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Metabolic Interactions between the Gut Microbiome and Host
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Metabolic Interactions between the Gut Microbiome and Host

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

Deadline for manuscript submissions: 30 October 2025 | Viewed by 7824

Special Issue Editors

Prof. Dr. Weiwei Wang

E-Mail Website
Guest Editor
Academy of National Food and Strategic Reserves Administration, Beijing 100037, China
Interests: probiotics; intestinal microbiome; intestinal barrier; intestinal innate immunity; probiotics-encapsulation technology; biotransformation of grain by-products
Dr. Yun Ji

E-Mail Website
Guest Editor
State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Interests: nutrition; gut microbiota; IBD; NAFLD; intestinal barrier function
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The symbiotic relationship between the gut microbiota and the host imparts metabolic, immune, and intestinal protective functions to healthy individuals. This interaction is largely determined by factors such as nutritional status and lifestyle habits. Diet is a major driver in shaping the gut microecosystem, which provides selective growth advantages for specific species of bacteria. Long-term dietary intervention can regulate the composition and function of intestinal microbiota in both humans and animals. Simultaneously, the metabolic activity of gut microbes also has an important impact on host health and the metabolic phenotype of the host, which can be beneficial or harmful. Gut microbiota imbalance is closely related to the occurrence and development of chronic metabolic diseases, such as diabetes, obesity, inflammatory bowel disease, cardiovascular disease, depression, tumor, and so on. Therefore, it is vital to reveal the strain specificity that produces microbial metabolites, which will facilitate the identification and discovery of strains or specific metabolites for diseases for therapeutic purposes.

This Special Issue focuses on “Metabolic Interactions between the Gut Microbiome and Host” and welcomes the submission of original research and review articles focusing on the causal relationship and its intrinsic mechanisms between the gut microbiome and the host; however, research on new methods and technologies employed for studying key bacteria and their specific molecules, microbial heterogeneity, that will help us to understand the gut microbiota in depth is also welcome. This Special Issue will enlighten readers about new discoveries, advances, and developments in microbiome-related disease therapeutics.

Prof. Dr. Weiwei Wang
Dr. Yun Ji
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. Biology 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 microbiome
  • host
  • metabolome
  • microbial heterogeneity
  • biomolecules

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Published Papers (5 papers)

