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Microorganisms
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How Do Food and Probiotics Influence the Composition and Activity...
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How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 24260

Special Issue Editors

Prof. Dr. Gisèle LaPointe

E-Mail Website
Guest Editor
Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON N1G 2W1, Canada
Interests: dairy microbiology; milk quality; fermentation; probiotics; prebiotics; lactic acid bacteria; microbial ecosystems; gut microbiota
Dr. Michael Rogers

E-Mail Website
Guest Editor
Department of Food Science, University of Guelph, Guelph, ON, Canada
Interests: digestion; food structure; food processing; crystallization; self-assembly; soft matter; gels

Special Issue Information

Dear Colleagues,

We are a product of the foods we chronically consume, and our life expectancy correlates with the quality of our diet. What we eat influences the immune system, intestinal permeability, mental activity, and has long term effects on fat storage and the cardiovascular system. With rapid transformative advances to contemporary tools, how we shed light on microbial ecosystems to study them, alters perspective in both food and the gut. New sequencing technologies have evolved from single gene profiles to complete genomic panoramas of microbial communities that need interpreting. Coupled with physical and chemical techniques progressing apace provides nano resolution of food structure and microbial activity in the gut. Integrating this information represents the new frontier of current research and expands what we consider wholesome. Food, and the broader aspects of diet, are the primary modulator of the gut microbiota essential for homeostasis and the prevention of chronic and infectious diseases. Understanding how food composition and structure influence the microbiota-host interaction is a vital key to engineering the next generation of foods that meet not only our nutritional needs but address concerns arising around safety and long-term well-being. This widening of scope bridges gaps between disciplines to improve cross-feeding of ideas among experts interested in designing foods to be part of a diet that pushes at the boundaries of our life expectancy.

Prof. Gisèle LaPointe
Dr. Michael Rogers
Guest Editors

Manuscript Submission Information

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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

  • food
  • probiotics
  • processing
  • fermentation
  • metagenomics
  • metabonomics
  • metabolic activity
  • gut microbiota

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Published Papers (6 papers)

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Editorial

Jump to: Research, Review

2 pages, 203 KiB  
Editorial
Microorganisms Special Issue “How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?”
by Gisèle LaPointe and Michael A. Rogers
Microorganisms 2022, 10(11), 2097; https://doi.org/10.3390/microorganisms10112097 - 22 Oct 2022
Cited by 1 | Viewed by 1142
Abstract
We are a product of the foods we chronically consume, and life expectancy correlates with the quality of our diet [...] Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)

