Getting Good With Your Gut

A Guide to Healing Your Microbiome at Duke

February 27, 2023
Science Magazine

Like it or not, we’re covered in bacteria. From our skin to our gut, these microorganisms are so numerous that they may even outnumber our own cells (although the number of bacterial cells in our gut changes significantly with every bowel movement we take). Scientists working on the Human Microbiome Project estimate that our bodies house up to 10,000 different species of microbes. This fact might send shivers down your spine — after all, we just experienced a pandemic and so many other outbreaks of disease have been thanks to these nasty little bugs. The infamous pathogens Bacillus anthracis, Clostridium botulinum, and Yersinia pestis are responsible for outbreaks of anthrax, botulism, and Black Death, respectively. And, since the advent of antibiotic medicine, new strains of bacteria have emerged with acquired antibiotic resistance that makes infections even more difficult to treat. 

Yet, scientists estimate the total number of pathogenic bacteria species to be lower than a hundred. So what do all the rest of the bacteria do?

It turns out that they’re pretty useful. Bacteria form what’s called a microbiome on our epithelial tissue, inside and out. Balanced skin microbiomes containing the bacterium S. epidermidis help form the skin’s outermost barrier, protecting our largest organ from water loss and damage. It’s possible that curating a healthy skin microbiome could help slow visible aging or treat skin diseases and inflammation. Healthy skin microbiomes have even been linked to healthier immune systems

Meanwhile, in the gut, microbes in the genera Bacteroidetes, ​Bifidobacteria, and Firmicutes metabolize complex fibers and polyphenols (a class of antioxidants), allowing us to extract the maximum amount of nutrients possible from our diets. Thanks for the gains, Firmicutes! Bacteria in the gut also synthesize Vitamin K, protect vulnerable mucosal tissue from pathogens, and even regulate the autonomic nervous system. This last finding has led to a surge of research on what is called the gut-brain axis: an increasingly validated model of bidirectional communication between the central nervous system (CNS) and the digestive system. Scientists are finding that neuropsychiatric disorders of the CNS like anxiety and depression are often linked with dysbiosis, a state of imbalance in the gut microbiota. Dysbiosis is characterized by a lack of diversity in the gut microbiome and is typically caused by overconsumption of simple sugars and underconsumption of fiber or by treatment with certain antibiotics.

If you’re anything like me, this fact might make you even more anxious. How are Duke students supposed to make sure our microbiomes are happy and balanced while eating the same meal rotations from WU? What can we change in our diets to potentially decrease our feelings of anxiety and depression?

Above: The Brodhead Center (or, as we affectionately call it, WU) is home to 14 of Duke’s 34 dining locations. Searching for gut-healthy options can be overwhelming, but Vertices is here to help! Image courtesy of James Ewing.

The answer lies in two classes of foods: prebiotics and probiotics. Prebiotics are foods that help nourish beneficial bacteria, allowing them to colonize the gut. Probiotics are foods rich in active bacterial cultures; these kinds of foods introduce new bacteria to our digestive systems. Unfortunately, it’s not just as simple as eating cultured foods — nourishing your microbiome is all about curating a healthy ecosystem in your gut. The good news is that our microbiomes change day by day, hour by hour as we eat and excrete. Some colonies flourish and feed on our meals — and others die. Unlike our genes and epigenes, we are in control of our guts. But one question still remains: how do we find prebiotics and probiotics at Duke?

Fear not: Vertices has compiled a list of on-campus meals and snacks that are full of microbiome-enriching foods. If that’s not enough for you, we’ve also included some items to pick up on your next grocery run. 


To promote the growth of bacteria already living in our guts, we’re looking for foods that contain a lot of fiber to digest and extract energy from, namely polysaccharides found in the cell walls of plants. Whole grains, artichokes, garlic, onion, leeks, asparagus, chicory, and bananas are great sources of fiber for your bacterial besties.


  • Sprout: Oatmeal topped with banana slices and other toppings of your choice will supply the fiber your gut craves in the morning. Oats contain high levels of beta-glucan, a gut-healthy fiber.
  • Café: Organic oatmeal served in a convenient cup is also a great option if you’re on the go. 
  • Panera: Venture to the bottom floor of WU for a whole-grain bagel. If you’re lucky, they might even spell your name right.
  • Skillet: Consider ordering a side of oatmeal with your breakfast plate.
  • Pitchforks: If Pitch is your favorite campus eatery, fret not: they also have oatmeal. You can even get it dressed with berries, honey, and pumpkin seeds for some extra micronutrients like manganese and Vitamin K!


  • Twinnies: Head over to E-Quad for a Chicken Pita or Veggie Panini — both of which contain red onions.
  • Krafthouse: The Ginger Grilled Salmon Salad contains a healthy serving of red onions, plus ginger aids digestion and is full of antioxidants. The Mixed Arugula Salad also has raw onions and fresh fruit, if that’s more your speed!
  • Freeman Center: Try the Corned Beef on Rye or Pastrami on Rye with a Garden or Israeli salad on the side for a fiber combo of whole wheat and onions! Or, on a cold day, the lentil soup is full of fiber and will keep you warm.
  • Gyotaku: Grab an appetizer of edamame with your sushi roll; edamame, or immature soybeans, are rich in both soluble and insoluble fiber and are great for digestion as well as feeding your microbiome.
  • Sprout: The Chickpea Salad is rich in a fiber called raffinose, which bacteria in your gut love.
  • The Loop: The Mediterranean Chicken Wrap contains polyphenol-containing kalamata olives and red onions. In the mood for a salad? The Feta Mediterranean Salad contains artichoke, kalamata olives, and onions — a triple punch of fiber.


