Review
Microbiology
Sabina Leanti La Rosa, Matthew P. Ostrowski, Arturo Vera-Ponce de Leon, Lauren S. McKee, Johan Larsbrink, Vincent G. Eijsink, Elisabeth C. Lowe, Eric C. Martens, Phillip B. Pope
Summary: This review summarizes recent insights into nutrient processing in microbiomes across different gastrointestinal ecosystems and discusses the implications for microbiome reprogramming to improve host health.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Cell Biology
Belinda L. Spillings, Christopher J. Day, Albert Garcia-Minambres, Anupriya Aggarwal, Nicholas D. Condon, Thomas Haselhorst, Damian F. J. Purcell, Stuart G. Turville, Jennifer L. Stow, Michael P. Jennings, Johnson Mak
Summary: This study reveals that HIV is captured near the lymphocyte surface in a virion-glycan-dependent manner. Removing certain glycans impairs virus-cell binding and interfering with glycan interactions reduces HIV infectivity. These findings provide new insights into the interaction between HIV and host cells.
Article
Multidisciplinary Sciences
Joshua B. R. White, Augustinas Silale, Matthew Feasey, Tiaan Heunis, Yiling Zhu, Hong Zheng, Akshada Gajbhiye, Susan Firbank, Arnaud Basle, Matthias Trost, David N. Bolam, Bert van den Berg, Neil A. Ranson
Summary: This study reveals the formation of stable glycan-utilizing machines, called utilisomes, which consist of glycoside hydrolases and bacterial outer membrane proteins in Bacteroides thetaiotaomicron. The structures of these utilisomes show the mechanism and function of the interactions between their components.
Article
Chemistry, Applied
Yu-Ying Liu, Si-Dong Zhang, Jin-Jing Xiao, Wen-Zhe Feng, Dong Wei, Ya-Jing Deng, Hai-Qun Cao, Yan-Hong Shi
Summary: This study investigated the impact of gut microbiota on the bioaccessibility of triadimefon in strawberry and grape for the first time. The gut microbiota reduced the bioaccessibility of triadimefon in strawberry but not in grape, and a strain of triadimefon-degrading bacteria was isolated. The study also revealed a significant reduction in transepithelial transport of triadimefon due to the barrier effect of gut microbiota.
Article
Microbiology
Sage E. Foley, Christine Tuohy, Merran Dunford, Michael J. Grey, Heidi De Luca, Caitlin Cawley, Rose L. Szabady, Ana Maldonado-Contreras, Jean Marie Houghton, Doyle Ward, Randall J. Mrsny, Beth A. McCormick
Summary: The study finds that specific genera within the Clostridia and Bacilli classes of the intestinal microbiome are essential for inducing P-glycoprotein (P-gp) expression in the intestinal epithelium. Metabolites produced by these microbial communities, such as short-chain fatty acids and secondary bile acids, positively associate with P-gp expression and synergistically upregulate P-gp function. In patients with ulcerative colitis, reduced P-gp expression is linked to a decrease in anti-inflammatory endocannabinoids and luminal content that can induce P-gp expression, highlighting the important role of the microbiome in regulating intestinal inflammation.
Article
Food Science & Technology
Jun Wang, Yixin Qin, Jingjing Jiang, Hongyan Shan, Changyu Zhao, Songnan Li
Summary: This study investigates the effects of theaflavins (TFs) on blood glucose, blood lipid, and the gut microbiome in diabetic mice, as well as explores the underlying mechanism of TFs improvement in diabetes from the perspective of the gut microbiome. The results show that TFs intervention significantly improves hyperglycemia and hyperlipidemia in diabetic mice and affects the structure of the gut microbiome. Short-chain fatty acid changes and functional prediction analysis suggest that TFs may regulate carbohydrate and lipid metabolism through the gut microbiome.
