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Keywords = carbohydrate-binding module 1

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26 pages, 4020 KB  
Article
Study on the Plateau Adaptive Synergistic Mechanism of Rumen Microbiome-Metabolome-Resistome in Tibetan Sheep
by Xu Gao, Qianling Chen, Yuzhu Sha, Yanyu He, Xiu Liu, Xiaowei Chen, Pengyang Shao, Wei Huang, Yapeng He, Mingna Li, Zhiyun Hao, Bingang Shi and Jianfeng Xu
Microorganisms 2025, 13(9), 2049; https://doi.org/10.3390/microorganisms13092049 - 3 Sep 2025
Viewed by 493
Abstract
Tibetan sheep are an important livestock breed adapted to the extreme environment of the Qinghai–Tibet Plateau (QTP). Their energy metabolism and environmental adaptability are highly dependent on the rumen microbiome. However, systematic comparisons of the rumen microbiome, its functions, and the resistome between [...] Read more.
Tibetan sheep are an important livestock breed adapted to the extreme environment of the Qinghai–Tibet Plateau (QTP). Their energy metabolism and environmental adaptability are highly dependent on the rumen microbiome. However, systematic comparisons of the rumen microbiome, its functions, and the resistome between plateau-adapted breeds and lowland breeds remain insufficient. In this study, 6 Tibetan sheep (TS) and 6 Hu sheep (HS) were selected. All the selected sheep had a body weight of 34 kg (±0.5 kg) and an age of 1 year (±1 month) and were all managed under local traditional natural grazing (without supplementary feeding). Using metagenomics and metabolomics techniques, systematic comparative analysis was conducted on the differences in rumen microbial community structure, functions, resistome, and metabolites between the two breeds. Metagenomic analysis showed that at the phylum level, the abundance of Bacteroidetes in the rumen of TS was significantly higher than that in HS (p < 0.05); at the genus level, the abundance of Bacteroides in TS was also significantly higher (p < 0.05). Carbohydrate-active enzymes (CAZy) analysis indicated that the abundance of Glycosyltransferases (GTs) and Carbohydrate-Binding Modules (CBMs) in the rumen of TS were significantly upregulated (p < 0.05), while HS was rich in various Glycoside Hydrolases (GHs). Comprehensive Antibiotic Resistance Database (CARD) analysis revealed that more than 60% of the Antibiotic Resistance Genes (ARGs) in the rumen of HS were present at higher levels than those in TS. Metabolomics identified a large number of differential metabolites, among which metabolites such as 2E,6Z,8Z,12E-hexadecatetraenoic acid, Leukotriene F4, and Tenurin were significantly upregulated in the rumen of TS. Correlation analysis showed that rumen microbial flora and their metabolites jointly act to regulate rumen ARGs. Specifically, microorganisms including Firmicutes and Succiniclasticum had a significantly positive correlation with ARGs such as rpoB2 (p < 0.05), while differential metabolites like endomorphin-1 and Purothionin AII exhibited a significantly negative correlation with ARGs such as rpoB2 (p < 0.05). Therefore, compared with HS, the synergistic effect of the rumen microbial flora, their metabolites, and the resistome in TS is an important characteristic and strategy for their adaptation to the hypoxic environment of the QTP, and also contributes to the formation of their unique rumen resistome. Despite being reared in the same plateau environment, the rumen microbiome of HS still retains low-altitude characteristics, which are manifested as high GHs activity and high ARGs abundance. Full article
(This article belongs to the Section Veterinary Microbiology)
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19 pages, 2901 KB  
Article
Genome Sequencing and Comparative Genomics of the Hyper-Cellulolytic Fungus Talaromyces pinophilus Y117
by Ya Li, Siyuan Yue, Peng Li, Jing Zeng, Jianjun Guo, Dawei Xiong, Shuaiwen Zhang, Tao Deng and Lin Yuan
J. Fungi 2025, 11(9), 614; https://doi.org/10.3390/jof11090614 - 22 Aug 2025
Viewed by 805
Abstract
Talaromyces pinophilus is a filamentous fungus with notable lignocellulose-degrading capacity based on enzyme activities and protein secretion potential, making it a compelling candidate for industrial biotechnology applications. In this study, we present the genomic characterization of the highly cellulolytic strain Y117, a domesticated [...] Read more.
