Special Issue "Gut Microbiome in Health and Disease"

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 31 October 2023 | Viewed by 12211

Special Issue Editors

Prof. Dr. Fengqin Feng
E-Mail Website
Guest Editor
College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
Interests: bioactive peptides; fatty acids; hyperuricemia; metabolic syndrome; immune response; ‘gut-X’ axis
Dr. Hao Zhong
E-Mail Website
Guest Editor
College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
Interests: probiotics; insulin resistance; obesity; gut microbiota; bile acids

Special Issue Information

Dear Colleagues,

There is increasing interest in elucidating how the gut microbiome modulates our physiology, both in health and in disease. Recent technological advancements and expanded efforts have led to tremendous growth in our collective knowledge of the host microbiome. The purpose of this Special Issue is to collect what is known about the gut microbiome, how it is connected to the development of disease and to identify the bacterial and biochemical targets. In addition, this Special Issue is also concerned with the nutrition–gut microbiome–physiology axis. This Special Issue welcomes research papers and reviews that cover a wide range of topics, including food nutrition and the gut microbiome, as well as metabolite biomarkers and underlying mechanisms. We hope to expand upon what is currently known about the gut microbiota in this Special Issue, by collecting cutting-edge findings in order to shed light on how the gut microbiome can control health and disease.

Prof. Dr. Fengqin Feng
Dr. Hao Zhong
Guest Editors

Manuscript Submission Information

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Keywords

  • gut microbiota
  • ‘gut-X’ axis
  • dysbiosis
  • food nutrition
  • metabolites
  • type 2 diabetes mellitus
  • gut health
  • immunity

Published Papers (10 papers)

