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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 (30 March 2024) | Viewed by 24793

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Dr. Sunmin Park

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Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan 31499, Republic of Korea
Interests: Alzheimer’s disease; insulin resistance; nutritional epidemiology; nutrigenomics; gut microbiome; type 2 diabetes; bioinformatics
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Dear Colleagues,

The gut microbiome is believed to profoundly influence many metabolic processes of the host human metabolism. This is often the result of neuroactive signals between the brain and the microbiome bidirectionally, called the gut–brain axis. The gut–brain axis influences the intestinal permeability through the autonomous system to modulate gut microbiota and their products. Such signals may be mediated by small molecules that are byproducts of the metabolism of gut microbiota, or they may be the results of cytokines and neurotransmitters produced in response to the gut bacteria. The microbiome is believed to play a causative role in diverse diseases such as obesity, Alzheimer’s disease, cardiovascular disease, some cancers, diabetes, and fatty liver disease. However, a healthy microbiome can prevent such diseases. Diet is known to be a major factor in determining the composition of the gut microbiome by modulating digestive juices and providing prebiotics. Diets can either expand or suppress microbial diversity, the relative composition of the microbiome (Firmicutes/Bacteroidetes ratio), the network of bacteria, or even increase or decrease specific bacteria such as Akkermansia municiphila. Many of the benefits of healthy diets are a consequence of the subsequent actions of the microbiome in response. However, substantial gaps exist in our understanding of the signaling pathways that control microbial responses to dietary inputs and their subsequent signaling to the brain and other organs of the body. This Special Issue looks to further the understanding of how dietary modulations of the gut microbiome results in human health outcomes in diverse regions of the body.

A wide range of manuscripts will be considered for this Special Issue. We are especially interested in new research in human subjects, but we will also consider animal research that is applicable to humans. High-quality reviews and manuscripts that describe new research methods are also welcome. We will consider any manuscript that provides new and novel information about how human nutrition may contribute to human health or disease prevention through the gut microbiome.

This issue will cover topics related to interactions of diet and lifestyle with the microbiome that result in either beneficial or harmful outcomes for human health. Especially important are the pathways that link nutrition to changes in the microbiome, and how the changes in the microbiome result in signaling by gut-derived changes in inflammatory cytokines, neurotransmitters, and metabolic hormone signals.

Prof. Dr. Sunmin Park
Guest Editor

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Keywords

microbiome
gut
brain
obesity
diabetes
inflammation
liver
nutrition
probiotic
prebiotic

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Gut Microbiota and Nutrition in Human Health (2nd Edition) in International Journal of Molecular Sciences

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Editorial

Jump to: Research, Review

5 pages, 495 KiB

Open AccessEditorial

Special Issue: “Gut Microbiota and Nutrition in Human Health”

by Sunmin Park

Int. J. Mol. Sci. 2024, 25(21), 11589; https://doi.org/10.3390/ijms252111589 - 29 Oct 2024

Viewed by 348

Abstract

The microbiome is a singular term for a vast array of life forms that live symbiotically within the bodies of human and animal hosts, forming commensal, parasitic, or mutualistic relationships [...] Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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Research

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14 pages, 3536 KiB

Open AccessArticle

Evaluating the Impact of Probiotic Therapy on the Endocannabinoid System, Pain, Sleep and Fatigue: A Randomized, Double-Blind, Placebo-Controlled Trial in Dancers

by Jakub Wiącek, Tomasz Podgórski, Krzysztof Kusy, Igor Łoniewski, Karolina Skonieczna-Żydecka and Joanna Karolkiewicz

Int. J. Mol. Sci. 2024, 25(11), 5611; https://doi.org/10.3390/ijms25115611 - 21 May 2024