Talaromyces pinophilus is a filamentous fungus with notable lignocellulose-degrading capacity based on enzyme activities and protein secretion potential, making it a compelling candidate for industrial biotechnology applications. In this study, we present the genomic characterization of the highly cellulolytic strain Y117, a domesticated variant of T. pinophilus, based on whole-genome sequencing and comparative genomic analysis with eleven related strains. Comprehensive analysis of CAZymes, transcription factors, and secondary metabolite diversity in T. pinophilus strains revealed that the exceptional lignocellulose degradation capacity of Y117 is driven by its unique genomic architecture. Key genomic features that distinguish Y117 include (1) significant expansion of glycoside hydrolase (GH) and carbohydrate-binding module (CBM) families, (2) loss of fungal-RiPP-like clusters, and (3) absence of the developmental regulator BrlA. These genomic adaptations could indicate a metabolic trade-off favoring hydrolytic enzyme production over secondary metabolism and sporulation. Our findings provide fundamental insights into fungal lignocellulose degradation mechanisms while establishing Y117 as a promising chassis for metabolic engineering applications in industrial enzyme production and heterologous protein expression. Full article
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13 pages, 2060 KB  
Article
Catalytic Efficiency Improvement in Cellobiohydrolase I by Cross-Species Domain Exchange Engineering
by Jing Xue, Xianzhang Jiang, Anjing Li, Jiaxin Li, Xiaoyun Su, Jianzhong Huang and Lina Qin
Int. J. Mol. Sci. 2025, 26(9), 4024; https://doi.org/10.3390/ijms26094024 - 24 Apr 2025
Cited by 1 | Viewed by 680
Abstract
Understanding the molecular mechanisms of cellobiohydrolase I (CBHI), a key enzyme in cellulase complexes, is crucial for developing efficient enzymes for the degradation of lignocellulosic biomasses (LCB). Building on our previous discovery that Chaetomium thermophilum CBHI (C-CBH) exhibits significantly higher specific activity than [...] Read more.
Understanding the molecular mechanisms of cellobiohydrolase I (CBHI), a key enzyme in cellulase complexes, is crucial for developing efficient enzymes for the degradation of lignocellulosic biomasses (LCB). Building on our previous discovery that Chaetomium thermophilum CBHI (C-CBH) exhibits significantly higher specific activity than Trichoderma reesei CBHI (T-CBH), systematic domain-swapping experiments were conducted to elucidate the structural determinants of catalytic efficiency in CBHI. Herein, the carbohydrate-binding modules (CBM) of the CBHIs from Trichoderma reesei (T-CBH) and Chaetomium thermophilum (C-CBH) were interchanged and to obtain two chimeric mutants TC-CBH and CT-CBH. These four CBHs were expressed in T. reesei, and the enzyme properties were analyzed. Comparative characterization revealed that while module exchange preserved native temperature/pH adaptability, it significantly altered substrate specificity and catalytic performance. The CT-CBH variant was identified as the most efficient biocatalyst, exhibiting four key advantages over T-CBH: (1) protein expression levels that far exceed those of T-CBH, (2) specific activity enhanced by 2.6-fold (734.5 U/μM vs. 282.5 U/μM on MU-cellobiose), (3) superior degradation capacities for filter paper (1.6-fold) and xylan, and (4) improved binding affinity for crystalline cellulose. These findings establish cross-species domain engineering as a viable strategy for creating high-performance cellulases, providing both mechanistic insights and practical solutions for lignocellulose degradation. Full article
(This article belongs to the Special Issue Lignocellulose Bioconversion and High-Value Utilization)
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21 pages, 3685 KB  
Article
The Effect of CBM1 and Linker on the Oxidase, Peroxidase and Monooxygenase Activities of AA9 LPMOs: Insight into Their Correlation with the Nature of Reductants and Crystallinity of Celluloses
by Xu Zhao, Fei Xie, Kaixiang Chen, Liangkun Long and Shaojun Ding
Int. J. Mol. Sci. 2024, 25(23), 12616; https://doi.org/10.3390/ijms252312616 - 24 Nov 2024
Cited by 3 | Viewed by 1660
Abstract
This study explores the effect of carbohydrate-binding module 1 (CBM1) and the linker on the function of auxiliary activity 9 (AA9) lytic polysaccharide monooxygenases (LPMOs), with a particular focus on monooxygenase activity, using different crystallinity celluloses and electron donors. The tested C1/C4-oxidizing AA9 [...] Read more.