Review
Nutrition & Dietetics
Cassandre Bedu-Ferrari, Paul Biscarrat, Philippe Langella, Claire Cherbuy
Summary: This review highlights the importance of the gut microbiota in human health and diseases, and discusses dietary strategies, particularly the use of prebiotics, to modulate microbial composition and metabolic function. It provides insights into the concept of prebiotics, their sources and breakdown mechanisms, and explores the potential of prebiotics in metabolic diseases and personalized responses.
Review
Microbiology
Sandra M. Kelly, Jose Munoz-Munoz, Douwe van Sinderen
Summary: Bifidobacterium, a genus of beneficial gut bacteria, is abundant in the microbiota of healthy infants but tends to decrease with age. Due to the negative correlation between Bifidobacterium abundance and health, there is a growing interest in maintaining or restoring their populations in the gut of individuals of all ages.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Nutrition & Dietetics
Matthew G. Pontifex, Aleena Mushtaq, Gwenaelle Le Gall, Ildefonso Rodriguez-Ramiro, Britt Anne Blokker, Mara E. M. Hoogteijling, Matthew Ricci, Michael Pellizzon, David Vauzour, Michael Muller
Summary: The addition of inulin and psyllium individually resulted in distinct changes in gut microbiota, with psyllium also leading to reductions in blood sugar and diabetes-associated metabolites. A combination diet benefitted from both inulin and psyllium related microbial changes.
Article
Pharmacology & Pharmacy
Bo Zhang, Yuzhou Wan, Xuefeng Zhou, Haojun Zhang, Hailing Zhao, Liang Ma, Xi Dong, Meihua Yan, Tingting Zhao, Ping Li
Summary: This study investigated the relationship between serum metabolites and gut microbiota in the progression of diabetic kidney disease (DKD). The results showed significant alterations in serum metabolites and the composition and function of gut microbiota in DKD. The study also identified potential metabolic and microbial targets for the treatment of DKD.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Gastroenterology & Hepatology
Mei Qi-Xiang, Fu Yang, Huang Ze-Hua, Yin Nuo-Ming, Wang Rui-Long, Xu Bin-Qiang, Fan Jun-Jie, Huang Chun-Lan, Zeng Yue
Summary: This study revealed that intestinal TLR4 exacerbates pancreatic and intestinal damage during AP, which is related to dysbiosis of gut microbiota, especially the depleted Lactobacillus. Furthermore, L. reuteri treatment can maintain intestinal homeostasis and alleviate AP through modulation of Paneth cells.
Article
Chemistry, Applied
Fen Li, Meng-Meng Wang, Qing-Hua Liu, Zhang-Wen Ma, Jun-Jiao Wang, Zi-Yi Wang, Jia-Wei Tang, Jing-Wen Lyu, Zuo-Bin Zhu, Liang Wang
Summary: This study investigates the important roles of two glycogen degradation enzymes in the structural alterations of glycogen in E. coli. The research concludes that glycogen phosphorylase plays a dominant role in glycogen structural stability control.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Applied
Bowei Zhang, Yingchuan Xu, Huan Lv, Wenwen Pang, Jin Wang, Hui Ma, Shuo Wang
Summary: This study investigated the intestinal pharmacokinetics of resveratrol in mice using HPLC-MS/MS and found that resveratrol and its metabolites were present in significant amounts in the entire intestinal tract and feces, with a peak concentration at 4 hours post-administration. The study also demonstrated the promotion of Lactobacillus reuteri growth by resveratrol-3-O-sulfate during in vitro fermentation and the up-regulation of tight junction and mucin-related proteins mRNA expressions by resveratrol-3-O-sulfate during incubation with Caco-2 cells.
Article
Plant Sciences
Yun Ren, Jianfang Zhu, Hui Zhang, Baogang Lin, Pengfei Hao, Shuijin Hua
Summary: The current study investigated the regulation of leaf carbohydrate metabolism in rapeseed by a late planting date at the reproductive stage. The results showed that leaf dry matter and chlorophyll content varied with different planting dates. The activity of carbohydrate catabolic and biosynthetic enzymes also differed among planting dates.
