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Microorganisms
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The Human Gut Microbiome, Diets and Health
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The Human Gut Microbiome, Diets and Health

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 102966

Special Issue Editor

Dr. Patrick Veiga

E-Mail Website
Guest Editor
Health & Microbiome Science Director, Innovation, Science & Nutrition Department, Danone Nutricia Research, Paris, France
Interests: gut microbiota; health; symbiosis; diets; food; probiotics; well-being

Special Issue Information

Dear Colleagues,

For millions of years, humans have co-evolved with their gut microbiota in a symbiotic relationship.

Today, this symbiosis might be jeopardized by unprecedented changes recently introduced in human lifestyles, such as the impoverishment of diets in microbiota-accessible carbohydrates or phytochemicals (polyphenols, glucosinolates, etc.), decreased exposure to exogenous bacteria, antibiotic use, etc. This altered human–microbe symbiosis may remain silent or, on the contrary, contribute to the development of non-communicable diseases in susceptible individuals (i.e., inflammatory bowel diseases, allergies, diabetes, cardiovascular diseases) and may even affect mental health and well-being. In this context, there is a need to understand the different configurations of the human gut microbiome that can support health and well-being.  Since diet is the most attainable approach for modulating the gut microbiome at the population scale, there is a need to understand which dietary patterns or components (fibers, prebiotics, polyphenols, fermented foods, probiotics, etc.) are critical to favor the human–gut microbiome symbiosis. Are those relevant across different countries, cuisines, cultures, and traditions?

The objective of this Special Issue is to contribute the common knowledge on the link between human diets, the gut microbiome, health, and well-being. I invite you to submit your manuscripts for this Special Issue: “The Human Gut Microbiome, Diets, and Health”.

As Guest Editor of this Special Issue, I look forward to reviewing your submissions and, together, defining the present state of the science.

Dr. Patrick Veiga
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • human
  • gut microbiome
  • diet
  • foods
  • health
  • well-being
  • gut–brain
  • probiotics
  • prebiotics
  • fermented foods
  • symbiosis
  • polyphenols

Published Papers (20 papers)