This study explores the effect of carbohydrate-binding module 1 (CBM1) and the linker on the function of auxiliary activity 9 (AA9) lytic polysaccharide monooxygenases (LPMOs), with a particular focus on monooxygenase activity, using different crystallinity celluloses and electron donors. The tested C1/C4-oxidizing AA9 LPMOs exhibited higher oxidase and peroxidase activities compared to those of the C4-oxidizing AA9 LPMOs. While the presence of CBM1 promoted cellulose-binding affinity, it reduced the oxidase activity of modular AA9 LPMOs. The effect of CBM1 on peroxidase activity was variable and enzyme-specific. Its influence on monooxygenase activity was linked to the type of reductants and the crystallinity of celluloses. Overall, CBM1 improved the monooxygenase activity on high-, medium-, and low-crystallinity celluloses when ascorbic acid (AscA) was used as the electron donor. CBM1 also facilitated monooxygenase activity on high-crystallinity cellulose, but significantly inhibited monooxygenase activity on low-crystallinity cellulose when cellobiose dehydrogenase (CDH) was the electron donor. Linker truncation of NcLOMO9C enhanced the cellulose-binding affinity but decreased both the oxidase and peroxidase activities. Linker truncation also impacted the monooxygenase activity in both the AscA-AA9 LPMO and AfCDH-AA9 LPMO systems, though its effect was less pronounced compared to that of CBM1. This work provides new insights into the role of the reductant type and cellulose crystallinity in the functionality of CBM1 and the linker in AA9 LPMOs. Full article
(This article belongs to the Section Biochemistry)
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20 pages, 5436 KB  
Article
Phytochemical Profiling and Bioactive Potential of Grape Seed Extract in Enhancing Salinity Tolerance of Vicia faba
by Doaa E. Elsherif, Fatmah A. Safhi, Prasanta K. Subudhi, Abdelghany S. Shaban, Mai A. El-Esawy and Asmaa M. Khalifa
Plants 2024, 13(12), 1596; https://doi.org/10.3390/plants13121596 - 8 Jun 2024
Cited by 3 | Viewed by 1827
Abstract
Salinity stress poses a significant threat to crop productivity worldwide, necessitating effective mitigation strategies. This study investigated the phytochemical composition and potential of grape seed extract (GSE) to mitigate salinity stress effects on faba bean plants. GC–MS analysis revealed several bioactive components in [...] Read more.
Salinity stress poses a significant threat to crop productivity worldwide, necessitating effective mitigation strategies. This study investigated the phytochemical composition and potential of grape seed extract (GSE) to mitigate salinity stress effects on faba bean plants. GC–MS analysis revealed several bioactive components in GSE, predominantly fatty acids. GSE was rich in essential nutrients and possessed a high antioxidant capacity. After 14 days of germination, GSE was applied as a foliar spray at different concentrations (0, 2, 4, 6, and 8 g/L) to mitigate the negative effects of salt stress (150 mM NaCl) on faba bean plants. Foliar application of 2–8 g/L GSE significantly enhanced growth parameters such as shoot length, root length, fresh weight, and dry weight of salt-stressed bean plants compared to the control. The Fv/Fm ratio, indicating photosynthetic activity, also improved with GSE treatment under salinity stress compared to the control. GSE effectively alleviated the oxidative stress induced by salinity, reducing malondialdehyde, hydrogen peroxide, praline, and glycine betaine levels. Total soluble proteins, amino acids, and sugars were enhanced in GSE-treated, salt-stressed plants. GSE treatment under salinity stress modulated the total antioxidant capacity, antioxidant responses, and enzyme activities such as peroxidase, ascorbate peroxidase, and polyphenol oxidase compared to salt-stressed plants. Gene expression analysis revealed GSE (6 g/L) upregulated photosynthesis (chlorophyll a/b-binding protein of LHCII type 1-like (Lhcb1) and ribulose bisphosphate carboxylase large chain-like (RbcL)) and carbohydrate metabolism (cell wall invertase I (CWINV1) genes) while downregulating stress response genes (ornithine aminotransferase (OAT) and ethylene-responsive transcription factor 1 (ERF1)) in salt-stressed bean plants. The study demonstrates GSE’s usefulness in mitigating salinity stress effects on bean plants by modulating growth, physiology, and gene expression patterns, highlighting its potential as a natural approach to enhance salt tolerance. Full article
(This article belongs to the Special Issue Mechanism of Drought and Salinity Tolerance in Crops)
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26 pages, 17083 KB  
Article
Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood
by Yili Liu, Liangliang Ma, Daojie Riqing, Jiu Qu, Jiyong Chen, Danzeng Zhandu, Biao Li and Mingfeng Jiang
Animals 2024, 14(9), 1365; https://doi.org/10.3390/ani14091365 - 30 Apr 2024
Cited by 2 | Viewed by 2674
Abstract
Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen’s survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of [...] Read more.
Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen’s survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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18 pages, 2439 KB  
Review
Sirtuin 6—A Key Regulator of Hepatic Lipid Metabolism and Liver Health
by X. Charlie Dong
Cells 2023, 12(4), 663; https://doi.org/10.3390/cells12040663 - 19 Feb 2023
Cited by 39 | Viewed by 11663
Abstract
Sirtuin 6 (SIRT6) is an NAD-dependent deacetylase/deacylase/mono-ADP ribosyltransferase, a member of the sirtuin protein family. SIRT6 has been implicated in hepatic lipid homeostasis and liver health. Hepatic lipogenesis is driven by several master regulators including liver X receptor (LXR), carbohydrate response element binding [...] Read more.
Sirtuin 6 (SIRT6) is an NAD-dependent deacetylase/deacylase/mono-ADP ribosyltransferase, a member of the sirtuin protein family. SIRT6 has been implicated in hepatic lipid homeostasis and liver health. Hepatic lipogenesis is driven by several master regulators including liver X receptor (LXR), carbohydrate response element binding protein (ChREBP), and sterol regulatory element binding protein 1 (SREBP1). Interestingly, these three transcription factors can be negatively regulated by SIRT6 through direct deacetylation. Fatty acid oxidation is regulated by peroxisome proliferator activated receptor alpha (PPARα) in the liver. SIRT6 can promote fatty acid oxidation by the activation of PPARα or the suppression of miR-122. SIRT6 can also directly modulate acyl-CoA synthetase long chain family member 5 (ACSL5) activity for fatty acid oxidation. SIRT6 also plays a critical role in the regulation of total cholesterol and low-density lipoprotein (LDL)-cholesterol through the regulation of SREBP2 and proprotein convertase subtilisin/kexin type 9 (PCSK9), respectively. Hepatic deficiency of Sirt6 in mice has been shown to cause hepatic steatosis, inflammation, and fibrosis, hallmarks of alcoholic and nonalcoholic steatohepatitis. SIRT6 can dampen hepatic inflammation through the modulation of macrophage polarization from M1 to M2 type. Hepatic stellate cells are a key cell type in hepatic fibrogenesis. SIRT6 plays a strong anti-fibrosis role by the suppression of multiple fibrogenic pathways including the transforming growth factor beta (TGFβ)-SMAD family proteins and Hippo pathways. The role of SIRT6 in liver cancer is quite complicated, as both tumor-suppressive and tumor-promoting activities have been documented in the literature. Overall, SIRT6 has multiple salutary effects on metabolic homeostasis and liver health, and it may serve as a therapeutic target for hepatic metabolic diseases. To date, numerous activators and inhibitors of SIRT6 have been developed for translational research. Full article
(This article belongs to the Special Issue Lipid Metabolism and Metabolic Disorders)
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15 pages, 3169 KB  
Article
Differentially Expressed Genes and Signalling Pathways Regulated by High Selenium Involved in Antioxidant and Immune Functions of Goats Based on Transcriptome Sequencing
by Xu Wang, Chao Ban, Jia-Xuan Li, Qing-Yuan Luo, Ji-Xiao Qin, Yi-Qing Xu, Qi Lu and Xing-Zhou Tian
Int. J. Mol. Sci. 2023, 24(2), 1124; https://doi.org/10.3390/ijms24021124 - 6 Jan 2023
Cited by 5 | Viewed by 2871
Abstract
The objective of this study is to observe the effect of high selenium on the antioxidant and immune functions of growing goats based on transcriptome sequencing. Eighteen goats were randomly divided into three groups: (1) the control (CON) group was fed a basal [...] Read more.
The objective of this study is to observe the effect of high selenium on the antioxidant and immune functions of growing goats based on transcriptome sequencing. Eighteen goats were randomly divided into three groups: (1) the control (CON) group was fed a basal diet, and (2) the treatment 1 group (LS) and treatment 2 group (HS) were fed a basal diet with 2.4 and 4.8 mg/kg selenium-yeast (SY), respectively. The results indicate that HS treatment significantly (p < 0.05) increased the apparent digestibility of either extract and significantly increased (p < 0.05) total antioxidant capacity, whereas it significantly (p < 0.05) decreased plasma aspartate aminotransferase and malondialdehyde relative to the control group. The LS treatment had significantly (p < 0.05) increased glutathione S-transferase and catalase compared to CON. A total of 532 differentially expressed genes (DEGs) between the CON and HS were obtained using transcriptome sequencing. Kyoto Encyclopedia of Genes and Genomes analysis identified upregulated (p < 0.05) DEGs mainly related to vascular smooth muscle contraction, alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, the VEGF signalling pathway, and proteoglycans in cancer; downregulated (p < 0.05) DEGs mainly related to the NOD-like receptor signalling pathway, influenza A, cytokine-cytokine receptor interaction, haematopoietic cell lineage, and African trypanosomiasis. Ontology analyses of the top genes show that the identified DEGs are mainly involved in the regulation of granulocyte macrophage colony-stimulating factor production for biological processes, the external side of the plasma membrane for cellular components, and carbohydrate derivative binding for molecular functions. Seven genes are considered potential candidate genes for regulating antioxidant activity, including selenoprotein W, 1, glutathione peroxidase 1, glutathione S-transferase A1, tumour necrosis factor, tumour necrosis factor superfamily member 10, tumour necrosis factor superfamily member 8, and tumour necrosis factor superfamily member 13b. The experimental observations indicate that dietary supplementation with 4.8 mg/kg SY can enhance antioxidant and immune functions by improving muscle immunity, reducing the concentrations of inflammatory molecules, and modulating antioxidant and inflammatory signalling pathways in growing goats. Full article
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19 pages, 4847 KB  
Article
The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
by Guopeng Lin, Qian Liu, Luyao Wang, Haitao Li, Jianxin Zhao, Hao Zhang, Gang Wang and Wei Chen
Nutrients 2022, 14(11), 2347; https://doi.org/10.3390/nu14112347 - 4 Jun 2022
Cited by 14 | Viewed by 4002
Abstract
Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase [...] Read more.
Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase families of the carbohydrate active enzyme (CAZy). A total of 30 kinds of glycoside hydrolases (GHs), 14 kinds of glycosyl transferases (GTs), 13 kinds of carbohydrate-binding modules (CBMs), 6 kinds of carbohydrate-esterases (CEs), and 2 kinds of auxiliary activities (AAs) gene families were identified across the genomes of the 88 B. pseudocatenulatum strains. Specifically, this showed that significant differences were also present in the number of 10 carbohydrate-active enzyme gene families (GT51, GH13_32, GH26, GH42, GH121, GH3, AA3, CBM46, CE2, and CE6) among the strains derived from the hosts of different age groups, particularly between strains from infants and those from other human age groups. Twelve different individuals of B. pseudocatenulatum from four main clusters were selected for further study to reveal the genetic diversity of carbohydrate metabolism-related genes within the same phylogenetics. The animal experiment showed that 3 weeks of oral administration and 1 week after cessation of administration of these strains did not markedly alter the serum routine inflammatory indicators in mice. Furthermore, the administration of these strains did not significantly cause adverse changes in the gut microbiota, as indicated by the α- and β-diversity indexes, relative to the control group (normal diet). Beyond that, FAHBZ9L5 significantly increased the abundance of B. pseudocatenulatum after 3 weeks and significantly increased the abundance of acetic acid and butyric acid in the host’s intestinal tract 3 and 4 weeks after the first administration, respectively, compared with the control group. Corresponding to this, comparative genomic analyses of 12 B. pseudocatenulatum suggest that FAHBZ9L5-specific genes were rich in ABC transporters and carbohydrate esterase. Combining the results of comparative genomics analyses and animal experiment, it is suggested that the strains containing certain gene clusters contribute to another competitive growth advantage of B. pseudocatenulatum, which facilitates its intestinal carbohydrate metabolism in a host. Full article
(This article belongs to the Special Issue Role of Lactobacillus and Probiotics in Human Health and Diseases)
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20 pages, 5251 KB  
Article
Effects of Bile Acid Modulation by Dietary Fat, Cholecystectomy, and Bile Acid Sequestrant on Energy, Glucose, and Lipid Metabolism and Gut Microbiota in Mice
by Sunmin Park, Ting Zhang, Yu Yue and Xuangao Wu
Int. J. Mol. Sci. 2022, 23(11), 5935; https://doi.org/10.3390/ijms23115935 - 25 May 2022
Cited by 35 | Viewed by 6461
Abstract
Bile acid metabolism, involved with the digestion and absorption of nutrients in the gut, is linked to the gut microbiota community, greatly impacting the host’s metabolism. We examined the hypothesis that the modulation of bile acid metabolism by dietary fat contents, gallbladder removal [...] Read more.