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Research

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Article
Analyzing Predominant Bacterial Species and Potential Short-Chain Fatty Acid-Associated Metabolic Routes in Human Gut Microbiome Using Integrative Metagenomics
Biology 2023, 12(1), 21; https://doi.org/10.3390/biology12010021 - 22 Dec 2022
Viewed by 640
Abstract
Gut microbiome plays an essential role in host health, and there is interest in utilizing diet to modulate the composition and function of microbial communities. Copra meal hydrolysate (CMH) is commonly used as a natural additive to enhance health. However, the gut microbiome [...] Read more.
Gut microbiome plays an essential role in host health, and there is interest in utilizing diet to modulate the composition and function of microbial communities. Copra meal hydrolysate (CMH) is commonly used as a natural additive to enhance health. However, the gut microbiome is largely unknown at species level and is associated with metabolic routes involving short-chain fatty acids (SCFAs). In this study, we aimed to analyze, using integrative metagenomics, the predominant species and metabolic routes involved in SCFAs production in the human gut microbiome after treatment with CMH. The effect of CMH treatment on the Thai gut microbiome was demonstrated using 16S rRNA genes with whole-metagenome shotgun (WMGS) sequencing technology. Accordingly, these results revealed that CMH has potentially beneficial effects on the gut microbiome. Twelve predominant bacterial species, as well as their potential metabolic routes, were involved in cooperative microbiome networks under sugar utilization (e.g., glucose, mannose, or xylose) and energy supply (e.g., NADH and ATP) in relation to SCFAs biosynthesis. These findings suggest that CMH may be used as a potential prebiotic diet for modulating and maintaining the gut microbiome. To our knowledge, this is the first study to reveal the predominant bacterial species and metabolic routes in the Thai gut microbiome after treatment with potential prebiotics. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Article
Gut Microbiome Suffers from Hematopoietic Stem Cell Transplantation in Childhood and Its Characteristics Are Positively Associated with Intra-Hospital Physical Exercise
Biology 2022, 11(5), 785; https://doi.org/10.3390/biology11050785 - 21 May 2022
Viewed by 1526
Abstract
Gut microbiome impairment is a serious side effect of cancer treatment. The aim of this study was to identify the effects of hematopoietic stem cell transplantation (HSCT) treatment on gut microbiota composition in children with acute lymphoblastic leukemia (ALL). Fecal microbiotas were categorized [...] Read more.
Gut microbiome impairment is a serious side effect of cancer treatment. The aim of this study was to identify the effects of hematopoietic stem cell transplantation (HSCT) treatment on gut microbiota composition in children with acute lymphoblastic leukemia (ALL). Fecal microbiotas were categorized using specific primers targeting the V1–V3 region of 16S rDNA in eligible pediatric ALL patients after HSCT (n = 16) and in healthy controls (Ctrl, n = 13). An intra-hospital exercise program was also organized for child patients during HSCT treatment. Significant differences in gut microbiota composition were observed between ALL HSCT and Ctrl with further negative effects. Plasma C-reactive protein correlated positively with the pathogenic bacteria Enterococcus spp. and negatively with beneficial bacteria Butyriccocus spp. or Akkermansia spp., respectively (rs = 0.511, p = 0.05; rs = −0.541, p = 0.04; rs = −0.738, p = 0.02). Bacterial alpha diversity correlated with the exercise training characteristics. Therefore, specific changes in the microbiota of children were associated with systemic inflammation or the ability to exercise physically during HSCT treatment. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Article
Dietary Supplementation of a New Probiotic Compound Improves the Growth Performance and Health of Broilers by Altering the Composition of Cecal Microflora
Biology 2022, 11(5), 633; https://doi.org/10.3390/biology11050633 - 21 Apr 2022
Cited by 2 | Viewed by 1014
Abstract
The current study aimed to investigate the effects of a new probiotic compound developed as a potential alternative to synthetic antibiotics for broilers. A total of 360 newly hatched Arbor Acres male chicks were randomly divided into three treatment groups. Each treatment consisted [...] Read more.
