Article
Multidisciplinary Sciences
Ivan Bulygin, Vladislav Shatov, Anton Rykachevskiy, Arsenii Raiko, Alexander Bernstein, Evgeny Burnaev, Mikhail S. Gelfand
Summary: This study explores the space of the human gut microbiome using multiple published datasets and finds a lower-dimensional structure, but no distinct and stable clusters representing enterotypes.
Article
Multidisciplinary Sciences
R. Gacesa, A. Kurilshikov, A. Vich Vila, T. Sinha, M. A. Y. Klaassen, L. A. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. A. M. Dekens, V. C. Lenters, J. R. Bjork, J. C. Swarte, M. A. Swertz, B. H. Jansen, J. Gelderloos-Arends, S. Jankipersadsing, M. Hofker, R. C. H. Vermeulen, S. Sanna, H. J. M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R. K. Weersma
Summary: This study analyzed the gut microbiome of 8,208 individuals from the Netherlands and found that the microbiome is primarily shaped by the environment and cohabitation. Only about 6.6% of microbial taxa are heritable, while around 48.6% of taxa are significantly influenced by cohabitation. Additionally, the study identified numerous associations between the microbiome and health, diet, socioeconomic factors, and early-life and current exposome.
Article
Multidisciplinary Sciences
Julien Tap, Franck Lejzerowicz, Aurelie Cotillard, Matthieu Pichaud, Daniel McDonald, Se Jin Song, Rob Knight, Patrick Veiga, Muriel Derrien
Summary: By analyzing over 35,000 samples, the study identifies three major branches of the human gut microbiome and reveals differential abundances of species and metabolic functions among these branches. The study also demonstrates the importance of considering both intrinsic and extrinsic factors when studying the gut microbiome.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sally L. Bornbusch, Tara A. Clarke, Sylvia Hobilalaina, Honore Soatata Reseva, Marni LaFleur, Christine M. Drea
Summary: Microbial rewilding, a method that modulates or enhances gut microbiomes and improves host-microbe symbiosis through exposure to natural environments, has been found effective in ring-tailed lemurs. The study showed that lemurs transitioned from unnatural to naturalistic environments exhibited increased similarity with wild lemurs' gut communities, decreased proportions of antibiotic resistance genes acquired from human contact during pethood, and greater covariation with soil microbiomes from natural habitats.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Correction
Endocrinology & Metabolism
Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C. Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T. Yurkovich, Deborah M. Kado, Jane A. Cauley, Joseph Zmuda, Nancy E. Lane, Andrew T. Magis, Jennifer C. Lovejoy, Leroy Hood, Sean M. Gibbons, Eric S. Orwoll, Nathan D. Price
Summary: A correction to the paper has been published.
Article
Gastroenterology & Hepatology
Juan P. Molina Ortiz, Mark Norman Read, Dale David McClure, Andrew Holmes, Fariba Dehghani, Erin Rose Shanahan
Summary: This study used genomic reconstruction modeling to infer the metabolic attributes and nutritional requirements of 816 gut strains, focusing on vitamin exchanges at different levels of community organization. The results showed that only 91 strains could satisfy their vitamin requirements, while the rest showed various degrees of dependence on external sources. The study also revealed marked metabolic differences in human gut microbial community enterotype indicators. Additionally, pre-defined interaction modules of gut species driven by, or independent of vitamin exchanges were identified.
Review
Immunology
Eleanor M. Townsend, Lucy Kelly, George Muscatt, Joshua D. Box, Nicole Hargraves, Daniel Lilley, Eleanor Jameson
Summary: The investigation of the human microbiome has revolutionized our understanding of the impact of microorganisms on human development and health. While most research has focused on bacteria and fungi, the exploration of gut viruses is still in its early stages. Bacteriophages, which influence bacterial populations in various ecosystems, remain relatively understudied in the context of the human gut microbiome.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Milla F. Brandao Gois, Asier Fernandez-Pato, Anke Huss, Ranko Gacesa, Cisca Wijmenga, Rinse K. Weersma, Jingyuan Fu, Roel C. H. Vermeulen, Alexandra Zhernakova, Virissa C. Lenters, Alexander Kurilshikov
Summary: The increasing use of pesticides in modern agriculture has led to changes in disease burden, with exposure to these chemicals playing an increasingly important role. The human gut microbiome, responsible for biotransformation of xenobiotics, is also known to promote the biotransformation of environmental pollutants. Understanding the effects of occupational pesticide exposure on the gut microbiome can provide valuable insights into the impact of pesticide exposure on health.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Luis F. Camarillo-Guerrero, Alexandre Almeida, Guillermo Rangel-Pineros, Robert D. Finn, Trevor D. Lawley
Summary: The study reveals the diversity of viruses in the human gut and gene flow networks between different bacterial species, as well as the globally distributed viral populations and a highly prevalent phage clade reminiscent of p-crAssphage.
