Prebiotic Type Spotlight: Whole Food Matrix

May 2024

Each edition of GPA’s Prebiotic Spotlight focuses on a specific prebiotic type to raise awareness about the prebiotic itself, its sources, any notable and/or recent research, and how it is used in the marketplace. In this issue, GPA goes beyond specific prebiotic types to highlight the interplay between natural food components, known as the whole food matrix. 


The whole food matrix refers to the complex and synergistic interactions between the natural components of whole foods, including nutrients, minerals, bioactive compounds, food structures, and others (e.g., phospholipids, prebiotics, and probiotics) (Mozaffarian, 2019). These interactions involve chemical and physical processes that affect the release, mass transfer, accessibility, digestibility, and stability of the food components, consequently influencing how these components are utilized by the body to impact health and disease (Aguilera, 2019). Advances in nutrition science have revealed the importance of consuming a variety of whole foods compared to focusing on individual nutrients; as such, stepping away from the old approach commonly adopted in the 20th century, known as the reductionist approach (Mozaffarian, 2019). Ingestion of whole foods not only offers an additive benefit of the individual components, but consuming foods in their natural forms can also enhance nutrient absorption and bioavailability in most cases.


The whole food diet is rich in prebiotic sources, including dietary fiber and phytochemicals (Esquivel, 2022). A sensible diet, characterized by high consumption of vegetables, fruits, fish, poultry, and wholegrain foods, contains a wealth of prebiotic components, and is associated with several health benefits, including decreased type-2 diabetes risk and glucose intolerance (Villegas et al., 2004). Several whole foods contribute to prebiotic effects on the microbiome, including:

  • Dietary fiber sources such as chicory roots, baobab, acacia fiber, etc., contain various prebiotic components, including beta-glucans, brans, oligosaccharides, and inulin. Dietary fiber sources can offer numerous health benefits, including improving cardiovascular health, diabetes control, digestion and laxation, microbiome composition, immunity, inflammation, insulin sensitivity, and weight maintenance (Esquivel, 2022; John, 2022). Manufacturers in the prebiotic field are increasingly developing innovative formulations to incorporate whole foods rich in fiber into their products. For example, Nexira has incorporated baobab, a plant with 70-80% fiber dry mass (Foltz et al., 2021), and acacia fiber as dietary supplements either combined or as standalone components to retain their natural form health benefits (Nexira, 2024). 
  • Walnuts, a food source of omega-3 fatty acids, have shown prebiotic benefits. Daily consumption of walnuts for 16 weeks has demonstrated protective effects in alleviating academic stress-induced gut microbiota disturbances in female students, as well as improving sleep over the long term (Herselman et al., 2022).
  • Fruits and vegetables. Fruits like berries and kiwi are rich in polyphenols, which display prebiotic effects on the microbiome. However, polyphenols have poor bioavailability in the body (Alves-Santos et al., 2020). Instead of using isolated polyphenols and phenolic acids, manufacturers in the prebiotic industry are utilizing whole foods rich in these prebiotic components to improve bioavailability. For example, products such as Livaux® by Anagenix, which utilizes gold kiwi powder, provide the whole-food matrix benefits from polyphenols. Studies have shown that Livaux® has targeted effects on Faecalibacterium prausnitzii, a commensal bacterium that maintains the balance of the gut microbiota with its anti-inflammatory, immunomodulatory, and gut permeability support effects (Anagenix, 2024; Blatchford et al., 2017).
  • Resistant starch (RS) sources such as green bananas, grains, beans, and cooked and cooled rice. RS content changes with heat as it decreases with heating oats, green bananas, and plantains; meanwhile, it increases with heating and cooling of grains such as wholegrains, lentils, and rice (Patterson et al., 2020; Sonia et al., 2015). RS has various benefits such as reducing cholesterol and improving glycemic control and insulin sensitivity (Patterson et al., 2020).   