Review
Microbiology
Jonathon A. Briggs, Julie M. Grondin, Harry Brumer
Summary: The human gut microbiota (HGM) relies on a complex and diverse range of glycan structures from both dietary and host sources for glycan deconstruction, with the glycan utilization profile of individual taxa determined by various factors such as carbohydrate-active enzymes. Different taxa in the HGM may compete or cooperate in glycan deconstruction, and diet plays a significant role in shaping the composition of the HGM.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hao-Wei Chang, Nathan P. McNulty, Matthew C. Hibberd, David O'Donnell, Jiye Cheng, Vincent Lombard, Bernard Henrissat, Olga Ilkayeva, Michael J. Muehlbauer, Christopher B. Newgard, Michael J. Barratt, Xi Lin, Jack Odle, Jeffrey Gordon
Summary: The study found that microbiomes associated with diet restriction have specific features in amino acid metabolism, which affect ponderal growth and health. Experimental colonization of gnotobiotic mice further confirmed the impact of microbiomes on host energy metabolism and the selection of energy substrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Feng Zhang, Aurore Labourel, Mireille Haon, Minna Kemppainen, Emilie Da Silva Machado, Nicolas Brouilly, Claire Veneault-Fourrey, Annegret Kohler, Marie-Noelle Rosso, Alejandro Pardo, Bernard Henrissat, Jean-Guy Berrin, Francis Martin
Summary: This study characterizes the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A in the ectomycorrhizal fungus Laccaria bicolor and confirms its key role in symbiosis. The enzyme is involved in the formation of the Hartig net and is an important determinant for successful symbiotic colonization.
Article
Plant Sciences
Brian Looney, Shingo Miyauchi, Emmanuelle Morin, Elodie Drula, Pierre Emmanuel Courty, Annegret Kohler, Alan Kuo, Kurt LaButti, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, William Andreopoulos, Guifen He, Jenifer Johnson, Matt Nolan, Andrew Tritt, Kerrie W. Barry, Igor Grigoriev, Laszlo G. Nagy, David Hibbett, Bernard Henrissat, P. Brandon Matheny, Jesse Labbe, Francis M. Martin
Summary: In this study, the researchers identified genomic signatures of the transition to ectomycorrhizal habit within the Russulaceae family. They found that the genomes of ectomycorrhizal Russulaceae species have a loss of genes for plant cell wall-degrading enzymes, an expansion of genome size through increased transposable element content, a reduction in secondary metabolism clusters, and an association of small secreted proteins with transposable element 'nests'. Some plant cell wall-degrading enzyme genes have been retained or expanded in a species-specific manner. The genome of a saprotrophic member of Russulaceae also showed some characteristics of ectomycorrhizal genomes. Functional specialization in ectomycorrhizal decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ectomycorrhizal habit, suggesting that changes in genome architecture and gene content may be necessary for the evolutionary switch.
Article
Plant Sciences
Mario E. E. Franco, Jennifer H. Wisecaver, A. Elizabeth Arnold, Yu-Ming Ju, Jason C. Slot, Steven Ahrendt, Lillian P. Moore, Katharine E. Eastman, Kelsey Scott, Zachary Konkel, Stephen J. Mondo, Alan Kuo, Richard D. Hayes, Sajeet Haridas, Bill Andreopoulos, Robert Riley, Kurt LaButti, Jasmyn Pangilinan, Anna Lipzen, Mojgan Amirebrahimi, Juying Yan, Catherine Adam, Keykhosrow Keymanesh, Vivian Ng, Katherine Louie, Trent Northen, Elodie Drula, Bernard Henrissat, Huei-Mei Hsieh, Ken Youens-Clark, Francois Lutzoni, Jolanta Miadlikowska, Daniel C. Eastwood, Richard C. Hamelin, Igor Grigoriev, Jana M. U'Ren
Summary: Endophytic fungi in the Xylariales exhibit high bioactivity and broad host ranges, with genomic factors related to secondary metabolite gene clusters (SMGCs) influencing symbiotic interactions and ecological roles. Xylariaceae endophytes show increased metabolic diversity, gene duplications, horizontal gene transfers (HGTs), and SMGCs compared to Hypoxylaceae species, likely driven by selection pressures from host and substrate generalism. The study highlights the importance of microbial symbioses in driving fungal metabolic diversity and facilitating symbiosis with phylogenetically diverse hosts.
