A vegan or vegetarian diet substantially alters the human colonic faecal microbiota
Open accessAbstract
Background/objectives Consisting of ≈10(14) microbial cells, the intestinal microbiota represents the largest and the most complex microbial community inhabiting the human body. However, the influence of regular diets on the microbiota is widely unknown.Subjects/methods We examined faecal samples of vegetarians (n=144), vegans (n=105) and an equal number of control subjects consuming ordinary omnivorous diet who were matched for age and gender. We used classical bacteriological isolation, identification and enumeration of the main anaerobic and aerobic bacterial genera and computed absolute and relative numbers that were compared between groups.Results Total counts of Bacteroides spp., Bifidobacterium spp., Escherichia coli and Enterobacteriaceae spp. were significantly lower (P=0.001, P=0.002, P=0.006 and P=0.008, respectively) in vegan samples than in controls, whereas others (E. coli biovars, Klebsiella spp., Enterobacter spp., other Enterobacteriaceae, Enterococcus spp., Lactobacillus spp., Citrobacter spp. and Clostridium spp.) were not. Subjects on a vegetarian diet ranked between vegans and controls. The total microbial count did not differ between the groups. In addition, subjects on a vegan or vegetarian diet showed significantly (P=0.0001) lower stool pH than did controls, and stool pH and counts of E. coli and Enterobacteriaceae were significantly correlated across all subgroups.Conclusions Maintaining a strict vegan or vegetarian diet results in a significant shift in the microbiota while total cell numbers remain unaltered.
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Eating vegetables, fiber and/or resistant starch along with animal protein seems to diminish the negative effects of the potentially harmful byproducts from amino acids fermented by the gut microbiota.
“While the amounts of Bacteroides and Firmicutes associated with vegan, vegetarian and omnivore diets from these studies and others [137, 138] are conflicting, it can be concluded that eating vegetables, fiber and/or resistant starch along with animal protein seems to diminish the negative effects of the potentially harmful byproducts from amino acids fermented by the gut microbiota.”
From Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes (2016) · cites this paper as [137]
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Intestinal Barrier and Permeability in Health, Obesity and NAFLD
Portincasa, P., Bonfrate, L., Khalil, M., Angelis, M. D., Calabrese, F. M., D’Amato, M., Wang, D. Q. ‐., & Ciaula, A. D. (2021) · Biomedicines · doi:10.3390/biomedicines10010083 · Cited by 212 · see citing works
“[378], decreased Enterobacteriaceae and increased Bacteroides [379], increased Bacteroidetes, and decreased Firmicutes and Enterobacteriaceae [380].”
BackgroundModulation of the human gut microbiota by phenolics and phenolic fiber‐rich foods
Loo, Y. T., Howell, K. S., Chan, M., Zhang, P., & Ng, K. (2020) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12563 · Cited by 216 · see citing works
Ghoshal, U. C., Shukla, R., & Ghoshal, U. (2017) · Gut and Liver · doi:10.5009/gnl16126 · Cited by 210 · see citing works
“Dietary manipulation of gut microbiota Dietary manipulation may help patients with IBS in general and those with SIBO in particular.132,133 In patients with SIBO, bacteria in the small bowel may ferment carbohydrates such as lactose, fructose and also the dietary fermentable oligo-, di-, monosaccharides and polyols (F…”
BackgroundAguirre, M., Eck, A., Koenen, M. E., Savelkoul, P. H. M., Budding, A. E., & Venema, K. (2016) · Research in Microbiology · doi:10.1016/j.resmic.2015.09.006 · Cited by 204 · see citing works
Diet-microbiota interactions and their implications for healthy living
Jeffery, I., & O'Toole, P. (2013) · Nutrients · doi:10.3390/nu5010234 · Cited by 199 · see citing works
“High amounts of SCFAs may decrease the intestinal pH [41] and prevent the growth of potentially pathogenic bacteria, such as E. coli and other members of the Enterobacteriaceae [42].”
BackgroundThe role of the gut microbiota in metabolic health
Janssen, A. W. F., & Kersten, S. (2015) · The FASEB Journal · doi:10.1096/fj.14-269514 · Cited by 199 · see citing works
“In general, it can be concluded thatdietmarkedly affects gutmicrobial composition at the phylum level and especially at the lower taxonomic levels (32, 34, 36, 37), although not necessarily in amanner that is consistent between individuals.”