Review
Gastroenterology & Hepatology
Muireann Egan, Eugene Dempsey, C. Anthony Ryan, R. Paul Ross, Catherine Stanton
Summary: The human gut microbiome is a diverse ecosystem that is integral to human health. Studies have shown that the formation of endospores by specific members of the gut microbiome is linked to antibiotic resistance and the spread of resistance genes, known as the resistome. This has important implications for human health, disease, and biotechnology.
Article
Genetics & Heredity
Oliver Aasmets, Kertu Liis Krigul, Elin Org
Summary: The human gut microbiome exhibits high variability, making it challenging to develop microbiome-based applications. Enterotyping, a method of categorizing microbiome profiles, has been proposed as a solution. However, the clinical relevance of enterotypes is not well characterized. In this study, we used a large microbiome dataset to evaluate the potential of using enterotypes for disease diagnostics and susceptibility prediction. We proposed a new 5-cluster model based on our data, which provides further insights into enterotype-specific characteristics.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Daniel A. Schwartz, Josue A. Rodriguez-Ramos, Michael Shaffer, Rory M. Flynn, Rebecca A. Daly, Kelly C. Wrighton, Jay T. Lennon
Summary: Spore-forming bacteria are common in mammalian guts and affect host health and nutrition. Dormant spore production plays a crucial role in the colonization, persistence, and transmission of these bacteria. Recent studies have shown that phages can counteract dormancy-mediated defense mechanisms and alter the transitions between active and inactive states through the expression of phage-carried sporulation genes during infection. Identification of sporulation genes preferentially carried by phages that infect spore-forming bacteria can help in understanding the complex genetic network responsible for spore development.
Article
Cell Biology
Sanzhima Garmaeva, Anastasia Gulyaeva, Trishla Sinha, Andrey N. Shkoporov, Adam G. Clooney, Stephen R. Stockdale, Johanne E. Spreckels, Thomas D. S. Sutton, Lorraine A. Draper, Bas E. Dutilh, Cisca Wijmenga, Alexander Kurilshikov, Jingyuan Fu, Colin Hill, Alexandra Zhernakova
Summary: The study found that there is a high diversity of gut virome composition in healthy adults, with individual viromes stable at the family level but varying significantly at the genera and species levels. Lower initial diversity of the human gut virome leads to a more pronounced effect of dietary intervention on its composition.
Article
Ecology
Weizhong Li, Karen E. Nelson
Summary: Recent studies suggest that many species of human gut microbiota acquired in early childhood can persist into senior adulthood, with some species showing a higher likelihood of being shared between twins, indicating a potential genetic component in microbiota transmission.
Article
Biochemistry & Molecular Biology
Juan Jose Pierella Karlusich, Eric Pelletier, Lucie Zinger, Fabien Lombard, Adriana Zingone, Sebastien Colin, Josep M. Gasol, Richard G. Dorrell, Nicolas Henry, Eleonora Scalco, Silvia G. Acinas, Patrick Wincker, Colomban de Vargas, Chris Bowler
Summary: Phytoplankton, accounting for over 45% of global primary production, play a significant role in aquatic food webs and the Earth System. However, current genetic surveys using PCR amplification of rRNA genes have limitations. This study introduces a PCR-free method targeting the photosynthetic gene psbO, showing improved correlations with flow cytometry and microscopy and providing new insights into the ecology of phytoplankton communities.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Sara Deleu, Kaline Arnauts, Lowie Deprez, Kathleen Machiels, Marc Ferrante, Geert R. B. Huys, Johan M. M. Thevelein, Jeroen Raes, Severine Vermeire
Summary: Short-chain fatty acids and their bacterial producers are gaining increasing attention in inflammatory bowel diseases. Acetate, although less studied compared to butyrate, shows potential in being less toxic to epithelial cells, stimulating butyrate-producing bacteria, and having anti-inflammatory and barrier-protective properties. In a study using organoid-based monolayer cultures from ulcerative colitis patients, high acetate concentrations were found to improve epithelial resistance, decrease pro-inflammatory markers, and enhance barrier gene expression. These findings suggest that acetate may offer a promising approach for managing barrier defects and inflammation in IBD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Charlotte van de Velde, Clemence Joseph, Kenneth Simoens, Jeroen Raes, Kristel Bernaerts, Karoline Faust
Summary: Synthetic communities grown in well-controlled conditions are important for understanding community dynamics. We used an automated fermentation system to study a synthetic human gut bacterial community and found that technical variability is the main source of variability in community profiling with 16S rRNA sequencing. HPLC and flow cytometry data showed low variability, suggesting a highly deterministic system.
