It is well-established that a dynamic population of microorganisms residing in the gastrointestinal tract—namely, the gut microbiota—partakes in regulating various host signaling pathways and physiological functions including energy homeostasis, glucose and lipid metabolism, and inflammatory responses (1–3). These processes have been shown to be partly mediated by the production of microbial metabolites such as short-chain fatty acids (SCFAs)—primarily acetate, propionate, and butyrate—from the fermentation of dietary fiber and resistant starch in the gut (1, 2). Disruption of intestinal microbiota function can alter its derived metabolites and byproducts, which may trigger a broad range of physiological responses linked to increased risk of developing metabolic diseases such as obesity and type 2 diabetes (T2D) (2, 3).

Diet is a key factor shaping the composition and function of gut microbiota (2, 4). Dietary patterns such as vegetarian or vegan diets and animal-based diets demonstrate distinct effects on gut microbiota composition (5, 6). Plant-based diets contain a variety of whole grains and are typically rich in fiber, while lower in saturated fat and protein as opposed to omnivorous diets (5, 7). Greater adherence to plant-based diets was reported to have favorable outcomes on body weight homeostasis and cardiometabolic heath (7–9) potentially and partly via promoting the preservation of a more diverse and stable ecosystem of beneficial bacteria residing in the gut (6). Different types of dietary fibers—depending on their chemical structure and physical properties—may stimulate the growth of specific taxa that express specific genes encoding enzymes required for their metabolism (4, 10). For example, inulin-type fructans (ITFs) are a type of fermentable dietary fibers known as prebiotics that induce beneficial health effects resulting from cross-feeding interactions between bifidobacteria and butyrate-producing bacteria (11). ITF-prebiotics, including fructo-oligosaccharides, oligofructose and inulin, are among the most investigated and well-established prebiotics, and have been shown to affect intestinal health and metabolism (11–14). However, there is a notable variation in the effects of dietary fiber on gut microbiota (15) and host health, which may be attributed to the unique microbial community that each individual harbors and its fiber-fermentation capacity (16, 17). This highly individualized response is opening the door to discover new potential microbiota-targeted therapeutics for the prevention and management of obesity and its metabolic comorbidities through precision nutrition (18). From this perspective, profiling the gut microbiome is emerging as a promising prognostic marker to predict response to dietary interventions (19). For instance, recent studies have found that individuals with high Prevotella-to-Bacteroides (P/B) ratio lose more weight than individuals with low P/B ratio when consuming a diet rich in whole grains and fiber (20–22), presumably due to the distinct fermentation responses dependent on Prevotella species (16, 19). Accordingly, in this secondary exploratory analysis from the PREVENTOMICS study (23, 24), the main objective was to investigate the impact of consuming an ad libitum high-fiber plant-based diet with or without the addition of isolated ITF-prebiotics on changes in gut microbiota in subjects with obesity, and explored associations with different metabolic health markers. In addition, we investigated whether weight loss can be predicted based on baseline P/B ratio as previously suggested.

The present study explored changes in gut microbiota and host metabolism after 10 weeks on a high fiber plant-based diet with or without the addition of isolated ITF-prebiotics. Our results reinforce current evidence demonstrating that plant-based diets are effective in reducing body weight and improving glucose and lipid profiles (7–9). We found that a predominantly plant-based diet (with a fiber content of ∼38 g/d) consumed ad libitum for a period of 10 weeks reduced fasting glucose, insulin, total cholesterol, and LDL-C levels, concomitant with improvements in measurements of body composition including fat mass, body fat percentage, total and visceral adipose tissue, and waist circumference. However, the addition of 20 g/d isolated ITF-prebiotics to the already high fiber diet did not provide additional benefits on various physiological parameters. If anything, ITF supplementation mitigated some of the beneficial effects of the plant-based diet on cardiometabolic risk factor profile, for the same amount of weight loss. This is in line with previous studies that found supplementation with inulin and/or FOS does not have significant independent effects on fasting glycemia and insulinemia, HOMA-IR index or lipid profile (31–35). Nonetheless, others demonstrated that ITF-prebiotics may have lipid-lowering (36) or glucose-lowering (13, 37, 38) effects, particularly among those with impaired fasting glycemia or hypercholesterolemia. In the present study we recruited individuals with obesity who were otherwise healthy (i.e., without hypertension, glucose abnormalities, and dyslipidemia), and found trends for attenuated reduction in glucose and LDL-C and augmented reduction in HDL-C in the ITF-subgroup relative to control, despite similar weight loss. These observations raise the possibility that the glucose and lipid-modifying ability of ITF-prebiotics mostly benefits those with compromised glycemic control and lipid profile at baseline. From a mechanistic perspective, a review by McRorie et al. (39) proposed that the cholesterol-lowering and improved glycemic effects of soluble fibers are highly correlated with their high viscosity gel-forming properties. Accordingly, non-viscous soluble fibers such as inulin and FOS do not exhibit these viscosity/gel-dependent beneficial health effects (39, 40).

