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Connection between Microbiome, Lifestyle and Diet

A topical collection in Nutrients (ISSN 2072-6643). This collection belongs to the section "Nutritional Immunology".

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Editors


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Guest Editor
Institite of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
Interests: gastrointestinal barrier; immunomodulation; microbiota; immunonutrition; allergy; gastrointestinal inflammation
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
D&R Institute of Pathology, Medical University of Graz, MedCampus, A-8010 Graz, Austria
Interests: metabolism; metabolic liver disease; mitochondrial function; microbiome–metabolism interaction; gut–liver axis

Topical Collection Information

Dear Colleagues,

Over the past 10 years, microbiome research has yielded tremendous insights into the composition of the gut microbiome and has identified possible associations between the gut microbiome and several nutrition- and/or lifestyle-related diseases. A growing body of evidence suggests that the intestinal microbiome modulates the risk of several chronic diseases, including type 2 diabetes, allergy, cardiovascular disease, systemic low-grade inflammation (obesity, inflammaging), inflammatory bowel disease, and colorectal cancer. Dietary habits and nutrient composition influence the chronic disease risk and modulate the composition and function of the gut microbiome. However, detailed knowledge on the relationship between the diet, the microbiome, and chronic disease risk is still limited. Many confounding factors influence the associations of the gut microbiome with disease and require large study groups to determine a more direct relation. Through this Special Issue, we aim to provide a collection of authoritative updates on the association between health, nutrition and the body’s microbiota, which represents a rapidly developing field, addressing the topic from multiple aspects and involving scientists specialized in different fields of health- or disease-associated microbiology, immunology and nutrition research.

Dr. Eva Untersmayr
Dr. Peter M. Abuja
Guest Editors

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Keywords

  • microbiota
  • dietary influences
  • metabolism
  • healthy aging
  • disease prevention

Published Papers (24 papers)

2023

Jump to: 2022, 2021, 2020

28 pages, 7377 KiB  
Article
Basal Diet Fed to Recipient Mice Was the Driving Factor for Colitis and Colon Tumorigenesis, despite Fecal Microbiota Transfer from Mice with Severe or Mild Disease
by Daphne M. Rodriguez, Korry J. Hintze, Giovanni Rompato, Eliza C. Stewart, Abbey H. Barton, Emily Mortensen-Curtis, Porter A. Green, Arnaud J. Van Wettere, Aaron J. Thomas and Abby D. Benninghoff
Nutrients 2023, 15(6), 1338; https://doi.org/10.3390/nu15061338 - 09 Mar 2023
Viewed by 1723
Abstract
Consumption of the total Western diet (TWD) in mice has been shown to increase gut inflammation, promote colon tumorigenesis, and alter fecal microbiome composition when compared to mice fed a healthy diet, i.e., AIN93G (AIN). However, it is unclear whether the gut microbiome [...] Read more.
Consumption of the total Western diet (TWD) in mice has been shown to increase gut inflammation, promote colon tumorigenesis, and alter fecal microbiome composition when compared to mice fed a healthy diet, i.e., AIN93G (AIN). However, it is unclear whether the gut microbiome contributes directly to colitis-associated CRC in this model. The objective of this study was to determine whether dynamic fecal microbiota transfer (FMT) from donor mice fed either the AIN basal diet or the TWD would alter colitis symptoms or colitis-associated CRC in recipient mice, which were fed either the AIN diet or the TWD, using a 2 × 2 factorial experiment design. Time-matched FMT from the donor mice fed the TWD did not significantly enhance symptoms of colitis, colon epithelial inflammation, mucosal injury, or colon tumor burden in the recipient mice fed the AIN diet. Conversely, FMT from the AIN-fed donors did not impart a protective effect on the recipient mice fed the TWD. Likewise, the composition of fecal microbiomes of the recipient mice was also affected to a much greater extent by the diet they consumed than by the source of FMT. In summary, FMT from the donor mice fed either basal diet with differing colitis or tumor outcomes did not shift colitis symptoms or colon tumorigenesis in the recipient mice, regardless of the basal diet they consumed. These observations suggest that the gut microbiome may not contribute directly to the development of disease in this animal model. Full article
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2022