BackgroundBarrea, L., Muscogiuri, G., Frías-Toral, E., Laudisio, D., Pugliese, G., Castellucci, B., Garcia-Velasquez, E., Savastano, S., & Colao, A. (2020) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2020.1792826 · Cited by 200 · see citing works
Gaohua, L., Miao, X., & Liu, D. (2021) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1080/17425255.2021.1951223 · Cited by 204 · see citing works
Microbiota and Lifestyle: A Special Focus on Diet
Redondo-Useros, N., Nova, E., González-Zancada, N., Díaz, L. E., Gómez-Martínez, S., & Marcos, A. (2020) · Nutrients · doi:10.3390/nu12061776 · Cited by 189 · see citing works
A Critical Look at Prebiotics Within the Dietary Fiber Concept
Verspreet, J., Damen, B., Broekaert, W. F., Verbeke, K., Delcour, J. A., & Courtin, C. M. (2016) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-081315-032749 · Cited by 186 · see citing works
“Vegans and vegetarians, who typically consume more DF, had lower stool pH levels and Enterobacteriaceae numbers than omnivorous subjects (Zimmer et al. 2012).”
BackgroundRapidly expanding knowledge on the role of the gut microbiome in health and disease
Cénit, M. C., Matzaraki, V., Tigchelaar, E. F., & Zhernakova, A. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.05.023 · Cited by 185 · see citing works
Alcohol or gut microbiota: who is the guilty?
Meroni, M., Longo, M., & Dongiovanni, P. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184568 · Cited by 183 · see citing works
“Also, diet-enriched in carbohydrates and fibers was responsible for lower stool pH (between 5.5 and 6.5) probably due to the end-products of gut fermentative metabolism thereby inhibiting pathogenic bacteria overgrowth like Escherichia coli and Enterobacteriacee [82,88,90,91].”
BackgroundInfluentialIntestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases
Opazo, M. C., Ortega-Rocha, E. M., Coronado-Arrázola, I., Bonifaz, L. C., Boudin, H., Neunlist, M., Bueno, S. M., Kalergis, A. M., & Riedel, C. A. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00432 · Cited by 179 · see citing works
“Also, a significant reduction for the loads for Lactic Acid Bacteria (LAB) was observed for the dietary groups ovo-lacto vegetarian and vegan, which may be due to the absence or low intake of some food such as cheese and yogurt (Zimmer et al., 2012).”
BackgroundHuman gut microbiota: Does diet matter?
Maukonen, J., & Saarela, M. (2015) · Proceedings of The Nutrition Society · doi:10.1017/s0029665114000688 · Cited by 177 · see citing works
“Strict vegetarians have higher percentages and/or numbers of Lachnospiraceae and Clostridium ramosum group (Clostridial cluster XVIII) bacteria than omnivorous people(135,136), whereas vegans have lower faecal numbers of Bacteroides spp., bifidobacteria and Enterobacteriaceae(137).”
InfluentialIntestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?
Cénit, M. C., Olivares, M., Codoñer‐Franch, P., & Sanz, Y. (2015) · Nutrients · doi:10.3390/nu7085314 · Cited by 179 · see citing works
“one of the main drivers of gut microbiota composition and function [45,88–91].”
BackgroundDietary Factors: Major Regulators of the Gut's Microbiota
Moschen, A. R., Wieser, V., & Tilg, H. (2012) · Gut and Liver · doi:10.5009/gnl.2012.6.4.411 · Cited by 173 · see citing works
“,(18) that long-term diets might indeed affect the microbiota.(23) Another study compared the fecal microbiota of vegetarian and omnivorous young women in southern India.”
BackgroundInfluentialWarinner, C., Speller, C., Collins, M. J., & Lewis, C. M. (2015) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.10.016 · Cited by 171 · see citing works
“…of bile-tolerant organisms (e.g., Bacteroides) and/or plant polysaccharide metabolizers (e.g., Prevotella) have been observed among individuals consuming vegan, vegetarian, and ‘omnivorous’ diets (Zimmer et al., 2012), as well as between rural and urban populations (Yatsunenko et al., 2012).”
