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

Deadline for manuscript submissions: closed (28 February 2019) | Viewed by 122566

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Special Issue Editors

Prof. Dr. Miguel Gueimonde

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Guest Editor

Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
Interests: microbiota; probiotics; prebiotics; bifidobacterium
Special Issues, Collections and Topics in MDPI journals

Dr. Kirsi Laitinen

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Guest Editor

Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, 20520 Turku, Finland
Interests: nutrition; diet; probiotics; fish oil; RCTs; allergy; obesity; gestation; children; eating behavior
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the last decade, our knowledge on the composition of the human microbiota has increased enormously. It has become clear that the human microbiota plays a key role for maintaining health, and that dysbiosis of this microbiota is involved in different communicable and non-communicable diseases. Diet has been identified as a major driver of microbiota composition and function. However, our knowledge on the impact of specific foods and nutrients and other dietary components upon the intestinal microbiota, along the different life stages, is still limited. Currently, a great research effort is being done for understanding the influence of different dietary components on the microbiota as a mediator of human health. In this context, this Special Issue, “Microbiota, Food and Health”, will cover a selection of current research topics, including, but not limited to, the following:

Role of microbiota-food interaction in the maintenance of human health.
Impact of both long and short-term nutritional and dietary interventions on the intestinal microbiota composition and function in different age groups.
Effects of dietary patterns on the human intestinal microbiota.
Influence of the gut microbiota in the transformation of dietary components and effects on bioavailability of the nutrients, bioactivity and health.
Modulation of intestinal microbiota and beneficial effects of functional foods or specific dietary ingredients.
Experimental studies on the mechanisms involved in the microbiota-food-health interaction.

We are particularly interested in human intervention and observational studies deciphering the role of food in the modulation of the microbiota composition/function and the consequences for human health.

Prof. Miguel Gueimonde
Prof. Kirsi Laitinen
Guest Editors

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Keywords

Microbiota
diet
food
health
functional foods
bioactivity
mechanisms

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 170 KiB

Open AccessEditorial

Microbiota, Food, and Health

by Kirsi Laitinen and Miguel Gueimonde

Int. J. Mol. Sci. 2019, 20(24), 6329; https://doi.org/10.3390/ijms20246329 - 15 Dec 2019

Cited by 4 | Viewed by 2932

Abstract

The effects of specific foods, such as products containing probiotics or prebiotics, on human health and the role of intestinal microbiota in this interaction have been a subject of scientific interest for several decades [...] Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

Research

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16 pages, 1103 KiB

Open AccessArticle

A Small In Vitro Fermentation Model for Screening the Gut Microbiota Effects of Different Fiber Preparations

by Irina Tsitko, Fanny Wiik-Miettinen, Outi Mattila, Natalia Rosa-Sibakov, Tuulikki Seppänen-Laakso, Johanna Maukonen, Emilia Nordlund and Maria Saarela

Int. J. Mol. Sci. 2019, 20(8), 1925; https://doi.org/10.3390/ijms20081925 - 18 Apr 2019

Cited by 42 | Viewed by 8066

Abstract

The development of prebiotic fibers requires fast high-throughput screening of their effects on the gut microbiota. We demonstrated the applicability of a mictotiter plate in the in vitro fermentation models for the screening of potentially-prebiotic dietary fibers. The effects of seven rye bran-, oat- and linseed-derived fiber preparations on the human fecal microbiota composition and short-chain fatty acid production were studied. The model was also used to study whether fibers can alleviate the harmful effects of amoxicillin-clavulanate on the microbiota. The antibiotic induced a shift in the bacterial community in the absence of fibers by decreasing the relative amounts of Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Lachnospiraceae and Ruminococcaceae, and increasing proteobacterial Sutterilaceae levels from 1% to 11% of the total microbiota. The fermentation of rye bran, enzymatically treated rye bran, its insoluble fraction, soluble oat fiber and a mixture of rye fiber:soluble oat fiber:linseed resulted in a significant increase in butyrate production and a bifidogenic effect in the absence of the antibiotic. These fibers were also able to counteract the negative effects of the antibiotic and prevent the decrease in the relative amount of bifidobacteria. Insoluble and soluble rye bran fractions and soluble oat fiber were the best for controlling the level of proteobacteria at the level below 2%. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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12 pages, 973 KiB