Bile acid metabolism, involved with the digestion and absorption of nutrients in the gut, is linked to the gut microbiota community, greatly impacting the host’s metabolism. We examined the hypothesis that the modulation of bile acid metabolism by dietary fat contents, gallbladder removal (GBX; cholecystectomy), and bile acid sequestrant (BAS; cholestyramine) treatment could alter energy, glucose, and lipid metabolism through the changes in the gut microbiota. Mice were randomly assigned to the following six groups: (1) Sham GBX surgery (Sham) + low fat/high carbohydrate diet (LFD), (2) Sham + high fat diet (HFD), (3) Sham + HFD + BAS, (4) GBX + LFD, (5) GBX + HFD, and (6) GBX + HFD + BAS. BAS groups received 2% cholestyramine. After an 8-week intervention, energy, glucose, and lipid metabolism, and the gut microbiota community were measured. HFD groups exhibited higher body weight gain than LFD, and GBX increased the weight gain comped to Sham groups regardless of BAS in HFD (p < 0.05). Homeostatic model assessment for insulin resistance (HOMA-IR) was higher in HFD than LFD, and GBX increased it regardless of BAS. Serum lipid profiles were worsened in GBX + HFD compared to Sham + LFD, whereas BAS alleviated them, except for serum HDL cholesterol. Hepatic tumor-necrosis-factor-α (TNF-α) mRNA expression and lipid peroxide contents increased with GBX and BAS treatment compared to Sham and no BAS treatment (p < 0.05). Hepatic mRNA expression of sterol regulatory element-binding transcription factor 1c (SREBP1c) and peroxisome proliferator-activated receptor gamma (PPAR-γ) exhibited the same trend as that of tumor necrosis factor-α (TNF-α). The α-diversity of gut bacteria decreased in GBX + HFD and increased in GBX + HFD + BAS. Akkermentia, Dehalobacterium, SMB53, and Megamonas were high in the Sham + LFD, and Veillonella and Streptococcus were rich in the Sham + HFD, while Oscillospira and Olsenella were high in Sham + HFD + BAS (p < 0.05). GBX + LFD increased Lactobacillus and Sutterella while GBX + HFD + BAS elevated Clostridium, Alistipes, Blautia, Eubacterium, and Coprobacillus (p < 0.05). In conclusion, the modulation of bile acid metabolism influences energy, glucose, and lipid metabolisms, and it might be linked to changes in the gut microbiota by bile acid metabolism modulation. Full article
(This article belongs to the Special Issue Gut Microbiota Colonization and Food Impact)
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13 pages, 1727 KB  
Article
The Effects of Selenium on Rumen Fermentation Parameters and Microbial Metagenome in Goats
by Xingzhou Tian, Xu Wang, Jiaxuan Li, Qingyuan Luo, Chao Ban and Qi Lu
Fermentation 2022, 8(5), 240; https://doi.org/10.3390/fermentation8050240 - 21 May 2022
Cited by 17 | Viewed by 3788
Abstract
This study evaluated the effects of selenium yeast (SY) on rumen fermentation parameters, rumen bacterial diversity, and expression pathways in goats. A total of 18 Qianbei-pockmarked weather goats from Guizhou (body weight, 25.75 ± 1.75 kg; mean ± standard deviation) were assigned to [...] Read more.
This study evaluated the effects of selenium yeast (SY) on rumen fermentation parameters, rumen bacterial diversity, and expression pathways in goats. A total of 18 Qianbei-pockmarked weather goats from Guizhou (body weight, 25.75 ± 1.75 kg; mean ± standard deviation) were assigned to three groups according to a completely randomized design. Control group (CON, n = 6) kids were fed a basal diet, while treatment 1 (LS, n = 6) and treatment 2 (HS, n = 6) kids were fed a basal diet with 2.4 and 4.8 mg/kg SY, respectively. The feeding trial lasted for 74 days. The results indicated that the ruminal fluid of LS goats had significantly higher levels of propionic, caproic, isobutyric, and isovaleric acids than that of the CON. The levels of butyric and valeric acids were higher in the HS group than in the CON. The acetate:propionate ratio was significantly higher in the CON than in the two treatments. In addition, the inclusion of 2.4 mg/kg SY can lead to a significant decrease in the relative abundances of Euryarchaeota, and Proteobacteria at the phylum level compared to the CON and the HS groups. At the genus level, the LS group had a significant decrease in the relative abundance of Methanobrevibacter and Sarcina, whereas it could lead to a significant increase in the relative abundance of Clostridium in the ruminal fluid relative of the other two groups. At the species level, the LS group had a significant decrease in the relative abundance of bacterium_P3, bacterium_P201, and Sarcina_sp._DSM_11001 compared to the other groups. Moreover, the CON group had a significant decrease in the relative abundance of bacterium_P201 compared to the other two treatments. Compared to the CON, the addition of 2.4 mg/kg SY significantly enriched carbohydrate metabolism pathways in the ruminal fluid for gene encoding. Additionally, goats receiving SY showed a significant upregulation of glycosyl transferase and carbohydrate binding module pathways. These results suggest that dietary supplementation with SY modulates fermentation parameters, and it affects microbial diversity and microbial metagenome in the rumen of Qianbei-pockmarked goats. Full article
(This article belongs to the Special Issue Recent Advances in Rumen Fermentation Efficiency)
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23 pages, 4671 KB  
Article
Comparison of the Biochemical Properties and Roles in the Xyloglucan-Rich Biomass Degradation of a GH74 Xyloglucanase and Its CBM-Deleted Variant from Thielavia terrestris
by Beibei Wang, Kaixiang Chen, Peiyu Zhang, Liangkun Long and Shaojun Ding
Int. J. Mol. Sci. 2022, 23(9), 5276; https://doi.org/10.3390/ijms23095276 - 9 May 2022
Cited by 9 | Viewed by 3690
Abstract
Xyloglucan is closely associated with cellulose and still retained with some modification in pretreated lignocellulose; however, its influence on lignocellulose biodegradation is less understood. TtGH74 from Thielavia terrestris displayed much higher catalytic activity than previously characterized fungal GH74 xyloglucanases. The carbohydrate-binding [...] Read more.