Benefit Areas

Compared to the benefits of individual dietary ingredients, the significance of the whole food matrix lies in offering a complex combination of components with numerous health benefits. While these benefits start at the molecular level with nutrient synergy and bioavailability, nutrient interactions may increase or reinforce the gained benefit and the enhanced absorption of the individual components more readily than when taken as standalone nutrients. Some of the general benefits of prebiotic whole foods include: 

  • Gut health. Prebiotic whole food sources can support the enrichment of the gut microbiome and improve gut health (Migliozzi et al., 2015).
  • Metabolic and cardiovascular health. Prebiotic whole food consumption results in weight loss, improved weight management, cardiovascular conditions, and metabolic health (Greger, 2020; Rinott et al., 2022).
  • Anti-inflammatory and immune function. Polyphenol-rich foods contribute to an anti-inflammatory and immunomodulatory effects in the body (Blatchford et al., 2017; Plamada & Vodnar, 2021). 
  • Mental health. Whole foods rich in prebiotics can contribute to mental health via the gut-brain axis (Balasubramanian et al., 2024; Herselman et al., 2022). The Mediterranean diet, rich in polyphenols and omega-3 fatty acids, has been shown to have neuroprotective effects (Kaplan et al., 2022).

Dose Range

The consumption of whole foods has no specific recommended dose range. It usually depends on the individual’s age, sex, height, genetics, health status, body composition, physical activity, and other factors. However, the dietary components of food usually have daily recommended intake values. For example, the recommended intake for dietary fiber is 14 grams per 1000 kcal consumed daily (Esquivel, 2022), which accounts for the different types of prebiotic fibers such as inulin, oligosaccharides, etc. Regarding polyphenols, population statistics report an estimated intake of 900-1000 mg/day, primarily consumed from sources like tea, coffee, red wine, fruits, and vegetables (Plamada & Vodnar, 2021).

Recent Research

Interest in the consumption of whole foods has increased in recent years. On, searching the term “whole food sources” retrieved thirteen trials that are currently recruiting and use a variety of interventions, including different protein-rich whole foods, ketogenic diet versus saturated and unsaturated fat sources, poultry foods naturally enriched with omega-3 polyunsaturated fatty acid, etc. (, 2024). A PubMed search using the terms “(whole food matrix) and (prebiotics)” retrieved ten results published between October 2009 and January 2024, with most studies focusing on the benefits of consuming dairy whole foods and dietary fiber (PubMed, 2024). Li et al. (2023) summarized the single and combined effects of dietary fiber and polyphenols on blood glucose homeostasis by regulating relevant factors in the upper and lower gastrointestinal tract. The review found that combining polyphenols with dietary fiber enhances the adsorption capacity of dietary fiber for glucose. Combining the two also demonstrated a lower inhibitory effect on glucose uptake than the effect of polyphenols alone. As such, it was concluded that in the lower gastrointestinal tract, the combination of polyphenols and dietary fiber has both synergistic and antagonistic effects on the gut microbiota. In the same study, the consumption of whole foods was reported to have a significant influence on glucose regulation via the modification of gut microbiota compared to consuming individual dietary fibers, polyphenols, or a combination thereof (Li et al., 2023). Another study by Maleki et al. (2024) reviewed existing research on seed germination on the seed’s bioactive compounds and the effects of these compounds on the gut microbiome. The study highlighted two parameters that may influence the gut microbiome: the food matrix (diet) and food processing. The study found that legume sprouts containing prebiotics, including RS, galactooligosaccharides, and phenolic compounds, can positively affect the gut microbiome and feed the probiotic bacteria (Maleki et al., 2024).

How is the Whole Food Matrix used in the marketplace?

 In recent years, there has been a rising trend of consuming plant-based diets and whole foods including those rich in prebiotics and probiotics. The health and wellness food market, which encompasses organic food, dietary supplements, plant-based alternatives, and natural remedies, is estimated to increase by USD 452.93 million by 2027, increasing at a compound annual growth rate of 8.5%, with North America as the major performing market contribution with 31% (technavio, 2022).


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