Research

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15 pages, 1202 KiB  
Article
Isolation and Characterization of Commensal Bifidobacteria Strains in Gut Microbiota of Neonates Born Preterm: A Prospective Longitudinal Study
by Sandra Wydau-Dematteis, Johanne Delannoy, Anne-Claire Téolis, Agnès Giuseppi, Florence Campeotto, Alexandre Lapillonne, Marie-José Butel and Julio Aires
Microorganisms 2022, 10(3), 654; https://doi.org/10.3390/microorganisms10030654 - 18 Mar 2022
Cited by 5 | Viewed by 2761
Abstract
Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, [...] Read more.
Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, and identification of the dominant bifidobacteria strains. The genetic relationship of the isolates was investigated via pulsed field gel electrophoresis (PFGE) genotyping, and PCR was used to screen the specific genetic marker tet genes. Additionally, all of the isolated strains were phenotypically characterized by their response to gastro-intestinal stresses and the MIC determination of tetracycline. In the same individual, our results showed a turnover of the bifidobacteria dominant population not only at species but also at strain levels. In addition, we found clonally related strains between twins. A minority of strains were tolerant to gastric (6%) and intestinal (16%) stresses. Thirteen percent of the strains were resistant to tetracycline. This work is original as it provides insights at the strain level of the early life in vivo dynamics of gut microbiota bifidobacteria in preterm neonates. It highlights the need to take into consideration the fluctuation of bifidobacteria populations that may occur for one individual. Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)
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12 pages, 2821 KiB  
Article
Effects of L. plantarum HY7715 on the Gut Microbial Community and Riboflavin Production in a Three-Stage Semi-Continuous Simulated Gut System
by Dong-Ki Hong, Myeong-Seok Yoo, Keon Heo, Jae-Jung Shim and Jung-Lyoul Lee
Microorganisms 2021, 9(12), 2478; https://doi.org/10.3390/microorganisms9122478 - 30 Nov 2021
Cited by 7 | Viewed by 2211
Abstract
Probiotics should be well established in the gut, passing through the digestive tract with a high degree of viability, and produce metabolites that improve the gut environment by interacting with the gut microbiome. Our previous study revealed that the Lactiplantibacillus plantarum HY7715 strain [...] Read more.
Probiotics should be well established in the gut, passing through the digestive tract with a high degree of viability, and produce metabolites that improve the gut environment by interacting with the gut microbiome. Our previous study revealed that the Lactiplantibacillus plantarum HY7715 strain shows good bile acid resistance and a riboflavin production capacity. To confirm the interaction between HY7715 and gut microbiome, we performed a metabolite and microbiome study using a simulated gut system (SGS) that mimics the intestinal environment. Changes in the microbiome were confirmed and compared with L. plantarum NCDO1752 as the control. After 14 days, the HY7715 treatment group showed a relatively high butyrate content compared to the control group, which showed increased acetate and propionate concentrations. Moreover, the riboflavin content was higher in the HY7715 treatment group, whereas the NCDO1752 treatment group produced only small amounts of riboflavin during the treatment period and showed a tendency to decrease during the washout stage; however, the HY7715 group produced riboflavin continuously in the ascending colon during the washout period. A correlation analysis of the genus that increased as the content of riboflavin increased revealed butyrate-producing microorganisms, such as Blautia and Flavonifractor. In conclusion, treatment with L. plantarum HY7715 induced the production and maintenance of riboflavin and the enrichment of the intestinal microbiome Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)
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25 pages, 5122 KiB  
Article
In Vitro Selection of Probiotics, Prebiotics, and Antioxidants to Develop an Innovative Synbiotic (NatuREN G) and Testing Its Effect in Reducing Uremic Toxins in Fecal Batches from CKD Patients
by Mirco Vacca, Giuseppe Celano, Marcello Salvatore Lenucci, Sergio Fontana, Flavia Maria la Forgia, Fabio Minervini, Aurelia Scarano, Angelo Santino, Giuseppe Dalfino, Loreto Gesualdo and Maria De Angelis
Microorganisms 2021, 9(6), 1316; https://doi.org/10.3390/microorganisms9061316 - 17 Jun 2021
Cited by 18 | Viewed by 4018
Abstract
We aimed to develop an innovative synbiotic formulation for use in reducing dysbiosis, uremic toxins (e.g., p-cresol and indoxyl sulfate), and, consequently, the pathognomonic features of patients with chronic kidney disease (CKD). Twenty-five probiotic strains, belonging to lactobacilli and Bifidobacterium, were [...] Read more.