Xyloglucan is closely associated with cellulose and still retained with some modification in pretreated lignocellulose; however, its influence on lignocellulose biodegradation is less understood. TtGH74 from Thielavia terrestris displayed much higher catalytic activity than previously characterized fungal GH74 xyloglucanases. The carbohydrate-binding module 1 (CBM1) deleted variant (TtGH74ΔCBM) had the same optimum temperature and pH but an elevated thermostability. TtGH74 displayed a high binding affinity on xyloglucan and cellulose, while TtGH74ΔCBM completely lost the adsorption capability on cellulose. Their hydrolysis action alone or in combination with other glycoside hydrolases on the free xyloglucan, xyloglucan-coated phosphoric acid-swollen cellulose or pretreated corn bran and apple pomace was compared. CBM1 might not be essential for the hydrolysis of free xyloglucan but still effective for the associated xyloglucan to an extent. TtGH74 alone or synergistically acting with the CBH1/EG1 mixture was more effective in the hydrolysis of xyloglucan in corn bran, while TtGH74ΔCBM showed relatively higher catalytic activity on apple pomace, indicating that the role and significance of CBM1 are substrate-specific. The degrees of synergy for TtGH74 or TtGH74ΔCBM with the CBH1/EG1 mixture reached 1.22–2.02. The addition of GH10 xylanase in TtGH74 or the TtGH74ΔCBM/CBH1/EG1 mixture further improved the overall hydrolysis efficiency, and the degrees of synergy were up to 1.50–2.16. Full article
(This article belongs to the Section Biochemistry)
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11 pages, 1861 KB  
Article
Bifidobacterium animalis ssp. lactis MG741 Reduces Body Weight and Ameliorates Nonalcoholic Fatty Liver Disease via Improving the Gut Permeability and Amelioration of Inflammatory Cytokines
by Moon Ho Do, Mi-Jin Oh, Hye-Bin Lee, Chang-Ho Kang, Guijae Yoo and Ho-Young Park
Nutrients 2022, 14(9), 1965; https://doi.org/10.3390/nu14091965 - 7 May 2022
Cited by 31 | Viewed by 4606
Abstract
Diet-induced obesity is one of the major causes of the development of metabolic disorders such as insulin resistance and nonalcoholic fatty liver disease (NAFLD). Recently, specific probiotic strains have been found to improve the symptoms of NAFLD. We examined the effects of Bifidobacterium [...] Read more.
Diet-induced obesity is one of the major causes of the development of metabolic disorders such as insulin resistance and nonalcoholic fatty liver disease (NAFLD). Recently, specific probiotic strains have been found to improve the symptoms of NAFLD. We examined the effects of Bifidobacterium animalis ssp. lactis MG741 (MG741) on NAFLD and weight gain, using a mouse model of high-fat-diet (HFD)-induced obesity. HFD-fed mice were supplemented daily with MG741. After 12 weeks, MG741-administered mice exhibited reduced fat deposition, and serum metabolic alterations, including fasting hyperinsulinemia, were modulated. In addition, MG741 regulated Acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), sterol regulatory element-binding protein 1 (SREBP-1), and carbohydrate-responsive element-binding protein (ChREBP) expression and lipid accumulation in the liver, thereby reducing the hepatic steatosis score. To determine whether the effects of MG741 were related to improvements in gut health, MG741 improved the HFD-induced deterioration in gut permeability by reducing toxic substances and inflammatory cytokine expression, and upregulating tight junctions. These results collectively demonstrate that the oral administration of MG741 could prevent NAFLD and obesity, thereby improving metabolic health. Full article
(This article belongs to the Topic Probiotics, Prebiotics and Postbiotics in Human Health)
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47 pages, 6250 KB  
Systematic Review
Re-Expression of Poly/Oligo-Sialylated Adhesion Molecules on the Surface of Tumor Cells Disrupts Their Interaction with Immune-Effector Cells and Contributes to Pathophysiological Immune Escape
by Mostafa Jarahian, Faroogh Marofi, Marwah Suliman Maashi, Mahnaz Ghaebi, Abdolrahman Khezri and Martin R. Berger
Cancers 2021, 13(20), 5203; https://doi.org/10.3390/cancers13205203 - 16 Oct 2021
Cited by 14 | Viewed by 5837 | Correction
Abstract
Glycans linked to surface proteins are the most complex biological macromolecules that play an active role in various cellular mechanisms. This diversity is the basis of cell–cell interaction and communication, cell growth, cell migration, as well as co-stimulatory or inhibitory signaling. Our review [...] Read more.
