Microbiology Metabolomics

Topic Information

Dear Colleagues,

Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics are extensively used for the identification and characterization of new molecular signatures. The significance of the metabolome is further underlined by its competence in manipulating the genome, transcriptome, and proteome. To better understand the roles of genes in biological systems, bioscience adopts metabolomic profiling, which provides detailed metabolic activities within the cell. The analysis of the metabolome provides deeper insight into cellular physiology and critical qualitative and quantitative information that help to understand related metabolic pathways and their alterations. Microbial metabolomics in intestinal flora provides an understanding of host interaction, host health, and disease status, while metabolome profiling of infective microbe offers information related to the diagnosis of the disease. Microbial metabolomics has often been used in food and nutrition to assess the impact of nutrient deficiency. Further, the dynamic microbial metabolome also provides information about microbial adaptation as well as the impact of environmental changes. Mass-spectrometry-based metabolomics analyses have made significant contributions to microbial metabolomics research in the environment and human disease. The aim of this topic entitled “Microbiology Metabolomics” is to provide targeted and untargeted microbial metabolome profiles of the gut microbiome, pathogenic microbes, microbial metabolome associated with food and nutrition, and microbial metabolome describing the impact of environmental changes on metabolites and metabolic pathways. This topic will consider original articles, commentaries, and review articles.

Dr. Sunil S. Adav
Prof. Dr. Gilles Comte
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Genes genes	2.8	5.2	2010	14.9 Days	CHF 2600
Metabolites metabolites	3.5	5.7	2011	16.1 Days	CHF 2700
Microbiology Research microbiolres	2.1	1.9	2010	15.4 Days	CHF 1600
Microorganisms microorganisms	4.1	7.4	2013	11.7 Days	CHF 2700
Proteomes proteomes	4.0	6.5	2013	27.3 Days	CHF 1800

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Published Papers (17 papers)

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18 pages, 2876 KiB  

Open AccessArticle

Lipidomic Analysis Reveals Differences in Bacteroides Species Driven Largely by Plasmalogens, Glycerophosphoinositols and Certain Sphingolipids

by Eileen Ryan, Belén Gonzalez Pastor, Lee A. Gethings, David J. Clarke and Susan A. Joyce

Metabolites 2023, 13(3), 360; https://doi.org/10.3390/metabo13030360 - 28 Feb 2023

Cited by 14 | Viewed by 3678

Abstract

There has been increasing interest in bacterial lipids in recent years due, in part, to their emerging role as molecular signalling molecules. Bacteroides thetaiotaomicron is an important member of the mammalian gut microbiota that has been shown to produce sphingolipids (SP) that pass [...] Read more.

There has been increasing interest in bacterial lipids in recent years due, in part, to their emerging role as molecular signalling molecules. Bacteroides thetaiotaomicron is an important member of the mammalian gut microbiota that has been shown to produce sphingolipids (SP) that pass through the gut epithelial barrier to impact host SP metabolism and signal into host inflammation pathways. B. thetaiotaomicron also produces a novel family of N-acyl amines (called glycine lipids) that are potent ligands of host Toll-like receptor 2 (TLR2). Here, we specifically examine the lipid signatures of four species of gut-associated Bacteroides. In total we identify 170 different lipids, and we report that the range and diversity of Bacteroides lipids is species specific. Multivariate analysis reveals that the differences in the lipid signatures are largely driven by the presence and absence of plasmalogens, glycerophosphoinositols and certain SP. Moreover, we show that, in B. thetaiotaomicron, mutations altering either SP or glycine lipid biosynthesis result in significant changes in the levels of other lipids, suggesting the existence of a compensatory mechanisms required to maintain the functionality of the bacterial membrane. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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11 pages, 2013 KiB  

Open AccessArticle

Comparative Analysis of Volatile and Non-Volatile Metabolites Derived from Bacillus subtilis Strains Producing Different Levels of Biogenic Amines

by Kyuwon Lee, Seo-Hee Kwon, Sumin Song, Do-Yup Lee, Min Kyung Park and Young-Suk Kim

Metabolites 2023, 13(2), 219; https://doi.org/10.3390/metabo13020219 - 2 Feb 2023

Cited by 2 | Viewed by 2503

Abstract

Biogenic amines (BAs), which are mainly generated by the microbial decarboxylation of amino acids, are important nitrogen compounds in fermented foods because of their toxicology. However, amino acids, the precursors of BAs, also play an important role in generating volatile and non-volatile metabolites, [...] Read more.