Jump to: 2023, 2021, 2020

11 pages, 661 KiB  
Article
FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota
by Paola Zinno, Francesco Maria Calabrese, Emily Schifano, Paolo Sorino, Raffaella Di Cagno, Marco Gobbetti, Eugenio Parente, Maria De Angelis and Chiara Devirgiliis
Nutrients 2022, 14(21), 4581; https://doi.org/10.3390/nu14214581 - 01 Nov 2022
Cited by 3 | Viewed by 2016
Abstract
Background: Fermented foods are attracting increasing interest due to their nutritional and health benefits, including a positive impact on gut microbiota exerted by their associated microbes. However, information relative to traditional fermented dairy products, along with their autochthonous microbiota, is still fragmented and [...] Read more.
Background: Fermented foods are attracting increasing interest due to their nutritional and health benefits, including a positive impact on gut microbiota exerted by their associated microbes. However, information relative to traditional fermented dairy products, along with their autochthonous microbiota, is still fragmented and poorly standardized. Therefore, our aim was to collect and aggregate data useful for obtaining a comprehensive overview translated in a classical database interface that can be easily handled by users. Methods: a preliminary inventory was built up by systematically collecting data from publicly available resources for the creation of a list of traditional dairy foods produced worldwide, including additional metadata useful for stratifying, and collapsing subgroups. Results: we developed the Fermented Dairy Food Database (FDF-DB), a feasible resource comprising 1852 traditional dairy foods (cheeses, fermented milks, and yogurt) for which microbial content and other associated metadata such as geographical indication label, country/region of origin, technological aspects were gathered. Conclusions: FDF-DB is a useful and user-friendly resource where taxonomic information and processing production details converge. This resource will be of great aid for researchers, food industries, stakeholders and any user interested in the identification of technological and microbiological features characterizing traditional fermented dairy products. Full article
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25 pages, 2581 KiB  
Review
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept
by Itai Sharon, Narciso Martín Quijada, Edoardo Pasolli, Marco Fabbrini, Francesco Vitali, Valeria Agamennone, Andreas Dötsch, Evelyne Selberherr, José Horacio Grau, Martin Meixner, Karsten Liere, Danilo Ercolini, Carlotta de Filippo, Giovanna Caderni, Patrizia Brigidi and Silvia Turroni
Nutrients 2022, 14(14), 2872; https://doi.org/10.3390/nu14142872 - 13 Jul 2022
Cited by 15 | Viewed by 8734
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to [...] Read more.
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome. Full article
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26 pages, 1248 KiB  
Systematic Review
Effects of Dietary Fibers on Short-Chain Fatty Acids and Gut Microbiota Composition in Healthy Adults: A Systematic Review
by Valentina Vinelli, Paola Biscotti, Daniela Martini, Cristian Del Bo’, Mirko Marino, Tomás Meroño, Olga Nikoloudaki, Francesco Maria Calabrese, Silvia Turroni, Valentina Taverniti, Andrea Unión Caballero, Cristina Andrés-Lacueva, Marisa Porrini, Marco Gobbetti, Maria De Angelis, Patrizia Brigidi, Mariona Pinart, Katharina Nimptsch, Simone Guglielmetti and Patrizia Riso
Nutrients 2022, 14(13), 2559; https://doi.org/10.3390/nu14132559 - 21 Jun 2022
Cited by 30 | Viewed by 6282
Abstract
There is an increasing interest in investigating dietary strategies able to modulate the gut microbial ecosystem which, in turn, may play a key role in human health. Dietary fibers (DFs) are widely recognized as molecules with prebiotic effects. The main objective of this [...] Read more.
There is an increasing interest in investigating dietary strategies able to modulate the gut microbial ecosystem which, in turn, may play a key role in human health. Dietary fibers (DFs) are widely recognized as molecules with prebiotic effects. The main objective of this systematic review was to: (i) analyze the results available on the impact of DF intervention on short chain fatty acids (SCFAs) production; (ii) evaluate the interplay between the type of DF intervention, the gut microbiota composition and its metabolic activities, and any other health associated outcome evaluated in the host. To this aim, initially, a comprehensive database of literature on human intervention studies assessing the effect of confirmed and candidate prebiotics on the microbial ecosystem was developed. Subsequently, studies performed on DFs and analyzing at least the impact on SCFA levels were extracted from the database. A total of 44 studies from 42 manuscripts were selected for the analysis. Among the different types of fiber, inulin was the DF investigated the most (n = 11). Regarding the results obtained on the ability of fiber to modulate total SCFAs, seven studies reported a significant increase, while no significant changes were reported in five studies, depending on the analytical methodology used. A total of 26 studies did not show significant differences in individual SCFAs, while the others reported significant differences for one or more SCFAs. The effect of DF interventions on the SCFA profile seemed to be strictly dependent on the dose and the type and structure of DFs. Overall, these results underline that, although affecting microbiota composition and derived metabolites, DFs do not produce univocal significant increase in SCFA levels in apparently healthy adults. In this regard, several factors (i.e., related to the study protocols and analytical methods) have been identified that could have affected the results obtained in the studies evaluated. Future studies are needed to better elucidate the relationship between DFs and gut microbiota in terms of SCFA production and impact on health-related markers. Full article
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76 pages, 6791 KiB  
Review
Medicinal Plants and Their Impact on the Gut Microbiome in Mental Health: A Systematic Review
by Eva-Maria Pferschy-Wenzig, Manuela R. Pausan, Karin Ardjomand-Woelkart, Stefanie Röck, Ramy M. Ammar, Olaf Kelber, Christine Moissl-Eichinger and Rudolf Bauer
Nutrients 2022, 14(10), 2111; https://doi.org/10.3390/nu14102111 - 18 May 2022
Cited by 14 | Viewed by 9621
Abstract
Background: Various neurocognitive and mental health-related conditions have been associated with the gut microbiome, implicating a microbiome–gut–brain axis (MGBA). The aim of this systematic review was to identify, categorize, and review clinical evidence supporting medicinal plants for the treatment of mental disorders and [...] Read more.
