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Human Gut Microbiome and Diet in Health and Disease

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Bioactives and Nutraceuticals".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 43177

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Special Issue Editors

Dr. Francesco Asnicar

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Guest Editor

Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
Interests: human microbiome; metagenomics; phylogenomics; bioinformatics

Dr. Serena Manara

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Guest Editor

Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
Interests: human microbiome; metagenomics; microbiome vertical transmission; clinical microbiology

Special Issue Information

Dear Colleagues,

In the last several decades, many studies have shown that the microbial communities associated with the human host play a fundamental role in maintaining health and preventing or causing some diseases. Other works have shown that human-associated microbial communities are shaped by several factors, including age, sex, antibiotics usage, and lifestyle. Among lifestyle-related factors, diet plays a key role in shaping the microbiome of the human digestive tract, as it provides different food sources for microbes and strongly affects the host metabolism. Human diet moreover forges the cross-talk between the host and the associated microbial communities by influencing the availability and production of different host- or microbiome-produced metabolites. While disentangling the links between diet, gut microbiome, and host metabolism is a complex matter, studies shedding light on these relationships are of key importance to identify potential diet interventions that could help to prevent or treat diseases through modulation of the gut microbiome.

Dr. Francesco Asnicar
Dr. Serena Manara
Guest Editors

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Keywords

Human gut microbiome
Diet
Nutrition
Gut metabolites
Fasting metabolism
Postprandial metabolism
Cardiometabolic health

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Published Papers (8 papers)

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Research

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22 pages, 3942 KiB

Open AccessArticle

The Human Milk Microbiota Produces Potential Therapeutic Biomolecules and Shapes the Intestinal Microbiota of Infants

by Martina Banić, Katarina Butorac, Nina Čuljak, Andreja Leboš Pavunc, Jasna Novak, Barbara Bellich, Saša Kazazić, Snježana Kazazić, Paola Cescutti, Jagoda Šušković, Jurica Zucko and Blaženka Kos

Int. J. Mol. Sci. 2022, 23(22), 14382; https://doi.org/10.3390/ijms232214382 - 19 Nov 2022

Cited by 7 | Viewed by 3581

Abstract

Human milk not only provides a perfect balance of nutrients to meet all the needs of the infant in the first months of life but also contains a variety of bacteria that play a key role in tailoring the neonatal faecal microbiome. Microbiome analysis of human milk and infant faeces from mother-breastfed infant pairs was performed by sequencing the V1–V3 region of the 16S rRNA gene using the Illumina MiSeq platform. According to the results, there is a connection in the composition of the microbiome in each mother-breastfed infant pair, supporting the hypothesis that the infant’s gut is colonised with bacteria from human milk. MiSeq sequencing also revealed high biodiversity of the human milk microbiome and the infant faecal microbiome, whose composition changes during lactation and infant development, respectively. A total of 28 genetically distinct strains were selected by hierarchical cluster analysis of RAPD-PCR (Random Amplified Polymorphic DNA-Polymerase Chain Reaction) electrophoresis profiles of 100 strains isolated from human milk and identified by 16S RNA sequencing. Since certain cellular molecules may support their use as probiotics, the next focus was to detect (S)-layer proteins, bacteriocins and exopolysaccharides (EPSs) that have potential as therapeutic biomolecules. SDS-PAGE (Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis) coupled with LC-MS (liquid chromatography-mass spectrometry) analysis revealed that four Levilactobacillus brevis strains expressed S-layer proteins, which were identified for the first time in strains isolated from human milk. The potential biosynthesis of plantaricin was detected in six Lactiplantibacillus plantarum strains by PCR analysis and in vitro antibacterial studies. ¹H NMR (Proton Nuclear Magnetic Resonance) analysis confirmed EPS production in only one strain, Limosilactobacillus fermentum MC1. The overall microbiome analysis suggests that human milk contributes to the establishment of the intestinal microbiota of infants. In addition, it is a promising source of novel Lactobacillus strains expressing specific functional biomolecules. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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14 pages, 2032 KiB

Open AccessArticle

Discovering Biomarkers for Non-Alcoholic Steatohepatitis Patients with and without Hepatocellular Carcinoma Using Fecal Metaproteomics

by Svenja Sydor, Christian Dandyk, Johannes Schwerdt, Paul Manka, Dirk Benndorf, Theresa Lehmann, Kay Schallert, Maximilian Wolf, Udo Reichl, Ali Canbay, Lars P. Bechmann and Robert Heyer