Biogenic amines (BAs), which are mainly generated by the microbial decarboxylation of amino acids, are important nitrogen compounds in fermented foods because of their toxicology. However, amino acids, the precursors of BAs, also play an important role in generating volatile and non-volatile metabolites, which are strongly associated with quality indicators for foods. Bacillus subtilis is one of dominant fermentative microorganism in various fermented foods and is well known as a BA-producing bacterium. In this study, B. subtilis strains which have different BAs-producing capacities, higher level of BAs production strain (BH) and lower level of BAs production strain (BL), were applied to compare the formations of volatile and non-volatile metabolite profiles according to cultivation times. In this study, histamine, putrescine, and spermidine were detected in all strains, however, 2-phenylethylamine was detected only in BH. Partial least squares discriminant analysis (PLS-DA) was applied to investigate the difference of metabolic profiles according to strains. In BH, some amino acids (phenylalanine, leucine, and threonine) and related volatile metabolites (3-methylbutanoic acid, pyrazines, styrene, and 1H-indole) were produced higher levels. On the other hand, BL produced significantly higher contents of metabolites associated with metabolism of fatty acids and nucleotides. It is necessary to consider the formation of metabolites in terms of quality as well as that of BAs during fermentation. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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21 pages, 5067 KiB  

Open AccessArticle

Optimized Fast Filtration-Based Sampling and Extraction Enables Precise and Absolute Quantification of the Escherichia coli Central Carbon Metabolome

by Lilja Brekke Thorfinnsdottir, Laura García-Calvo, Gaute Hovde Bø, Per Bruheim and Lisa Marie Røst

Metabolites 2023, 13(2), 150; https://doi.org/10.3390/metabo13020150 - 18 Jan 2023

Cited by 9 | Viewed by 3247

Abstract

Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have [...] Read more.

Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have also been proven highly dependent on species-specific properties. For Escherichia coli, unspecific leakage has been demonstrated for conventional microbial metabolomics sampling protocols. We herein present a fast filtration-based sampling protocol for this widely applied model organism, focusing on pitfalls such as inefficient filtration, selective loss of biomass, matrix contamination, and membrane permeabilization and leakage. We evaluate the effect of and need for removal of extracellular components and demonstrate how residual salts can challenge analytical accuracy of hyphenated mass spectrometric analyses, even when sophisticated correction strategies are applied. Laborious extraction procedures are bypassed by direct extraction in cold acetonitrile:water:methanol (3:5:2, v/v%), ensuring compatibility with sample concentration and thus, any downstream analysis. By applying this protocol, we achieve and demonstrate high precision and low metabolite turnover, and, followingly, minimal perturbation of the inherent metabolic state. This allows us to herein report absolute intracellular concentrations in E. coli and explore its central carbon metabolome at several commonly applied cultivation conditions. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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10 pages, 610 KiB  

Open AccessReview

Multi-Omics Nutritional Approaches Targeting Metabolic-Associated Fatty Liver Disease

by Omar Ramos-Lopez

Genes 2022, 13(11), 2142; https://doi.org/10.3390/genes13112142 - 17 Nov 2022

Cited by 4 | Viewed by 3313

Abstract

Currently, metabolic-associated fatty liver disease (MAFLD) is a leading global cause of chronic liver disease, and is expected to become one of the most common indications of liver transplantation. MAFLD is associated with obesity, involving multiple mechanisms such as alterations in lipid metabolism, [...] Read more.