  • Tandoor: This is the place to go if you’re looking for prebiotics. Grab a serving of cabbage, chana masala, or dal for a kick of fiber. Bonus: the spices in these dishes aid in absorption of micronutrients!
  • Farmstead: Farmstead’s famous brussels sprouts will also help nourish your microbiome.
  • Ginger and Soy: Add a helping of edamame beans to your next bowl for an extra serving of fiber.
  • JB’s: Grab a side of grilled asparagus with your dinner for a serving of healthy fibers.

Snacks and Beverages

  • Café: Organic Masala Chai contains beneficial spices like chicory root extract (probably not a ton, but this is a good excuse to buy yourself a warm chai this winter).
  • Krafthouse: If you’re in the mood for something fried but don’t want to wreck your gut, try the onion rings to make sure you’re getting some fiber.


These are foods containing live cultures. It’s best to get a diverse collection of bacteria in your diet, so be sure to try out all of these amazing options here on campus.


  • Sprout: Start your day with a delicious yogurt parfait with the toppings of your choice! You can even choose your flavor of yogurt.
  • Pitchforks: If you live on the other side of campus, stop by Pitch for your parfait of the day (POTD?).
  • Red Mango: Grab some Overnight Yoats with blueberries from the Grab and Go section for a yummy blend of active cultures and prebiotics! Another option for yogurt lovers is the blueberry parfait.


  • Twinnies: Try a Reuben complete with sauerkraut, a German recipe of fermented cabbage rich in active cultures. Not into that? No problem — their Cuban comes with pickles, another valuable source of probiotics!
  • Pitchforks: On the other side of West Campus? No problem! Grab a Reuben at Pitch. For veggie lovers, try the Falafel sandwich on whole wheat pita. This sandwich comes with tzatziki, a yogurt sauce, and the whole wheat pita supplies some prebiotics. Two for one!
  • Nasher Museum Cafe: Next time you have some food points to blow, pick up the Nasher’s Avocado Smash, Giorgio’s Falafel Bowl, or Smoked Salmon Bowl for lunch. All of these contain pickled onions as well as prebiotics like whole grains and fiber-rich veggies!


  • Gyotaku: Grab a side of Miso Soup with your sushi roll! It’s only $2.15 and miso is chock-full of active cultures. If you’re grabbing a poke bowl, be sure to get the pickled toppings.
  • Ginger and Soy: Be sure to top your bowl with pickled radish, pickled cabbage, pickled carrot, or kimchi for some extra probiotic benefits. Pickled vegetables are an excellent source of probiotics.
  • Bulkogi: When this KBBQ food truck is on campus, make sure to grab a side of fresh kimchi!
  • Bon Frittay: Next time you see this Haitian food truck on campus, pick up a side of pikliz, a spicy fermented mix of cabbage, carrots, and peppers.

Snacks and Beverages

  • Red Mango: Grab any yogurt-based smoothie for a probiotic-packed snack! I love the PB&J one.
  • Beyu Blue: For your next caffeine boost, pick up a kombucha. This fermented sweetened black tea contains active cultures and comes in creative flavors. If you get a bit peckish for some more probiotics, Beyu also has yogurt parfaits!
  • Trinity Cafe: This convenient East Campus cafe supplies cups of both regular and Greek yogurt in various yummy flavors
  • Saladelia: Pick up a kombucha during your next Perkins grind session.
  • Krafthouse: Whether it’s a late-night snack or a game-day treat, give the fried pickles a try! Okay, probably not the healthiest suggestion on this list, but at least it’s a bit better than the fried cheese curds.

Above: Pickled veggies are one great source of gut-friendly bacterial cultures. Image courtesy of Harvard Health Blog.

Still not satisfied? Here are a few items you can pick up on your next grocery run.

  • Kefir: A fermented milk beverage popular in Eastern Europe, this drink has recently risen in popularity in the U.S. It can now be found in various fun flavors like peach, strawberry, and mango in addition to the classic plain variety.
  • Kimchi: This crunchy, spicy, fermented cabbage is a delicious staple of Korean cuisine.
  • Miso: Gyotaku’s miso soup is like a warm hug full of friendly bacteria. If you want to recreate that feeling in your dorm room, pick up a tub of Carolina-made miso at Whole Foods!
  • Pickles: Find these sour snacks at any grocery store in the area.
  • Yogurt: If you need yogurt access at all hours of the day, pick up a big tub at Harris Teeter!
  • Sauerkraut: This Central European pickled cabbage dish is perfect on sandwiches, as a side to a hearty meal, or even in soups and stews. (By the way, there are usually other kinds of pickled veggies near the sauerkraut jars — if you’re feeling adventurous, you could try some pickled beets, carrots, or radishes!)
  • Tempeh: This fermented soybean product originated in Indonesia. A unique culture of bacteria and friendly fungi work together to produce a high-protein, B12-rich probiotic option. This is a great option for anyone worried about indigestion or lactose intolerance from probiotic-packed foods: the fermentation process reduces the oligosaccharides and other carbohydrates in soy that are associated with gas and indigestion.
  • Kombucha: If Perkins and Beyu don’t have enough flavor options for you, browse a wider selection of this fermented tea at any grocery store in the area! Conveniently for Duke students, Whole Foods has a whole wall of fresh ‘booch options.
  • Cottage cheese: This controversially-textured cheese is having a moment right now. If it still makes you squeamish, try it on bread with some honey or build it into a parfait with fruit and granola on top!
  • Olives: These are great on snacks or in salads! If you’re a real olive fiend, grab some to stash in your mini-fridge.
Katherine Long

Katherine (Trinity ’24) is majoring in biology and chemistry with a concentration in cell and molecular biology. She is passionate about scientific communication and research and is excited to contribute to Vertices as a staff writer and peer reviewer. When she’s not in the lab or doing homework, she loves to paint, hike, and hang out with the Duke cat.

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