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Research

16 pages, 5926 KiB  
Article
Imbalance of Bile Acids Metabolism Mediated by Gut Microbiota Contributed to Metabolic Disorders in Diabetic Model Mice
by Hongwang Dong, Xinguo Liu, Ge Song, Wenting Peng, Xihan Sun, Wei Fang and Wentao Qi
Biology 2025, 14(3), 291; https://doi.org/10.3390/biology14030291 - 13 Mar 2025
Viewed by 639
Abstract
Type 2 diabetes (T2D) is a chronic disease prevalent in the world, accompanied by a variety of diseases, endangering human health and safety. Bile acids (BAs) play an important role in the regulation of host glucose and lipid metabolism homeostasis, and are strictly [...] Read more.
Type 2 diabetes (T2D) is a chronic disease prevalent in the world, accompanied by a variety of diseases, endangering human health and safety. Bile acids (BAs) play an important role in the regulation of host glucose and lipid metabolism homeostasis, and are strictly regulated by gut microbiota. However, the relationship between key BAs, BAs transporters and signaling, as well as gut microbiota, and host metabolism in T2D remains elusive. In this study, 9-week-old db/db mice were used as diabetes model (db/db group, n = 10), and their wild-type (wt) littermates of same age were used as the healthy control (CON group, n = 10). After 8 weeks of feeding, the BA profiles and microbial composition in the colon, and gene expression level of BA regulatory factors were analyzed in the db/db and CON groups to explore the underlying mechanisms of T2D. Compared with healthy mice, the body weight, blood glucose and lipid levels of db/db mice were significantly increased. The concentrations of total BAs, primary BAs, conjugated BAs and non-12α–hydroxylated BAs (non-12–OH BAs) were significantly decreased, while Deoxycholic acid (DCA) in secondary BAs was increased in db/db group. Compared with wt mice, the synthesis of BAs in the liver was transformed from the alternative pathway to the classical pathway, and hepatic BAs transporters (NTCP, BSEP, MRP2, OATP–1 and OSTβ) and receptors (FXR and TGR5) were significantly down-regulated in the db/db mice. In the colon, the mRNA level of FXR was up-regulated, while TGR5 was down-regulated. The diabetic (db/db) mice presented a changed gut microbiota composition, including an increased abundance of secondary BAs-producing bacteria, Escherichia–Shigella, and a decreased the abundance of Akkermansia, which are involved in the synthesis of non-12–OH BAs. We further found that the reduced BA types in db/db mice were negatively correlated with metabolic-disorder-related indicators, while an increased DCA level had the opposite correlation. Our results shed light into how the imbalance of BAs’ metabolism mediated by intestinal flora may be potential mechanisms of T2D. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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17 pages, 6555 KiB  
Article
Exploring the Mechanism of Clostridium autoethanogenum Protein for Broiler Growth Based on Gut Microbiota and Serum Metabolomics
by Chunqiao Shan, Yan Liu, Sisi Liu, Chuang Li, Chaoxin Ma, Hongmin Yu, Juan Li, Guotuo Jiang and Jing Tian
Biology 2025, 14(1), 29; https://doi.org/10.3390/biology14010029 - 2 Jan 2025
Viewed by 911
Abstract
Intestinal health is vital for poultry production, and protein plays a key role in intestinal nutrition. The present study used 16S rRNA gene sequencing and serum metabolomics to investigate the effect of CAP on the cecal microflora structure and serum metabolites in 42-day-old [...] Read more.
Intestinal health is vital for poultry production, and protein plays a key role in intestinal nutrition. The present study used 16S rRNA gene sequencing and serum metabolomics to investigate the effect of CAP on the cecal microflora structure and serum metabolites in 42-day-old broiler chickens. A total of 480 one-day-old Arbor Acres broiler chickens were randomly divided into four treatments with twelve replicates comprising 10 chickens each, evenly divided by sex. The four groups were basal diet group (CAP0), treatment group 1 (CAP2), treatment group 2 (CAP3), and treatment group 3 (CAP4). The broilers in the CAP0 group were fed a basal diet (without CAP), while those in the CAP2, CAP3, and CAP4 groups received diets containing 2%, 3%, and 4% CAP, respectively. Growth performance results showed that dietary CAP supplementation significantly ameliorated the feed conversion rate (FCR) of broilers at 42 days in the CAP3 and CAP4 groups (p < 0.05). Microbial results revealed that CAP did not alter the dominant microorganisms in the cecum at the phylum, family, and genus levels. LEfSe analysis showed significantly higher relative abundances of p_Desulfobacterota, f_Desulfovibrionaceae, and g_Ruminococcus in the CAP3 group compared to the CAP0 and CAP4 groups. Metabolomic analyses indicated that the effect of incorporating CAP into the diet on serum metabolites primarily focused on organic acids and their derivatives, small peptides, amino acid derivatives, and oxidized lipids. The addition of 3% or 4% CAP to the diet can enhance metabolic pathways such as the citrate cycle (TCA cycle) and arginine and proline metabolism. In summary, incorporating CAP into the diet can increase the relative abundance of beneficial bacteria in the cecum and improve the feed conversion efficiency of broilers by enhancing amino acid and energy metabolism. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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18 pages, 2244 KiB  
Article
Transcriptional Responses of Lacticaseibacillus rhamnosus to TNFα, IL-6, IL-8, and IL-10 Cytokines
by Ksenia M. Klimina, Marina S. Dyachkova, Vladimir A. Veselovsky, Natalia V. Zakharevich, Aleksandra A. Strokach, Oksana V. Selezneva, Egor A. Shitikov, Dmitry A. Bespiatykh, Roman A. Yunes, Elena U. Poluektova, Maya V. Odorskaya, Polina S. Ostroukhova, Sergey A. Bruskin, Valeriy N. Danilenko and Evgenii I. Olekhnovich
Biology 2024, 13(11), 931; https://doi.org/10.3390/biology13110931 - 15 Nov 2024
Viewed by 1302
Abstract
The interaction between gut microbiota and the host immune system is a complex and understudied field, with cytokines like TNFα, IL-6, IL-8, and IL-10 playing pivotal roles. Commensal bacteria, including lactobacilli, respond to these cytokines through adaptive mechanisms that support their survival and [...] Read more.