Currently, metabolic-associated fatty liver disease (MAFLD) is a leading global cause of chronic liver disease, and is expected to become one of the most common indications of liver transplantation. MAFLD is associated with obesity, involving multiple mechanisms such as alterations in lipid metabolism, insulin resistance, hyperinflammation, mitochondrial dysfunction, cell apoptosis, oxidative stress, and extracellular matrix formation. However, the onset and progression of MAFLD is variable among individuals, being influenced by intrinsic (personal) and external environmental factors. In this context, sequence structural variants across the human genome, epigenetic phenomena (i.e., DNA methylation, histone modifications, and long non-coding RNAs) affecting gene expression, gut microbiota dysbiosis, and metabolomics/lipidomic fingerprints may account for differences in MAFLD outcomes through interactions with nutritional features. This knowledge may contribute to gaining a deeper understanding of the molecular and physiological processes underlying MAFLD pathogenesis and phenotype heterogeneity, as well as facilitating the identification of biomarkers of disease progression and therapeutic targets for the implementation of tailored nutritional strategies. This comprehensive literature review highlights the potential of nutrigenetic, nutriepigenetic, nutrimetagenomic, nutritranscriptomics, and nutrimetabolomic approaches for the prevention and management of MAFLD in humans through the lens of precision nutrition. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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14 pages, 5932 KiB  

Open AccessArticle

Impact of Visceral Leishmaniasis on Local Organ Metabolism in Hamsters

by Mahbobeh Lesani, Camil Gosmanov, Andrea Paun, Michael D. Lewis and Laura-Isobel McCall

Metabolites 2022, 12(9), 802; https://doi.org/10.3390/metabo12090802 - 27 Aug 2022

Cited by 5 | Viewed by 2667

Abstract

Leishmania is an intracellular parasite with different species pathogenic to humans and causing the disease leishmaniasis. Leishmania donovani causes visceral leishmaniasis (VL) that manifests as hepatosplenomegaly, fever, pancytopenia and hypergammaglobulinemia. If left without treatment, VL can cause death, especially in immunocompromised people. Current [...] Read more.

Leishmania is an intracellular parasite with different species pathogenic to humans and causing the disease leishmaniasis. Leishmania donovani causes visceral leishmaniasis (VL) that manifests as hepatosplenomegaly, fever, pancytopenia and hypergammaglobulinemia. If left without treatment, VL can cause death, especially in immunocompromised people. Current treatments have often significant adverse effects, and resistance has been reported in some countries. Determining the metabolites perturbed during VL can lead us to find new treatments targeting disease pathogenesis. We therefore compared metabolic perturbation between L. donovani-infected and uninfected hamsters across organs (spleen, liver, and gut). Metabolites were extracted, analyzed by liquid chromatography-mass spectrometry, and processed with MZmine and molecular networking to annotate metabolites. We found few metabolites commonly impacted by infection across all three sites, including glycerophospholipids, ceramides, acylcarnitines, peptides, purines and amino acids. In accordance with VL symptoms and parasite tropism, we found a greater overlap of perturbed metabolites between spleen and liver compared to spleen and gut, or liver and gut. Targeting pathways related to these metabolite families would be the next focus that can lead us to find more effective treatments for VL. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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15 pages, 2350 KiB  

Open AccessArticle

Interactions between Jumbo Phage SA1 and Staphylococcus: A Global Transcriptomic Analysis

by Bingyan Zhang, Jiayi Xu, Xiaoqi He, Yigang Tong and Huiying Ren

Microorganisms 2022, 10(8), 1590; https://doi.org/10.3390/microorganisms10081590 - 7 Aug 2022

Cited by 2 | Viewed by 3100

Abstract

Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that poses a serious health concern to humans and cattle worldwide. Although it has been proven that lytic phages may successfully kill S. aureus, the interaction between the host [...] Read more.

Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that poses a serious health concern to humans and cattle worldwide. Although it has been proven that lytic phages may successfully kill S. aureus, the interaction between the host and the phage has yet to be thoroughly investigated, which will likely limit the clinical application of phage. Here, RNA sequencing (RNA-seq) was used to examine the transcriptomics of jumbo phage SA1 and Staphylococcus JTB1-3 during a high multiplicity of infection (MOI) and RT-qPCR was used to confirm the results. The RNA-seq analysis revealed that phage SA1 took over the transcriptional resources of the host cells and that the genes were categorized as early, middle, and late, based on the expression levels during infection. A minor portion of the resources of the host was employed to enable phage replication after infection because only 35.73% (997/2790) of the host genes were identified as differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the phage infection mainly affected the nucleotide metabolism, protein metabolism, and energy-related metabolism of the host. Moreover, the expression of the host genes involved in anti-phage systems, virulence, and drug resistance significantly changed during infection. This research gives a fresh understanding of the relationship between jumbo phages and their Gram-positive bacteria hosts and provides a reference for studying phage treatment and antibiotics. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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16 pages, 1666 KiB  