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14 pages, 1910 KiB  
Article
Relation between Mood and the Host-Microbiome Co-Metabolite 3-Indoxylsulfate: Results from the Observational Prospective NutriNet-Santé Study
by Catherine Philippe, Fabien Szabo de Edelenyi, Laurent Naudon, Nathalie Druesne-Pecollo, Serge Hercberg, Emmanuelle Kesse-Guyot, Paule Latino-Martel, Pilar Galan and Sylvie Rabot
Microorganisms 2021, 9(4), 716; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040716 - 31 Mar 2021
Cited by 12 | Viewed by 3455
Abstract
Gut microbiota metabolizes tryptophan into indole, which can influence brain and behavior. Indeed, some oxidized derivatives of indole, formed in the liver, have neuroactive properties, and indole overproduction by the gut microbiota induces an anxio-depressive phenotype in rodents. The aim of this study [...] Read more.
Gut microbiota metabolizes tryptophan into indole, which can influence brain and behavior. Indeed, some oxidized derivatives of indole, formed in the liver, have neuroactive properties, and indole overproduction by the gut microbiota induces an anxio-depressive phenotype in rodents. The aim of this study was to investigate in humans whether there was a relationship between recurrent depressive symptoms and indole production by the gut microbiota. A case-control study was conducted in 45–65-year-old women, who were participants in the observational prospective NutriNet-Santé Study. Cases were defined as having two Center for Epidemiological Studies-Depression Scales (CES-D) scores ≥ 23 at a two-year interval (recurrent depressive symptoms, n = 87). Each case was matched with two controls (two CES-D <23; n = 174). Urinary excretion of 3-indoxylsulfate, the major final metabolite of indole, was used as a biomarker of indole production by the gut microbiota. Conditional logistic regression models for paired data showed a positive association between urinary 3-indoxylsulfate concentrations, grouped in tertiles, and recurrent depressive symptoms (odds ratio = 2.46, p for trend = 0.0264 in the final model adjusted for confounding factors). This association suggested that indole production by the gut microbiota may play a role in the onset of mood disorders in humans. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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13 pages, 596 KiB  
Article
Gut Microbiota Profile and Changes in Body Weight in Elderly Subjects with Overweight/Obesity and Metabolic Syndrome
by Alessandro Atzeni, Serena Galié, Jananee Muralidharan, Nancy Babio, Francisco José Tinahones, Jesús Vioque, Dolores Corella, Olga Castañer, Josep Vidal, Isabel Moreno-Indias, Laura Torres-Collado, Rebeca Fernández-Carrión, Montserrat Fitó, Romina Olbeyra, Miguel Angel Martínez-González, Monica Bulló and Jordi Salas-Salvadó
Microorganisms 2021, 9(2), 346; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020346 - 10 Feb 2021
Cited by 15 | Viewed by 3391
Abstract
Gut microbiota is essential for the development of obesity and related comorbidities. However, studies describing the association between specific bacteria and obesity or weight loss reported discordant results. The present observational study, conducted within the frame of the PREDIMED-Plus clinical trial, aims to [...] Read more.
Gut microbiota is essential for the development of obesity and related comorbidities. However, studies describing the association between specific bacteria and obesity or weight loss reported discordant results. The present observational study, conducted within the frame of the PREDIMED-Plus clinical trial, aims to assess the association between fecal microbiota, body composition and weight loss, in response to a 12-month lifestyle intervention in a subsample of 372 individuals (age 55–75) with overweight/obesity and metabolic syndrome. Participants were stratified by tertiles of baseline body mass index (BMI) and changes in body weight after 12-month intervention. General assessments, anthropometry and biochemical measurements, and stool samples were collected. 16S amplicon sequencing was performed on bacterial DNA extracted from stool samples and microbiota analyzed. Differential abundance analysis showed an enrichment of Prevotella 9, Lachnospiraceae UCG-001 and Bacteroides, associated with a higher weight loss after 12-month of follow-up, whereas in the cross-sectional analysis, Prevotella 2 and Bacteroides were enriched in the lowest tertile of baseline BMI. Our findings suggest that fecal microbiota plays an important role in the control of body weight, supporting specific genera as potential target in personalized nutrition for obesity management. A more in-depth taxonomic identification method and the need of metabolic information encourages to further investigation. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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27 pages, 5871 KiB  
Article
Fecal Microbiota Transplant from Human to Mice Gives Insights into the Role of the Gut Microbiota in Non-Alcoholic Fatty Liver Disease (NAFLD)
by Sebastian D. Burz, Magali Monnoye, Catherine Philippe, William Farin, Vlad Ratziu, Francesco Strozzi, Jean-Michel Paillarse, Laurent Chêne, Hervé M. Blottière and Philippe Gérard
Microorganisms 2021, 9(1), 199; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010199 - 19 Jan 2021
Cited by 32 | Viewed by 6101
Abstract
Non-alcoholic fatty liver diseases (NAFLD) are associated with changes in the composition and metabolic activities of the gut microbiota. However, the causal role played by the gut microbiota in individual susceptibility to NAFLD and particularly at its early stage is still unclear. In [...] Read more.