Open AccessArticle

Overall Dietary Quality Relates to Gut Microbiota Diversity and Abundance

by Kirsi Laitinen and Kati Mokkala

Int. J. Mol. Sci. 2019, 20(8), 1835; https://doi.org/10.3390/ijms20081835 - 13 Apr 2019

Cited by 67 | Viewed by 7418

Abstract

Disturbances in gut microbiota homeostasis may have metabolic consequences with potentially serious clinical manifestations. Diet influences the host’s metabolic health in several ways, either directly or indirectly by modulating the composition and function of gut microbiota. This study investigated the extent to which dietary quality is reflected in gut microbiota diversity in overweight and obese pregnant women at risk for metabolic complications. Dietary quality was measured by a validated index of diet quality (IDQ) and microbiota composition was analyzed using 16SrRNA gene sequencing from 84 women pregnant less than 18 weeks. The alpha diversity, measured as Chao1, observed operational taxonomic units (OTUs), phylogenetic diversity, and the Shannon index were calculated. The IDQ score correlated positively with the Shannon index (rho = 0.319, p = 0.003), but not with the other indexes. The women who had the highest dietary quality (highest IDQ quartile) had higher gut microbiota diversity in all the investigated indexes, when compared to the women with the lowest dietary quality (lowest IDQ quartile; p < 0.032). Consequently, a higher dietary quality was reflected in a higher gut microbiota diversity. The presented approach may aid in devising new tools for dietary counseling aiming at holistic health, as well as in microbiome studies, to control for dietary variance. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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16 pages, 3461 KiB

Open AccessArticle

Characterization of Microbiota Associated with Digesta and Mucosa in Different Regions of Gastrointestinal Tract of Nursery Pigs

by Bishnu Adhikari, Sung Woo Kim and Young Min Kwon

Int. J. Mol. Sci. 2019, 20(7), 1630; https://doi.org/10.3390/ijms20071630 - 2 Apr 2019

Cited by 62 | Viewed by 5830

Abstract

Weaning is a crucial period when piglets have to cope with sudden dietary, social, and environmental stressors that often lead to serious intestinal dysbiosis and mortality. In this study, five mucosal and five digesta samples from each proximate jejunum, distal jejunum, and mid-colon were collected from 7- and 27-day post-weaned pigs and subjected to microbiota analysis using 16S rRNA gene profiling. Taxonomic analysis at phylum level revealed that Proteobacteria was significantly higher at 7 days (13.54%), while Bacteriodetes was higher at 27 days (30.72%) post weaning. Genera such as Campylobacter, Veillonella, Helicobacter, and Blautia that were previously reported in intestinal dysbiosis were significantly enriched in seven-day post-weaned pigs. However, microbial communities shifted as post weaning age increased with a significant increase in alpha diversity, and genera such as Moryella, Dialister, Clostridium, Streptococcus, Prevotella, and Bacteroides become significantly abundant in 27-day post-weaned pigs. Interestingly, the genus Campylobacter was significantly abundant on seven-day post-weaning in two piglets with diarrhea, implicating its role in post-weaning diarrhea. The results of this study suggest that gut microbiota in pigs with dysbiosis on 7-day post weaning undergoes significant changes toward a more normal state as the post-weaning age reaches 27 days. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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15 pages, 2547 KiB

Open AccessArticle

Structural Determinants of Substrate Specificity of Omega-3 Desaturases from Mortierella alpina and Rhizophagus irregularis by Domain-Swapping and Molecular Docking

by Chunchi Rong, Haiqin Chen, Xin Tang, Zhennan Gu, Jianxin Zhao, Hao Zhang, Yongquan Chen and Wei Chen

Int. J. Mol. Sci. 2019, 20(7), 1603; https://doi.org/10.3390/ijms20071603 - 30 Mar 2019

Cited by 5 | Viewed by 3372

Abstract

Although various ω-3 fatty acid desaturases (ω3Des) have been identified and well-studied regarding substrate preference and regiospecificity, the molecular mechanism of their substrate specificities remains to be investigated. Here we compared two ω3Des, FADS15 from Mortierella alpina and oRiFADS17 from Rhizophagus irregularis, which possessed a substrate preference for linoleic acid and arachidonic acid, respectively. Their sequences were divided into six sections and a domain-swapping strategy was used to test the role of each section in catalytic activity. Heterologous expression and fatty acid experiments of hybrid enzymes in Saccharomyces cerevisiae INVSc1 indicated that the sequences between his-boxes I and II played critical roles in influencing substrate preference. Based on site-directed mutagenesis and molecular docking, the amino acid substitutions W129T and T144W, located in the upper part of the hydrocarbon chain, were found to be involved in substrate specificity, while V137T and V152T were confirmed to interfere with substrate recognition. This study provides significant insight into the structure-function relationship of ω3Des. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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15 pages, 2148 KiB