Open AccessReview

The Role of Rumen Microbiota and Its Metabolites in Subacute Ruminal Acidosis (SARA)-Induced Inflammatory Diseases of Ruminants

by Yunhe Fu, Yuhong He, Kaihe Xiang, Caijun Zhao, Zhaoqi He, Min Qiu, Xiaoyu Hu and Naisheng Zhang

Microorganisms 2022, 10(8), 1495; https://doi.org/10.3390/microorganisms10081495 - 25 Jul 2022

Cited by 41 | Viewed by 8707

Abstract

Subacute ruminal acidosis (SARA) is a common metabolic disease in ruminants. In the early stage of SARA, ruminants do not exhibit obvious clinical symptoms. However, SARA often leads to local inflammatory diseases such as laminitis, mastitis, endometritis and hepatitis. The mechanism by which [...] Read more.

Subacute ruminal acidosis (SARA) is a common metabolic disease in ruminants. In the early stage of SARA, ruminants do not exhibit obvious clinical symptoms. However, SARA often leads to local inflammatory diseases such as laminitis, mastitis, endometritis and hepatitis. The mechanism by which SARA leads to inflammatory diseases is largely unknown. The gut microbiota is the totality of bacteria, viruses and fungi inhabiting the gastrointestinal tract. Studies have found that the gut microbiota is not only crucial to gastrointestinal health but also involved in a variety of disease processes, including metabolic diseases, autoimmune diseases, tumors and inflammatory diseases. Studies have shown that intestinal bacteria and their metabolites can migrate to extraintestinal distal organs, such as the lung, liver and brain, through endogenous pathways, leading to related diseases. Combined with the literature, we believe that the dysbiosis of the rumen microbiota, the destruction of the rumen barrier and the dysbiosis of liver function in the pathogenesis of SARA lead to the entry of rumen bacteria and/or metabolites into the body through blood or lymphatic circulation and place the body in the “chronic low-grade” inflammatory state. Meanwhile, rumen bacteria and/or their metabolites can also migrate to the mammary gland, uterus and other organs, leading to the occurrence of related inflammatory diseases. The aim of this review is to describe the mechanism by which SARA causes inflammatory diseases to obtain a more comprehensive and profound understanding of SARA and its related inflammatory diseases. Meanwhile, it is also of great significance for the joint prevention and control of diseases. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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17 pages, 2468 KiB  

Open AccessFeature PaperArticle

The Effects of Catabolism Relationships of Leucine and Isoleucine with BAT2 Gene of Saccharomyces cerevisiae on High Alcohols and Esters

by Lin Zhang, Yiqian Zhang and Zhongqiu Hu

Genes 2022, 13(7), 1178; https://doi.org/10.3390/genes13071178 - 30 Jun 2022

Cited by 6 | Viewed by 2493

Abstract

This study sought to provide a theoretical basis for effectively controlling the content of higher alcohols and esters in fermented foods. In this work, isoleucine (Ile) or leucine (Leu) at high levels was used as the sole nitrogen source for a BAT2 mutant [...] Read more.

This study sought to provide a theoretical basis for effectively controlling the content of higher alcohols and esters in fermented foods. In this work, isoleucine (Ile) or leucine (Leu) at high levels was used as the sole nitrogen source for a BAT2 mutant and its parental Saccharomyces. cerevisiae 38 to investigate the effects of the addition of amounts of Ile or Leu and BAT2 on the aroma components in the flavor profile using gas chromatography mass spectrometer (GC-MS). The results showed that 2-methyl-butyraldehyde, 2-methyl-1-butanol, and 2-methylbutyl-acetate were the products positively correlated with the Ile addition amount. In addition, 3-methyl-butyraldehyde, 3-methyl-1-butanol, and 3-methylbutyl-acetate were the products positively correlated with Leu addition amount. BAT2 deletion resulted in a significant decline in the yields of 2-methyl-butyraldehyde, 3-methyl-butyraldehyde,2-methyl-1-butanol, and 3-methyl-1-butanol, but also an increase in the yields of 2-methylbutyl-acetate and 3-methylbutyl-acetate. We speculated that BAT2 regulated the front and end of this metabolite chain in a feedback manner. Improved metabolic chain analyses, including the simulated energy metabolism of Ile or Leu, indicated that reducing the added amount of branched-chain amino acids, BAT mutation, and eliminating the role of energy cofactors such as NADH/NAD+ were three important ways to control the content of high alcohols and esters in fermented foods. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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41 pages, 10342 KiB  