Non-alcoholic fatty liver diseases (NAFLD) are associated with changes in the composition and metabolic activities of the gut microbiota. However, the causal role played by the gut microbiota in individual susceptibility to NAFLD and particularly at its early stage is still unclear. In this context, we transplanted the microbiota from a patient with fatty liver (NAFL) and from a healthy individual to two groups of mice. We first showed that the microbiota composition in recipient mice resembled the microbiota composition of their respective human donor. Following administration of a high-fructose, high-fat diet, mice that received the human NAFL microbiota (NAFLR) gained more weight and had a higher liver triglycerides level and higher plasma LDL cholesterol than mice that received the human healthy microbiota (HR). Metabolomic analyses revealed that it was associated with lower and higher plasma levels of glycine and 3-Indolepropionic acid in NAFLR mice, respectively. Moreover, several bacterial genera and OTUs were identified as differently represented in the NAFLR and HR microbiota and therefore potentially responsible for the different phenotypes observed. Altogether, our results confirm that the gut bacteria play a role in obesity and steatosis development and that targeting the gut microbiota may be a preventive or therapeutic strategy in NAFLD management. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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22 pages, 4808 KiB  
Article
Duodenal Metatranscriptomics to Define Human and Microbial Functional Alterations Associated with Severe Obesity: A Pilot Study
by Ilaria Granata, Carmela Nardelli, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone and Lucia Sacchetti
Microorganisms 2020, 8(11), 1811; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111811 - 17 Nov 2020
Cited by 13 | Viewed by 2758
Abstract
Obesity is a multifactorial disorder, and the gut microbiome has been suggested to contribute to its onset. In order to better clarify the role of the microbiome in obesity, we evaluated the metatranscriptome in duodenal biopsies from a cohort of 23 adult severely [...] Read more.
Obesity is a multifactorial disorder, and the gut microbiome has been suggested to contribute to its onset. In order to better clarify the role of the microbiome in obesity, we evaluated the metatranscriptome in duodenal biopsies from a cohort of 23 adult severely obese and lean control subjects using next generation sequencing. Our aim was to provide a general picture of the duodenal metatranscriptome associated with severe obesity. We found altered expressions of human and microbial genes in the obese compared to lean subjects, with most of the gene alterations being present in the carbohydrate, protein, and lipid metabolic pathways. Defects were also present in several human genes involved in epithelial intestinal cells differentiation and function, as well as in the immunity/inflammation pathways. Moreover, the microbial taxa abundance inferred by our transcriptomic data differed in part from the data that we previously evaluated by 16S rRNA in 13/23 individuals of our cohort, particularly concerning the Firmicutes and Proteobacteria phyla abundances. In conclusion, our pilot study provides the first taxonomic and functional characterization of duodenal microbiota in severely obese subjects and lean controls. Our findings suggest that duodenal microbiome and human genes both play a role in deregulating metabolic pathways, likely affecting energy metabolism and thus contributing to the obese phenotype. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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22 pages, 2259 KiB  
Article
Correlation between the Antimicrobial Activity and Metabolic Profiles of Cell Free Supernatants and Membrane Vesicles Produced by Lactobacillus reuteri DSM 17938
by Alessandro Maccelli, Simone Carradori, Valentina Puca, Francesca Sisto, Paola Lanuti, Maria Elisa Crestoni, Alba Lasalvia, Raffaella Muraro, Helena Bysell, Antonella Di Sotto, Stefan Roos and Rossella Grande
Microorganisms 2020, 8(11), 1653; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111653 - 24 Oct 2020
Cited by 21 | Viewed by 3839
Abstract
The aim of the work is to assess the antimicrobial activities of Cell Free Supernatants (CFS) and Membrane Vesicles (MVs), produced by Lactobacillus reuteri DSM 17938, versus Gram-positive and Gram-negative bacteria and investigate their metabolic profiles. The Minimum Inhibitory Concentration was determined through [...] Read more.
The aim of the work is to assess the antimicrobial activities of Cell Free Supernatants (CFS) and Membrane Vesicles (MVs), produced by Lactobacillus reuteri DSM 17938, versus Gram-positive and Gram-negative bacteria and investigate their metabolic profiles. The Minimum Inhibitory Concentration was determined through the broth microdilution method and cell proliferation assay while the Minimum Bactericidal Concentration was determined by Colony Forming Units counts. The characteristics of the antimicrobial compounds were evaluated by pH adjustments, proteinase treatment, and size fractionation of the CFS. The cytotoxicity of CFS was tested on two human cell lines. A detailed snapshot of the L. reuteri metabolism was attained through an untargeted metabolic profiling by means of high resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) coupled with Electrospray Ionization Source (ESI). The results showed (i) a greater efficacy of CFS and its fractions towards Gram-negative compared to Gram-positive bacteria; (ii) an antimicrobial effect related to pH-dependent compounds but not to MVs; (iii) a molecular weight < 3 KDa as well as an a non-proteinaceous nature of the antimicrobial compounds; and (iv) more than 200 and 500 putative metabolites annotated in MVs and supernatants, covering several classes of metabolites, including amino acids, lipids, fatty and organic acids, polyalcohols, nucleotides, and vitamins. Some putative compounds were proposed not only as characteristic of specific fractions, but also possibly involved in antimicrobial activity. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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18 pages, 2546 KiB  
