Transcriptomics and metabolomics reveal the adaption of Akkermansia muciniphila to high mucin by regulating energy homeostasis

AbstractIn gut, Akkermansia muciniphila (A. muciniphila) probably exerts its probiotic activities by the positive modulation of mucus thickness and gut barrier integrity. However, the potential mechanisms between A. muciniphila and mucin balance have not been fully elucidated. In this study, we cultured the bacterium in a BHI medium containing 0% to 0.5% mucin, and transcriptome and gas chromatography mass spectrometry (GC–MS) analyses were performed. We found that 0.5% (m/v) mucin in a BHI medium induced 1191 microbial genes to be differentially expressed, and 49 metabolites to be changed. The metabolites of sorbose, mannose, 2,7-anhydro-β-sedoheptulose, fructose, phenylalanine, threonine, lysine, ornithine, asparagine, alanine and glutamic acid were decreased by 0.5% mucin, while the metabolites of leucine, valine and N-acetylneuraminic acid were increased. The association analysis between transcriptome and metabolome revealed that A. muciniphila gave strong responses to energy metabolism, amino sugar and nucleotide sugar metabolism, and galactose metabolism pathways to adapt to high mucin in the medium. This finding showed that only when mucin reached a certain concentration in a BHI medium, A. muciniphila could respond to the culture environment significantly at the level of genes and metabolites, and changed its metabolic characteristics by altering the effect on carbohydrates and amino acids.

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Study the Mechanism of Antileishmanial Action of Xanthium strumarium Against Amastigotes Stages in Leishmania major: A Metabolomics Approach

Jundishapur Journal of Natural Pharmaceutical Products ◽

10.5812/jjnpp.106431 ◽

2021 ◽

Vol In Press (In Press) ◽

Author(s):

Mohamad Ahmadi ◽

Ziba Akhbari ◽

Zahra Zamani ◽

Reza Hajhossieni ◽

Mohammad Arjmand

Keyword(s):

Metabolic Pathways ◽

Leaf Extract ◽

Leishmania Major ◽

Colorimetric Method ◽

Sugar Metabolism ◽

Amino Sugar ◽

Primary Treatment ◽

Antileishmanial Activity ◽

Xanthium Strumarium ◽

Galactose Metabolism

Background: Leishmaniasis is among the most important neglected tropical infections, affecting millions of people worldwide. Since 1945, chemotherapy has been the primary treatment for leishmaniasis; however, lengthy and costly treatments associated with various side effects and strains resistant to the conventional therapy have dramatically reduced chemotherapy compounds’ efficacy. Objectives: The antileishmanial activity of the leaf extract of Xanthium strumarium (Asteraceae) was studied. New insights into its mechanism of action toward Leishmania major were provided through a metabolomics-based study. Methods: J774 macrophages were cultured, infected with stationary promastigotes, and treated with different leaf extract concentrations for three days. Antileishmanial activity was assayed by the MTT colorimetric method, and cell metabolites were extracted. 1HNMR spectroscopy was applied, and outliers were analyzed using multivariate statistical analysis. Results: X. strumarium extract (0.15 µg/mL) showed the best activity against L. major amastigotes with the infection rate (IR) and multiplication index (MI) values of 51% and 57%, respectively. The action of X. strumarium extract on amastigotes was comparable with amphotericin B as the positive control (0.015 µg/mL). According to the obtained P-values, pentanoate and coenzyme, A biosynthesis, pentose, glucuronate metabolism, valine, leucine, isoleucine biosynthesis, galactose metabolism, and amino sugar and nucleotide sugar metabolism were the most important metabolic pathways affected by the plant extract in the amastigote stage of L. major. Conclusions: Our finding demonstrated that X. strumarium leaf extract could be used for discovering and producing novel leishmanicidal medicines. Moreover, the affected metabolic pathways observed in this study could be potential candidates for drug targeting against leishmaniasis.

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Effect of a Humanized Diet Profile on Colonization Efficiency and Gut Microbial Diversity in Human Flora-Associated Mice

Frontiers in Nutrition ◽

10.3389/fnut.2021.633738 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sashuang Dong ◽

BenHua Zeng ◽

Ling Hu ◽

Yuling Zhang ◽

Jiaqi Xiong ◽

...