Cited by 1 | Viewed by 1663

Abstract

Emerging research links the endocannabinoid system to gut microbiota, influencing nociception, mood, and immunity, yet the molecular interactions remain unclear. This study focused on the effects of probiotics on ECS markers—cannabinoid receptor type 2 (CB2) and fatty acid amide hydrolase (FAAH)—in dancers, a group selected due to their high exposure to physical and psychological stress. In a double-blind, placebo-controlled trial (ClinicalTrials.gov NCT05567653), 15 dancers were assigned to receive either a 12-week regimen of Lactobacillus helveticus Rosell-52 and Bifidobacterium longum Rosell-17 or a placebo (PLA: n = 10, PRO: n = 5). There were no significant changes in CB2 (probiotic: 0.55 to 0.29 ng/mL; placebo: 0.86 to 0.72 ng/mL) or FAAH levels (probiotic: 5.93 to 6.02 ng/mL; placebo: 6.46 to 6.94 ng/mL; p > 0.05). A trend toward improved sleep quality was observed in the probiotic group, while the placebo group showed a decline (PRO: from 1.4 to 1.0; PLA: from 0.8 to 1.2; p = 0.07841). No other differences were noted in assessed outcomes (pain and fatigue). Probiotic supplementation showed no significant impact on CB2 or FAAH levels, pain, or fatigue but suggested potential benefits for sleep quality, suggesting an area for further research. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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17 pages, 2443 KiB

Open AccessArticle

Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities

by Yaiza Carnicero-Mayo, Luis E. Sáenz de Miera, Miguel Ángel Ferrero, Nicolás Navasa and Javier Casqueiro

Int. J. Mol. Sci. 2024, 25(7), 4013; https://doi.org/10.3390/ijms25074013 - 4 Apr 2024

Viewed by 1339

Abstract

Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3–V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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17 pages, 6526 KiB

Open AccessArticle

Consumption of Limosilactobacillus fermentum Inhibits Corneal Damage and Inflammation in Dry Eye Disease Mouse Model through Regulating the Gut Microbiome

by Kippeum Lee, Hyeonjun Gwon, Jae Jung Shim, Joo Yun Kim and Jae Hwan Lee

Int. J. Mol. Sci. 2024, 25(6), 3528; https://doi.org/10.3390/ijms25063528 - 20 Mar 2024

Cited by 1 | Viewed by 1644

Abstract

The present study investigated the effect of orally administered Limosilactobacillus fermentum HY7302 (HY7302) on the relationship between ocular tissue and the microbiome in a corneal injury dry eye mouse model. Specifically, 0.1% benzalkonium chloride (BAC) was applied to the ocular surface for 14 days to induce corneal injury in male Balb/c mice. During the BAC treatment period, HY7302 (1 × 10⁸ CFU/kg/day or 1 × 10⁹ CFU/kg/day) or an omega-3 positive control (400 mg/kg/day) were administered orally (n = eight/group). To examine the signaling pathways affected by the HY7302 treatment, the in vitro effects of HY7302 on the tight junctions and the inflammatory response were investigated in the mouse colon epithelial cell line, CMT-93. BAC exposure decreased tear production, induced ocular inflammation and corneal epithelial detachment, and altered the gut microbiota. However, oral administration of HY7302 restored tear secretion and decreased corneal epithelial detachment in BAC-treated corneal injury mice. Further, HY7302 alleviated corneal inflammation via modulation of matrix metalloproteinase-9 (MMP-9) expression and affeted alterations in gut microbiota composition. These findings suggest that the gut–eye axis interaction between gut microbiota and corneal tissue affects disease severity in corneal injury, and that the alteration of the microbiota by HY7302 could improve eye health by regulating the inflammatory response. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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14 pages, 2489 KiB

Open AccessArticle

Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity

by Agata Anna Cisek, Edyta Szymańska, Aldona Wierzbicka-Rucińska, Tamara Aleksandrzak-Piekarczyk and Bożena Cukrowska

Int. J. Mol. Sci. 2024, 25(1), 673; https://doi.org/10.3390/ijms25010673 - 4 Jan 2024

Cited by 3 | Viewed by 1741

Abstract

The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens—especially those focused on children—are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn’s disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn’s Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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16 pages, 4016 KiB

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Strontium Chloride Improves Reproductive Function and Alters Gut Microbiota in Male Rats

by Xulai Huang, Yanan Gao, Yangdong Zhang, Jiaqi Wang and Nan Zheng

Int. J. Mol. Sci. 2023, 24(18), 13922; https://doi.org/10.3390/ijms241813922 - 10 Sep 2023