Background: Various neurocognitive and mental health-related conditions have been associated with the gut microbiome, implicating a microbiome–gut–brain axis (MGBA). The aim of this systematic review was to identify, categorize, and review clinical evidence supporting medicinal plants for the treatment of mental disorders and studies on their interactions with the gut microbiota. Methods: This review included medicinal plants for which clinical studies on depression, sleeping disorders, anxiety, or cognitive dysfunction as well as scientific evidence of interaction with the gut microbiome were available. The studies were reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Results: Eighty-five studies met the inclusion criteria and covered thirty mental health-related medicinal plants with data on interaction with the gut microbiome. Conclusion: Only a few studies have been specifically designed to assess how herbal preparations affect MGBA-related targets or pathways. However, many studies provide hints of a possible interaction with the MGBA, such as an increased abundance of health-beneficial microorganisms, anti-inflammatory effects, or MGBA-related pathway effects by gut microbial metabolites. Data for Panax ginseng, Schisandra chinensis, and Salvia rosmarinus indicate that the interaction of their constituents with the gut microbiota could mediate mental health benefits. Studies specifically assessing the effects on MGBA-related pathways are still required for most medicinal plants. Full article
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10 pages, 842 KiB  
Concept Paper
The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit?
by Conny Stumptner, Vanessa Stadlbauer, Dominic O’Neil, André Gessner, Andreas Hiergeist, Kurt Zatloukal and Peter M. Abuja
Nutrients 2022, 14(9), 1976; https://doi.org/10.3390/nu14091976 - 09 May 2022
Cited by 1 | Viewed by 2521
Abstract
Recently, CEN/TS 17626:2021, the European pre-analytical standard for human specimens intended for microbiome DNA analysis, was published. Although this standard relates to diagnostic procedures for microbiome analysis and is relevant for in vitro diagnostic (IVD) manufacturers and diagnostic laboratories, it also has implications [...] Read more.
Recently, CEN/TS 17626:2021, the European pre-analytical standard for human specimens intended for microbiome DNA analysis, was published. Although this standard relates to diagnostic procedures for microbiome analysis and is relevant for in vitro diagnostic (IVD) manufacturers and diagnostic laboratories, it also has implications for research and development (R&D). We present here why standards are needed in biomedical research, what pre-analytical standards can accomplish, and which elements of the pre-analytical workflow they cover. The benefits of standardization for the generation of FAIR (findable, accessible, interoperable, reusable) data and to support innovation are briefly discussed. Full article
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12 pages, 457 KiB  
Article
HDHL-INTIMIC: A European Knowledge Platform on Food, Diet, Intestinal Microbiomics, and Human Health
by Valeria Agamennone, Peter M. Abuja, Marijana Basic, Maria De Angelis, André Gessner, Bart Keijser, Martin Larsen, Mariona Pinart, Katharina Nimptsch, Estelle Pujos-Guillot, Kristina Schlicht, Itai Sharon, Eva Untersmayr, Matthias Laudes, Tobias Pischon, Jildau Bouwman and on behalf of the Consortium
Nutrients 2022, 14(9), 1881; https://doi.org/10.3390/nu14091881 - 29 Apr 2022
Cited by 3 | Viewed by 2274
Abstract
Studies indicate that the intestinal microbiota influences general metabolic processes in humans, thereby modulating the risk of chronic diseases such as type 2 diabetes, allergy, cardiovascular disease, and colorectal cancer (CRC). Dietary factors are also directly related to chronic disease risk, and they [...] Read more.
Studies indicate that the intestinal microbiota influences general metabolic processes in humans, thereby modulating the risk of chronic diseases such as type 2 diabetes, allergy, cardiovascular disease, and colorectal cancer (CRC). Dietary factors are also directly related to chronic disease risk, and they affect the composition and function of the gut microbiota. Still, detailed knowledge on the relation between diet, the microbiota, and chronic disease risk is limited. The overarching aim of the HDHL-INTIMIC (INtesTInal MICrobiomics) knowledge platform is to foster studies on the microbiota, nutrition, and health by assembling available knowledge of the microbiota and of the other aspects (e.g., food science and metabolomics) that are relevant in the context of microbiome research. The goal is to make this information findable, accessible, interoperable, and reusable (FAIR) to the scientific community, and to share information with the various stakeholders. Through these efforts a network of transnational and multidisciplinary collaboration has emerged, which has contributed to further develop and increase the impact of microbiome research in human health. The roles of microbiota in early infancy, during ageing, and in subclinical and clinically manifested disease are identified as urgent areas of research in this knowledge platform. Full article
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11 pages, 2143 KiB  
Article
A Comprehensive Analysis of Plasma Cytokines and Metabolites Shows an Association between Galectin-9 and Changes in Peripheral Lymphocyte Subset Percentages Following Coix Seed Consumption
by Yoshio Suzuki, Taisei Miyahara, Minami Jinnouchi, Yoshiki Miura, Hikari Taka, Naoko Kaga and Akiko Ohara-Takada
Nutrients 2022, 14(9), 1696; https://doi.org/10.3390/nu14091696 - 19 Apr 2022
Cited by 1 | Viewed by 1537
Abstract
We previously reported that healthy adult males who consumed coix seeds for 1 week demonstrated an increased intestinal abundance of Faecalibacterium prausnitzii and altered peripheral lymphocyte subset percentages. However, the mechanism underlining these effects has not been elucidated. Therefore, cytokines and metabolites in [...] Read more.
We previously reported that healthy adult males who consumed coix seeds for 1 week demonstrated an increased intestinal abundance of Faecalibacterium prausnitzii and altered peripheral lymphocyte subset percentages. However, the mechanism underlining these effects has not been elucidated. Therefore, cytokines and metabolites in plasma obtained in this study are comprehensively analyzed. A total of 56 cytokines and 52 metabolites in the plasma are quantified. Among them, 14 cytokines and 9 metabolites show significant changes in their levels following coix seed consumption. We examine the relationship between these changes and those in peripheral lymphocyte subset percentages and intestinal abundance of F. prausnitzii, which is also considerably altered following coix seed consumption. The galectin-9 concentration considerably decreased after coix seed consumption, and these changes correlate with those in cytotoxic T cells and pan T cells. Therefore, galectin-9 is possibly involved in the changes in peripheral lymphocyte subset percentages induced by coix seed consumption. Full article