Keyword(s):

Microbial Diversity ◽

Mouse Models ◽

Metabolic Pathways ◽

Intestinal Flora ◽

Sugar Metabolism ◽

Amino Sugar ◽

Nucleotide Sugar ◽

Human Donor ◽

Disease Research ◽

Human Flora

Human flora-associated (HFA) mouse models allow us to design interventions for human disease research to test specific hypotheses and explore the complex commensal microbiome while avoiding the ethical limitations of using humans as models to directly study intestinal flora diseases. However, few studies have investigated the effect of a humanized diet profile (coarse-feed diet; CFD) on colonization efficiency and gut microbial diversity in HFA mice. We tested the colonization efficiency and gut microbial diversity in germ-free Kunming (KM) mice fed a CFD or a purified feed diet (PFD) at 1, 2, and 4 weeks. Although the colonization efficiencies differed significantly (67.50–70.00% vs. 72.69–85.96%) in the HFA mice, the colonization efficiency of the PFD-fed HFA mice (85.96%) was significantly higher than that of the CFD-fed mice (69.61%) at 2 weeks. At 4 weeks, the colonization efficiency of the PFD-fed mice (72.69%) was comparable to that of the CFD-fed mice (70.00%). Additionally, the gut microbial diversity of the CFD-fed HFA mice was similar to that of a human fecal donor. Regarding the Kyoto Encyclopedia of Genes and Genomes colonic microbiota metabolic pathways, the CFD-fed HFA mice showed more similarities to the human donor than to the PFD-fed mice in amino sugar and nucleotide sugar metabolism, biosynthesis of amino acids, carbon metabolism, purine metabolism, and phosphotransferase systems. In conclusion, the humanized diet profiles of the CFD and PFD could help establish human microbiotas in mice. Constructing HFA mouse models fed a CFD for 4 weeks may be useful in researching human-derived intestinal diseases.

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Metabolic response induced by parasitic plant-fungus interactions hinder amino sugar and nucleotide sugar metabolism in the host

Scientific Reports ◽

10.1038/srep37434 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 20

Author(s):

Dong-Kyu Lee ◽

Soohyun Ahn ◽

Hae Yoon Cho ◽

Hye Young Yun ◽

Jeong Hill Park ◽

...

Keyword(s):

Metabolic Response ◽

Sugar Metabolism ◽

Amino Sugar ◽

Parasitic Plant ◽

Nucleotide Sugar

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Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

International Journal of Molecular Sciences ◽

10.3390/ijms20040997 ◽

2019 ◽

Vol 20 (4) ◽

pp. 997 ◽

Cited By ~ 3

Author(s):

Peng Zhang ◽

Zhuoran Ding ◽

Zhengzheng Zhong ◽

Hanhua Tong

Keyword(s):

Gene Expression ◽

Sulfur Metabolism ◽

Expression Patterns ◽

Sugar Metabolism ◽

Amino Sugar ◽

Transcriptomic Analysis ◽

Gene Expression Patterns ◽

Japonica Rice ◽

Al Tolerance ◽

Nucleotide Sugar

Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels; thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., “Terpenoid backbone biosynthesis”, “Ribosome”, “Amino sugar and nucleotide sugar metabolism”, “Plant hormone signal transduction”, “TCA cycle”, “Synthesis and degradation of ketone bodies”, and “Butanoate metabolism” were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., “Sulfur metabolism”) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in “Starch and sucrose metabolism”, “Metabolic pathway”, and “Amino sugar and nucleotide sugar metabolism”.

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Comparative Proteomic Analysis of Grapevine Rootstock in Response to Waterlogging Stress

Frontiers in Plant Science ◽

10.3389/fpls.2021.749184 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xicheng Wang ◽

Lichun Yan ◽

Bo Wang ◽

Yaming Qian ◽

Zhuangwei Wang ◽

...

Keyword(s):

Carbon Fixation ◽

Sugar Metabolism ◽

Enrichment Analysis ◽

Amino Sugar ◽

Resistance Mechanisms ◽

Glutathione Metabolism ◽

Waterlogging Tolerance ◽

Galactose Metabolism ◽

Waterlogging Stress ◽

Waterlogging Treatment

Waterlogging severely affects global agricultural production. Clarifying the regulatory mechanism of grapevine in response to waterlogging stress will help to improve the waterlogging tolerance of grapevine. In the present study, the physiological and proteomic responses of SO4 grapevine rootstock to different waterlogging tolerances were comparatively assayed. The results showed that the activities of SOD and POD first increased and then decreased, while the change trend of CAT and APX activities was the opposite. In addition, the MDA and H2O2 contents increased after waterlogging treatment, but the chlorophyll a and chlorophyll b contents decreased. A total of 5,578 grapevine proteins were identified by the use of the tandem mass tag (TMT) labeling technique. Among them, 214 (103 and 111 whose expression was upregulated and downregulated, respectively), 314 (129 and 185 whose expression was upregulated and downregulated, respectively), and 529 (248 and 281 whose expression was upregulated and downregulated, respectively) differentially expressed proteins (DEPs) were identified in T0d vs. T10d, T10d vs. T20d, and T0d vs. T20d comparison groups, respectively. Enrichment analysis showed that these DEPs were mainly involved in glutathione metabolism, carbon fixation, amino sugar and nucleotide sugar metabolism, biosynthesis of amino acids, photosynthesis, carbon metabolism, starch, and sucrose metabolism, galactose metabolism, protein processing and ribosomes. To further verify the proteomic data, the expression of corresponding genes that encode eight DEPs was confirmed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results of this study presented an important step toward understanding the resistance mechanisms of grapevine in response to waterlogging stress at the proteome level.