Supplementation with ITF-prebiotics for 10 weeks altered the fecal bacterial community of the participants. Overall, in agreement with previous findings (38), we observed a decrease in gut microbiota richness among the whole cohort, which was mainly driven by the ITF-prebiotics subgroup (reduced alpha diversity measures). Therefore, it may be inferred that providing one type of isolated fiber for enough time induces a decrease in diversity and promotes the growth of certain taxa attributable to their specific ability to metabolize this type of fiber. Of particular interest, the administration of 20 g/d ITF-prebiotics in the present study led to a selective increase in the abundances of Bifidobacterium (∼2.2 fold) and F. prausnitzii (∼1.6 fold), in line with previous studies (31, 41–44). Specific stimulation of these taxa as a function of prebiotics has been shown to be associated with various health parameters resulting from cross-feeding interactions between acetate-producing bifidobacteria with butyrate-producing F. prausnitzii (45). Despite the bifidogenic effect of ITF in the present study, no strong correlation was found between changes in Bifidobacterium and F. prausnitzii abundances with changes in glucose and triglyceride concentrations, as reported previously (46). However, Faecalibacterium species abundance was positively correlated with serum insulin levels and HOMA-IR, contrary to previous findings (47). Interestingly, a recent study analyzing Faecalibacterium-like metagenome-assembled genomes identified twelve clades of this genus in the human gut, suggesting different functional potential and diversity associated with diet, health, and disease (48). That said, investigating which clade or strain is associated with a particular function is yet to be explored.

Obesity and T2D are recognized as states of chronic low-grade inflammation associated with gut dysbiosis and manifested by higher levels of circulating proinflammatory cytokines (3). Current evidence on the potential influence of gut microbes on immune responses are largely derived from in vitro and animal models, whereas findings from human studies are few and equivocal. Several studies have reported that the microbial diversity and the abundance of Bifidobacterium species and butyrate-producing bacteria, e.g., F. prausnitzii, in the human colon is markedly decreased in patients with gut diseases such as inflammatory bowel disease (49). F. prausnitzii are involved in immunomodulation by downregulating the NF-κB pathway and consequently inhibiting the synthesis of pro-inflammatory cytokines IL-6 and IL-12, while facilitating the induction of anti-inflammatory IL-10 (50). An in vitro study by Pang et al. demonstrated that inulin-type fructans, derived from Platycodon grandifloras, induced a significant increase in IL-10 mRNA levels along with a minor increase in TNFα (51). Another study confirmed that FOS and inulin independently increased TNFα, IL-1β, and IL-10 in human peripheral blood monocytes mediated through TLR signaling (52). In fact, only TNFα and IL-10 were significantly induced (52). This direct role was investigated in vitro demonstrating that ITF-prebiotics act as TLR4 ligands in intestinal epithelial cells and induce the production of MCP-1 and macrophage inflammatory protein 2 (MIP2), with an efficacy that was 50–80% that of lipopolysaccharide (53). Our study yielded similar results with ITF supplementation significantly increasing IL-10 and MCP-1 levels and mildly increasing TNFα. On the other hand, Clarke et al. reported a decrease in serum IL-10 concentration following 28 days of 15 g/d fructans consumption among 30 healthy adults (54), and Dehghan et al. found a decrease in TNFα, CRP and lipopolysaccharide among women with T2D after 8 weeks of 10 g/d inulin supplementation together with a trend for increased IL-10 (55). The reasons for the conflicting results observed across studies remain to be clarified. Interestingly, however, Hippe et al. (56) reported that F. prausnitzii phylotypes found in individuals with obesity and T2D were different compared to those found in lean counterparts who had the highest in F. prausnitzii but the lowest in its butyrate production capacity (BUT gene). Notably, the highest BUT gene abundance was observed among patients with T2D, suggesting that butyrate-producing capacity differs between F. prausnitzii phylotypes, and its protective role may be concentration-dependent. The authors speculated that a specific threshold of butyrate production can be protective—improving adiposity and glucose homeostasis; whereas increased concentrations could be detrimental—promoting inflammation. There is still much to be learned by investigating the complex signaling pathways involved in the direct and indirect prebiotics-gut microbiota interactions with host health including the immune system, leading to either an anti-or a pro-inflammatory response.