Int. J. Mol. Sci. 2022, 23(16), 8841; https://doi.org/10.3390/ijms23168841 - 9 Aug 2022

Cited by 7 | Viewed by 3281

Abstract

High-calorie diets lead to hepatic steatosis and to the development of non-alcoholic fatty liver disease (NAFLD), which can evolve over many years into the inflammatory form of non-alcoholic steatohepatitis (NASH), posing a risk for the development of hepatocellular carcinoma (HCC). Due to diet and liver alteration, the axis between liver and gut is disturbed, resulting in gut microbiome alterations. Consequently, detecting these gut microbiome alterations represents a promising strategy for early NASH and HCC detection. We analyzed medical parameters and the fecal metaproteome of 19 healthy controls, 32 NASH patients, and 29 HCC patients, targeting the discovery of diagnostic biomarkers. Here, NASH and HCC resulted in increased inflammation status and shifts within the composition of the gut microbiome. An increased abundance of kielin/chordin, E3 ubiquitin ligase, and nucleophosmin 1 represented valuable fecal biomarkers, indicating disease-related changes in the liver. Although a single biomarker failed to separate NASH and HCC, machine learning-based classification algorithms provided an 86% accuracy in distinguishing between controls, NASH, and HCC. Fecal metaproteomics enables early detection of NASH and HCC by providing single biomarkers and machine learning-based metaprotein panels. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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10 pages, 5943 KiB

Open AccessArticle

Characteristics of an In Vitro Mesenteric Lymph Node Cell Suspension Model and Its Possible Association with In Vivo Functional Evaluation

by Saisai Feng, Jing Li, Dingwu Qu, Fengwei Tian, Leilei Yu, Hao Zhang, Wei Chen, Jianxin Zhao and Qixiao Zhai

Int. J. Mol. Sci. 2022, 23(2), 1003; https://doi.org/10.3390/ijms23021003 - 17 Jan 2022

Cited by 3 | Viewed by 2294

Abstract

In a previous study, we uncovered three immune-responsive patterns of gut microbes using an in vitro mesenteric lymph node cell suspension model, abbreviated as the MLN model hereafter. We used Akkermansia muciniphila and Clostridium butyricum as the first group directly inducing an immune response, Bifidobacterium sp. and Bacteroides sp. as the second group evoking an immune response with the help of stimuli (anti-CD3 and anti-CD28 antibodies), and Lactobacillus sp. as the third group blunting the immune response with or without stimuli. Our group previously clarified the immune-activation characteristics of A. muciniphila and linked its in vivo immune induction effect in GF and SPF mice under homeostasis. In the present study, we supplemented the characteristics of C. butyricum and B. bifidum in the in vitro MLN model and addressed the specific elements of the model. Finally, we used an in vivo TNBS-challenge model to show the functional differences between these species with different response patterns in vitro. The results showed that C. butyricum and B. bifidum evoked an immune response in vitro in a dose-dependent and strain-unique manner. Although TLR2, rather than TLR4, is indispensable for immune activation in the present in vitro model, it may not involve interaction between TLR2 and bacterial ligands. Like the PBMC model, the present in vitro MLN model is highly dependent on cell resources and should be given more attention when used to conduct a quantitative comparison. Finally, a mixture of two strong immunogenic strains, A. muciniphila and C. butyricum, significantly increased the mortality of TNBS-challenged (2,4,6-trinitrobenzene sulfonic acid, TNBS) mice, indicating a possible link between the in vitro MLN model and in vivo functional evaluation. However, more evidence is needed to clarify the associations and underlying mechanisms. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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21 pages, 4153 KiB

Open AccessArticle

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis

by Diego S. Vazquez, Hanna M. Schilbert and Veronica I. Dodero

Int. J. Mol. Sci. 2021, 22(17), 9278; https://doi.org/10.3390/ijms22179278 - 27 Aug 2021