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Alterations of gut microbiota in gestational diabetes patients during the second trimester of pregnancy in the Shanghai Han population

Journal of Translational Medicine ◽

10.1186/s12967-021-03040-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yao Su ◽

Hong-Kun Wang ◽

Xu-Pei Gan ◽

Li Chen ◽

Yan-Nan Cao ◽

...

Keyword(s):

Gestational Diabetes ◽

Gut Microbiota ◽

Gut Microbiome ◽

Sugar Metabolism ◽

16S Rrna Gene Sequencing ◽

Amino Sugar ◽

Fecal Microbiota ◽

Rrna Gene ◽

Second Trimester ◽

Metabolic Hormone

Abstract Background The causes of gestational diabetes mellitus (GDM) are still unclear. Recent studies have found that the imbalance of the gut microbiome could lead to disorders of human metabolism and immune system, resulting in GDM. This study aims to reveal the different gut compositions between GDM and normoglycemic pregnant women and find the relationship between gut microbiota and GDM. Methods Fecal microbiota profiles from women with GDM (n = 21) and normoglycemic women (n = 32) were assessed by 16S rRNA gene sequencing. Fasting metabolic hormone concentrations were measured using multiplex ELISA. Results Metabolic hormone levels, microbiome profiles, and inferred functional characteristics differed between women with GDM and healthy women. Additionally, four phyla and seven genera levels have different correlations with plasma glucose and insulin levels. Corynebacteriales (order), Nocardiaceae (family), Desulfovibrionaceae (family), Rhodococcus (genus), and Bacteroidetes (phylum) may be the taxonomic biomarkers of GDM. Microbial gene functions related to amino sugar and nucleotide sugar metabolism were found to be enriched in patients with GDM. Conclusion Our study indicated that dysbiosis of the gut microbiome exists in patients with GDM in the second trimester of pregnancy, and gut microbiota might be a potential diagnostic biomarker for the diagnosis, prevention, and treatment of GDM.

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The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

Biogeosciences Discussions ◽

10.5194/bgd-12-18103-2015 ◽

2015 ◽

Vol 12 (21) ◽

pp. 18103-18150 ◽

Cited By ~ 3

Author(s):

L. Purkamo ◽

M. Bomberg ◽

R. Kietäväinen ◽

H. Salavirta ◽

M. Nyyssönen ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Fixation ◽

Keystone Species ◽

Carbon Assimilation ◽

Sugar Metabolism ◽

Archaeal Community ◽

Amino Sugar ◽

Amplicon Sequencing ◽

Fracture Zones ◽

Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

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The Antifungal Effects of Citral on Magnaporthe oryzae Occur via Modulation of Chitin Content as Revealed by RNA-Seq Analysis

Journal of Fungi ◽

10.3390/jof7121023 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1023

Author(s):

Xingchen Song ◽

Qijun Zhao ◽

Aiai Zhou ◽

Xiaodong Wen ◽

Ming Li ◽

...

Keyword(s):

Cell Wall ◽

Magnaporthe Oryzae ◽

Amino Sugar ◽

Cell Wall Integrity ◽

Rna Seq ◽

Chitin Synthesis ◽

Nucleotide Sugar ◽

Qpcr Analysis ◽

Antifungal Effects ◽

Glucose Synthesis

The natural product citral has previously been demonstrated to possess antifungal activity against Magnaporthe oryzae. The purpose of this study was to screen and annotate genes that were differentially expressed (DEGs) in M. oryzae after treatment with citral using RNA sequencing (RNA-seq). Thereafter, samples were reprepared for quantitative real-time PCR (RT-qPCR) analysis verification of RNA-seq data. The results showed that 649 DEGs in M. oryzae were significantly affected after treatment with citral (100 μg/mL) for 24 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) and a gene ontology (GO) analysis showed that DEGs were mainly enriched in amino sugar and nucleotide sugar metabolic pathways, including the chitin synthesis pathway and UDP sugar synthesis pathway. The results of the RT-qPCR analysis also showed that the chitin present in M. oryzae might be degraded to chitosan, chitobiose, N-acetyl-D-glucosamine, and β-D-fructose-6-phosphate following treatment with citral. Chitin degradation was indicated by damaged cell-wall integrity. Moreover, the UDP glucose synthesis pathway was involved in glycolysis and gluconeogenesis, providing precursors for the synthesis of polysaccharides. Galactose-1-phosphate uridylyltransferase, which is involved in the regulation of UDP-α-D-galactose and α-D-galactose-1-phosphate, was downregulated. This would result in the inhibition of UDP glucose (UDP-Glc) synthesis, a reduction in cell-wall glucan content, and the destruction of cell-wall integrity.