Article
Chemistry, Analytical
P. Vangeenderhuysen, J. Van Arnhem, B. Pomian, M. De Graeve, L. De Commer, G. Falony, J. Raes, A. Zhernakova, J. Fu, L. Y. Hemeryck, L. Vanhaecke
Summary: In recent years, feces has emerged as the ideal matrix for studying the connection between the gut microbiome and health due to its non-invasive sampling and ability to reflect an individual's lifestyle. To facilitate large cohort studies with limited availability, there is a need for high-throughput analyses that require minimal sample and resources. This study presents a workflow that combines fecal extraction and ultra high performance liquid chromatography-high resolution-quadrupole-orbitrap-mass spectrometry (UHPLC-HR-Q-Orbitrap-MS) to enable targeted and untargeted metabolome and lipidome analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Gastroenterology & Hepatology
Daan Jansen, Gwen Falony, Sara Vieira-Silva, Ceren Simsek, Tine Marcelis, Clara Caenepeel, Kathleen Machiels, Jeroen Raes, Severine Vermeire, Jelle Matthijnssens
Summary: This study found that the composition of gut viruses is associated with the pathophysiology and therapeutic success of inflammatory bowel disease (IBD), identifying two distinct gut viral configurations. These findings suggest a potential clinical relevance of gut viruses in the development and treatment of IBD.
JOURNAL OF CROHNS & COLITIS
(2023)
Article
Nutrition & Dietetics
Charlene Goosen, Sebastian Proost, Jeannine Baumgartner, Kashish Mallick, Raul Y. Tito, Shaun L. Barnabas, Mark F. Cotton, Michael B. Zimmermann, Jeroen Raes, Renee Blaauw
Summary: This study aimed to determine the associations of HIV and iron status with gut microbiota composition, gut inflammation, and gut integrity in South African school-age children. The findings showed that iron deficiency is associated with gut inflammation, and both HIV and iron status have an impact on gut microbiota.
JOURNAL OF HUMAN NUTRITION AND DIETETICS
(2023)
Article
Multidisciplinary Sciences
Jessica Coraiola Nevoa, Jose Manuel Latorre-Estivalis, Fabiano Sviatopolk-Mirsky Pais, Newmar Pinto Marliere, Gabriel da Rocha Fernandes, Marcelo Gustavo Lorenzo, Alessandra Aparecida Guarneri
Summary: This study characterized the gene expression profiles in the brain of starved R. prolixus nymphs through RNA sequencing. Neuromodulatory-related genes, such as neuropeptide precursors, neurohormones, and their receptors, as well as enzymes involved in neuropeptide and biogenic amine biosynthesis, were identified and analyzed. Other important genes, including neurotransmitter receptors, nuclear receptors, clock genes, sensory receptors, and takeouts genes, were also identified. The study suggests that further functional characterization of these highly expressed genes in starved R. prolixus brain could lead to the development of bug control tools.
Article
Nutrition & Dietetics
Ana Paula Aguiar Prudencio, Danielle Cristina Fonseca, Natasha Mendonca Machado, Juliana Tepedino Martins Alves, Priscila Sala, Gabriel R. R. Fernandes, Raquel Susana Torrinhas, Dan Linetzky Waitzberg
Summary: This study aimed to investigate the relationship between food intake, tryptophan metabolism, and gut microbiota on the glycemic control of obese T2D women after RYGB surgery. The results showed that red meat intake decreased, while indole-3-acetate and Dorea longicatena increased three months after bariatric surgery, and these changes were associated with better insulin resistance in T2D women after RYGB.
Article
Cell Biology
Valdemar Brimnes Ingemann Johansen, Daisy Faero, Karsten Buschard, Karsten Kristiansen, Flemming Pociot, Pia Kiilerich, Knud Josefsen, Martin Haupt-Jorgensen, Julie Christine Antvorskov
Summary: The incidence of type 1 diabetes is increasing and environmental factors are believed to contribute to it. A gluten-free diet has been shown to improve autoimmune diabetes in non-obese diabetic (NOD) mice and humans. This study conducted analysis of gut microbiota and pancreatic immune environment in NOD mice fed a gluten-free (GF) diet and a gluten-containing standard (STD) diet. The results revealed distinct microbiota compositions and reduced insulitis in GF mice, suggesting a protective effect of a GF diet in humans.