The current study aimed to investigate the effects of a new probiotic compound developed as a potential alternative to synthetic antibiotics for broilers. A total of 360 newly hatched Arbor Acres male chicks were randomly divided into three treatment groups. Each treatment consisted of six replicates with 20 birds in each replicate. The negative control group was fed the basal diet. The positive control group was fed the basal diet supplemented with a commercial antimicrobial, virginiamycin, at 30 mg/kg of basal feed. The compound probiotics group was fed a basal diet containing 4.5 × 106 CFU of Lactobacillus LP184 and 2.4 × 106 CFU of Yeast SC167 per gram of basal feed. The feeding trial lasted for 42 days. The results showed that the compound probiotics were a competent alternative to synthetic antibiotics for improving the growth performance and carcass traits of broilers. The compound probiotics enhanced the immune and antioxidant capacities of the broilers, while antibiotics lacked such merits. The positive effects of compound probiotics could be attributed to an improvement in the intestinal morphology and cecal microbial diversity of broilers, effects which are distinct from those of antibiotics. These findings revealed the differences between probiotics and antibiotics in terms of improving broilers’ performance and enriched the basic knowledge surrounding the intestinal microbial structure of broilers. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Article
Anti-Osteoporotic Effect of Lactobacillus brevis AR281 in an Ovariectomized Mouse Model Mediated by Inhibition of Osteoclast Differentiation
Biology 2022, 11(3), 359; https://doi.org/10.3390/biology11030359 - 24 Feb 2022
Viewed by 1155
Abstract
Osteoporosis is a global disease characterized by weakened bone microarchitecture, leading to osteoporotic fractures. Estrogen replacement therapy is the traditional treatment for osteoporosis but carries with it an increased risk of cardiac events. In search of a safe and effective treatment, we used [...] Read more.
Osteoporosis is a global disease characterized by weakened bone microarchitecture, leading to osteoporotic fractures. Estrogen replacement therapy is the traditional treatment for osteoporosis but carries with it an increased risk of cardiac events. In search of a safe and effective treatment, we used Lactobacillus brevis AR281, which has anti-inflammatory properties, to conduct a 7-week experiment, investigating its inhibitory effects on osteoporosis in an ovariectomized (ovx) mouse model. The results demonstrated that AR281 significantly improved bone microarchitecture and biomechanical strength in ovx mice by attenuating bone resorption. AR281 significantly decreased the critical osteoclast activator, the ratio of the receptor activator for nuclear factor kappa B (NF-κB) ligand (RANKL) to osteoprotegerin, and pro-inflammatory osteoclastogenic mediators, such as IL-1, IL-6, and IL-17, which can increase the RANKL expression. Moreover, AR281 modulated intestinal microbiota in ovx mice increased the abundance of Akkermansia, which is responsible for the improvement of gut epithelial barrier integrity. In an in vitro trial, AR281 suppressed the number of osteoclasts differentiated from the osteoclast precursor RAW264.7 cells caused by RANKL through the tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6)/NF-κB/nuclear factor of activated T cells c1 (NFATc1) pathway. Therefore, AR281 may be a natural alternative for combating osteoporosis. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Article
Two Blautia Species Associated with Visceral Fat Accumulation: A One-Year Longitudinal Study
Biology 2022, 11(2), 318; https://doi.org/10.3390/biology11020318 - 16 Feb 2022
Cited by 6 | Viewed by 2163
Abstract
Intestinal microflora has been associated with obesity. While visceral fat is more strongly associated with cardiovascular disorder, a complication linked to obesity, than the body mass index (BMI), the association between intestinal microflora and obesity (as defined in terms of BMI) has been [...] Read more.
Intestinal microflora has been associated with obesity. While visceral fat is more strongly associated with cardiovascular disorder, a complication linked to obesity, than the body mass index (BMI), the association between intestinal microflora and obesity (as defined in terms of BMI) has been studied widely. However, the link between visceral fat area (VFA) and intestinal microflora has been little studied. In this study, we investigate the association between intestinal microflora and VFA and BMI using a longitudinal study on Japanese subjects with different VFA statuses (N = 767). Principal component analysis of the changes in intestinal microflora composition over the one-year study period revealed the different associations between intestinal microflora and VFA and BMI. As determined by 16S rRNA amplicon sequencing, changes in the abundance ratio of two microbial genera—Blautia and Flavonifractor—were significantly associated with VFA changes and changes in the abundance ratio of four different microbial genera were significantly associated with BMI changes, suggesting that the associated intestinal microbes are different. Furthermore, as determined by metagenomic shotgun sequences, changes in the abundance ratios of two Blautia species—Blautia hansenii and Blautia producta—were significantly and negatively associated with VFA changes. Our findings might be used to develop a new treatment for visceral fat. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Review