Glycans linked to surface proteins are the most complex biological macromolecules that play an active role in various cellular mechanisms. This diversity is the basis of cell–cell interaction and communication, cell growth, cell migration, as well as co-stimulatory or inhibitory signaling. Our review describes the importance of neuraminic acid and its derivatives as recognition elements, which are located at the outermost positions of carbohydrate chains linked to specific glycoproteins or glycolipids. Tumor cells, especially from solid tumors, mask themselves by re-expression of hypersialylated neural cell adhesion molecule (NCAM), neuropilin-2 (NRP-2), or synaptic cell adhesion molecule 1 (SynCAM 1) in order to protect themselves against the cytotoxic attack of the also highly sialylated immune effector cells. More particularly, we focus on α-2,8-linked polysialic acid chains, which characterize carrier glycoproteins such as NCAM, NRP-2, or SynCam-1. This characteristic property correlates with an aggressive clinical phenotype and endows them with multiple roles in biological processes that underlie all steps of cancer progression, including regulation of cell–cell and/or cell–extracellular matrix interactions, as well as increased proliferation, migration, reduced apoptosis rate of tumor cells, angiogenesis, and metastasis. Specifically, re-expression of poly/oligo-sialylated adhesion molecules on the surface of tumor cells disrupts their interaction with immune-effector cells and contributes to pathophysiological immune escape. Further, sialylated glycoproteins induce immunoregulatory cytokines and growth factors through interactions with sialic acid-binding immunoglobulin-like lectins. We describe the processes, which modulate the interaction between sialylated carrier glycoproteins and their ligands, and illustrate that sialic acids could be targets of novel therapeutic strategies for treatment of cancer and immune diseases. Full article
(This article belongs to the Special Issue Feature Paper from Journal Reviewers)
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14 pages, 2187 KB  
Article
Ginger Water Reduces Body Weight Gain and Improves Energy Expenditure in Rats
by Samy Sayed, Mohamed Ahmed, Ahmed El-Shehawi, Mohamed Alkafafy, Saqer Al-Otaibi, Hanan El-Sawy, Samy Farouk and Samir El-Shazly
Foods 2020, 9(1), 38; https://doi.org/10.3390/foods9010038 - 2 Jan 2020
Cited by 41 | Viewed by 11761
Abstract
Obesity is a serious global problem that causes predisposition to numerous serious diseases. The current study aims to investigate the effect of ginger water on body weight and energy expenditure through modulation of mRNA expression of carbohydrate and lipid metabolism. A white colored [...] Read more.
Obesity is a serious global problem that causes predisposition to numerous serious diseases. The current study aims to investigate the effect of ginger water on body weight and energy expenditure through modulation of mRNA expression of carbohydrate and lipid metabolism. A white colored liquid obtained during freeze-drying of fresh rhizomes of Zingiber officinal was collected and named ginger water. It was used to treat rats, then blood and tissue samples were collected from the liver and white adipose at the end of the experiment. The serum was prepared and used for biochemical assays, while tissue samples were used for RNA isolation and gene expression analysis via Reverse transcription polymerase chain reaction (RT-PCR). Results of High Performance Liquid Chromatography (HPLC) analysis of ginger water revealed the presence of chrysin and galangin at concentrations of 0.24 µg/mL and 0.53 µg/mL, respectively. Average body weight gain decreased significantly in groups that received ginger water. In addition, both total cholesterol and serum triacylglycerol were reduced in the groups that received ginger water. Furthermore, mRNA expression of Sterol regulatory element-binding protein 1 (SREBP-1c) in the liver and leptin in adipose tissues were downregulated, while those of adiponectin, hepatic carnitine palmitoyltransferase1 (CPT-1), acyl-coA oxidase (ACO), Glucose transporter 2 (GLUT-2), and pyruvate kinase (PK) were upregulated in ginger water-treated groups. These results clearly revealed the lowering body weight gain effect of ginger water, which most likely occurs at the transcriptional level of energy metabolizing proteins. Full article
(This article belongs to the Special Issue Nutraceuticals in Human Health)
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