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Microorganisms
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Diet, Nutrition, and Gut Microbiota
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Diet, Nutrition, and 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 October 2022) | Viewed by 12449

Special Issue Editor

Dr. Oleg Paliy

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Wright State University, 260 Diggs Laboratory, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
Interests: human gut microbiota; diet; human nutrition; molecular ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is focused on the roles of gut microbes in modulating the effects of human nutrition and dietary components on our health and wellbeing. In recent years, we have begun to gradually uncover the indispensable role our gut microbiota plays in the transformation of consumed compounds, in the degradation of dietary fibers, and in the production of short chain fatty acids and other metabolites that have significant impact on our physiology. The foods we consume contain hundreds of metabolites and bioactive compounds, and we have only just started to investigate the sheer variety of the microbiome involvement in the transformation of these nutrients. Increasing our understanding of the mechanisms linking gut microbes to these dietary components will facilitate the development of pro-, pre- , and synbiotic treatments and functional foods and will pave the way to personalized nutrition and microbe-based therapeutics.

We welcome all manuscript submissions that are focused on the interplay of diet and nutrition with the host-associated microbiota, whether that host is human, other vertebrate or invertebrate species, or in vitro community systems. We are happy to consider both primary research articles as well as reviews on the appropriate topic. Especially encouraged are manuscripts that go beyond the description of microbiome changes on different diets and supplement such information with data on the functional consequences of dietary alterations, including profiling metabolic end- and by-products, interrogating gene and protein expression alterations (e.g., metatranscriptomics and metaproteomics), delineating the genetic determinants of microbes’ ability to digest and transform dietary components, or providing evidence for the effects of microbiota-derived metabolites on the host.

The deadline for the submission of manuscripts for this Special Issue is 17 April 2022. For this issue, the Editorial office is granting a 400 CHF reduction of the fee. Authors who wish to inquire about the suitability of their manuscript for this Special Issue are encouraged to contact the Special Issue editor, Dr. Oleg Paliy, at [email protected].

Dr. Oleg Paliy
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

  • gut microbiota
  • microbiome
  • nutrition
  • diet
  • dietary fiber
  • high fat

Published Papers (6 papers)