Article
A Multi-Omic Analysis for Low Bone Mineral Density in Postmenopausal Women Suggests a Relationship between Diet, Metabolites, and Microbiota
by Berenice Palacios-González, Eric G. Ramírez-Salazar, Berenice Rivera-Paredez, Manuel Quiterio, Yvonne N. Flores, Luis Macias-Kauffer, Sofía Moran-Ramos, Edgar Denova-Gutiérrez, Isabel Ibarra-González, Marcela Vela-Amieva, Samuel Canizales-Quinteros, Jorge Salmerón and Rafael Velázquez-Cruz
Microorganisms 2020, 8(11), 1630; https://doi.org/10.3390/microorganisms8111630 - 22 Oct 2020
Cited by 27 | Viewed by 2551
Abstract
The effect of microbiota composition and its health on bone tissue is a novel field for research. However, their associations with bone mineral density (BMD) have not been established in postmenopausal women. The present study investigates the relation of diet, the microbiota composition, [...] Read more.
The effect of microbiota composition and its health on bone tissue is a novel field for research. However, their associations with bone mineral density (BMD) have not been established in postmenopausal women. The present study investigates the relation of diet, the microbiota composition, and the serum metabolic profile in postmenopausal women with normal-BMD or with low-BMD. Ninety-two Mexican postmenopausal women were classified into normal-BMD (n = 34) and low-BMD (n = 58). The V4 hypervariable region was sequenced using the Miseq platform. Serum vitamin D was determined by chemiluminescence immunoassay. Serum concentrations of acyl-carnitines and amino acids were determined by electrospray tandem mass spectrometry. Diet was assessed by a food frequency questionnaire. The low-BMD group had fewer observed species, higher abundance of γ-Proteobacteria, lower consumption of lycopene, and lower concentrations of leucine, valine, and tyrosine compared with the normal-BMD group. These amino acids correlated positively with the abundance of Bacteroides. Lycopene consumption positively correlated with Oscillospira and negatively correlated with Pantoea genus abundance. Finally, the intestinal microbiota of women with vitamin D deficiency was related to Erysipelotrichaceae and Veillonellaceae abundance compared to the vitamin D non-deficient group. Associations mediated by the gut microbiota between diet and circulating metabolites with low-BMD were identified. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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16 pages, 2122 KiB  
Article
Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes
by Andrés Sánchez-Quinto, Daniel Cerqueda-García, Luisa I. Falcón, Osiris Gaona, Santiago Martínez-Correa, Javier Nieto and Isaac G-Santoyo
Microorganisms 2020, 8(10), 1592; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101592 - 16 Oct 2020
Cited by 11 | Viewed by 6766
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years [...] Read more.
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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15 pages, 1257 KiB  
Article
Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria
by Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer and Muriel Derrien
Microorganisms 2020, 8(10), 1528; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101528 - 05 Oct 2020
Cited by 13 | Viewed by 4083
Abstract
Interest in preventive or therapeutic strategies targeting gut microbiota is increasing. Such strategies may involve the direct replenishment of the gut microbiota with single strains or strain mixtures, or the manipulation of strain abundance through dietary intervention, including lactic acid bacteria. A few [...] Read more.
Interest in preventive or therapeutic strategies targeting gut microbiota is increasing. Such strategies may involve the direct replenishment of the gut microbiota with single strains or strain mixtures, or the manipulation of strain abundance through dietary intervention, including lactic acid bacteria. A few candidate species associated with health benefits have been identified, including Faecalibacterium prausnitzii. Given its growth requirements, modulation of this bacterium has not been extensively studied. In this investigation, we explored the capacity of cell-free supernatants of different Lactobacillus, Streptococcus, Lactococcus, and Bifidobacterium strains to stimulate the growth of F. prausnitzii A2-165. Modulation by four strains with the greatest capacity to stimulate growth or delay lysis, Lactococcus lactis subsp. lactis CNCM I-1631, Lactococcus lactis subsp. cremoris CNCM I-3558, Lactobacillus paracasei CNCM I-3689, and Streptococcus thermophilus CNCM I-3862, was further characterized by transcriptomics. The response of F. prausnitzii to cell-free supernatants from these four strains revealed several shared characteristics, in particular, upregulation of carbohydrate metabolism and cell wall-related genes and downregulation of replication and mobilome genes. Overall, this study suggests differential responses of F. prausnitzii to metabolites produced by different strains, providing protection against cell death, with an increase in peptidoglycan levels for cell wall formation, and reduced cell mobilome activity. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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13 pages, 1433 KiB  
Article
Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates
by Loo Wee Chia, Marko Mank, Bernadet Blijenberg, Steven Aalvink, Roger S. Bongers, Bernd Stahl, Jan Knol and Clara Belzer
Microorganisms 2020, 8(10), 1513; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101513 - 01 Oct 2020
Cited by 27 | Viewed by 4629
Abstract
The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides [...] Read more.