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23 pages, 2722 KiB  
Article
Preventive Effect of a Postbiotic and Prebiotic Mixture in a Rat Model of Early Life Rotavirus Induced-Diarrhea
by Carla Morales-Ferré, Ignasi Azagra-Boronat, Malén Massot-Cladera, Sebastian Tims, Karen Knipping, Johan Garssen, Jan Knol, Àngels Franch, Margarida Castell, Francisco J. Pérez-Cano and María J. Rodríguez-Lagunas
Nutrients 2022, 14(6), 1163; https://doi.org/10.3390/nu14061163 - 10 Mar 2022
Cited by 9 | Viewed by 2807
Abstract
Rotavirus (RV) is the main cause of gastroenteritis in children. Prebiotics and, more recently, postbiotics are used for preventing and treating gastrointestinal infections. The aim of this study was to analyze the effects of a LactofidusTM, short-chain galacto-oligosaccharides (scGOS) and long-chain [...] Read more.
Rotavirus (RV) is the main cause of gastroenteritis in children. Prebiotics and, more recently, postbiotics are used for preventing and treating gastrointestinal infections. The aim of this study was to analyze the effects of a LactofidusTM, short-chain galacto-oligosaccharides (scGOS) and long-chain fructo-oligosaccharides (lcFOS) mixture, and their combination on RV infection, in a rat model, for early life diarrhea. Fifteen litters of suckling rats were intragastrically administered daily with the vehicle, the prebiotic mixture, the postbiotic or the combination. The RV was inoculated on day 5 and then fecal samples were clinically evaluated daily. Viral shedding, intestinal permeability assay, in vitro blocking assay, immunoglobulin profiles, and anti-RV response were assessed at day 8 and 16 of life. Cecal microbiota composition, intestinal gene expression, and short chain fatty acids (SCFAs) were analyzed at day 16. The incidence and severity of diarrhea were significantly reduced by all the supplementations. Moreover, they showed blocking activity, changes in the immunoglobulin profiles, in gut microbiota, and in the intestinal gene expression. The prebiotic mixture reduced gut permeability and changed the SCFA profile, whereas the postbiotic enhanced the expression of Toll-like receptors (TLRs). The combination preserved most of the individual observed effects, and furthermore, complementary effects, such as an increase in white blood cells and lymphocytes recruitment, as well as upregulation of TLR7 and TLR9 gene expression. Full article
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20 pages, 832 KiB  
Review
The Intestinal Barrier Dysfunction as Driving Factor of Inflammaging
by Eva Untersmayr, Annette Brandt, Larissa Koidl and Ina Bergheim
Nutrients 2022, 14(5), 949; https://doi.org/10.3390/nu14050949 - 23 Feb 2022
Cited by 25 | Viewed by 7862
Abstract
The intestinal barrier, composed of the luminal microbiota, the mucus layer, and the physical barrier consisting of epithelial cells and immune cells, the latter residing underneath and within the epithelial cells, plays a special role in health and disease. While there is growing [...] Read more.
The intestinal barrier, composed of the luminal microbiota, the mucus layer, and the physical barrier consisting of epithelial cells and immune cells, the latter residing underneath and within the epithelial cells, plays a special role in health and disease. While there is growing knowledge on the changes to the different layers associated with disease development, the barrier function also plays an important role during aging. Besides changes in the composition and function of cellular junctions, the entire gastrointestinal physiology contributes to essential age-related changes. This is also reflected by substantial differences in the microbial composition throughout the life span. Even though it remains difficult to define physiological age-related changes and to distinguish them from early signs of pathologies, studies in centenarians provide insights into the intestinal barrier features associated with longevity. The knowledge reviewed in this narrative review article might contribute to the definition of strategies to prevent the development of diseases in the elderly. Thus, targeted interventions to improve overall barrier function will be important disease prevention strategies for healthy aging in the future. Full article
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15 pages, 2469 KiB  
Article
Effect of Different Functional Food Supplements on the Gut Microbiota of Prediabetic Indonesian Individuals during Weight Loss
by Ingrid S. Surono, Abraham Simatupang, Pratiwi D. Kusumo, Priyo Waspodo, Sanne Verbruggen, Jessica Verhoeven and Koen Venema
Nutrients 2022, 14(4), 781; https://doi.org/10.3390/nu14040781 - 13 Feb 2022
Cited by 5 | Viewed by 2710
Abstract
The gut microbiota has been shown in recent years to be involved in the development and severity of type 2 diabetes (T2D). The aim of the present study was to test the effect of a 2-week functional food intervention on the gut microbiota [...] Read more.
The gut microbiota has been shown in recent years to be involved in the development and severity of type 2 diabetes (T2D). The aim of the present study was to test the effect of a 2-week functional food intervention on the gut microbiota composition in prediabetic individuals. A randomized double-blind, cross-over trial was conducted on prediabetic subjects. Fifteen volunteers were provided products made of: (i) 50% taro flour + 50% wheat flour; (ii) these products and the probiotic L. plantarum IS-10506; or (iii) these products with beetroot adsorbed for a period of 2 weeks with 2 weeks wash-out in between. Stool and blood samples were taken at each baseline and after each of the interventions. The gut microbiota composition was evaluated by sequencing the V3–V4 region of the 16S rRNA gene and anthropometric measures were recorded. The total weight loss over the entire period ranged from 0.5 to 11 kg. The next-generation sequencing showed a highly personalized microbiota composition. In the principal coordinate analyses, the samples of each individual clustered closer together than the samples of each treatment. For six individuals, the samples clustered closely together, indicating a stable microbiota. For nine individuals, the microbiota was less resilient and, depending on the intervention, the beta-diversity transiently differed greatly only to return to the composition close to the baseline during the wash-out. The statistical analyses showed that 202 of the total 304 taxa were significantly different between the participants. Only Butyricimonas could be correlated with taro ingestion. The results of the study show that the highly variable interindividual variation observed in the gut microbiota of the participants clouded any gut microbiota modulation that might be present due to the functional food interventions. Full article
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2021