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Research

20 pages, 2933 KiB  
Article
Effect of Yeast Saccharomyces cerevisiae as a Probiotic on Diet Digestibility, Fermentative Metabolites, and Composition and Functional Potential of the Fecal Microbiota of Dogs Submitted to an Abrupt Dietary Change
by Taís Silvino Bastos, Camilla Mariane Menezes Souza, Héloïse Legendre, Nadège Richard, Rachel Pilla, Jan S. Suchodolski, Simone Gisele de Oliveira, Achraf Adib Lesaux and Ananda Portella Félix
Microorganisms 2023, 11(2), 506; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020506 - 17 Feb 2023
Cited by 6 | Viewed by 3050
Abstract
The aim was to evaluate the effects of yeast probiotic on diet digestibility, fermentative metabolites, and fecal microbiota of dogs submitted to dietary change. Sixteen dogs were divided into two groups of eight dogs each: control, without, and with probiotic, receiving 0.12 g/dog/day [...] Read more.
The aim was to evaluate the effects of yeast probiotic on diet digestibility, fermentative metabolites, and fecal microbiota of dogs submitted to dietary change. Sixteen dogs were divided into two groups of eight dogs each: control, without, and with probiotic, receiving 0.12 g/dog/day of live Saccharomyces cerevisiae yeast. The dogs were fed a lower protein and fiber diet for 21 days and then changed to a higher protein and fiber diet until day 49. Yeast supplementation did not statistically influence diet digestibility. The probiotic group had a lower fecal concentration of total biogenic amines (days 21 and 49), ammonia (day 23), and aromatic compounds and a higher fecal concentration of butyrate (p < 0.05). The probiotic group showed a lower dysbiosis index, a higher abundance (p < 0.05) of Bifidobacterium (days 35 and 49) and Turicibacter, and a lower abundance of Lactobacillus and E. coli (p < 0.05). Beta diversity demonstrated a clear differentiation in the gut microbiota between the control and probiotic groups on day 49. The control group showed upregulation in genes related to virulence factors, antibiotic resistance, and osmotic stress. The results indicated that the live yeast evaluated can have beneficial effects on intestinal functionality of dogs. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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17 pages, 7792 KiB  
Article
Average Daily Gain in Lambs Weaned at 60 Days of Age Is Correlated with Rumen and Rectum Microbiota
by Xuejiao Yin, Chunhui Duan, Shoukun Ji, Peizhi Tian, Sisi Ju, Hui Yan, Yingjie Zhang and Yueqin Liu
Microorganisms 2023, 11(2), 348; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11020348 - 30 Jan 2023
Cited by 1 | Viewed by 1187
Abstract
Colonization of gastrointestinal microbiota in mammals during early life is vital to host health. The objective of this study was to investigate whether lambs with high and low ADG have a different rumen and rectum microbial community. Thus, we investigated potential relationships between [...] Read more.
Colonization of gastrointestinal microbiota in mammals during early life is vital to host health. The objective of this study was to investigate whether lambs with high and low ADG have a different rumen and rectum microbial community. Thus, we investigated potential relationships between rumen and rectum microbiota and average daily gain (ADG) in weaned lambs. Sixteen lambs with similar body weights (7.63 ± 1.18 kg) were selected at 30 days of age. At 60 days of age, lambs were weaned, and ADG was calculated from 60 to 90 days. Then, two groups were generated: higher ADG (HG, 134.17 ± 13.48 g/day) and lower ADG (LG, 47.50 ± 19.51 g/day). Microbiota was evaluated at 30, 60, and 90 days of age. The final live weight and ADG at 90 days of age was higher (p < 0.05) in the HG group compared to the LG group. The maturity of bacterial and fungal communities was increased (p < 0.05) in the HG group for the 30 days vs. 90 days comparison and 60 days vs. 90 days comparison. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 18 bacterial biomarkers that are ADG-specific in the rumen and 35 bacterial biomarkers in the rectum. Meanwhile, 15 fungal biomarkers were found in the rumen and 8 biomarkers were found in the rectum. Our findings indicated that ADG is related to the rumen and rectum microbiota in lambs. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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10 pages, 1658 KiB  
Article
Effects of Helicobacter pylori and Nitrate-Reducing Bacteria Coculture on Cells
by Hinako Ojima, Sakiko Kuraoka, Shyoutarou Okanoue, Hiroyuki Okada, Kazuyoshi Gotoh, Osamu Matsushita, Akari Watanabe and Kenji Yokota
Microorganisms 2022, 10(12), 2495; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122495 - 16 Dec 2022
Cited by 3 | Viewed by 1541
Abstract
Helicobacter pylori infection is an important risk factor for developing gastric cancer. However, only a few H. pylori-infected people develop gastric cancer. Thus, other risk factors aside from H. pylori infection may be involved in gastric cancer development. This study aimed to [...] Read more.
Helicobacter pylori infection is an important risk factor for developing gastric cancer. However, only a few H. pylori-infected people develop gastric cancer. Thus, other risk factors aside from H. pylori infection may be involved in gastric cancer development. This study aimed to investigate whether the nitrate-reducing bacteria isolated from patients with atrophic gastritis caused by H. pylori infection are risk factors for developing atrophic gastritis and gastric neoplasia. Nitrate-reducing bacteria were isolated from patients with atrophic gastritis caused by H. pylori infection. Among the isolated bacteria, Actinomyces oris, Actinomyces odontolyticus, Rothia dentocariosa, and Rothia mucilaginosa were used in the subsequent experiments. Cytokine inducibility was evaluated in monocytic cells, and mitogen-activated protein kinase (MAPK) activity and cell cycle were assessed in the gastric epithelial cells. The cytotoxicities and neutrophil-inducing abilities of the Actinomyces and Rothia species were enhanced when cocultured with H. pylori. Th1/Th2-related cytokines were also expressed, but their expression levels differed depending on the bacterial species. Moreover, H. pylori and Actinomyces activated MAPK (ERK and p38) and affected cell cycle progression. Some nitrate-reducing bacteria cocultured with H. pylori may promote inflammation and atrophy by inducing cytokine production. In addition, the MAPK activation and cell cycle progression caused by these bacteria can contribute to gastric cancer development. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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15 pages, 2048 KiB  