The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides thetaiotaomicron and the butyrate-producing Anaerostipes caccae in the presence of early-life carbohydrates. Anaerobic bioreactors were set up to study the monocultures of B. thetaiotaomicron and the co-cultures of B. thetaiotaomicron with A. caccae in minimal media supplemented with lactose or a total human milk carbohydrate fraction. Bacterial growth (qPCR), metabolites (HPLC), and HMOS utilization (LC-ESI-MS2) were monitored. B. thetaiotaomicron displayed potent glycan catabolic capability with differential preference in degrading specific low molecular weight HMOSs, including the neutral trioses (2′-FL and 3-FL), neutral tetraoses (DFL, LNT, LNnT), neutral pentaoses (LNFP I, II, III, V), and acidic trioses (3′-SL and 6′-SL). In contrast, A. caccae was not able to utilize lactose and HMOSs. However, the signature metabolite of A. caccae, butyrate, was detected in co-culture with B. thetaiotaomicron. As such, A. caccae cross-fed on B. thetaiotaomicron-derived monosaccharides, acetate, and d-lactate for growth and concomitant butyrate production. This study provides a proof of concept that B. thetaiotaomicron could drive the butyrogenic metabolic network in the infant gut. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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19 pages, 2579 KiB  
Article
The Infant-Derived Bifidobacterium bifidum Strain CNCM I-4319 Strengthens Gut Functionality
by Rebeca Martín, Francesca Bottacini, Muireann Egan, Celia Chamignon, Valérie Tondereau, Raphaël Moriez, Jan Knol, Philippe Langella, Hélène Eutamene, Tamara Smokvina and Douwe van Sinderen
Microorganisms 2020, 8(9), 1313; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091313 - 28 Aug 2020
Cited by 10 | Viewed by 3290
Abstract
Bifidobacteria are among the first colonisers of the gastrointestinal tract of breast-fed newborns due to, among other things, their ability to metabolise oligosaccharides naturally occurring in human milk. The presence of bifidobacteria in the infant gut has been shown to promote intestinal health [...] Read more.
Bifidobacteria are among the first colonisers of the gastrointestinal tract of breast-fed newborns due to, among other things, their ability to metabolise oligosaccharides naturally occurring in human milk. The presence of bifidobacteria in the infant gut has been shown to promote intestinal health and homeostasis as well as to preserve a functional gut barrier, thus positively influencing host health and well-being. Among human-associated gut commensals, Bifidobacterium bifidum has been described as the only species capable of the extracellular degradation of both mucin-type glycans and HMOs, thereby giving this species a special role as a commensal gut forager of both host and diet-derived glycans. In the present study, we assess the possible beneficial properties and probiotic potential of B. bifidum strain CNCM I-4319. In silico genome analysis and growth experiments confirmed the expected ability of this strain to consume HMOs and mucin. By employing various animal models, we were also able to assess the ability of B. bifidum CNCM I-4319 to preserve gut integrity and functionality from stress-induced and inflammatory damage, thereby enforcing its potential as an effective probiotic strain. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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20 pages, 935 KiB  
Article
Association of the Gut Microbiota with Weight-Loss Response within a Retail Weight-Management Program
by Samitinjaya Dhakal, Lacey McCormack and Moul Dey
Microorganisms 2020, 8(8), 1246; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8081246 - 16 Aug 2020
Cited by 19 | Viewed by 4102
Abstract
Retail programs offer popular weight-loss options amid the ongoing obesity crisis. However, research on weight-loss outcomes within such programs is limited. This prospective-cohort observational study enrolled 58 men and women between ages 20 and 72 years from a retail program to assess the [...] Read more.
Retail programs offer popular weight-loss options amid the ongoing obesity crisis. However, research on weight-loss outcomes within such programs is limited. This prospective-cohort observational study enrolled 58 men and women between ages 20 and 72 years from a retail program to assess the influence of client features on energy-restriction induced weight-loss response. DESeq2 in R-studio, a linear regression model adjusting for significantly correlating covariates, and Wilcoxon signed-rank and Kruskal–Wallis for within- and between-group differences, respectively, were used for data analyses. An average 10% (~10 kg) reduction in baseline-weight along with lower total-, android-, gynoid-, and android:gynoid-fat were observed at Week 12 (all, p < 0.05). Fifty percent of participants experienced a higher response, losing an average of 14.5 kg compared to 5.9 kg in the remaining low-response group (p < 0.0001). Hemoglobin-A1C (p = 0.005) and heart rate (p = 0.079) reduced in the high-response group only. Fat mass and A1C correlated when individuals had high android:gynoid fat (r = 0.55, p = 0.008). Gut-microbial β-diversity was associated with BMI, body fat%, and android-fat (all, p < 0.05). Microbiota of the high-response group had a higher baseline OTU-richness (p = 0.02) as well as differential abundance and/or associations with B. eggerthi, A. muciniphila, Turicibacter, Prevotella, and Christensenella (all, p/padj < 0.005). These results show that intestinal microbiota as well as sex and body composition differences may contribute to variable weight-loss response. This highlights the importance of various client features in the context of real-world weight control efforts. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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17 pages, 4939 KiB  
Article
Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
by Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao and Chenhong Zhang
Microorganisms 2020, 8(8), 1225; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8081225 - 12 Aug 2020
Cited by 24 | Viewed by 3623
Abstract
Supplementation of probiotics is a promising gut microbiota-targeted therapeutic method for hyperlipidemia and atherosclerosis. However, the selection of probiotic candidate strains is still empirical. Here, we obtained a human-derived strain, Lactobacillus mucosae A1, which was shown by metagenomic analysis to be promoted by [...] Read more.
Supplementation of probiotics is a promising gut microbiota-targeted therapeutic method for hyperlipidemia and atherosclerosis. However, the selection of probiotic candidate strains is still empirical. Here, we obtained a human-derived strain, Lactobacillus mucosae A1, which was shown by metagenomic analysis to be promoted by a high-fiber diet and associated with the amelioration of host hyperlipidemia, and validated its effect on treating hyperlipidemia and atherosclerosis as well as changing structure of gut microbiota in ApoE-/- mice on a Western diet. L. mucosae A1 attenuated the severe lipid accumulation in serum, liver and aortic sinus of ApoE-/- mice on a Western diet, while it also reduced the serum lipopolysaccharide-binding protein content of mice, reflecting the improved metabolic endotoxemia. In addition, L. mucosae A1 shifted the gut microbiota structure of ApoE-/- mice on a Western diet, including recovering a few members of gut microbiota enhanced by the Western diet. This study not only suggests the potential of L. mucosae A1 to be a probiotic in the treatment of hyperlipidemia and atherosclerosis, but also highlights the advantage of such function-based rather than taxonomy-based strategies for the selection of candidate strains for the next generation probiotics. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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15 pages, 3239 KiB  
Article
Evaluation of the Probiotic Properties and the Capacity to Form Biofilms of Various Lactobacillus Strains
by Célia Chamignon, Virgile Guéneau, Sonia Medina, Julien Deschamps, Angel Gil-Izquierdo, Romain Briandet, Pierre-Yves Mousset, Philippe Langella, Sophie Lafay and Luis G. Bermúdez-Humarán
Microorganisms 2020, 8(7), 1053; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8071053 - 15 Jul 2020
Cited by 21 | Viewed by 3374
Abstract
Over the last 20 years, Lactobacillus species inhabiting the gastrointestinal tract (GIT) have received much attention, and their health-promoting properties are now well-described. Probiotic effects cannot be generalized, and their uses cover a wide range of applications. It is thus important to proceed [...] Read more.
Over the last 20 years, Lactobacillus species inhabiting the gastrointestinal tract (GIT) have received much attention, and their health-promoting properties are now well-described. Probiotic effects cannot be generalized, and their uses cover a wide range of applications. It is thus important to proceed to an accurate selection and evaluation of probiotic candidates. We evaluate the probiotic potential of six strains of Lactobacillus in different in vitro models representing critical factors of either survival, efficacy, or both. We characterized the strains for their ability to (i) modulate intestinal permeability using transepithelial electrical resistance (TEER), (ii) form biofilms and resist stressful conditions, and (iii) produce beneficial host and/or bacteria metabolites. Our data reveal the specificity of Lactobacillus strains to modulate intestinal permeability depending on the cell type. The six isolates were able to form spatially organized biofilms, and we provide evidence that the biofilm form is beneficial in a strongly acidic environment. Finally, we demonstrated the ability of the strains to produce γ-aminobutyric acid (GABA) that is involved in the gut-brain axis and beneficial enzymes that promote the bacterial tolerance to bile salts. Overall, our study highlights the specific properties of Lactobacillus strains and their possible applications as biofilms. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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14 pages, 2074 KiB  
Article
Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children
by Maria Julia Golloso-Gubat, Quinten R. Ducarmon, Robby Carlo A. Tan, Romy D. Zwittink, Ed J. Kuijper, Jacus S. Nacis and Noelle Lyn C. Santos
Microorganisms 2020, 8(7), 1015; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8071015 - 08 Jul 2020
Cited by 17 | Viewed by 5303
Abstract
Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban [...] Read more.
Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban Filipino children, and determined the relationship between their energy, macronutrient and dietary fiber intakes, and their gut microbiota composition and diversity. Forty-three children (normal-weight, n = 32; overweight, n = 11) participated in the study. Energy and fiber intakes were collected using a semi-quantitative Food Frequency Questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing of the V3–V4 region. The diet of the children was a mixture of traditional and Western patterns. There were no significant differences in energy, macronutrients and energy-adjusted fiber intakes between the normal-weight and overweight groups, but there were significantly more children meeting the recommended fiber intake in the overweight group. Alpha and beta bacterial diversities did not significantly differ between weight groups. Relative abundance of Bifidobacterium, Turicibacter and Clostridiaceae 1 were higher in the normal-weight than overweight children, and Lachnospira was higher in overweight children. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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Review