Cited by 7 | Viewed by 4776

Abstract

Gluten-related disorders (GRDs) are a group of diseases that involve the activation of the immune system triggered by the ingestion of gluten, with a worldwide prevalence of 5%. Among them, Celiac disease (CeD) is a T-cell-mediated autoimmune disease causing a plethora of symptoms from diarrhea and malabsorption to lymphoma. Even though GRDs have been intensively studied, the environmental triggers promoting the diverse reactions to gluten proteins in susceptible individuals remain elusive. It has been proposed that pathogens could act as disease-causing environmental triggers of CeD by molecular mimicry mechanisms. Additionally, it could also be possible that unrecognized molecular, structural, and physical parallels between gluten and pathogens have a relevant role. Herein, we report sequence, structural and physical similarities of the two most relevant gluten peptides, the 33-mer and p31-43 gliadin peptides, with bacterial pathogens using bioinformatics going beyond the molecular mimicry hypothesis. First, a stringent BLASTp search using the two gliadin peptides identified high sequence similarity regions within pathogen-derived proteins, e.g., extracellular proteins from Streptococcus pneumoniae and Granulicatella sp. Second, molecular dynamics calculations of an updated α-2-gliadin model revealed close spatial localization and solvent-exposure of the 33-mer and p31-43 peptide, which was compared with the pathogen-related proteins by homology models and localization predictors. We found putative functions of the identified pathogen-derived sequence by identifying T-cell epitopes and SH3/WW-binding domains. Finally, shape and size parallels between the pathogens and the superstructures of gliadin peptides gave rise to novel hypotheses about activation of innate immunity and dysbiosis. Based on our structural findings and the similarities with the bacterial pathogens, evidence emerges that these pathologically relevant gluten-derived peptides could behave as non-replicating pathogens opening new research questions in the interface of innate immunity, microbiome, and food research. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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19 pages, 3764 KiB

Open AccessArticle

Screening of Human Gut Bacterial Culture Collection Identifies Species That Biotransform Quercetin into Metabolites with Anticancer Properties

by Ranjini Sankaranarayanan, Prabhjot Kaur Sekhon, Achuthan Ambat, Julia Nelson, Davis Jose, G. Jayarama Bhat and Joy Scaria

Int. J. Mol. Sci. 2021, 22(13), 7045; https://doi.org/10.3390/ijms22137045 - 30 Jun 2021

Cited by 22 | Viewed by 4000

Abstract

We previously demonstrated that flavonoid metabolites inhibit cancer cell proliferation through both CDK-dependent and -independent mechanisms. The existing evidence suggests that gut microbiota is capable of flavonoid biotransformation to generate bioactive metabolites including 2,4,6-trihydroxybenzoic acid (2,4,6-THBA), 3,4-dihydroxybenzoic acid (3,4-DHBA), 3,4,5-trihyroxybenzoic acid (3,4,5-THBA) and 3,4-dihydroxyphenylacetic acid (DOPAC). In this study, we screened 94 human gut bacterial species for their ability to biotransform flavonoid quercetin into different metabolites. We demonstrated that five of these species were able to degrade quercetin including Bacillus glycinifermentans, Flavonifractor plautii, Bacteroides eggerthii, Olsenella scatoligenes and Eubacterium eligens. Additional studies showed that B. glycinifermentans could generate 2,4,6-THBA and 3,4-DHBA from quercetin while F. plautii generates DOPAC. In addition to the differences in the metabolites produced, we also observed that the kinetics of quercetin degradation was different between B. glycinifermentans and F. plautii, suggesting that the pathways of degradation are likely different between these strains. Similar to the antiproliferative effects of 2,4,6-THBA and 3,4-DHBA demonstrated previously, DOPAC also inhibited colony formation ex vivo in the HCT-116 colon cancer cell line. Consistent with this, the bacterial culture supernatant of F. plautii also inhibited colony formation in this cell line. Thus, as F. plautii and B. glycinifermentans generate metabolites possessing antiproliferative activity, we suggest that these strains have the potential to be developed into probiotics to improve human gut health. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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Review

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13 pages, 488 KiB

Open AccessReview

The Black Box Orchestra of Gut Bacteria and Bile Acids: Who Is the Conductor?

by Soumia Majait, Max Nieuwdorp, Marleen Kemper and Maarten Soeters

Int. J. Mol. Sci. 2023, 24(3), 1816; https://doi.org/10.3390/ijms24031816 - 17 Jan 2023