Open AccessReview

Microbiological Aspects of Unique, Rare, and Unusual Fatty Acids Derived from Natural Amides and Their Pharmacological Profile

by Valery M. Dembitsky

Microbiol. Res. 2022, 13(3), 377-417; https://doi.org/10.3390/microbiolres13030030 - 26 Jun 2022

Cited by 7 | Viewed by 4365

Abstract

In the proposed review, the pharmacological profile of unique, rare, and unusual fatty acids derived from natural amides is considered. These amides are produced by various microorganisms, lichens, and fungi. The biological activity of some natural fatty acid amides has been determined by [...] Read more.

In the proposed review, the pharmacological profile of unique, rare, and unusual fatty acids derived from natural amides is considered. These amides are produced by various microorganisms, lichens, and fungi. The biological activity of some natural fatty acid amides has been determined by their isolation from natural sources, but the biological activity of fatty acids has not been practically studied. According to QSAR data, the biological activity of fatty acids is shown, which demonstrated strong antifungal, antibacterial, antiviral, antineoplastic, anti-inflammatory activities. Moreover, some fatty acids have shown rare activities such as antidiabetic, anti-infective, anti-eczematic, antimutagenic, and anti-psoriatic activities. For some fatty acids that have pronounced biological properties, 3D graphs are shown that show a graphical representation of unique activities. These data are undoubtedly of both theoretical and practical interest for chemists, pharmacologists, as well as for the pharmaceutical industry, which is engaged in the synthesis of biologically active drugs. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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23 pages, 464 KiB  

Open AccessReview

Deoxynivalenol: An Overview on Occurrence, Chemistry, Biosynthesis, Health Effects and Its Detection, Management, and Control Strategies in Food and Feed

by Madhu Kamle, Dipendra Kumar Mahato, Akansha Gupta, Shikha Pandhi, Bharti Sharma, Kajal Dhawan, Vasundhara, Sadhna Mishra, Manoj Kumar, Abhishek Dutt Tripathi, Prasad Rasane, Raman Selvakumar, Arvind Kumar, Shirani Gamlath and Pradeep Kumar

Microbiol. Res. 2022, 13(2), 292-314; https://doi.org/10.3390/microbiolres13020023 - 1 Jun 2022

Cited by 43 | Viewed by 9030

Abstract

Mycotoxins are fungi-produced secondary metabolites that can contaminate many foods eaten by humans and animals. Deoxynivalenol (DON), which is formed by Fusarium, is one of the most common occurring predominantly in cereal grains and thus poses a significant health risk. When DON [...] Read more.

Mycotoxins are fungi-produced secondary metabolites that can contaminate many foods eaten by humans and animals. Deoxynivalenol (DON), which is formed by Fusarium, is one of the most common occurring predominantly in cereal grains and thus poses a significant health risk. When DON is ingested, it can cause both acute and chronic toxicity. Acute signs include abdominal pain, anorexia, diarrhea, increased salivation, vomiting, and malaise. The most common effects of chronic DON exposure include changes in dietary efficacy, weight loss, and anorexia. This review provides a succinct overview of various sources, biosynthetic mechanisms, and genes governing DON production, along with its consequences on human and animal health. It also covers the effect of environmental factors on its production with potential detection, management, and control strategies. Full article

(This article belongs to the Topic Microbiology Metabolomics)

11 pages, 2730 KiB  

Open AccessArticle

Transcriptome Analysis of Bacillus amyloliquefaciens Reveals Fructose Addition Effects on Fengycin Synthesis

by Hedong Lu, Hai Xu, Panping Yang, Muhammad Bilal, Shaohui Zhu, Mengyuan Zhong, Li Zhao, Chengyuan Gu, Shuai Liu, Yuping Zhao and Chengxin Geng

Genes 2022, 13(6), 984; https://doi.org/10.3390/genes13060984 - 31 May 2022

Cited by 17 | Viewed by 3104

Abstract

Fengycin is a lipopeptide produced by Bacillus that has a strong inhibitory effect on filamentous fungi; however, its use is restricted due to poor production and low yield. Previous studies have shown that fengycin biosynthesis in B. amyloliquefaciens was found to be [...] Read more.