We aimed to develop an innovative synbiotic formulation for use in reducing dysbiosis, uremic toxins (e.g., p-cresol and indoxyl sulfate), and, consequently, the pathognomonic features of patients with chronic kidney disease (CKD). Twenty-five probiotic strains, belonging to lactobacilli and Bifidobacterium, were tested for their ability to grow in co-culture with different vegetable (pomegranate, tomato, and grapes) sources of antioxidants and prebiotics (inulin, fructo-oligosaccharides, and β-glucans). Probiotics were selected based on the acidification rates and viable cell counts. Inulin and fructo-oligosaccharides reported the best prebiotic activity, while a pomegranate seed extract was initially chosen as antioxidant source. The investigation was also conducted in fecal batches from healthy and CKD subjects, on which metabolomic analyses (profiling volatile organic compounds and total free amino acids) were conducted. Two out of twenty-five probiotics were finally selected. After the stability tests, the selective innovative synbiotic formulation (named NatuREN G) comprised Bifidobacterium animalis BLC1, Lacticaseibacillus casei LC4P1, fructo-oligosaccharides, inulin, quercetin, resveratrol, and proanthocyanidins. Finally, NatuREN G was evaluated on fecal batches collected from CKD in which modified the viable cell densities of some cultivable bacterial patterns, increased the concentration of acetic acid and decane, while reduced the concentration of nonanoic acid, dimethyl trisulfide, and indoxyl sulfate. Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)
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16 pages, 2408 KiB  
Article
Enterotypes of the Gut Microbial Community and Their Response to Plant Secondary Compounds in Plateau Pikas
by Chao Fan, Liangzhi Zhang, Haibo Fu, Chuanfa Liu, Wenjing Li, Qi Cheng, He Zhang, Shangang Jia and Yanming Zhang
Microorganisms 2020, 8(9), 1311; https://doi.org/10.3390/microorganisms8091311 - 28 Aug 2020
Cited by 17 | Viewed by 4401
Abstract
Animal gut microbiomes can be clustered into “enterotypes” characterized by an abundance of signature genera. The characteristic determinants, stability, and resilience of these community clusters remain poorly understood. We used plateau pika (Ochotona curzoniae) as a model and identified three enterotypes [...] Read more.
Animal gut microbiomes can be clustered into “enterotypes” characterized by an abundance of signature genera. The characteristic determinants, stability, and resilience of these community clusters remain poorly understood. We used plateau pika (Ochotona curzoniae) as a model and identified three enterotypes by 16S rDNA sequencing. Among the top 15 genera, 13 showed significantly different levels of abundance between the enterotypes combined with different microbial functions and distinct fecal short-chain fatty acids. We monitored changes in the microbial community associated with the transfer of plateau pikas from field to laboratory and observed that feeding them a single diet reduced microbial diversity, resulting in a single enterotype with an altered composition of the dominant bacteria. However, microbial diversity, an abundance of some changed dominant genera, and enterotypes were partially restored after adding swainsonine (a plant secondary compound found in the natural diet of plateau pikas) to the feed. These results provide strong evidence that gut microbial diversity and enterotypes are directly related to specific diet, thereby indicating that the formation of different enterotypes can help animals adapt to complex food conditions. Additionally, natural plant secondary compounds can maintain dominant bacteria and inter-individual differences of gut microbiota and promote the resilience of enterotypes in small herbivorous mammals. Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)
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Review

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24 pages, 3018 KiB  
Review
Role of Gut Microbiota and Probiotics in Colorectal Cancer: Onset and Progression
by Edgar Torres-Maravilla, Anne-Sophie Boucard, Amir Hossein Mohseni, Sedigheh Taghinezhad-S, Naima G. Cortes-Perez and Luis G. Bermúdez-Humarán
Microorganisms 2021, 9(5), 1021; https://doi.org/10.3390/microorganisms9051021 - 10 May 2021
Cited by 47 | Viewed by 8635
Abstract
The gut microbiota plays an important role in maintaining homeostasis in the human body, and the disruption of these communities can lead to compromised host health and the onset of disease. Current research on probiotics is quite promising and, in particular, these microorganisms [...] Read more.
The gut microbiota plays an important role in maintaining homeostasis in the human body, and the disruption of these communities can lead to compromised host health and the onset of disease. Current research on probiotics is quite promising and, in particular, these microorganisms have demonstrated their potential for use as adjuvants for the treatment of colorectal cancer. This review addresses the possible applications of probiotics, postbiotics, synbiotics, and next-generation probiotics in colorectal cancer research. Full article
(This article belongs to the Special Issue How Do Food and Probiotics Influence the Composition and Activity of the Gut Microbiota?)
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