Jump to: 2023, 2022, 2020

17 pages, 591 KiB  
Review
Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review
by Francesco Maria Calabrese, Annalisa Porrelli, Mirco Vacca, Blandine Comte, Katharina Nimptsch, Mariona Pinart, Tobias Pischon, Estelle Pujos-Guillot and Maria De Angelis
Nutrients 2022, 14(1), 47; https://doi.org/10.3390/nu14010047 - 23 Dec 2021
Cited by 8 | Viewed by 3482
Abstract
Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol [...] Read more.
Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies. Full article
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41 pages, 3726 KiB  
Review
Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis
by Mariona Pinart, Andreas Dötsch, Kristina Schlicht, Matthias Laudes, Jildau Bouwman, Sofia K. Forslund, Tobias Pischon and Katharina Nimptsch
Nutrients 2022, 14(1), 12; https://doi.org/10.3390/nu14010012 - 21 Dec 2021
Cited by 121 | Viewed by 10837
Abstract
Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing [...] Read more.
Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (−0.06, 95% CI −0.24, 0.12, I2 = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, I2 = 81%) and non-significantly lower Bacteroidetes (−4.79, 95% CI −10.77, 1.20, I2 = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers. Full article
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21 pages, 1143 KiB  
Review
Synthetic Microbiomes on the Rise—Application in Deciphering the Role of Microbes in Host Health and Disease
by Silvia Bolsega, André Bleich and Marijana Basic
Nutrients 2021, 13(11), 4173; https://doi.org/10.3390/nu13114173 - 21 Nov 2021
Cited by 10 | Viewed by 3695
Abstract
The intestinal microbiota conveys significant benefits to host physiology. Although multiple chronic disorders have been associated with alterations in the intestinal microbiota composition and function, it is still unclear whether these changes are a cause or a consequence. Hence, to translate microbiome research [...] Read more.
The intestinal microbiota conveys significant benefits to host physiology. Although multiple chronic disorders have been associated with alterations in the intestinal microbiota composition and function, it is still unclear whether these changes are a cause or a consequence. Hence, to translate microbiome research into clinical application, it is necessary to provide a proof of causality of host–microbiota interactions. This is hampered by the complexity of the gut microbiome and many confounding factors. The application of gnotobiotic animal models associated with synthetic communities allows us to address the cause–effect relationship between the host and intestinal microbiota by reducing the microbiome complexity on a manageable level. In recent years, diverse bacterial communities were assembled to analyze the role of microorganisms in infectious, inflammatory, and metabolic diseases. In this review, we outline their application and features. Furthermore, we discuss the differences between human-derived and model-specific communities. Lastly, we highlight the necessity of generating novel synthetic communities to unravel the microbial role associated with specific health outcomes and disease phenotypes. This understanding is essential for the development of novel non-invasive targeted therapeutic strategies to control and modulate intestinal microbiota in health and disease. Full article
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13 pages, 2900 KiB  
Article
A Citrus Fruit Extract High in Polyphenols Beneficially Modulates the Gut Microbiota of Healthy Human Volunteers in a Validated In Vitro Model of the Colon
by Mônica Maurer Sost, Sanne Ahles, Jessica Verhoeven, Sanne Verbruggen, Yala Stevens and Koen Venema
Nutrients 2021, 13(11), 3915; https://doi.org/10.3390/nu13113915 - 01 Nov 2021
Cited by 22 | Viewed by 4984
Abstract
The effect of a Citrus Fruit Extract high in the polyphenols hesperidin and naringin (CFE) on modulation of the composition and activity of the gut microbiota was tested in a validated, dynamic in vitro model of the colon (TIM-2). CFE was provided at [...] Read more.
The effect of a Citrus Fruit Extract high in the polyphenols hesperidin and naringin (CFE) on modulation of the composition and activity of the gut microbiota was tested in a validated, dynamic in vitro model of the colon (TIM-2). CFE was provided at two doses (250 and 350 mg/day) for 3 days. CFE led to a dose-dependent increase in Roseburia, Eubacterium ramulus, and Bacteroides eggerthii. There was a shift in production of short-chain fatty acids, where acetate production increased on CFE, while butyrate decreased. In overweight and obesity, acetate has been shown to increase fat oxidation when produced in the distal gut, and stimulate secretion of appetite-suppressive neuropeptides. Thus, the data in the in vitro model point towards mechanisms underlying the effects of the polyphenols in CFE with respect to modulation of the gut microbiota, both in composition and activity. These results should be confirmed in a clinical trial. Full article
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13 pages, 647 KiB  
Review
Microbiota in Health and Disease—Potential Clinical Applications
by Matthias Laudes, Corinna Geisler, Nathalie Rohmann, Jildau Bouwman, Tobias Pischon and Kristina Schlicht
Nutrients 2021, 13(11), 3866; https://doi.org/10.3390/nu13113866 - 29 Oct 2021
Cited by 9 | Viewed by 4533
Abstract
Within the last two decades tremendous efforts in biomedicine have been undertaken to understand the interplay of commensal bacteria living in and on our human body with our own human physiology. It became clear that (1) a high diversity especially of the microbial [...] Read more.
Within the last two decades tremendous efforts in biomedicine have been undertaken to understand the interplay of commensal bacteria living in and on our human body with our own human physiology. It became clear that (1) a high diversity especially of the microbial communities in the gut are important to preserve health and that (2) certain bacteria via nutrition-microbe-host metabolic axes are beneficially affecting various functions of the host, including metabolic control, energy balance and immune function. While a large set of evidence indicate a special role for small chain fatty acids (SCFA) in that context, recently also metabolites of amino acids (e.g., tryptophan and arginine) moved into scientific attention. Of interest, microbiome alterations are not only important in nutrition associated diseases like obesity and diabetes, but also in many chronic inflammatory, oncological and neurological abnormalities. From a clinician’s point of view, it should be mentioned, that the microbiome is not only interesting to develop novel therapies, but also as a modifiable factor to improve efficiency of modern pharmaceutics, e.g., immune-therapeutics in oncology. However, so far, most data rely on animal experiments or human association studies, whereas controlled clinical intervention studies are spare. Hence, the translation of the knowledge of the last decades into clinical routine will be the challenge of microbiome based biomedical research for the next years. This review aims to provide examples for future clinical applications in various entities and to suggest bacterial species and/or microbial effector molecules as potential targets for intervention studies. Full article