Fengycin is a lipopeptide produced by Bacillus that has a strong inhibitory effect on filamentous fungi; however, its use is restricted due to poor production and low yield. Previous studies have shown that fengycin biosynthesis in B. amyloliquefaciens was found to be significantly increased after fructose addition. This study investigated the effect of fructose on fengycin production and its regulation mechanism in B. amyloliquefaciens by transcriptome sequencing. According to the RNA sequencing data, 458 genes were upregulated and 879 genes were downregulated. Transcriptome analysis results showed that fructose changed the transcription of amino acid synthesis, fatty acid metabolism, and energy metabolism; alterations in these metabolic pathways contribute to the synthesis of fengycin. In an MLF medium (modified Landy medium with fructose), the expression level of the fengycin operon was two-times higher than in an ML medium (modified Landy medium). After fructose was added to B. amyloliquefaciens, the fengycin-synthesis-associated genes were activated in the process of fengycin synthesis. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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15 pages, 3885 KiB  

Open AccessArticle

Effects of Different Pesticides on the Brewing of Wine Investigated by GC-MS-Based Metabolomics

by Beibei Song, Yaoyao Zhou, Rong Zhan, Linjiang Zhu, Hanchi Chen, Zhi Ma, Xiaolong Chen and Yuele Lu

Metabolites 2022, 12(6), 485; https://doi.org/10.3390/metabo12060485 - 27 May 2022

Cited by 20 | Viewed by 3168

Abstract

The application of pesticides is critical during the growth of high-quality grape for wine making. However, pesticide residues have significant influence on the wine flavor. In this study, gas chromatography-mass spectrometry (GC-MS) was performed and the obtained datasets were analyzed with multivariate statistical [...] Read more.

The application of pesticides is critical during the growth of high-quality grape for wine making. However, pesticide residues have significant influence on the wine flavor. In this study, gas chromatography-mass spectrometry (GC-MS) was performed and the obtained datasets were analyzed with multivariate statistical methods to investigate changes in flavor substances in wine during fermentation. The principal component analysis (PCA) score plot showed significant differences in the metabolites of wine treated with various pesticides. In trials using five pesticides (hexaconazole, difenoconazole, flutriafol, tebuconazole, and propiconazole), more than 86 metabolites were changed. Most of these metabolites were natural flavor compounds, like carbohydrates, amino acids, and short-chain fatty acids and their derivatives, which essentially define the appearance, aroma, flavor, and taste of the wine. Moreover, the five pesticides added to grape pulp exhibited different effects on the metabolic pathways, involving mainly alanine, aspartate and glutamate metabolism, butanoate metabolism, arginine, and proline metabolism. The results of this study will provide new insight into the potential impact of pesticide residues on the metabolites and sensory profile of wine during fermentation. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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17 pages, 10449 KiB  

Open AccessArticle

Metabolomics Study Suggests the Mechanism of Different Types of Tieguanyin (Oolong) Tea in Alleviating Alzheimer’s Disease in APP/PS1 Transgenic Mice

by Youying Tu, Hyunuk Kang, Eunhye Kim, Jiangfan Yang, Puming He, Yuanyuan Wu, Bo Li, Xiaobo Liu and Junsheng Liu

Metabolites 2022, 12(5), 466; https://doi.org/10.3390/metabo12050466 - 22 May 2022

Cited by 4 | Viewed by 2923

Abstract

Previously, we found that three types of Tieguanyin tea (Tgy-Q, Tgy-N and Tgy-C) extracts could alleviate Alzheimer’s disease (AD) in a mouse model among which Tgy-C was more effective. In this study, APP/PS1 transgenic mice were used to investigate the metabolomic changes in [...] Read more.