The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile
Biagi, E., Rampelli, S., Turroni, S., Quercia, S., Candela, M., & Brigidi, P. (2017) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2016.12.013 · Cited by 166 · see citing works
Association between the gut microbiota and diet: Fetal life, early childhood, and further life
Kashtanova, D. A., Popenko, A., Ткачева, О. Н., Tyakht, A., Alexeev, D. G., & Boytsov, S. A. (2016) · Nutrition · doi:10.1016/j.nut.2015.12.037 · Cited by 166 · see citing works
Linking dietary patterns with gut microbial composition and function
Sheflin, A. M., Melby, C. L., Carbonero, F., & Weir, T. L. (2017) · Gut Microbes · doi:10.1080/19490976.2016.1270809 · Cited by 162 · see citing works
“For example, in a comparative study of vegans, lacto-ovo vegetarians, and omnivores, Zimmer et al.20 used culture-based methods and found lower counts of Bacteroides spp., Bifodobacterium spp, E. coli, and Enterobacteriaceae (P D 0.001, P D 0.002, P D 0.006 and P D 0.008, respectively) in vegans compared with the non-…”
ResultInfluentialGut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities
Pandey, H., Tang, D. W. T., Wong, S. H., & Lal, D. (2023) · Cancers · doi:10.3390/cancers15030866 · Cited by 165 · see citing works
Lin, R., Piao, M., & Song, Y. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01092 · Cited by 161 · see citing works
“stated that strict vegan or vegetarian diets significantly decrease Bacteroides, Enterobacteriaceae, and Bifidobacterium populations (Zimmer et al., 2012).”
BackgroundChu, F., Shi, M., Lang, Y., Shen, D., Jin, T., Zhu, J., & Cui, L. (2018) · Mediators of Inflammation · doi:10.1155/2018/8168717 · Cited by 159 · see citing works
Jefferson, A., & Adolphus, K. (2019) · Frontiers in Nutrition · doi:10.3389/fnut.2019.00033 · Cited by 149 · see citing works
Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation
Korpela, K. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012830 · Cited by 153 · see citing works
“The overall fermentation and organic acid production slow down along the length of the colon, and the pH increases, allowing the acid-sensitive Bacteroides and Proteobacteria to increase in abundance (Duncan et al. 2009, Walker et al. 2005).”
BackgroundInfluentialCharoensiddhi, S., Conlon, M. A., Franco, C. M. M., & Zhang, W. Y. (2017) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2017.10.002 · Cited by 148 · see citing works
Intestinal Microbiota as a Contributor to Chronic Inflammation and Its Potential Modifications
Potrykus, M., Czaja-Stolc, S., Stankiewicz, M., Kaska, Ł., & Małgorzewicz, S. (2021) · Nutrients · doi:10.3390/nu13113839 · Cited by 146 · see citing works
“In people on a plant-based diet, the amounts of Bifidobacteria, Escherichia coli, and Enterobacteria were lower than in omnivores [52,53].”
BackgroundCorrelation of diet, microbiota and metabolite networks in inflammatory bowel disease
Yi, W., Gan, H. Y., Li, X., Huang, Y., Li, Z. C., Deng, H., Chen, S. Z., Zhou, Y. J., Wang, L. S., Han, Y. P., et al. (2019) · Journal of Digestive Diseases · doi:10.1111/1751-2980.12795 · Cited by 142 · see citing works
“Compared with short-term changes, long-term dietary patterns affect more significantly the ratios of Firmicutes, Bacteroides, and Prevotella in the gut;(7) while a strict vegan or vegetarian diet is associated with an obvious decrease in the abundance of Enterobacteriaceae, Bacteroides, and Bifidobacterium species.(8)…”
BackgroundModulation of Gut Microbiota in the Management of Metabolic Disorders: The Prospects and Challenges
Erejuwa, O. O., Sulaiman, S. A., & Wahab, M. S. A. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms15034158 · Cited by 136 · see citing works
“The type of diet (whether vegetarian diet or Western diet) may alter the gut microbiota composition [116].”
BackgroundHabitual Dietary Intake Is Associated with Stool Microbiota Composition in Monozygotic Twins
Simões, C., Maukonen, J., Kaprio, J. A., Rissanen, A., Pietiläinen, K. H., & Saarela, M. (2013) · Journal of Nutrition · doi:10.3945/jn.112.166322 · Cited by 137 · see citing works
“, vegetarians or vegans versus omnivores (9,10)] or from geographically distinct areas (11,12) have been characterized.”
BackgroundDiet, the intestinal microbiota, and immune health in aging
Clements, S. J., & Carding, S. R. (2016) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2016.1211086 · Cited by 163 · see citing works
“One comparative study showed a significant reduction in Enterobacteriaceae in vegans compared with omnivorous control subjects (Zimmer et al., 2012).”