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21 pages, 2805 KiB  
Article
BMI, Alcohol Consumption and Gut Microbiome Species Richness Are Related to Structural and Functional Neurological Abnormalities
by Corinna Geisler, Jil Pankoke, Kristina Schlicht, Carina Knappe, Nathalie Rohmann, Katharina Hartmann, Ute Settgast, Kathrin Türk, Anna Katharina Seoudy, Andre Franke, Stefan Schreiber, Dominik M. Schulte and Matthias Laudes
Nutrients 2021, 13(11), 3743; https://doi.org/10.3390/nu13113743 - 23 Oct 2021
Cited by 2 | Viewed by 2715
Abstract
Background: The incidence of neurological diseases is increasing throughout the world. The aim of the present study was to identify nutrition and microbiome factors related to structural and functional neurological abnormalities to optimize future preventive strategies. Methods: Two hundred thirty-eight patients suffering from [...] Read more.
Background: The incidence of neurological diseases is increasing throughout the world. The aim of the present study was to identify nutrition and microbiome factors related to structural and functional neurological abnormalities to optimize future preventive strategies. Methods: Two hundred thirty-eight patients suffering from (1) structural (neurodegeneration) or (2) functional (epilepsy) neurological abnormalities or (3) chronic pain (migraine) and 612 healthy control subjects were analyzed by validated 12-month food frequency questionnaire (FFQ) and 16S rRNA microbiome sequencing (from stool samples). A binomial logistic regression model was applied for risk calculation and functional pathway analysis to show which functional pathway could discriminate cases and healthy controls. Results: Detailed analysis of more than 60 macro- and micronutrients revealed no distinct significant difference between cases and controls, whereas BMI, insulin resistance and metabolic inflammation in addition to alcohol consumption were major drivers of an overall neurological disease risk. The gut microbiome analysis showed decreased alpha diversity (Shannon index: p = 9.1× 10−7) and species richness (p = 1.2 × 10−8) in the case group as well as significant differences in beta diversity between cases and controls (Bray–Curtis: p = 9.99 × 10−4; Jaccard: p = 9.99 × 10−4). The Shannon index showed a beneficial effect (OR = 0.59 (95%-CI (0.40, 0.87); p = 8 × 10−3). Cases were clearly discriminated from healthy controls by environmental information processing, signal transduction, two component system and membrane transport as significantly different functional pathways. Conclusions: In conclusion, our data indicate that an overall healthy lifestyle, in contrast to supplementation of single micro- or macronutrients, is most likely to reduce overall neurological abnormality risk and that the gut microbiome is an interesting target to develop novel preventive strategies. Full article
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16 pages, 317 KiB  
Article
Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis
by Mariona Pinart, Katharina Nimptsch, Sofia K. Forslund, Kristina Schlicht, Miguel Gueimonde, Patrizia Brigidi, Silvia Turroni, Wolfgang Ahrens, Antje Hebestreit, Maike Wolters, Andreas Dötsch, Ute Nöthlings, Kolade Oluwagbemigun, Rafael R. C. Cuadrat, Matthias B. Schulze, Marie Standl, Michael Schloter, Maria De Angelis, Patricia Iozzo, Maria Angela Guzzardi, Geertrui Vlaemynck, John Penders, Daisy M. A. E. Jonkers, Maya Stemmer, Giulia Chiesa, Duccio Cavalieri, Carlotta De Filippo, Danilo Ercolini, Francesca De Filippis, David Ribet, Najate Achamrah, Marie-Pierre Tavolacci, Pierre Déchelotte, Jildau Bouwman, Matthias Laudes and Tobias Pischonadd Show full author list remove Hide full author list
Nutrients 2021, 13(9), 3292; https://doi.org/10.3390/nu13093292 - 21 Sep 2021
Cited by 5 | Viewed by 4040
Abstract
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational [...] Read more.
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease. Full article
21 pages, 637 KiB  
Review
Human Microbiota Network: Unveiling Potential Crosstalk between the Different Microbiota Ecosystems and Their Role in Health and Disease
by Jose E. Martínez, Augusto Vargas, Tania Pérez-Sánchez, Ignacio J. Encío, Miriam Cabello-Olmo and Miguel Barajas
Nutrients 2021, 13(9), 2905; https://doi.org/10.3390/nu13092905 - 24 Aug 2021
Cited by 24 | Viewed by 5578
Abstract
The human body is host to a large number of microorganisms which conform the human microbiota, that is known to play an important role in health and disease. Although most of the microorganisms that coexist with us are located in the gut, microbial [...] Read more.
The human body is host to a large number of microorganisms which conform the human microbiota, that is known to play an important role in health and disease. Although most of the microorganisms that coexist with us are located in the gut, microbial cells present in other locations (like skin, respiratory tract, genitourinary tract, and the vaginal zone in women) also play a significant role regulating host health. The fact that there are different kinds of microbiota in different body areas does not mean they are independent. It is plausible that connection exist, and different studies have shown that the microbiota present in different zones of the human body has the capability of communicating through secondary metabolites. In this sense, dysbiosis in one body compartment may negatively affect distal areas and contribute to the development of diseases. Accordingly, it could be hypothesized that the whole set of microbial cells that inhabit the human body form a system, and the dialogue between the different host microbiotas may be a contributing factor for the susceptibility to developing diseased states. For this reason, the present review aims to integrate the available literature on the relationship between the different human microbiotas and understand how changes in the microbiota in one body region can influence other microbiota communities in a bidirectional process. The findings suggest that the different microbiotas may act in a coordinated way to decisively influence human well-being. This new integrative paradigm opens new insights in the microbiota field of research and its relationship with human health that should be taken into account in future studies. Full article
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20 pages, 1821 KiB  
Article
Gut Microbiota Differences According to Ultra-Processed Food Consumption in a Spanish Population