With respect to weight management in relation to microbial enterotypes, in contrast to previous findings (20, 21), baseline P/B ratio in this study did not predict weight loss success. However, in accordance with previous observations (19, 22), the association between the Prevotella enterotype and weight loss was observed only among a subgroup of individuals having low salivary amylase gene copy number. Here, we did not evaluate this gene variant. Also, about half of the participants (51%) had no detectable fecal Prevotella at baseline. This is higher than previously reported (19–21) and basically excluded half of the participants from the analysis, resulting in low statistical power for detecting significant relationships with health outcomes. Moreover, previous research suggests that individuals with no detectable Prevotella have a differential weight loss response compared to those with low P/B ratio (20).

To our knowledge, this is the first study that compared the health effects of consuming a diet naturally rich in fiber, with prebiotic properties, and its effects on gut microbiota composition and physiological outcomes relative to a similar plant-based diet supplemented with inulin and FOS. We demonstrate that improvements in various health parameters can be achieved with a varied high-fiber diet rather than supplementation with an isolated nutrient which in fact was associated with reduced microbial diversity and attenuated cardiometabolic benefits. However, these results should be interpreted with caution given the exploratory nature of our analysis. Intriguingly, other studies (57, 58) reported favorable changes in metabolic markers following dietary intervention with ITF-prebiotic despite observed reduced gut microbiota diversity, which appear to contradict the notion that overall greater diversity and/or richness translates to better health. Therefore, the relationships between decreased gut microbial diversity and health outcomes in addition to what constitutes a healthy gut microbiome require further investigation. In addition, we did not measure bowel habits or gastrointestinal symptoms but we nevertheless encountered only 4 dropouts in the ITF-prebiotics subgroup. It has previously been reported that inulin fructans are generally well-tolerated up to a level of 20 g/d (59). An important limitation concerning research with gut microbiome is the lack of quantitative data on actual fluxes of SCFAs and of relevant metabolic processes and interconversions resulting from prebiotics fermentation. Similarly, our study provides no insight into gut microbial SCFA production. Considering that the majority of SCFAs are rapidly utilized by colonocytes (butyrate being the primary energy source), or consumed in cross-feeding between different gut microbiota (leaving only ∼5% of total SCFAs excreted in stool), interpretation of concentrations in peripheral blood and/or urine may not accurately reflect the amounts produced in the gut and subsequently absorbed in the systemic circulation. Lastly, it is possible that the absence of significant differences between the two subgroups in our study was due to the control diet being already very high in fiber (33 g/d) and plant foods; inulin is naturally present in a wide variety of plants such as onions, garlic, leek, bananas, asparagus, artichoke, wheat, and chicory (60).

Collectively, while evidence for direct and indirect health effects of prebiotics is rapidly accumulating, results from interventions in human subjects are inconsistent and make it challenging to draw comprehensive conclusions, thereby limiting translation to practice. This could be related to (1) the heterogeneity of study designs and the generally small sample sizes, (2) the habitual intake of dietary fiber, (3) the duration of supplementation as well as factors related to differences in the type, dose, and physicochemical properties of the prebiotics, and (4) the gut microbiota’s fermentation capacity. The bidirectional relationship between gut microbiota and host adds further complexity. Therefore, future research efforts should focus on unraveling the potential mechanisms underlying these complex pathways and microbial functionality through metagenomic analysis before targeted dietary advice can be implemented. Well-powered large-scale prospective randomized multi-omics trials designed to tailor a diet based on baseline microbiota profile, amongst others, are warranted to provide more concrete evidence. Consideration of individual factors, including, but not limited to, health status, age and sex could also explain the variation of the microbiota responses to diet among individuals.

In summary, our results indicate that ad libitum consumption of a balanced plant-based diet that is naturally rich in fiber significantly decreases body weight and improves glycemic and lipid profiles, whereas the addition of ∼20 g/d of isolated inulin-type fructans has no additional benefits in generally healthy individuals with obesity despite modulating gut microbiota composition. There is insufficient evidence at present to support precision dietary advice for weight loss merely informed by individual gut microbiota profile.

The original contributions presented in the study are publicly available. This data can be found at: https://www.ncbi.nlm.nih.gov/sra/PRJNA908225.

The studies involving human participants were reviewed and approved by the ethical committee of the Capital Region of Denmark (H-20029882). The patients/participants provided their written informed consent to participate in this study.

MA, KP, MH, and FM: designed and conducted the original trial. MA, LC, MH, and FM: conceived the idea and designed the current analysis. XM and ML: carried gut microbiota characterization analyses. MA and KP: undertook data acquisition of the original study. MA: conducted data analysis and acquired fund for gut microbiome analyses. MA and FM wrote the original draft. MA, XM, ML, KP, LC, HR, DN, MH, and FM critically revised and edited the manuscript. All authors contributed to the article and approved the submitted version.

The PREVENTOMICS project was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 818318, but no additional funding was received for the current analysis. Work on gut microbiome quantification in feces in addition to some of the study materials was funded by a PhD scholarship from King Saud bin Abdulaziz University for Health Sciences via The Saudi Arabian Cultural Office.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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