The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders?
Ochoa‐Repáraz, J., & Kasper, L. H. (2016) · Current Obesity Reports · doi:10.1007/s13679-016-0191-1 · Cited by 134 · see citing works
Peng, Y., Yan, Y., Wan, P., Dong, W., Huang, K., Ran, L., Mi, J., Lu, L., Zeng, X., & Cao, Y. (2019) · Food Research International · doi:10.1016/j.foodres.2019.108952 · Cited by 132 · see citing works
de León-Rodríguez, M. D. C. P., Guyot, J., & Laurent-Babot, C. (2018) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2018.1506734 · Cited by 129 · see citing works
“In addition to dietary factors, TJ and immune dysregulation and a potential microbiota disequilibrium, genetic, environmental and socioeconomic factors may also influence the development of IBD and are reviewed elsewhere (Cho 2008; Khor, Gardet, and Xavier 2011; Liu and Stappenbeck 2016; Ng et al. 2013).”
BackgroundInfluentialVegetable-Based Diets for Chronic Kidney Disease? It Is Time to Reconsider
Cases, A., Cigarrán, S., Mas, S., & González‐Parra, E. (2019) · Nutrients · doi:10.3390/nu11061263 · Cited by 126 · see citing works
“In contrast, in vegan or vegetarian patients there is a reduced abundance of pathobionts and a greater abundance of symbionts [25].”
BackgroundFrame, L. A., Costa, E., & Jackson, S. A. (2019) · Nutrition Reviews · doi:10.1093/nutrit/nuz106 · Cited by 127 · see citing works
The influence of antibiotics and dietary components on gut microbiota
Dudek-Wicher, R. K., Junka, A., & Bartoszewicz, M. (2018) · Gastroenterology Review · doi:10.5114/pg.2018.76005 · Cited by 126 · see citing works
A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes
Davis‐Richardson, A. G., & Triplett, E. W. (2015) · Diabetologia · doi:10.1007/s00125-015-3614-8 · Cited by 126 · see citing works
Reischer, G. H., Ebdon, J., Bauer, J. M., Schuster, N., Ahmed, W., Åström, J., Blanch, A. R., Blöschl, G., Byamukama, D., Coakley, T., et al. (2013) · Environmental Science & Technology · doi:10.1021/es304367t · Cited by 124 · see citing works
Nutrition and Genetics in NAFLD: The Perfect Binomium
Meroni, M., Longo, M., Rustichelli, A., & Dongiovanni, P. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082986 · Cited by 122 · see citing works
“Indeed, fecal samples of vegan and vegetarian individuals showed a significant decrease in Bidifobacterium and Bacteroides species, as well as Africans fed a high-carbohydrate vegetarian diet compared to English subjects assuming a mixed Western diet [155,156].”
BackgroundDismicrobism in inflammatory bowel disease and colorectal cancer: Changes in response of colocytes
Tomasello, G. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i48.18121 · Cited by 122 · see citing works
Ijssennagger, N., Derrien, M., van Doorn, G. M., Rijnierse, A., van den Bogert, B., Müller, M. M., Dekker, J. P., Kleerebezem, M., & van der Meer, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049868 · Cited by 121 · see citing works
Zheng, J., Hoffman, K. L., Chen, J., Shivappa, N., Sood, A., Browman, G. J., Dirba, D. D., Hanash, S., Wei, P., Hébert, J. R., et al. (2020) · British Journal Of Nutrition · doi:10.1017/s0007114520001853 · Cited by 119 · see citing works
Campmans-Kuijpers, M. J. E., & Dijkstra, G. D. H. (2021) · Nutrients · doi:10.3390/nu13041067 · Cited by 116 · see citing works
“The faecal microbiota of vegetarians and vegans showed lower abundance of Bifidobacteria and Bacteroides species than omnivores living on the same continent [39].”