Article
Identification of Human Gut Microbiome Associated with Enterolignan Production
by Kento Sawane, Koji Hosomi, Jonguk Park, Kouta Ookoshi, Hinako Nanri, Takashi Nakagata, Yi-An Chen, Attayeb Mohsen, Hitoshi Kawashima, Kenji Mizuguchi, Motohiko Miyachi and Jun Kunisawa
Microorganisms 2022, 10(11), 2169; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112169 - 31 Oct 2022
Cited by 2 | Viewed by 2182
Abstract
Dietary plant lignans are converted inside the gut to enterolignans enterodiol (ED) and enterolactone (EL), which have several biological functions, and health benefits. In this study, we characterized the gut microbiome composition associated with enterolignan production using data from a cross-sectional study in [...] Read more.
Dietary plant lignans are converted inside the gut to enterolignans enterodiol (ED) and enterolactone (EL), which have several biological functions, and health benefits. In this study, we characterized the gut microbiome composition associated with enterolignan production using data from a cross-sectional study in the Japanese population. We identified enterolignan producers by measuring ED and EL levels in subject’s serum using liquid chromatography-tandem mass spectrometry. Enterolignan producers show more abundant proportion of Ruminococcaceae and Lachnospiraceae than non-enterolignan producers. In particular, subjects with EL in their serum had a highly diverse gut microbiome that was rich in Ruminococcaceae and Rikenellaceae. Moreover, we built a random forest classification model to classify subjects to either EL producers or not using three characteristic bacteria. In conclusion, our analysis revealed the composition of gut microbiome that is associated with lignan metabolism. We also confirmed that it can be used to classify the microbiome ability to metabolize lignan using machine learning approach. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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14 pages, 3080 KiB  
Article
A Cohort Study of the Effects of Daily-Diet Water-Soluble Dietary Fiber on Butyric Acid-Producing Gut Microbiota in Middle-Aged and Older Adults in a Rural Region
by Satoshi Sato, Daisuke Chinda, Tadashi Shimoyama, Chikara Iino, Sae Kudo, Kaori Sawada, Tatsuya Mikami, Shigeyuki Nakaji, Hirotake Sakuraba and Shinsaku Fukuda
Microorganisms 2022, 10(9), 1813; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10091813 - 10 Sep 2022
Cited by 1 | Viewed by 1840
Abstract
Water-soluble dietary fiber is primarily a substrate for degradation of short chain fatty acids (SCFAs), particularly butyric acid, by gut microbiota. SCFAs have beneficial effects on the whole body. However, epidemiological studies on the association between water-soluble dietary fiber from daily food intake [...] Read more.
Water-soluble dietary fiber is primarily a substrate for degradation of short chain fatty acids (SCFAs), particularly butyric acid, by gut microbiota. SCFAs have beneficial effects on the whole body. However, epidemiological studies on the association between water-soluble dietary fiber from daily food intake and butyric acid-producing bacteria are inconsistent. The purpose of this study was to determine the association between levels of water-soluble dietary fiber from daily food intake and gut microbiota, particularly butyric acid producers, in middle-aged and older adults in a rural area in Japan. We examined the effects of water-soluble dietary fiber intake on gut microbiota after adjusting for confounding factors. After propensity score matching, 520 subjects (260 in the low-intake group and 260 in the high-intake group) were selected. One year later after a follow-up survey, we re-classified the participants and again compared low- and high-intake groups. As a result, people with a high intake had a higher relative abundance of butyric acid-producing bacteria. It was also revealed that butyric acid-producing bacteria remained high in the group that maintained high intake the next year. We concluded that continuous intake of water-soluble dietary fiber from daily food is necessary to maintain sufficient amounts of butyric acid-producing bacteria. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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14 pages, 1677 KiB  
Article
Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota
by Sumudu Rajakaruna, Sergio Pérez-Burillo, Denise Lynette Kramer, José Ángel Rufián-Henares and Oleg Paliy
Microorganisms 2022, 10(7), 1268; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071268 - 22 Jun 2022
Cited by 8 | Viewed by 1654
Abstract
Melanoidins are the products of the Maillard reaction between carbonyl and amino groups of macromolecules and are readily formed in foods, especially during heat treatment. In this study we utilized the three-stage Human Gut Simulator system to assess the effect of providing melanoidins [...] Read more.
Melanoidins are the products of the Maillard reaction between carbonyl and amino groups of macromolecules and are readily formed in foods, especially during heat treatment. In this study we utilized the three-stage Human Gut Simulator system to assess the effect of providing melanoidins extracted from either biscuits or bread crust to the human gut microbiota. Addition of melanoidins to the growth medium led to statistically significant alterations in the microbial community composition, and it increased short-chain fatty acid and antioxidant production by the microbiota. The magnitude of these changes was much higher for cultures grown with biscuit melanoidins. Several lines of evidence indicate that such differences between these melanoidin sources might be due to the presence of lipid components in biscuit melanoidin structures. Because melanoidins are largely not degraded by human gastrointestinal enzymes, they provide an additional source of microbiota-accessible nutrients to our gut microbes. Full article
(This article belongs to the Special Issue Diet, Nutrition, and Gut Microbiota)
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