Previously, we found that three types of Tieguanyin tea (Tgy-Q, Tgy-N and Tgy-C) extracts could alleviate Alzheimer’s disease (AD) in a mouse model among which Tgy-C was more effective. In this study, APP/PS1 transgenic mice were used to investigate the metabolomic changes in the feces of mice treated with Tieguanyin tea extracts. Results showed that the profile of fecal metabolites was obviously changed in AD mice. Metabolomics analysis found the effects of Tgy-C, especially its decreasing effect on the fecal metabolites in AD mice—132 of the 155 differential metabolites were decreased. KEGG enrichment revealed that differential metabolites could participate in functional pathways including protein digestion and absorption, biosynthesis of amino acids and ABC transporters. Further comparisons of the metabolites between groups showed that although Tgy-N and Tgy-Q exerted a decreasing effect on the fecal metabolites, Tgy-C was more effective. Moreover, correlation analysis found that the levels of the fecal metabolites were highly correlated with the contents of functional components in tea extracts. Finally, 16S rDNA sequencing presented that Tieguanyin extracts modified the gut microbiota by targeting diverse bacteria. In this study, we investigated the differences of three types of Tieguanyin tea extracts on the fecal metabolites as well as the bacterial community of the gut microbiota in AD mice. The identified differential metabolites and the changed intestinal bacteria might provide potential diagnostic biomarkers for the occurrence and progression of AD. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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5 pages, 3084 KiB  

Open AccessEditorial

Microbiota and Kidney: Is There a Correlation?

by Giuseppe Merra, Annunziata Capacci, Giuseppe Cenname, Ernesto Esposito, Maria Dri, Laura Di Renzo and Marco Marchetti

Microbiol. Res. 2022, 13(2), 183-187; https://doi.org/10.3390/microbiolres13020015 - 20 Apr 2022

Cited by 1 | Viewed by 2083

Abstract

The relationship between microbiota and chronic kidney disease (CKD) has long been known [...] Full article

(This article belongs to the Topic Microbiology Metabolomics)

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20 pages, 3546 KiB  

Open AccessArticle

Microbiomics Revealed the Disturbance of Intestinal Balance in Rabbits with Diarrhea Caused by Stopping the Use of an Antibiotic Diet

by Jie Wang, Siqi Xia, Huimei Fan, Jiahao Shao, Tao Tang, Li Yang, Wenqiang Sun, Xianbo Jia, Shiyi Chen and Songjia Lai

Microorganisms 2022, 10(5), 841; https://doi.org/10.3390/microorganisms10050841 - 20 Apr 2022

Cited by 5 | Viewed by 3070

Abstract

The harmful effects of diarrhea on the growth performance of rabbits have been well documented, but the details of the potential mechanism of intestinal diarrhea when antibiotics are stopped are still unclear. Here, PacBio sequencing technology was used to sequence the full length [...] Read more.

The harmful effects of diarrhea on the growth performance of rabbits have been well documented, but the details of the potential mechanism of intestinal diarrhea when antibiotics are stopped are still unclear. Here, PacBio sequencing technology was used to sequence the full length 16S rRNA gene of the microbiota of intestinal content samples, in order to characterize the bacterial communities in the small intestine (duodenum and jejunum) and large intestine (colon and cecum) in normal Hyplus rabbits and those with diarrhea. The histopathological examination showed that intestinal necrosis occurred in different degrees in the diarrhea group, and that the mucosal epithelium was shed and necrotic, forming erosion, and the clinical manifestation was necrosis. However, the intestinal tissue structure of the normal group was normal. The results revealed that there were significant differences in bacterial communities and structure between the diarrhea and normal groups of four intestinal segments (p < 0.05). In general, 16 bacterial phyla, 144 bacterial genera and 22 metabolic pathways were identified in the two groups. Tax4Fun functional prediction analysis showed that KEGG related to amino acid metabolism and energy metabolism was enriched in the large intestines of rabbits with diarrhea, whereas lipid metabolism was more abundant in the small intestine of rabbits with diarrhea. In conclusion, the change in the relative abundance of the identified dominant microbiota, which could deplete key anti-inflammatory metabolites and lead to bacterial imbalance and diarrhea, resulted in diarrhea in Hyplus rabbits that stopped using antibiotics. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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10 pages, 2996 KiB  