Open AccessArticle

Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome

by Laetitia Cortes, Harm Wopereis, Aude Tartiere, Julie Piquenot, Joost W. Gouw, Sebastian Tims, Jan Knol and Daniel Chelsky

Int. J. Mol. Sci. 2019, 20(6), 1430; https://doi.org/10.3390/ijms20061430 - 21 Mar 2019

Cited by 13 | Viewed by 6048

Abstract

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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12 pages, 1264 KiB

Open AccessArticle

Characteristics of Gut Microbiota in Sows and Their Relationship with Apparent Nutrient Digestibility

by Qing Niu, Pinghua Li, Shuaishuai Hao, Sung Woo Kim, Taoran Du, Jindi Hua and Ruihua Huang

Int. J. Mol. Sci. 2019, 20(4), 870; https://doi.org/10.3390/ijms20040870 - 18 Feb 2019

Cited by 51 | Viewed by 4733

Abstract

The gut microbiota plays important roles in animal health and nutrient digestibility. The characteristics of gut microbiota population in grower pigs and their correlation with apparent nutrient digestibility were assessed in previous study. Here we studied characteristics of intestinal microbiota of sows and analyzed their relationships with apparent nutrient (ether extract (EE), crude protein (CP), crude fiber (CF), neutral detergent fiber (NDF) and acid detergent fiber (ADF)) digestibility. Firmicutes and Bacteroidetes were the most dominant phyla, approximately 73% of the total sequences. Treponema, Oscillibacter and Lactobacillus were the most dominant generas, more than 49% of the total sequences. The microbiota of sows clustered separately from the microbiota of grower pigs at the age of D28 D60, D90 and D150. The abundance of Clostridium and Turicibacter was positively correlated with apparent EE digestibility. The abundance of Anaerofustis and Robinsoniella in sow fecal samples was positively correlated with apparent CF digestibility. The abundance of Collinsella and Sutterella was positively correlated with apparent NDF digestibility. The abundance of Clostridium, Collinsella, Robinsoniella and Turicibacter was positively correlated with apparent ADF digestibility. Sows have their unique gut microbial structure compared with grower pigs and some of them participate in the digestive process of different nutrients. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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12 pages, 1831 KiB

Open AccessArticle

The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls

by Jonna Jalanka, Giles Major, Kathryn Murray, Gulzar Singh, Adam Nowak, Caroline Kurtz, Inmaculada Silos-Santiago, Jeffrey M. Johnston, Willem M. de Vos and Robin Spiller

Int. J. Mol. Sci. 2019, 20(2), 433; https://doi.org/10.3390/ijms20020433 - 20 Jan 2019

Cited by 124 | Viewed by 29744

Abstract

Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We performed two randomised, placebo-controlled, double-blinded trials comparing 7 days of psyllium with a placebo (maltodextrin) in 8 healthy volunteers and 16 constipated patients respectively. We measured the patients’ gastrointestnal (GI) transit, faecal water content, short-chain fatty acid (SCFA) and the stool microbiota composition. While psyllium supplement had a small but significant effect on the microbial composition of healthy adults (increasing Veillonella and decreasing Subdoligranulum), in constipated subjects there were greater effects on the microbial composition (increased Lachnospira, Faecalibacterium, Phascolarctobacterium, Veillonella and Sutterella and decreased uncultured Coriobacteria and Christensenella) and alterations in the levels of acetate and propionate. We found several taxa to be associated with altered GI transit, SCFAs and faecal water content in these patients. Significant increases in three genera known to produce butyrate, Lachnospira, Roseburia and Faecalibacterium, correlated with increased faecal water. In summary, psyllium supplementation increased stool water and this was associated with significant changes in microbiota, most marked in constipated patients. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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Review

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23 pages, 582 KiB

Open AccessReview

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond

by Carrie A. M. Wegh, Sharon Y. Geerlings, Jan Knol, Guus Roeselers and Clara Belzer

Int. J. Mol. Sci. 2019, 20(19), 4673; https://doi.org/10.3390/ijms20194673 - 20 Sep 2019

