To Eat, or Not to Eat Spinach: That is the Question with Oxalates

From a childhood idol to reality

The image of the beloved Popeye with his bulging forearms and a hefty dose of spinach has taught all of us the superpower of spinach. ‘I'm strong to the "finich", 'cause I eats me spinach’, says the lyric from I'm Popeye the Sailor Man. Many of us were indeed inspired or persuaded by Popeye to eat more spinach growing up. Loving it or eating it with the hope of being like Popeye, you will learn in this blog that this commonly considered healthy and nutritious food is not necessarily everyone’s source to harvest the superpower. It depends on your individual gut biochemistry!


Turns out it specifically has to do with oxalates and how much capacity your body, specifically your gut microbiome, has to break down and use (i.e., metabolize) them. Oxalates are organic salts naturally present in many vegetables, fruits, nuts, and other plant foods. In plants oxalates serve beneficial roles in defense from insects, heavy metal detoxification, and pH regulation.1 Spinach is one of the highest-oxalate-containing foods, as are some other leafy greens like beet greens, purslane, rhubarb, chard, endive, and dandelion greens. Our body can also produce oxalates internally (endogenously) by breaking down proteins (amino acid metabolism).2 3 If the body cannot metabolize oxalates efficiently, high levels of oxalates in urine can lead to the development of kidney stones! It has been reported that close to 80% of all kidney stones are formed from calcium oxalate (CaOx).4 5 This binding to calcium in the gut can also inhibit calcium absorption by the host, which is undesirable.6 7 

Oxalates, the specialist, and the biochemistry

So how are oxalates broken down in our body? One of the main specialists you need to know is Oxalobacter formigenes, or O. formigenes, a bacteria that requires oxygen-free conditions (i.e., it’s an anaerobe) that lives in your gut. As illustrated in Figure 2 (upper right), O. formigenes use oxalates to extract energy for growth. Employing a two-step process that uses catalysts to bring about a specific biochemical reaction (i.e., enzymes called formyl-CoA transferase (frc), and oxalyl-CoA decarboxylase (oxc), they degrade oxalates to produce carbon dioxide and formate that can be consumed by other microbes in the gut. A lower prevalence of O. formigenes has been associated with increased urinary oxalate excretion and the development of kidney stones.8 9 10 There are hundreds of species, including lactic acid-producing bacteria (LAB), that possess oxc and frc enzymes required to break-down oxalates.11 12 This functional characteristic of breaking down oxalates is captured in the Oxalate Metabolism Pathways score to better assess your gut’s oxalate biochemistry, as described in our scores blog.

gut lining

In the Viome customer cohort used for this study, we see active O. formigenes in ~27% of the individuals, which is similar to the estimated ~30% detection for the US.13 14 15 The word “active” is very important in this instance, since we are detecting only those organisms that are alive and expressing their genes, not the ones that are dormant. So how can you know whether your body has sufficient oxalate degradation functional activity? Viome can help!  

Spinach: superfood or avoid?

Viome’s Nutrition 2.0 platform is a strategy to leverage your specific biochemical functionality and tailor food and supplement recommendations that meet your needs. Viome’s wellness tests and App provide comprehensive food and supplementation recommendations based on your gut microbiome activities. As introduced in our previous blog about the journey of your sample, and illustrated in Figure 3, Viome’s Glycemic Response Model first predicts whether a food, in this case spinach, is ‘enjoy’ or ‘minimize’ based on macronutrients curated in Viome’s food database and your gut microbiome. Combined with your health scores, by analyzing the biochemical pathways, spinach is further categorized into ‘superfood’ if your Viome App Oxalate Metabolism Pathways score is high (‘good’), and ‘avoid’ if it is low (‘not optimal’).

food database

Let’s dive into how Viome’s customers are doing with spinach. We sampled 10K customers and reviewed their food recommendations on spinach. Figure 4 shows the breakdown of spinach recommendations from these customers. Interestingly (and unlike Popeye), almost 60% of this population was recommended to avoid or minimize spinach!   

figure 4

Why is such a healthy vegetable recommended as a minimize or avoid food for so many people? Turns out that this is not because there is a big difference in one particular organism like O.formigenes between the superfood-recommended population and the avoid-or-minimize-recommended population, but rather, a systematic difference in the oxalate metabolism functional pathways between these two populations.  This is the essence of the score OxalateMetabolismPathways.


Let’s see some data based on a case/control comparison analysis. We sub-selected approximately 1500 people with spinach recommended as a ‘superfood’ (Superfood group) and selected a matched group of 1500 people randomly with spinach as ‘avoid’ (Avoid group). From a 2-group differential analysis on microbes, the ‘oxalate specialist’ O. formigenes, is not shown to have different abundance in the Superfood group and in the Avoid group (Figure 5).

figure 5

On the other hand, when we compare the Oxalate Metabolism Pathways scores from the same Superfood and Avoid group individuals used in Figure 5, we see that their scores are significantly different, as expected (Figure 6).  As mentioned earlier, all of the oxalate metabolism functions within the microbiome are consolidated into the Oxalate Metabolism Pathways score shown in the Viome App.

figure 6

This analysis confirms that the function of oxalate metabolism in your microbiome is needed to be able to take advantage of the nutrients in spinach. For this reason, certain generally considered healthy foods, such as spinach and kale, may not necessarily be healthy for you depending on your microbiome’s biochemical activity. 