Cited by 10 | Viewed by 5540

Abstract

Over the past decades the potential role of the gut microbiome and bile acids in type 2 diabetes mellitus (T2DM) has been revealed, with a special reference to low bacterial alpha diversity. Certain bile acid effects on gut bacteria concern cytotoxicity, or in the case of the microbiome, bacteriotoxicity. Reciprocally, the gut microbiome plays a key role in regulating the bile acid pool by influencing the conversion and (de)conjugation of primary bile acids into secondary bile acids. Three main groups of bacterial enzymes responsible for the conversion of bile acids are bile salt hydrolases (BSHs), hydroxysteroid dehydrogenases (HSDHs) and enzymes encoded in the bile acid inducible (Bai) operon genes. Interventions such as probiotics, antibiotics and fecal microbiome transplantation can impact bile acids levels. Further evidence of the reciprocal interaction between gut microbiota and bile acids comes from a multitude of nutritional interventions including macronutrients, fibers, prebiotics, specific individual products or diets. Finally, anatomical changes after bariatric surgery are important because of their metabolic effects. The heterogeneity of studies, diseases, bacterial species and (epi)genetic influences such as nutrition may challenge establishing specific and detailed interventions that aim to tackle the gut microbiome and bile acids. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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27 pages, 1897 KiB

Open AccessReview

The Gut Microbiome in Depression and Potential Benefit of Prebiotics, Probiotics and Synbiotics: A Systematic Review of Clinical Trials and Observational Studies

by Sauliha R. Alli, Ilona Gorbovskaya, Jonathan C. W. Liu, Nathan J. Kolla, Lisa Brown and Daniel J. Müller

Int. J. Mol. Sci. 2022, 23(9), 4494; https://doi.org/10.3390/ijms23094494 - 19 Apr 2022

Cited by 76 | Viewed by 14542

Abstract

An emerging body of literature demonstrates differences in the gut microbiome (GMB) of patients with major depressive disorder (MDD) compared to healthy controls (HC), as well as the potential benefits of prebiotic, probiotic, and synbiotic treatment. We conducted a systematic review of 24 observational studies (n = 2817), and 19 interventional trials (n = 1119). We assessed alpha diversity, beta diversity, and taxa abundance changes in patients with MDD relative to HC, as well as the effect of prebiotics, probiotics, and synbiotics on depressive symptoms in individuals with clinical or subclinical depression. We observed no significant differences in alpha diversity but a significant difference in beta diversity between patients with MDD and HC. There were fluctuations in the abundance of specific taxa in patients with MDD relative to HC. Probiotic and synbiotic, but not prebiotic, treatment showed a modest benefit in reducing depressive symptoms in patients with MDD over four to nine weeks. The GMB profiles of patients with MDD differ significantly from HC, but further studies are needed to elucidate the benefits of prebiotic, probiotic and synbiotic treatments relative to antidepressants and over longer follow-up before these therapies are implemented into clinical practice. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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35 pages, 2002 KiB

Open AccessReview

Effects of Non-Polar Dietary and Endogenous Lipids on Gut Microbiota Alterations: The Role of Lipidomics

by Konstantinos Tsiantas, Spyridon J. Konteles, Eftichia Kritsi, Vassilia J. Sinanoglou, Thalia Tsiaka and Panagiotis Zoumpoulakis

Int. J. Mol. Sci. 2022, 23(8), 4070; https://doi.org/10.3390/ijms23084070 - 7 Apr 2022

Cited by 13 | Viewed by 3643

Abstract

Advances in sequencing technologies over the past 15 years have led to a substantially greater appreciation of the importance of the gut microbiome to the health of the host. Recent outcomes indicate that aspects of nutrition, especially lipids (exogenous or endogenous), can influence the gut microbiota composition and consequently, play an important role in the metabolic health of the host. Thus, there is an increasing interest in applying holistic analytical approaches, such as lipidomics, metabolomics, (meta)transcriptomics, (meta)genomics, and (meta)proteomics, to thoroughly study the gut microbiota and any possible interplay with nutritional or endogenous components. This review firstly summarizes the general background regarding the interactions between important non-polar dietary (i.e., sterols, fat-soluble vitamins, and carotenoids) or amphoteric endogenous (i.e., eicosanoids, endocannabinoids-eCBs, and specialized pro-resolving mediators-SPMs) lipids and gut microbiota. In the second stage, through the evaluation of a vast number of dietary clinical interventions, a comprehensive effort is made to highlight the role of the above lipid categories on gut microbiota and vice versa. In addition, the present status of lipidomics in current clinical interventions as well as their strengths and limitations are also presented. Indisputably, dietary lipids and most phytochemicals, such as sterols and carotenoids, can play an important role on the development of medical foods or nutraceuticals, as they exert prebiotic-like effects. On the other hand, endogenous lipids can be considered either prognostic indicators of symbiosis or dysbiosis or even play a role as specialized mediators through dietary interventions, which seem to be regulated by gut microbiota. Full article

(This article belongs to the Special Issue Human Gut Microbiome and Diet in Health and Disease)

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