Cited by 2 | Viewed by 1936

Abstract

Strontium (Sr) is an essential trace element in the human body and plays an important role in regulating male reproductive health. Recent studies have shown that gut flora plays a key role in maintaining spermatogenesis, as well as testicular health, through the gut–testis axis. At present, it is unclear whether gut microbiota can mediate the effects of Sr on sperm quality, and what the underlying mechanisms may be. We investigated the effects of different concentrations of strontium chloride (SrCl₂) solutions (0, 50, 100, and 200 mg/kg BW) on reproductive function and gut microbiota in male Wistar rats (6–8 weeks, 250 ± 20 g). All the animals were euthanized after 37 days of treatment. The Sr-50 group significantly increased sperm concentration, sperm motility, and sperm viability in rats. After Sr treatment, serum and testicular testosterone (T) and Sr levels increased in a dose-dependent manner with increasing Sr concentration. At the same time, we also found that testicular marker enzymes (ACP, LDH) and testosterone marker genes (StAR, 3β-HSD, and Cyp11a1) increased significantly in varying degrees after Sr treatment, while serum NO levels decreased significantly in a dose-dependent manner. Further investigation of intestinal flora showed that SrCl₂ affected the composition of gut microbiome, but did not affect the richness and diversity of gut microbiota. Sr treatment reduced the number of bacteria with negative effects on reproductive health, such as Bacteroidetes, Tenericutes, Romboutsia, Ruminococcaceae_UCG_014, Weissella, and Eubacterium_coprostanoligenes_group, and added bacteria with negative effects on reproductive health, such as Jeotgalicoccus. To further explore the Sr and the relationship between the gut microbiota, we conducted a Spearman correlation analysis, and the results showed that the gut microbiota was closely correlated with Sr content in serum and testicular tissue, sex hormone levels, and testicular marker enzymes. Additionally, gut microbiota can also regulate each other and jointly maintain the homeostasis of the body’s internal environment. However, we found no significant correlation between intestinal flora and sperm quality in this study, which may be related to the small sample size of our 16S rDNA sequencing. In conclusion, the Sr-50 group significantly increased T levels and sperm quality, and improved the levels of testicular marker enzymes and testosterone marker genes in the rats. Sr treatment altered the gut flora of the rats. However, further analysis of the effects of gut microbiota in mediating the effects of SrCl₂ on male reproductive function is needed. This study may improve the current understanding of the interaction between Sr, reproductive health, and gut microbiota, providing evidence for the development of Sr-rich foods and the prevention of male fertility decline. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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15 pages, 3882 KiB

Open AccessArticle

Effect of Liver Fibrosis on Oral and Gut Microbiota in the Japanese General Population Determined by Evaluating the FibroScan–Aspartate Aminotransferase Score

by Satoshi Sato, Chikara Iino, Daisuke Chinda, Takafumi Sasada, Tetsuyuki Tateda, Masatoshi Kaizuka, Hiroki Nomiya, Go Igarashi, Kaori Sawada, Tatsuya Mikami, Shigeyuki Nakaji, Hirotake Sakuraba and Shinsaku Fukuda

Int. J. Mol. Sci. 2023, 24(17), 13470; https://doi.org/10.3390/ijms241713470 - 30 Aug 2023

Cited by 1 | Viewed by 1657

Abstract

The association between liver fibrosis and oral or gut microbiota has been studied before. However, epidemiological studies in the general population are limited owing to the difficulty of noninvasive liver-fibrosis assessment. FibroScan–asparate aminotransferase (FAST) scores can be used to accurately and non-invasively evaluate liver fibrosis. This study aimed to determine the association between liver fibrosis and oral or gut microbiota using the FAST score in the general population. After propensity score matching of 1059 participants based on sex, age, body mass index, homeostasis model assessment of insulin resistance, and triglyceride levels, 125 (non-liver-fibrosis group, 100; liver fibrosis group, 25) were included. The diversity of gut microbiota differed significantly between the two groups; however, no significant differences were noted in their oral microbiota. The liver fibrosis group showed an increase in the relative abundance of Fusobacteria strains and a decrease in the relative abundance of Faecalibacterium, with the presence of Fusicatenibacter in the gut microbiota. Feacalibacterium was not identified as an independent factor of liver fibrosis in adjusting the fatty liver index. In the general population, gut microbiota may be more involved in liver fibrosis than oral microbiota. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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23 pages, 5002 KiB