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Review
The Gut Microbiota in Kidney Transplantation: A Target for Personalized Therapy?
Biology 2023, 12(2), 163; https://doi.org/10.3390/biology12020163 - 20 Jan 2023
Viewed by 414
Abstract
Kidney transplantation improves quality of life, morbidity, and mortality of patients with kidney failure. However, integrated immunosuppressive therapy required to preserve graft function is associated with the development of post-transplant complications, including infections, altered immunosuppressive metabolism, gastrointestinal toxicity, and diarrhea. The gut microbiota [...] Read more.
Kidney transplantation improves quality of life, morbidity, and mortality of patients with kidney failure. However, integrated immunosuppressive therapy required to preserve graft function is associated with the development of post-transplant complications, including infections, altered immunosuppressive metabolism, gastrointestinal toxicity, and diarrhea. The gut microbiota has emerged as a potential therapeutic target for personalizing immunosuppressive therapy and managing post-transplant complications. This review reports current evidence on gut microbial dysbiosis in kidney transplant recipients, alterations in their gut microbiota associated with kidney transplantation outcomes, and the application of gut microbiota intervention therapies in treating post-transplant complications. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Review
The Interaction between Mushroom Polysaccharides and Gut Microbiota and Their Effect on Human Health: A Review
Biology 2023, 12(1), 122; https://doi.org/10.3390/biology12010122 - 12 Jan 2023
Viewed by 728
Abstract
Mushroom polysaccharides are a kind of biological macromolecule extracted from the fruiting body, mycelium or fermentation liquid of edible fungi. In recent years, the research on mushroom polysaccharides for alleviating metabolic diseases, inflammatory bowel diseases, cancers and other symptoms by changing the intestinal [...] Read more.
Mushroom polysaccharides are a kind of biological macromolecule extracted from the fruiting body, mycelium or fermentation liquid of edible fungi. In recent years, the research on mushroom polysaccharides for alleviating metabolic diseases, inflammatory bowel diseases, cancers and other symptoms by changing the intestinal microenvironment has been increasing. Mushroom polysaccharides could promote human health by regulating gut microbiota, increasing the production of short-chain fatty acids, improving intestinal mucosal barrier, regulating lipid metabolism and activating specific signaling pathways. Notably, these biological activities are closely related to the molecular weight, monosaccharide composition and type of the glycosidic bond of mushroom polysaccharide. This review aims to summarize the latest studies: (1) Regulatory effects of mushroom polysaccharides on gut microbiota; (2) The effect of mushroom polysaccharide structure on gut microbiota; (3) Metabolism of mushroom polysaccharides by gut microbiota; and (4) Effects of mushroom polysaccharides on gut microbe-mediated diseases. It provides a theoretical basis for further exploring the mechanism of mushroom polysaccharides for regulating gut microbiota and gives a reference for developing and utilizing mushroom polysaccharides as promising prebiotics in the future. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Review
Commensal Intestinal Protozoa—Underestimated Members of the Gut Microbial Community
Biology 2022, 11(12), 1742; https://doi.org/10.3390/biology11121742 - 30 Nov 2022
Viewed by 1299
Abstract
The human gastrointestinal microbiota contains a diverse consortium of microbes, including bacteria, protozoa, viruses, and fungi. Through millennia of co-evolution, the host–microbiota interactions have shaped the immune system to both tolerate and maintain the symbiotic relationship with commensal microbiota, while exerting protective responses [...] Read more.
The human gastrointestinal microbiota contains a diverse consortium of microbes, including bacteria, protozoa, viruses, and fungi. Through millennia of co-evolution, the host–microbiota interactions have shaped the immune system to both tolerate and maintain the symbiotic relationship with commensal microbiota, while exerting protective responses against invading pathogens. Microbiome research is dominated by studies describing the impact of prokaryotic bacteria on gut immunity with a limited understanding of their relationship with other integral microbiota constituents. However, converging evidence shows that eukaryotic organisms, such as commensal protozoa, can play an important role in modulating intestinal immune responses as well as influencing the overall health of the host. The presence of several protozoa species has recently been shown to be a common occurrence in healthy populations worldwide, suggesting that many of these are commensals rather than invading pathogens. This review aims to discuss the most recent, conflicting findings regarding the role of intestinal protozoa in gut homeostasis, interactions between intestinal protozoa and the bacterial microbiota, as well as potential immunological consequences of protozoa colonization. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Review
Gut–Liver Axis and Non-Alcoholic Fatty Liver Disease: A Vicious Circle of Dysfunctions Orchestrated by the Gut Microbiome
Biology 2022, 11(11), 1622; https://doi.org/10.3390/biology11111622 - 06 Nov 2022
Cited by 1 | Viewed by 1016
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a prevalent, multifactorial, and poorly understood liver disease with an increasing incidence worldwide. NAFLD is typically asymptomatic and coupled with other symptoms of metabolic syndrome. The prevalence of NAFLD is rising in tandem with the prevalence of [...] Read more.
Non-alcoholic fatty liver disease (NAFLD) is a prevalent, multifactorial, and poorly understood liver disease with an increasing incidence worldwide. NAFLD is typically asymptomatic and coupled with other symptoms of metabolic syndrome. The prevalence of NAFLD is rising in tandem with the prevalence of obesity. In the Western hemisphere, NAFLD is one of the most prevalent causes of liver disease and liver transplantation. Recent research suggests that gut microbiome dysbiosis may play a significant role in the pathogenesis of NAFLD by dysregulating the gut–liver axis. The so-called “gut–liver axis” refers to the communication and feedback loop between the digestive system and the liver. Several pathological mechanisms characterized the alteration of the gut–liver axis, such as the impairment of the gut barrier and the increase of the intestinal permeability which result in endotoxemia and inflammation, and changes in bile acid profiles and metabolite levels produced by the gut microbiome. This review will explore the role of gut–liver axis disruption, mediated by gut microbiome dysbiosis, on NAFLD development. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Review
Roles of Gut Microbiome in Bone Homeostasis and Its Relationship with Bone-Related Diseases
Biology 2022, 11(10), 1402; https://doi.org/10.3390/biology11101402 - 26 Sep 2022
Cited by 1 | Viewed by 1294
Abstract
The extended microbial genome—the gut microbiome (GM)—plays a significant role in host health and disease. It is able to influence a number of physiological functions. During dysbiosis, GM is associated with the development of various chronic diseases with impaired bone quality. In general, [...] Read more.
The extended microbial genome—the gut microbiome (GM)—plays a significant role in host health and disease. It is able to influence a number of physiological functions. During dysbiosis, GM is associated with the development of various chronic diseases with impaired bone quality. In general, GM is important for bone homeostasis and can affect it via several mechanisms. This review describes the roles of GM in bone homeostasis through influencing the immune and endocrine functions, short-chain fatty acids production, calcium absorption and the gut–brain axis. The relationship between GM composition and several bone-related diseases, specifically osteoporosis, osteoarthritis, rheumatoid arthritis, diabetes mellitus, obesity and bone cancer, is also highlighted and summarized. GM manipulation may become a future adjuvant therapy in the prevention of many chronic diseases. Therefore, the beneficial effects of probiotic therapy to improve the health status of individuals with aforementioned diseases are provided, but further studies are needed to clearly confirm its effectiveness. Recent evidence suggests that GM is responsible for direct and indirect effects on drug efficacy. Accordingly, various GM alterations and interactions related to the treatment of bone-related diseases are mentioned as well. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Gut microbiome: An "invisible organ" interplays with drug metabolism in metabolic disorders
Author:
Highlights: Trillions of bacteria live in gut, exerting various functions, especially for the influence of host Both synthetic and herbal medicines alter gut microbiota composition; gut microbiota also changes drug metabolism We summarized the relationship between the gut microbiome and drugs metabolism in metabolic disorders These will assist the drug application and contribute to personalized drug development on metabolic diseases

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