by Amanda Cuevas-Sierra, Fermín I. Milagro, Paula Aranaz, Jose Alfredo Martínez and José I. Riezu-Boj
Nutrients 2021, 13(8), 2710; https://doi.org/10.3390/nu13082710 - 06 Aug 2021
Cited by 42 | Viewed by 10019
Abstract
Ultra-processed foods (UPFs) consumption could affect gut microbiota diversity and profile. We aimed to evaluate the effects of UPFs on microbiota, considering the role of sex. The consumption of UPFs (using NOVA criteria) was assessed with a validated 137-item food-frequency questionnaire. Participants ( [...] Read more.
Ultra-processed foods (UPFs) consumption could affect gut microbiota diversity and profile. We aimed to evaluate the effects of UPFs on microbiota, considering the role of sex. The consumption of UPFs (using NOVA criteria) was assessed with a validated 137-item food-frequency questionnaire. Participants (n = 359) were classified into less than three servings per day (n = 96) of UPFs and more than five (n = 90). Women and men were subclassified following the same criteria. 16S rRNA sequencing was performed from DNA fecal samples, and differences in microbiota were analyzed using EdgeR. The relationship between UPFs and bacteria was assessed by Spearman correlation and comparison of tertiles of consumption. Women who consumed more than five servings/day of UPFs presented an increase in Acidaminococcus, Butyrivibrio, Gemmiger, Shigella, Anaerofilum, Parabacteroides, Bifidobacterium, Enterobacteriales, Bifidobacteriales and Actinobacteria and a decrease in Melainabacter and Lachnospira. Bifidobacterium, Bifidobacteriales and Actinobacteria was positively associated with pizza and Actinobacteria with industrially processed dairy in women. Men who consumed more than five servings/day presented an increase of Granulicatella, Blautia, Carnobacteriaceae, Bacteroidaceae, Peptostreptococcaceae, Bacteroidia and Bacteroidetes and a decrease of Anaerostipes and Clostridiaceae. Bacteroidia and Bacteroidetes correlated positively with industrially processed meat. This study suggests that UPFs may affect microbiota composition differently in women and men. Full article
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18 pages, 2965 KiB  
Article
Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
by Chiara-Maria Homann, Connor A. J. Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best and Jennifer C. Stearns
Nutrients 2021, 13(8), 2639; https://doi.org/10.3390/nu13082639 - 30 Jul 2021
Cited by 21 | Viewed by 6299
Abstract
The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the [...] Read more.
The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food & Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray–Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced. Full article
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32 pages, 935 KiB  
Review
The Effects of Lifestyle and Diet on Gut Microbiota Composition, Inflammation and Muscle Performance in Our Aging Society
by Barbara Strasser, Maike Wolters, Christopher Weyh, Karsten Krüger and Andrea Ticinesi
Nutrients 2021, 13(6), 2045; https://doi.org/10.3390/nu13062045 - 15 Jun 2021
Cited by 53 | Viewed by 12550
Abstract
Living longer is associated with an increased risk of chronic diseases, including impairments of the musculoskeletal and immune system as well as metabolic disorders and certain cancers, each of which can negatively affect the relationship between host and microbiota up to the occurrence [...] Read more.
Living longer is associated with an increased risk of chronic diseases, including impairments of the musculoskeletal and immune system as well as metabolic disorders and certain cancers, each of which can negatively affect the relationship between host and microbiota up to the occurrence of dysbiosis. On the other hand, lifestyle factors, including regular physical exercise and a healthy diet, can affect skeletal muscle and immune aging positively at all ages. Accordingly, health benefits could partly depend on the effect of such interventions that influence the biodiversity and functionality of intestinal microbiota. In the present review, we first discuss the physiological effects of aging on the gut microbiota, immune system, and skeletal muscle. Secondly, we describe human epidemiological evidence about the associations between physical activity and fitness and the gut microbiota composition in older adults. The third part highlights the relevance and restorative mechanisms of immune protection through physical activity and specific exercise interventions during aging. Fourth, we present important research findings on the effects of exercise and protein as well as other nutrients on skeletal muscle performance in older adults. Finally, we provide nutritional recommendations to prevent malnutrition and support healthy active aging with a focus on gut microbiota. Key nutrition-related concerns include the need for adequate energy and protein intake for preventing low muscle mass and a higher demand for specific nutrients (e.g., dietary fiber, polyphenols and polyunsaturated fatty acids) that can modify the composition, diversity, and metabolic capacity of the gut microbiota, and may thus provide a practical means of enhancing gut and systemic immune function. Full article
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12 pages, 1608 KiB  
Article
Gut Microbiota Prevents Sugar Alcohol-Induced Diarrhea
by Kouya Hattori, Masahiro Akiyama, Natsumi Seki, Kyosuke Yakabe, Koji Hase and Yun-Gi Kim
Nutrients 2021, 13(6), 2029; https://doi.org/10.3390/nu13062029 - 12 Jun 2021
Cited by 9 | Viewed by 11049
Abstract
While poorly-absorbed sugar alcohols such as sorbitol are widely used as sweeteners, they may induce diarrhea in some individuals. However, the factors which determine an individual’s susceptibility to sugar alcohol-induced diarrhea remain unknown. Here, we show that specific gut bacteria are involved in [...] Read more.
While poorly-absorbed sugar alcohols such as sorbitol are widely used as sweeteners, they may induce diarrhea in some individuals. However, the factors which determine an individual’s susceptibility to sugar alcohol-induced diarrhea remain unknown. Here, we show that specific gut bacteria are involved in the suppression of sorbitol-induced diarrhea. Based on 16S rDNA analysis, the abundance of Enterobacteriaceae bacteria increased in response to sorbitol consumption. We found that Escherichia coli of the family Enterobacteriaceae degraded sorbitol and suppressed sorbitol-induced diarrhea. Finally, we showed that the metabolism of sorbitol by the E. coli sugar phosphotransferase system helped suppress sorbitol-induced diarrhea. Therefore, gut microbiota prevented sugar alcohol-induced diarrhea by degrading sorbitol in the gut. The identification of the gut bacteria which respond to and degrade sugar alcohols in the intestine has implications for microbiome science, processed food science, and public health. Full article
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2020