The interaction between gut microbiota and the host immune system is a complex and understudied field, with cytokines like TNFα, IL-6, IL-8, and IL-10 playing pivotal roles. Commensal bacteria, including lactobacilli, respond to these cytokines through adaptive mechanisms that support their survival and function within the gut. While the influence of cytokines on pathogenic bacteria is well documented, their impact on commensal bacteria, particularly lactobacilli, remains underexplored. This study investigates the transcriptional responses of Lacticaseibacillus rhamnosus strains K32 and R19-3 to various cytokines using next-generation RNA sequencing (RNA-seq). Our findings reveal that cytokines, especially IL-8 and IL-10, significantly alter the L. rhamnosus transcriptome, affecting genes involved in carbohydrate metabolism, stress response, and transcriptional regulation. Notably, IL-8 and IL-10 induce a significant downregulation of genes related to the phosphotransferase system, suggesting a reduction in metabolic activity in response to inflammatory signals. This study unveils a previously unexplored aspect of L. rhamnosus adaptation, highlighting its intricate response to cytokine signals. By modulating gene expression, L. rhamnosus may mitigate the adverse effects of inflammation and promote gut health. These insights could inform the development of targeted probiotic therapies for inflammatory bowel disease (IBD) and other conditions with altered cytokine levels. Our results suggest that co-evolution between a host and gut microbiota enables bacteria to respond to specific cytokines through gene expression changes, revealing a unique and underexplored facet of the interaction between commensal bacteria and the host organism. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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12 pages, 4211 KiB  
Article
Generalized Ketogenic Diet Induced Liver Impairment and Reduced Probiotics Abundance of Gut Microbiota in Rat
by Ge Song, Dan Song, Yongwei Wang, Li Wang and Weiwei Wang
Biology 2024, 13(11), 899; https://doi.org/10.3390/biology13110899 - 4 Nov 2024
Cited by 1 | Viewed by 1493
Abstract
The ketogenic diet is becoming an assisted treatment to control weight, obesity, and even type 2 diabetes. However, there has been no scientific proof supporting that the ketogenic diet is absolutely safe and sustainable. In this study, Sprague–Dawley (SD) rats were fed different [...] Read more.
The ketogenic diet is becoming an assisted treatment to control weight, obesity, and even type 2 diabetes. However, there has been no scientific proof supporting that the ketogenic diet is absolutely safe and sustainable. In this study, Sprague–Dawley (SD) rats were fed different ratios of fat to carbohydrates under the same apparent metabolizable energy level to evaluate the effects of a ketogenic diet on healthy subjects. The results showed that the ketogenic diet could relatively sustain body weight and enhance the levels of serum alanine aminotransferase (ALT) and serum alkaline phosphatase (SAP), leading to more moderate lipoidosis and milder local non-specific inflammation in the liver compared with the high-carbohydrate diet. In addition, the abundance of probiotic strains such as Lactobacillus, Lactococcus, and Faecalitalea were reduced with the ketogenic diet in rats, while an abundance of pathogenic strains such as Anaerotruncus, Enterococcus, Rothia, and Enterorhabdus were increased with both the ketogenic diet and the high-carbohydrate diet. This study suggests that the ketogenic diet can lead to impairments of liver function and changed composition of the gut microbiota in rats, which to some extent indicates the danger of consuming a generalized ketogenic diet. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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16 pages, 1581 KiB  
Article
Blood Metabolites and Faecal Microbial Communities in Nonpregnant and Early Gestation Ewes in Highly Cold Areas
by Zhiwu Wu, Yanyan Yang, Biao Wang, Kefyalew Gebeyew, Shaoxun Tang, Xuefeng Han, Zhixiong He and Zhiliang Tan
Biology 2023, 12(11), 1436; https://doi.org/10.3390/biology12111436 - 16 Nov 2023
Cited by 2 | Viewed by 2040
Abstract
Ewes undergo complex metabolic changes during pregnancy. Understanding the specific process of these changes is a necessary prerequisite in ewes for regulating and intervening in order to maintain pregnancies. However, there have been relatively few studies on the specific changes that occur in [...] Read more.
Ewes undergo complex metabolic changes during pregnancy. Understanding the specific process of these changes is a necessary prerequisite in ewes for regulating and intervening in order to maintain pregnancies. However, there have been relatively few studies on the specific changes that occur in nutritional metabolism in pregnant ewes during early gestation, especially for some landrace ewes in highly cold areas. Therefore, this study aimed to (1) elucidate the changes in metabolites and microbial communities in pregnant ewes during early gestation using metabolomics and 16S ribosomal RNA gene (rDNA) amplicon sequencing approaches, and to (2) discover novel early pregnancy-induced biomarkers in the blood and faeces. Rams were placed together with ewes on D0 and removed on D45. During early gestation, blood and faecal samples were collected from ewes in a highly cold area for analysing the metabolites and microbial communities; these were retrospectively classified as the early gestation pregnant (EP) ewe group or the nonpregnant (NP) ewe group based on the lambing status recorded during the expected delivery period. The differences in the plasma biochemical parameters, plasma metabolites, and faecal microbial communities of pregnant and nonpregnant ewes were characterised. The GC, IL-6, O-acetyl-l-serine, L-glutamine, and 6-acetamido-2-oxohexanoic acid were screened out as potential biomarkers for evaluating the occurrence of early pregnancy. These novel early pregnancy-induced metabolites discovered in ewes might allow for the development of technologies to detect early pregnancies in sheep in highly cold areas. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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