Jump to: Research

31 pages, 978 KiB  
Review
Eukaryotic and Prokaryotic Microbiota Interactions
by Aly Kodio, Estelle Menu and Stéphane Ranque
Microorganisms 2020, 8(12), 2018; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8122018 - 17 Dec 2020
Cited by 11 | Viewed by 4463
Abstract
The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In [...] Read more.
The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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20 pages, 1124 KiB  
Review
The Bifidogenic Effect Revisited—Ecology and Health Perspectives of Bifidobacterial Colonization in Early Life
by Himanshu Kumar, Maria Carmen Collado, Harm Wopereis, Seppo Salminen, Jan Knol and Guus Roeselers
Microorganisms 2020, 8(12), 1855; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121855 - 25 Nov 2020
Cited by 35 | Viewed by 8414
Abstract
Extensive microbial colonization of the infant gastrointestinal tract starts after parturition. There are several parallel mechanisms by which early life microbiome acquisition may proceed, including early exposure to maternal vaginal and fecal microbiota, transmission of skin associated microbes, and ingestion of microorganisms present [...] Read more.
Extensive microbial colonization of the infant gastrointestinal tract starts after parturition. There are several parallel mechanisms by which early life microbiome acquisition may proceed, including early exposure to maternal vaginal and fecal microbiota, transmission of skin associated microbes, and ingestion of microorganisms present in breast milk. The crucial role of vertical transmission from the maternal microbial reservoir during vaginal delivery is supported by the shared microbial strains observed among mothers and their babies and the distinctly different gut microbiome composition of caesarean-section born infants. The healthy infant colon is often dominated by members of the keystone genus Bifidobacterium that have evolved complex genetic pathways to metabolize different glycans present in human milk. In exchange for these host-derived nutrients, bifidobacteria’s saccharolytic activity results in an anaerobic and acidic gut environment that is protective against enteropathogenic infection. Interference with early-life microbiota acquisition and development could result in adverse health outcomes. Compromised microbiota development, often characterized by decreased abundance of Bifidobacterium species has been reported in infants delivered prematurely, delivered by caesarean section, early life antibiotic exposure and in the case of early life allergies. Various microbiome modulation strategies such as probiotic, prebiotics, synbiotics and postbiotics have been developed that are able to generate a bifidogenic shift and help to restore the microbiota development. This review explores the evolutionary ecology of early-life type Bifidobacterium strains and their symbiotic relationship with humans and discusses examples of compromised microbiota development in which stimulating the abundance and activity of Bifidobacterium has demonstrated beneficial associations with health. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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24 pages, 1174 KiB  
Review
Probiotics: A Dietary Factor to Modulate the Gut Microbiome, Host Immune System, and Gut–Brain Interaction
by Tetsuji Hori, Kazunori Matsuda and Kenji Oishi
Microorganisms 2020, 8(9), 1401; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091401 - 11 Sep 2020
Cited by 40 | Viewed by 6834
Abstract
Various benefits of probiotics to the host have been shown in numerous human clinical trials. These organisms have been proposed to act by improving the balance of the gut microbiota and enhancing the production of short-chain fatty acids, as well as by interacting [...] Read more.
Various benefits of probiotics to the host have been shown in numerous human clinical trials. These organisms have been proposed to act by improving the balance of the gut microbiota and enhancing the production of short-chain fatty acids, as well as by interacting with host cells in the gastrointestinal tract, including immune cells, nerve cells, and endocrine cells. Although the stimulation of host cells by probiotics and subsequent signaling have been explained by in vitro experiments and animal studies, there has been some skepticism as to whether probiotics can actually interact with host cells in the human gastrointestinal tract, where miscellaneous indigenous bacteria coexist. Most recently, it has been shown that the ileal microbiota in humans after consumption of a fermented milk is occupied by probiotics for several hours, indicating that there is adequate opportunity for the ingested strain to stimulate the host cells continuously over a period of time. As the dynamics of ingested probiotics in the human gastrointestinal tract become clearer, further progress in this research area is expected to elucidate their behavior within the tract, as well as the mechanism of their physiological effects on the host. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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26 pages, 796 KiB  
Review
Role of the Gut Microbiota in the Pathophysiology of Autism Spectrum Disorder: Clinical and Preclinical Evidence
by Léa Roussin, Naika Prince, Paula Perez-Pardo, Aletta D. Kraneveld, Sylvie Rabot and Laurent Naudon
Microorganisms 2020, 8(9), 1369; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091369 - 07 Sep 2020
Cited by 31 | Viewed by 7593
