likely to be supported by adequate metal availability, helping maintain a healthy mucus layer, beneficial bacteria populations, and a strong intestinal barrier.

Actionable considerations: continue preventive steps that support gut health—eat a varied, fiber-rich diet, include fermented foods, maintain good sleep and stress habits, and limit processed foods. Routine clinical monitoring is typically not required based on genotype alone but consult your clinician if you have symptoms or other risk factors.

When to talk with your healthcare provider

  • If you have ongoing gastrointestinal symptoms such as persistent diarrhea, bloating, abdominal pain, or unexplained inflammation.
  • If you are considering mineral supplementation, especially manganese or zinc, because dosing and monitoring are important.
  • If you are on medications or have conditions that affect nutrient absorption or immune function.

PlexusDx does not provide medical advice. This information is meant to educate about genetic predispositions and possible lifestyle and dietary strategies. Always consult with your healthcare provider before starting supplements, making major diet changes, or interpreting genetic results in the context of your medical history.