Cited by 350 | Viewed by 25518

Abstract

Postbiotics are functional bioactive compounds, generated in a matrix during fermentation, which may be used to promote health. The term postbiotics can be regarded as an umbrella term for all synonyms and related terms of these microbial fermentation components. Therefore, postbiotics can include many different constituents including metabolites, short-chain fatty acids (SCFAs), microbial cell fractions, functional proteins, extracellular polysaccharides (EPS), cell lysates, teichoic acid, peptidoglycan-derived muropeptides and pili-type structures. Postbiotics is also a rather new term in the ‘-biotics’ field. Where consensus exists for the definitions of pre- and probiotics, this is not yet the case for postbiotics. Here we propose a working definition and review currently known postbiotic compounds, their proposed mechanisms, clinical evidence and potential applications. Research to date indicates that postbiotics can have direct immunomodulatory and clinically relevant effects and evidence can be found for the use of postbiotics in healthy individuals to improve overall health and to relief symptoms in a range of diseases such as infant colic and in adults atopic dermatitis and different causes of diarrhea. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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18 pages, 767 KiB

Open AccessReview

Xenobiotics Formed during Food Processing: Their Relation with the Intestinal Microbiota and Colorectal Cancer

by Alicja M. Nogacka, María Gómez-Martín, Adolfo Suárez, Oscar González-Bernardo, Clara G. de los Reyes-Gavilán and Sonia González

Int. J. Mol. Sci. 2019, 20(8), 2051; https://doi.org/10.3390/ijms20082051 - 25 Apr 2019

Cited by 52 | Viewed by 9849

Abstract

The colonic epithelium is exposed to a mixture of compounds through diet, among which some are procarcinogens, whereas others have a protective effect. Therefore, the net impact of these compounds on human health depends on the overall balance between all factors involved. Strong scientific evidence has demonstrated the relationship between nitrosamines (NA), heterocyclic amines (HCAs), and polycyclic aromatic hydrocarbons (PAHs), which are the major genotoxins derived from cooking and food processing, and cancer. The mechanisms of the relationship between dietary toxic xenobiotics and cancer risk are not yet well understood, but it has been suggested that differences in dietary habits affect the colonic environment by increasing or decreasing the exposure to mutagens directly and indirectly through changes in the composition and activity of the gut microbiota. Several changes in the proportions of specific microbial groups have been proposed as risk factors for the development of neoplastic lesions and the enrichment of enterotoxigenic microbial strains in stool. In addition, changes in the gut microbiota composition and activity promoted by diet may modify the faecal genotoxicity/cytotoxicity, which can be associated with a higher or lower risk of developing cancer. Therefore, the interaction between dietary components and intestinal bacteria may be a modifiable factor for the development of colorectal cancer in humans and deserves more attention in the near future. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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28 pages, 2735 KiB

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Causal Relationship between Diet-Induced Gut Microbiota Changes and Diabetes: A Novel Strategy to Transplant Faecalibacterium prausnitzii in Preventing Diabetes

by Kumar Ganesan, Sookja Kim Chung, Jairam Vanamala and Baojun Xu

Int. J. Mol. Sci. 2018, 19(12), 3720; https://doi.org/10.3390/ijms19123720 - 22 Nov 2018

Cited by 138 | Viewed by 17636

Abstract

The incidence of metabolic disorders, including diabetes, has elevated exponentially during the last decades and enhanced the risk of a variety of complications, such as diabetes and cardiovascular diseases. In the present review, we have highlighted the new insights on the complex relationships between diet-induced modulation of gut microbiota and metabolic disorders, including diabetes. Literature from various library databases and electronic searches (ScienceDirect, PubMed, and Google Scholar) were randomly collected. There exists a complex relationship between diet and gut microbiota, which alters the energy balance, health impacts, and autoimmunity, further causes inflammation and metabolic dysfunction, including diabetes. Faecalibacterium prausnitzii is a butyrate-producing bacterium, which plays a vital role in diabetes. Transplantation of F. prausnitzii has been used as an intervention strategy to treat dysbiosis of the gut’s microbial community that is linked to the inflammation, which precedes autoimmune disease and diabetes. The review focuses on literature that highlights the benefits of the microbiota especially, the abundant of F. prausnitzii in protecting the gut microbiota pattern and its therapeutic potential against inflammation and diabetes. Full article

(This article belongs to the Special Issue Microbiota, Food and Health)

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