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STRUCTURE AND FUNCTION OF THE FRUIT MICROBIOME IN HEALTHY AND DISEASED KIWIFRUIT

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/19.8820 ◽

2019 ◽

Vol 56 (03) ◽

pp. 577-585

Author(s):

Wenneng Wu

Keyword(s):

Microbial Diversity ◽

Relative Abundance ◽

Foodborne Pathogens ◽

Fungal Pathogens ◽

Sugar Metabolism ◽

Amino Sugar ◽

Disease Diagnosis ◽

Postharvest Disease ◽

Pathogen Infection ◽

Microbiome Composition

The fruit surface is an infection court where foodborne pathogens compete with indigenous microbiota for microsites to invade the fruits for nutrients acquisition. However, our current understanding of the structure and functions of fruit microbiome visa-vis postharvest pathogen infection is still nascent. Here, we sequenced the metagenomic DNA to understand the structural and functional attributes of healthy and diseased kiwifruit microbiome. The healthy fruits exhibited higher microbial diversity and distinct microbiome composition compared with diseased fruits. The microbiome of diseased fruit was dominated by fungal pathogens Neofusicoccum parvum and Diplodiaseriata, while the microbiome of healthy fruits were enriched by bacteria from Methylobacteriaceae, Sphingomonadaceae, Nocardioidaceae and fungi in Pleosporaceae. Importantly, the healthy fruit microbiome had a higher relative abundance of genes related to ABC transporter, two-component system, bacterial chemotaxis, bacterial secretion system, but had a lower relative abundance of genes associated with polycyclic aromatic hydrocarbon degradation, amino sugar and nucleotide sugar metabolism, glycine, serine and threonine metabolism compared with diseased fruits. Our results indicate that pathogen infection disrupts the fruit microbiome. The changes in microbiome composition and functions could also increase the possibility of secondary pathogen infection as the reduced microbial diversity may demonstrate less resistance to pathogens infection. Therefore, monitoring the microbiome dynamics and their functions using metagenomic approaches could be useful to build a predictive understanding of accurate postharvest disease diagnosis and management in the future

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Novel serine/threonine-O-glycosylation with N-acetylneuraminic acid and 3-deoxy-D-manno-octulosonic acid by bacterial flagellin glycosyltransferases

Glycobiology ◽

10.1093/glycob/cwaa084 ◽

2020 ◽

Cited By ~ 1

Author(s):

Aasawari Khairnar ◽

Sonali Sunsunwal ◽

Ponnusamy Babu ◽

T N C Ramya

Keyword(s):

Escherichia Coli ◽

Clostridium Botulinum ◽

Associated Factors ◽

Nucleotide Sugar ◽

Acetylneuraminic Acid ◽

Geobacillus Kaustophilus ◽

Nonulosonic Acid ◽

Glycosyl Donor ◽

Pseudaminic Acid ◽

Substrate Promiscuity

Abstract Some bacterial flagellins are O-glycosylated on surface-exposed serine/threonine residues with nonulosonic acids such as pseudaminic acid, legionaminic acid and their derivatives by flagellin nonulosonic acid glycosyltransferases, also called motility-associated factors (Maf). We report here two new glycosidic linkages previously unknown in any organism, serine/threonine-O-linked N-acetylneuraminic acid (Ser/Thr-O-Neu5Ac) and serine/threonine-O-linked 3-deoxy-D-manno-octulosonic acid or keto-deoxyoctulosonate (Ser/Thr-O-KDO), both catalyzed by Geobacillus kaustophilus Maf and Clostridium botulinum Maf. We identified these novel glycosidic linkages in recombinant G. kaustophilus and C. botulinum flagellins that were coexpressed with their cognate recombinant Maf protein in Escherichia coli strains producing the appropriate nucleotide sugar glycosyl donor. Our finding that both G. kaustophilus Maf (putative flagellin sialyltransferase) and C. botulinum Maf (putative flagellin legionaminic acid transferase) catalyzed Neu5Ac and KDO transfer on to flagellin indicates that Maf glycosyltransferases display donor substrate promiscuity. Maf glycosyltransferases have the potential to radically expand the scope of neoglycopeptide synthesis and posttranslational protein engineering.

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