Article
Plant Sciences
Gang Wu, Shingo Miyauchi, Emmanuelle Morin, Alan Kuo, Elodie Drula, Torda Varga, Annegret Kohler, Bang Feng, Yang Cao, Anna Lipzen, Christopher Daum, Hope Hundley, Jasmyn Pangilinan, Jenifer Johnson, Kerrie Barry, Kurt LaButti, Vivian Ng, Steven Ahrendt, Byoungnam Min, In-Geol Choi, Hongjae Park, Jonathan M. Plett, Jon Magnuson, Joseph W. Spatafora, Laszlo G. Nagy, Bernard Henrissat, Igor V. Grigoriev, Zhu-Liang Yang, Jianping Xu, Francis M. Martin
Summary: This study compared the genomes of 21 ectomycorrhizal species within Boletales with their saprotrophic brown-rot relatives, revealing that symbiotic boletes have become functionally diverse over their evolutionary history with reduced plant cell-wall-degrading enzymes but distinct sets of enzymes. Additionally, the study showed that transposable element proliferation contributed to the higher evolutionary rate of certain genes, while the loss of secreted CAZymes was related to DNA decay rather than TE activity. These findings provide new insights into the mechanisms influencing the evolutionary diversification of symbiotic boletes.
Article
Biochemistry & Molecular Biology
Elodie Drula, Marie-Line Garron, Suzan Dogan, Vincent Lombard, Bernard Henrissat, Nicolas Terrapon
Summary: The CAZy database, freely available for browsing and download, is deeply rooted in human curation and plays a crucial role in maintaining and updating family classification, classifying new sequences, and presenting functional information. Over the past 8 years, there has been an increase in novel families and extensive annotations conducted, highlighting the significant amount of work involved in analyzing and reporting biochemical data from the literature.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Peicheng Sun, Xinxin Li, Adiphol Dilokpimol, Bernard Henrissat, Ronald P. de Vries, Mirjam A. Kabel, Miia R. Makela
Summary: This article introduces xyloglucanases (XEGs) and the GH44 family, which have been found in bacteria and fungi. Through genome analysis, GH44 enzymes from Dichomitus squalens and Pleurotus ostreatus were discovered and characterized. The study reveals that these fungal GH44 XEGs have different cleavage patterns during cellulose hydrolysis, indicating their potential for plant biomass conversion and utilization.
Article
Biochemistry & Molecular Biology
Vania Cardoso, Joana L. A. Bras, Ines F. Costa, Luis M. A. Ferreira, Luis T. Gama, Renaud Vincentelli, Bernard Henrissat, Carlos M. G. A. Fontes
Summary: In this study, a high-throughput strategy was used to successfully isolate and clone a diverse library of carbohydrate-active enzyme genes. Most of the genes showed good yield during recombinant expression, with bacteria having the highest soluble protein percentage. Gene synthesis resulted in lower soluble protein production, but the use of a green fluorescent protein tag improved solubility. It was also observed that the amino acid composition of a protein influenced its solubility in Escherichia coli.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ao Li, Mounir Benkoulouche, Simon Ladeveze, Julien Durand, Gianluca Cioci, Elisabeth Laville, Gabrielle Potocki-Veronese
Summary: This article discusses the latest developments in the strategies employed to efficiently discover glycoside phosphorylases(GPs) and make the best use of their exceptional catalytic properties for glycoside bioproduction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Marie Couturier, Melanie Touvrey-Loiodice, Nicolas Terrapon, Elodie Drula, Laurine Buon, Christine Chirat, Bernard Henrissat, William Helbert
Summary: This study focuses on the functional characterization of GH113 family enzymes, revealing their specificity towards mannans with variations in product profiles and modes of action. Four clades of the family were assigned mannanase and mannosidase activities, increasing the number of characterized GH113 members by 200% and expanding the toolbox for fine-tuning of mannooligosaccharides.