BackgroundDiet Effects in Gut Microbiome and Obesity
Chen, J., He, X., & Huang, J. (2014) · Journal of Food Science · doi:10.1111/1750-3841.12397 · Cited by 116 · see citing works
Pathogenesis of Crohn's disease
Boyapati, R. K., Satsangi, J. J., & Ho, G. (2015) · F1000Prime Reports · doi:10.12703/p7-44 · Cited by 109 · see citing works
Spooren, C. E. G. M., Pierik, M. J., Zeegers, M. P., Feskens, E. J. M., Masclee, A., & Jonkers, D. M. A. E. (2013) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.12501 · Cited by 110 · see citing works
Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans
Link, V. M., Subramanian, P., Cheung, F., Han, K. L., Stacy, A., Chi, L., Sellers, B. A., Koroleva, G., Courville, A. B., Mistry, S., et al. (2024) · Nature Medicine · doi:10.1038/s41591-023-02761-2 · Cited by 109 · see citing works
Ferrocino, I., Di Cagno, R., De Angelis, M., Turroni, S., Vannini, L., Bancalari, E., Rantsiou, K., Cardinali, G., Neviani, E., & Cocolin, L. (2015) · PLOS ONE · doi:10.1371/journal.pone.0128669 · Cited by 107 · see citing works
“However, in a recent study it has been reported that there was no significant difference for Bifidobacterium between the three diets [35].”
BackgroundResultHerstad, K., Gajardo, K., Bakke, A., Moe, L., Ludvigsen, J., Rudi, K., Rud, I., Sekelja, M., & Skancke, E. (2017) · BMC Veterinary Research · doi:10.1186/s12917-017-1073-9 · Cited by 85 · see citing works
“Especially the fermentation of non-digestible carbohydrates by the colonic bacteria results in the formation of short chain fatty acids (SCFAs), mainly acetate, propionate and butyrate, and a lowering of the colonic pH [11, 15].”
BackgroundThe Role of Microbiome in Brain Development and Neurodegenerative Diseases
Nandwana, V., Nandwana, N. K., Das, Y., Saito, M., Panda, T., Das, S., Almaguel, F. A., Hosmane, N. S., & Das, B. C. (2022) · Molecules · doi:10.3390/molecules27113402 · Cited by 113 · see citing works
Díez-Sainz, E., Milagro, F. I., Riezu‐Boj, J. I., & Lorente‐Cebrián, S. (2021) · Journal of Physiology and Biochemistry · doi:10.1007/s13105-021-00837-6 · Cited by 104 · see citing works
“Therefore, promotion of a specific gut microbiota composition profile has been established for a wide range of diets, such as vegan/vegetarian diet, gluten-free diet, Western diet, or Mediterranean diet, which have an impact on metabolism and gut barrier and immune functions [2, 51, 110, 135].”
BackgroundCommunal living: glycan utilization by the human gut microbiota
Briggs, J. A., Grondin, J. M., & Brumer, H. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15317 · Cited by 103 · see citing works
“Interestingly, those consuming entirely plant-based (vegan) diets were found to have substantially lower populations of Bifidobacterium species in their faecal microbiota (Zimmer et al., 2012), hinting at the hierarchal consumption of polysaccharides within the gut ecosystem.”
Background
- Authors
- Zimmer, J., Lange, B., Frick, J.-S., Sauer, H., Zimmermann, K., Schwiertz, A., Rusch, K., Klosterhalfen, S., & Enck, P.
- Affiliations
- Universitätsklinikum Tübingen (DE)
- Herford Hospital (DE)
- Institut für Mikroökologie (DE)
- Corresponding author
- Enck, P
- Venue
- European Journal of Clinical Nutrition
- Published
- 2011-08-03
- Volume
- 66
- Issue
- 1
- Pages
- 53-60
- ISSN
- 0954-3007 (ISSN-L)
- 1476-5640
- OpenAlex
- W2152289100
- Cited by
- 465
- References
- 31
- Citations by year
- 2026: 11 · 2025: 11 · 2024: 31 · 2023: 35 · 2022: 35 · 2021: 48 · 2020: 52 · 2019: 49 · 2018: 45 · 2017: 48 · 2016: 27 · 2015: 27 · 2014: 27 · 2013: 13 · 2012: 5
- FWCI
- 5.82
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- European Journal of Clinical Nutrition (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Trinity's Access to Research Output (TARA) (Trinity College Dublin) (submittedVersion)
- Funders
- Eberhard Karls Universität Tübingen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- vegan diet, vegetarian diet, gut microbiota, fecal microbiota, diet and microbiome, Bacteroides, Bifidobacterium, Escherichia coli, Enterobacteriaceae, fecal pH, anaerobic bacteria, omnivorous diet
- MeSH terms
- Adult, Aged, Bacteria, Colon, Feces, Female, Humans, Hydrogen-Ion Concentration, Male, Middle Aged, Diet, Vegetarian, Colony Count, Microbial, Case-Control Studies, Metagenome
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