Open AccessArticle

Gut Microbiota Feature of Senile Osteoporosis by Shallow Shotgun Sequencing Using Aged Rats Model

by Ning Wang, Sicong Ma and Lingjie Fu

Genes 2022, 13(4), 619; https://doi.org/10.3390/genes13040619 - 29 Mar 2022

Cited by 22 | Viewed by 3459

Abstract

Senile osteoporosis is defined as an age-related bone metabolic disorder, which is characterized by bone loss and decreased bone fragility. Gut microbiota (GM) could regulate the bone metabolic process and be closely related to senile osteoporosis. Several genus-level GM were found to increase [...] Read more.

Senile osteoporosis is defined as an age-related bone metabolic disorder, which is characterized by bone loss and decreased bone fragility. Gut microbiota (GM) could regulate the bone metabolic process and be closely related to senile osteoporosis. Several genus-level GM were found to increase in osteoporotic animals and patients. However, to reveal the pathogenic bacteria in senile osteoporosis, further studies are still needed to investigate the complete characteristics of bacteria species. In the present study, the rats were equally divided into two groups: the control group (Con, 6-month-old) and the osteoporosis group (OP, 22-month-old). Fecal samples were freshly collected to conduct the shallow shotgun sequencing. Then, we compared the species numbers, microbial diversity, GM composition at genus and species-level, and functional metabolic pathways in the two groups. The results showed that the species number was lower in the OP group (1272) than in the control group (1413), and 1002 GM species were shared between the two groups. The OP group had the decreased α diversity compared with the control group. As for β diversity, The PCA revealed that samples in the two groups had distinguishable ecological distance in each coordinate. At the species level, Bacteroide coprocola (B. coprocola), Acinetobacter baumannii (A. baumannii), Parabacteroides distasonis (P. distasonis), and Prevotella copri (P. copri) were higher in the OP group, while Corynebacterium stationis (C. stationis), Akkermansia muciniphila (A. muciniphila), and Alistipes indistinctus (A. indistinctus) were decreased. Moreover, functional metabolic analysis revealed that metabolic pathways of fatty acid biosynthesis, valine/isoleucine biosynthesis, GABA biosynthesis, and ubiquinone biosynthesis were enriched in the senile osteoporotic rats. In conclusion, GM at the species level in senile osteoporotic rats was significantly altered in structure, composition, and function. The altered GM structure, increased GM species such as P. copri, and decreased GM species such as A. muciniphila might be linked with the development of senile osteoporosis. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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15 pages, 1571 KiB  

Open AccessArticle

Late-Stage Glioma Is Associated with Deleterious Alteration of Gut Bacterial Metabolites in Mice

by Aglae Herbreteau, Philippe Aubert, Mikaël Croyal, Philippe Naveilhan, Stéphanie Billon-Crossouard, Michel Neunlist, Yves Delneste, Dominique Couez and Laetitia Aymeric

Metabolites 2022, 12(4), 290; https://doi.org/10.3390/metabo12040290 - 25 Mar 2022

Cited by 11 | Viewed by 3169

Abstract

Brain-gut axis refers to the bidirectional functional connection between the brain and the gut, which sustains vital functions for vertebrates. This connection also underlies the gastrointestinal (GI) comorbidities associated with brain disorders. Using a mouse model of glioma, based on the orthotopic injection [...] Read more.

Brain-gut axis refers to the bidirectional functional connection between the brain and the gut, which sustains vital functions for vertebrates. This connection also underlies the gastrointestinal (GI) comorbidities associated with brain disorders. Using a mouse model of glioma, based on the orthotopic injection of GL261 cell line in syngeneic C57BL6 mice, we show that late-stage glioma is associated with GI functional alteration and with a shift in the level of some bacterial metabolites in the cecum. By performing cecal content transfer experiments, we further show that cancer-associated alteration in cecal metabolites is involved in end-stage disease progression. Antibiotic treatment results in a slight but significant delay in mice death and a shift in the proportion of myeloid cells in the brain tumor environment. This work rationally considers microbiota modulating strategies in the clinical management of patients with late-stage glioma. Full article

(This article belongs to the Topic Microbiology Metabolomics)

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