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder affecting 1 in 160 people in the world. Although there is a strong genetic heritability to ASD, it is now accepted that environmental factors can play a role in its onset. As the prevalence of [...] Read more.
Autism spectrum disorder (ASD) is a neurodevelopmental disorder affecting 1 in 160 people in the world. Although there is a strong genetic heritability to ASD, it is now accepted that environmental factors can play a role in its onset. As the prevalence of gastrointestinal (GI) symptoms is four-times higher in ASD patients, the potential implication of the gut microbiota in this disorder is being increasingly studied. A disturbed microbiota composition has been demonstrated in ASD patients, accompanied by altered production of bacterial metabolites. Clinical studies as well as preclinical studies conducted in rodents have started to investigate the physiological functions that gut microbiota might disturb and thus underlie the pathophysiology of ASD. The first data support an involvement of the immune system and tryptophan metabolism, both in the gut and central nervous system. In addition, a few clinical studies and a larger number of preclinical studies found that modulation of the microbiota through antibiotic and probiotic treatments, or fecal microbiota transplantation, could improve behavior. Although the understanding of the role of the gut microbiota in the physiopathology of ASD is only in its early stages, the data gathered in this review highlight that this role should be taken in consideration. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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26 pages, 1769 KiB  
Review
Probiotics for the Treatment of Overweight and Obesity in Humans—A Review of Clinical Trials
by Michał Wiciński, Jakub Gębalski, Jakub Gołębiewski and Bartosz Malinowski
Microorganisms 2020, 8(8), 1148; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8081148 - 29 Jul 2020
Cited by 65 | Viewed by 11911
Abstract
The World Health Organization (WHO) reports that 400 million people are obese, and over 1.6 billion adults are overweight worldwide. Annually, over 2.8 million people die from obesity-related diseases. The incidence of overweight and obesity is steadily increasing, and this phenomenon is referred [...] Read more.
The World Health Organization (WHO) reports that 400 million people are obese, and over 1.6 billion adults are overweight worldwide. Annually, over 2.8 million people die from obesity-related diseases. The incidence of overweight and obesity is steadily increasing, and this phenomenon is referred to as a 21st-century pandemic. The main reason for this phenomenon is an easy access to high-energy, processed foods, and a low-activity lifestyle. These changes lead to an energy imbalance and, as a consequence, to the development of body fat. Weight gain contributes to the development of heart diseases, skeletal system disorders, metabolic disorders such as diabetes, and certain types of cancer. In recent years, there have been many works linking obesity with intestinal microbiota. Experiments on germ-free animals (GFs) have provided much evidence for the contribution of bacteria to obesity. The composition of the gut microbiota (GM) changes in obese people. These changes affect the degree of energy obtained from food, the composition and secretory functions of adipose tissue, carbohydrate, and lipid metabolism in the liver, and the activity of centers in the brain. The study aimed to present the current state of knowledge about the role of intestinal microbiota in the development of obesity and the impact of supplementation with probiotic bacteria on the health of overweight and obese patients. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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10 pages, 232 KiB  
Review
The Infant Gut Microbiota and Risk of Asthma: The Effect of Maternal Nutrition during Pregnancy and Lactation
by Naser A. Alsharairi
Microorganisms 2020, 8(8), 1119; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8081119 - 25 Jul 2020
Cited by 27 | Viewed by 4715
Abstract
Research has amply demonstrated that early life dysbiosis of the gut microbiota influences the propensity to develop asthma. The influence of maternal nutrition on infant gut microbiota is therefore of growing interest. However, a handful of prospective studies have examined the role of [...] Read more.
Research has amply demonstrated that early life dysbiosis of the gut microbiota influences the propensity to develop asthma. The influence of maternal nutrition on infant gut microbiota is therefore of growing interest. However, a handful of prospective studies have examined the role of maternal dietary patterns during pregnancy in influencing the infant gut microbiota but did not assess whether this resulted in an increased risk of asthma later in life. The mechanisms involved in the process are also, thus far, poorly documented. There have also been few studies examining the effect of maternal dietary nutrient intake during lactation on the milk microbiota, the effect on the infant gut microbiota and, furthermore, the consequences for asthma development remain largely unknown. Therefore, the specific aim of this mini review is summarizing the current knowledge regarding the effect of maternal nutrition during pregnancy and lactation on the infant gut microbiota composition, and whether it has implications for asthma development. Full article
(This article belongs to the Special Issue The Human Gut Microbiome, Diets and Health)
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