Article
Immunology
Hong Ki Min, Hyun Sik Na, JooYeon Jhun, Seon-Yeong Lee, Sun Shim Choi, Go Eun Park, Jeong Su Lee, In Gyu Um, Seung Yoon Lee, Hochan Seo, Tae-Seop Shin, Yoon-Keun Kim, Jennifer Jooha Lee, Seung-Ki Kwok, Mi-La Cho, Sung-Hwan Park
Summary: In this study, we compared the gut microbiota of axSpA patients and healthy controls and found an association between specific gut microbiota and SpA pathogenesis. The results showed that axSpA patients had lower alpha-diversity and higher abundance of Bacteroides and Streptococcus, while Faecalibacterium prausnitzii, a butyrate-producing bacteria, was more abundant in healthy controls. Further experiments revealed that introducing F. prausnitzii or butyrate can reduce the polarization of CD4(+) IL-17A(+) T cells and the formation of osteoclasts, and decrease inflammation levels. Therefore, the reduced abundance of butyrate-producing microbes, especially F. prausnitzii, may be associated with axSpA pathogenesis.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Immunology
Tejpal Gill, James T. Rosenbaum
Summary: Spondyloarthritis (SpA) is a group of immune mediated inflammatory diseases strongly associated with the MHC class I molecule, HLA-B27. Although various hypotheses have been proposed to explain the HLA-B27 and disease association, the exact mechanisms underlying disease pathogenesis remain unclear. Evidence suggests that diseases related to HLA-B27 may have a microbial pathogenesis, and the influence of microbes on disease development is significant.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
James T. Rosenbaum, Michael H. Weisman, Hedley Hamilton, Cassie Shafer, Elin Aslanyan, Richard A. Howard, Kimberly Ogle, John D. Reveille, Kevin L. Winthrop, Dongseok Choi
Summary: HLA-B27 positive patients with axial spondyloarthritis (AxSpA) tend to have lower disease activity compared to HLA-B27 negative patients, as indicated by higher BASDAI scores. HLA-B27 positive patients with mild back pain are more likely to be diagnosed with AxSpA, suggesting a cognitive bias introduced by the HLA-B27 test.
SCIENTIFIC REPORTS
(2021)
Review
Immunology
Denis Wakefield, Daniel Clarke, Peter McCluskey
Summary: Over the past 5 years, there has been steady progress in understanding the pathogenesis, clinical features, and treatment of acute anterior uveitis (AU). Large gene wide association studies have confirmed AU as a polygenic disease with overlaps with other conditions. Recent research has shown the importance of the microbiome in AU, with evidence suggesting that HLA B27 may influence gut microbiome composition. Clinical investigations have confirmed the typical features of AU and the value of immunosuppressive treatments.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Gastroenterology & Hepatology
Van T. Pham, Sophie Fehlbaum, Nicole Seifert, Nathalie Richard, Maaike J. Bruins, Wilbert Sybesma, Ateequr Rehman, Robert E. Steinert
Summary: Recent research suggests that vitamins, particularly vitamin C, B2, and D, may modulate the human gut microbiome in terms of metabolic activity and bacterial composition. In a study involving human clinical trials and fermentation experiments, vitamin C was found to significantly increase microbial alpha diversity and fecal short-chain fatty acids compared to placebo, indicating a potential role of vitamins in regulating gut microbiota.
Article
Immunology
Tejpal Gill, Patrick Stauffer, Mark Asquith, Ted Laderas, Tammy M. Martin, Sean Davin, Matthew Schleisman, Claire Ramirez, Kimberly Ogle, Ingrid Lindquist, Justine Nguyen, Stephen R. Planck, Carley Shaut, Sarah Diamond, James T. Rosenbaum, Lisa Karstens
Summary: This study investigated the altered immunoglobulin A (IgA) response in the gut and oral microbial communities of patients with axial spondyloarthritis (axSpA). The results showed that axSpA patients had distinct populations of immunoreactive microbes in their fecal and salivary microbiomes. Predictive metagenomic analysis revealed perturbation of metabolites and metabolic pathways in axSpA patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Barbara Olendzki, Vanni Bucci, Caitlin Cawley, Rene Maserati, Margaret McManus, Effie Olednzki, Camilla Madziar, David Chiang, Doyle Ward, Randall Pellish, Christine Foley, Shakti Bhattarai, Beth A. McCormick, Ana Maldonado-Contreras
Summary: This study aims to investigate the impact of specific foods on the intestinal microbiome in patients with IBD and explore the interactions between diet and immunity to provide personalized nutrition guidance for IBD patients with dysbiosis-related conditions.