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19 pages, 979 KiB  
Review
The Gut Microbiome and the Big Eight
by Cassandra Suther, Matthew D. Moore, Avraham Beigelman and Yanjiao Zhou
Nutrients 2020, 12(12), 3728; https://doi.org/10.3390/nu12123728 - 03 Dec 2020
Cited by 17 | Viewed by 6365
Abstract
Food allergies are increasing at an alarming rate, with 6.5% of the general population affected. It has been hypothesized that the increase in allergies stems from the “hygiene hypothesis”. The gut microbiome, a collection of microbiota and their genetic contents from the gastrointestinal [...] Read more.
Food allergies are increasing at an alarming rate, with 6.5% of the general population affected. It has been hypothesized that the increase in allergies stems from the “hygiene hypothesis”. The gut microbiome, a collection of microbiota and their genetic contents from the gastrointestinal tract, has been shown to play a part in the development of food allergies. The Food and Drug Administration requires all regulated food companies to clearly state an inclusion of the major, or “big eight” food allergens on packaging. This review is to provide information on the significant advancements related to the gut microbiome and each of the eight major food allergies individually. Establishment of causal connection between the microbiome and food allergies has uncovered novel mechanisms. New strategies are discussed to prevent future sensitization and reaction through novel treatments involving functional additives and dietary changes that target the microbiome. Full article
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