Open AccessArticle

Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals

by Sunmin Park, Chen Li, Xuangao Wu and Tianshun Zhang

Int. J. Mol. Sci. 2023, 24(17), 13329; https://doi.org/10.3390/ijms241713329 - 28 Aug 2023

Cited by 5 | Viewed by 2393

Abstract

This study aimed to investigate alterations in the gut microbiota of patients with depression compared to those in the gut microbiota of healthy individuals based on enterotypes as a classification framework. Fecal bacteria FASTA/Q samples from 333 Chinese participants, including 107 healthy individuals (Healthy group) and 226 individuals suffering from depression (DP group), were analyzed. The participants were classified into three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). An α-diversity analysis revealed no significant differences in microbial diversity between the Healthy and DP groups across all enterotypes. However, there were substantial differences in the gut microbial composition for β-diversity, particularly within ET-L and ET-B. The DP group within ET-B exhibited a higher abundance of Proteobacteria, while a linear discriminant analysis (LDA) of the DP group showed an increased relative abundance of specific genera, such as Mediterraneibacter, Blautia, Bifidobacterium, and Clostridium. Within ET-L, Bifidobacterium, Blautia, Clostridium, Collinsella, and Corynebacterium were significantly higher in the DP group in the LDA and ANOVA-like differential expression-2 (ALDEx2) analyses. At the species level of ET-L, Blautia luti, Blautia provencensis, Blautia glucerasea, Clostridium innocuum, Clostridium porci, and Clostridium leptum were the primary bacteria in the DP group identified using the machine learning approach. A network analysis revealed a more tightly interconnected microbial community within ET-L than within ET-B. This suggests a potentially stronger functional relationship among the gut microbiota in ET-L. The metabolic pathways related to glucose metabolism, tryptophan and tyrosine metabolism, neurotransmitter metabolism, and immune-related functions showed strong negative associations with depression, particularly within ET-L. These findings provide insights into the gut–brain axis and its role in the pathogenesis of depression, thus contributing to our understanding of the underlying mechanisms in Asian individuals. Further research is warranted to explain the mechanistic links between gut microbiota and depression and to explore their potential for use in precision medicine interventions. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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Review

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50 pages, 3008 KiB

Open AccessReview

Unraveling the Microbiome–Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications

by Gabriel Olteanu, Maria-Alexandra Ciucă-Pană, Ștefan Sebastian Busnatu, Dumitru Lupuliasa, Sorinel Marius Neacșu, Magdalena Mititelu, Adina Magdalena Musuc, Corina-Bianca Ioniță-Mîndrican and Steluța Constanța Boroghină

Int. J. Mol. Sci. 2024, 25(10), 5561; https://doi.org/10.3390/ijms25105561 - 20 May 2024

Cited by 2 | Viewed by 3900

Abstract

This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host–microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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14 pages, 2133 KiB

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The Role of Prebiotics in Modulating Gut Microbiota: Implications for Human Health

by Suyeon Yoo, Suk-Chae Jung, Kihyuck Kwak and Jun-Seob Kim

Int. J. Mol. Sci. 2024, 25(9), 4834; https://doi.org/10.3390/ijms25094834 - 29 Apr 2024

Cited by 10 | Viewed by 7034

Abstract

The human gut microbiota, an intricate ecosystem within the gastrointestinal tract, plays a pivotal role in health and disease. Prebiotics, non-digestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of beneficial microorganisms, have emerged as a key modulator of this complex microbial community. This review article explores the evolution of the prebiotic concept, delineates various types of prebiotics, including fructans, galactooligosaccharides, xylooligosaccharides, chitooligosaccharides, lactulose, resistant starch, and polyphenols, and elucidates their impact on the gut microbiota composition. We delve into the mechanisms through which prebiotics exert their effects, particularly focusing on producing short-chain fatty acids and modulating the gut microbiota towards a health-promoting composition. The implications of prebiotics on human health are extensively reviewed, focusing on conditions such as obesity, inflammatory bowel disease, immune function, and mental health. The review further discusses the emerging concept of synbiotics—combinations of prebiotics and probiotics that synergistically enhance gut health—and highlights the market potential of prebiotics in response to a growing demand for functional foods. By consolidating current knowledge and identifying areas for future research, this review aims to enhance understanding of prebiotics’ role in health and disease, underscoring their importance in maintaining a healthy gut microbiome and overall well-being. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrition in Human Health)

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