Article
Multidisciplinary Sciences
Omar Delannoy-Bruno, Chandani Desai, Juan J. Castillo, Garret Couture, Ruteja A. Barve, Vincent Lombard, Bernard Henrissat, Jiye Cheng, Nathan Han, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Carlito B. Lebrilla, Stacey Marion, Andrew C. Heath, Michael J. Barratt, Jeffrey Gordon
Summary: This study investigated the effects of snack prototypes containing fiber preparations from peas and oranges on the fecal microbiome and plasma protein levels of human participants. The findings suggest that changes in microbiomes influenced by different fiber types can impact various physiological functions in hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Andrei S. Steindorff, Kyungyong Seong, Akiko Carver, Sara Calhoun, Monika S. Fischer, Kyra Stillman, Haowen Liu, Elodie Drula, Bernard Henrissat, Hunter J. Simpson, Jonathan S. Schilling, Anna Lipzen, Guifen He, Mi Yan, Bill Andreopoulos, Jasmyn Pangilinan, Kurt LaButti, Vivian Ng, Matthew Traxler, Thomas D. Bruns, Igor Grigoriev
Summary: Wildfires have a drastic impact on the soil environment, altering soil organic matter and reducing microorganism diversity. This study sequenced six new genomes of post-fire pyrophilous fungi and found enrichment of gene families involved in stress responses and the degradation of pyrolyzed organic matter. The protein sequence lengths and G+C content in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. Comparative transcriptome analysis revealed co-expressed gene modules in charcoal and light-induced sexual development conditions, suggesting a potential connection between charcoal tolerance and fruiting body formation in one pyrophilous fungus.
Article
Microbiology
Janneke P. Ouwerkerk, Hanne L. P. Tytgat, Janneke Elzinga, Jasper Koehorst, Pieter Van den Abbeele, Bernard Henrissat, Miguel Gueimonde, Patrice D. Cani, Tom Van de Wiele, Clara Belzer, Willem M. de Vos
Summary: This study isolated six novel strains of Akkermansia muciniphila from healthy human donors and compared their genomic, proteomic, and physiological characteristics to the type strains. The isolates clustered into two distinct subspecies, with one subspecies yet to be well characterized. All strains showed unique characteristics, and it was found that single healthy individuals can carry multiple strains of A. muciniphila. The strains exhibited strong conservation in mucin degradation pathways and showed potential as beneficial microbes without significant antibiotic resistance risks.
Article
Biochemistry & Molecular Biology
Marie Sofie Moller, Souad El Bouaballati, Bernard Henrissat, Birte Svensson
Summary: The study shows that a bacterium Saccharophagus degradans produces an endo-beta-mannanase with three phylogenetically distinct family 10 CBMs. Among these, only the C-terminal CBM10-3 binds strongly to microcrystalline cellulose. The different CBMs in the enzyme play specific roles in polysaccharide binding, with CBM10-3 being crucial.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kristian E. H. Frandsen, Mireille Haon, Sacha Grisel, Bernard Henrissat, Leila Lo Leggio, Jean-Guy Berrin
Summary: Understanding the enzymatic breakdown of plant biomass is crucial for the development of nature-inspired biotechnological processes. Lytic polysaccharide monooxygenases (LPMOs) play a significant role in this process by oxidatively cleaving polysaccharides, enhancing the efficiency of glycoside hydrolases, and contributing to wood decaying in nature. These microbial enzymes have broad substrate specificities and can recognize different types of polysaccharides, providing valuable insights for sustainable biorefineries.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)