Article
Pediatrics
An Samaey, Jorge Francisco Vazquez-Castellanos, Clara Caenepeel, Pieter Evenepoel, Severine Vermeire, Jeroen Raes, Noel Knops
Summary: This study investigated the clinical efficacy of fecal microbiota transplantation (FMT) for recurrent Clostridium difficile infection (rCDI) in children with chronic kidney disease (CKD), as well as the effect on dysbiosis and uremic retention molecules (URM) levels. Results showed that FMT was effective in treating rCDI in CKD patients, but had minimal impact on dysbiosis and URM levels.
PEDIATRIC NEPHROLOGY
(2023)
Article
Cell Biology
Mueez U-Din, Vanessa D. de Mello, Marjo Tuomainen, Juho Raiko, Tarja Niemi, Tobias Fromme, Anton Klavus, Nadine Gautier, Kimmo Haimilahti, Marko Lehtonen, Karsten Kristiansen, John W. Newman, Kirsi H. Pietilaeinen, Jussi Pihlajamaeki, Ez-Zoubir Amri, Martin Klingenspor, Pirjo Nuutila, Eija Pirinen, Kati Hanhineva, Kirsi A. Virtanen
Summary: Cold stimulates NAD+ metabolism in humans and may be regulated by multiple tissues.
Article
Chemistry, Multidisciplinary
Chuqing Sun, Jingchao Chen, Menglu Jin, Xueyang Zhao, Yun Li, Yanqi Dong, Na Gao, Zhi Liu, Peer Bork, Xing-Ming Zhao, Wei-Hua Chen
Summary: In this study, DNA methylation patterns in 8848 high-quality phages from 104 fecal samples were analyzed using single-molecule real-time sequencing. The results show that 97.60% of gut phages exhibit methylation, and certain factors correlate with methylation densities. Phages with higher methylation densities have potential viability advantages. More than one-third of the phages possess their own DNA methyltransferases (MTases), and increased MTase copies are associated with higher genome methylation densities and specific methylation motifs. These findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems.
Article
Immunology
Ana Paula Moreira Franco-Luiz, Nubia Monteiro Goncalves Soares Fernandes, Thais Barbara de Souza Silva, Wilma Patricia de Oliveira Santos Bernardes, Mateus Rodrigues Westin, Thais Garcia Santos, Gabriel da Rocha Fernandes, Taynana Cesar Simoes, Eduardo Fernandes E. Silva, Sandra Grossi Gava, Breno Magalhaes Alves, Mariana de Carvalho Melo, Rosiane A. da Silva-Pereira, Pedro Augusto Alves, Cristina Toscano Fonseca
Summary: This study tracked the humoral immune response and reinfection in 52 healthcare workers from Brazil over a period of 450 days. The results showed that vaccines can improve the clinical outcome of COVID-19, but they cannot fully prevent infection and reinfection, especially from new variants. Additionally, IgM and IgG antibody levels were not associated with the prevention of reinfection.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Rheumatology
Maja Skov Kragsnaes, Jesus Miguens Blanco, Benjamin H. Mullish, Jose Ivan Contreras-Serrano, Jens Kjeldsen, Hans Christian Horn, Jens Kristian Pedersen, Heidi Lausten Munk, Anna Christine Nilsson, Ash Salam, Matthew R. Lewis, Elena Chekmeneva, Karsten Kristiansen, Julian R. Marchesi, Torkell Ellingsen
Summary: This study investigated the intestinal permeability and metabolomic profiles in methotrexate-treated psoriatic arthritis patients, and their relationship with clinical response. The results showed that intestinal permeability and metabolomic profiles were associated with the primary clinical trial end point.
ACR OPEN RHEUMATOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Diego Lisboa Rios, Patricia Costa Lima da Silva, Cesar Silva Santana Moura, Camila Nair Batista Couto Villanoeva, Gabriel da Rocha Fernandes, Ana Agustina Bengoa, Graciela Liliana Garrote, Analia Graciela Abraham, Jacques Robert Nicoli, Elisabeth Neumann, alvaro Cantini Nunes
Summary: This study compared the bacterial and fungal diversity of kefir beverages produced using milk or sugared water as propagation matrices. The results showed that milk and water kefir have different microbial communities, but share similar main functional processes with slight quantitative variations.
INTERNATIONAL MICROBIOLOGY
(2023)