Spinach: Love the leaf, minus the troubles

The first thing you should do is go out and purchase a Viome kit to understand whether spinach is a ‘Superfood’ for you. However, if you are concerned about your oxalate consumption, but want to keep spinach as a staple of your diet, there are a couple of ways to decrease oxalate content. Boiling (or blanching) spinach seems to be the most effective way of reducing oxalate content - steaming, to a lesser degree, reduces oxalates as well.16 17 18 19 In case you are not a huge fan of the consistency or flavor of boiled spinach (like a lot of people), here is a quick and simple recipe to liven it up:


  • 8 oz bag of spinach

  • 2 tbsp olive oil

  • 2-3 cloves of garlic (minced or sliced thinly)

  • ½ tbsp of lemon zest

  • Pinch salt 

  • Optional: Pinch of crushed red chili flakes (for some heat)


  1. Spinach reduces in size as you cook it, so you’re going to want at least a bag (8oz) to start with. To a pot of boiling water (season with a teaspoon of salt), place in your spinach. Leave the pot uncovered and boil for 1-3 minutes. Use a spider strainer or a colander to drain the spinach of water and place it immediately in an ice-water bath (this stops the cooking process and leaves your spinach bright green). 

  2. Add 2 tablespoons of olive oil in a medium saute pan and saute the garlic and lemon zest until fragrant (about one minute). 

  3. Remove excess water from blanched spinach by squeezing it in your hand or by using a cheesecloth. 

  4. Add the spinach to your saute pan and continue cooking for 2-3 minutes to mix all the flavors together; top with some crushed red chili flakes, and enjoy!

This preparation can be used as a side dish for many meals or just on top of some rice as a healthy stand-alone.

spinach teeth

Taken together, this blog hopefully answers some questions about whether the so-called healthy foods are really healthy for you. Some key takeaways:

  1. About 60% of Viome’s customer cohort have recommendations to avoid or minimize spinach in their diet.

  2. We detected active oxalate metabolizer bacteria O. formigenes in  about 27% of our Viome customers, which is consistent with US-based estimates.

  3. The abundance of the “oxalate specialist” O. formigenes activity is not different in customers who were recommended spinach as a ‘Superfood’ compared to a recommendation of Avoid.

  4. Given that other bacteria are capable of breaking down oxalates, Viome developed an Oxalate Metabolism Pathways score to better assess your functional oxalate biochemistry.

  5. Oxalate Metabolism Pathways score is shown to be significantly higher (‘good’ direction) in customers who were recommended spinach as a ‘Superfood’ compared to a recommendation of ‘Avoid’.

  6. Boiling or blanching spinach can reduce the oxalate content during meal prep.  

With Viome’s Nutrition 2.0 platform, we can tease out the uniqueness of your microbiome, make recommendations tailored to you, and be a friend on your wellness journey!


1. Li, P. et al. J. Agric. Food Chem. 70, 16037–16049 (2022).

2. Noonan, S. C. & Savage, G. P. Asia Pac. J. Clin. Nutr. 8, 64–74 (1999).

3. Holmes, R. P. Mol. Urol. 4, 329–32 (2000).

4. Evan, A. P. Pediatr. Nephrol. 25, 831–841 (2010).

5. Curhan, G. C., Willett, W. C., Speizer, F. E. & Stampfer, M. J. Kidney Int. 59, 2290–2298 (2001).

6. Kelsay, J. L. & Prather, E. S. Am. J. Clin. Nutr. 38, 12–19 (1983).

7. Heaney, R. P. & Weaver, C. M. Am. J. Clin. Nutr. 50, 830–832 (1989).

8. Siener, R. et al. Kidney Int. 83, 1144–1149 (2013).

9. Kaufman, D. W. et al. J. Am. Soc. Nephrol. 19, 1197–1203 (2008).

10. Wigner, P., Bijak, M. & Saluk-Bijak, J. Cells 11, 284 (2022).

11. Allison, M. J., Dawson, K. A., Mayberry, W. R. & Foss, J. G. Arch. Microbiol. 141, 1–7 (1985).

12. Jiang, T. et al. Front. Microbiol. 11, 672 (2020).

13. Barnett, C., Nazzal, L., Goldfarb, D. S. & Blaser, M. J. T. J. Urol. 195, 499–506 (2016).

14. Kelly, J. P., Curhan, G. C., Cave, D. R., Anderson, T. E. & Kaufman, D. W. J. Endourol. 25, 673–679 (2011).

15. Daniel, S. L. et al. Appl. Environ. Microbiol. 87, e00544-21 (2021).

16. BENGTSSON, B. L. Int. J. Food Sci. Technol. 4, 141–145 (1969).

17. Chai, W. & Liebman, M. J Agr Food Chem 53, 3027–3030 (2005).

18. Hönow, R. & Hesse, A. Food Chem. 78, 511–521 (2002).

19. Savage, G. P., Vanhanen, L., Mason, S. M. & Ross, A. B. J. Food Compos. Anal. 13, 201–206 (2000).