Article
Ophthalmology
Douglas A. Jabs, Nisha R. Acharya, Soon-Phaik Chee, Debra Goldstein, Peter McCluskey, Philip Murray, Neal Oden, Alan G. Palestine, James T. Rosenbaum, Jennifer E. Thorne, Brett E. Trusko
Summary: This study aimed to establish classification criteria for spondyloarthritis/HLA-B27-associated anterior uveitis using machine learning, achieving high accuracy in both training and validation sets. Key criteria for this condition were identified, with a low misclassification rate, indicating their potential utility in clinical and translational research.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2021)
Review
Nutrition & Dietetics
Eleuterio A. Sanchez Romero, Erika Melendez Oliva, Jose Luis Alonso Perez, Sebastian Martin Perez, Silvia Turroni, Lorenzo Marchese, Jorge Hugo Villafane
Summary: This study aimed to review the association between gut microbiome and pain in OA patients and found only three out of 2084 studies supported a relationship, but the results were not conclusive. It also highlighted the lack of high-quality studies and significant technique disparities, making it impossible to draw firm conclusions on the topic.
Article
Multidisciplinary Sciences
Annelore Beterams, Marta Calatayud Arroyo, Kim De Paepe, Ann-Sophie De Craemer, Dirk Elewaut, Koen Venken, Tom Van de Wiele
Summary: Spondyloarthritis is a chronic inflammatory disease that primarily affects joints and non-joint sites. This study explores the differential impact of gut microbiota from healthy individuals and spondyloarthritis patients on host cell response. The results show that there are differences in the composition of gut microbiota and host cell response between healthy individuals and spondyloarthritis patients.
SCIENTIFIC REPORTS
(2022)
Article
Neurosciences
Min Hou, Gaolian Xu, Maosheng Ran, Wei Luo, Hui Wang
Summary: This study analyzed the gut microbiota composition and risk genetic variants in Alzheimer's disease (AD) patients and healthy controls, revealing a correlation between the APOE ε4 allele and AD development, as well as a positive association with certain pathogens. Targeting the microbiota might be an effective therapeutic strategy for AD patients susceptible to the APOE ε4 allele, but further investigation is needed.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Nutrition & Dietetics
Priyanka Sharma, Guojun Wu, Deeptha Kumaraswamy, Natalie Burchat, Hong Ye, Yongjia Gong, Liping Zhao, Yan Y. Lam, Harini Sampath
Summary: DHF supplementation in female mice significantly reduces fat mass, hepatic lipid accumulation, and adipose tissue inflammation, while in male mice, it does not provide protection against adiposity and may worsen hepatic lipid accumulation and adipose tissue inflammation. The effects of DHF on the female gut microbiome precede changes in body weight and play a crucial role in mediating the sexually dimorphic effects of DHF on body weight.
Review
Gastroenterology & Hepatology
Blaine Caslin, Kailey Mohler, Shreya Thiagarajan, Esther Melamed
Summary: Alcohol may have complex effects on autoimmune diseases, with potential pro-inflammatory and anti-inflammatory properties. These effects may be related to factors such as the dose, duration, type, cultural background, and sex of alcohol consumption.
Article
Immunology
Melissa N. van Tok, Mohamed Mandour, Joseph Wahle, Mark E. Labadia, Marleen G. H. van de Sande, Gerald Nabozny, Dominique L. Baeten, Leonie M. van Duivenvoorde
Summary: Although RORC inhibitor treatment significantly suppresses the IL-17 axis, it accelerates and aggravates experimental SpA in the HLA-B27 tg rat model.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Bassam Abomoelak, Veronica Pemberton, Chirajyoti Deb, Stephani Campion, Michelle Vinson, Jennifer Mauck, Joseph Manipadam, Sailendharan Sudakaran, Samit Patel, Miguel Saps, Hesham A. El Enshasy, Theodoros Varzakas, Devendra Mehta
Summary: This prospective longitudinal study revealed distinct differences in gut microbiome between pediatric patients with functional abdominal pain disorders (FAPDs) and healthy controls, with variations observed not only in bacterial populations but also in diversity levels. The severity of symptoms in patients was found to be correlated with the gut microbiome, highlighting a potential relationship between the two. Additionally, the Faecalibacterium/Bacteroides ratio may serve as a promising diagnostic biomarker for FAPDs.
Article
Gastroenterology & Hepatology
Eugeni Belda, Lise Voland, Valentina Tremaroli, Gwen Falony, Solia Adriouch, Karen E. Assmann, Edi Prifiti, Judith Aron-Wisnewsky, Jean Debedat, Tiphaine Le Roy, Trine Nielsen, Chloe Amouyal, Sebastien Andre, Fabrizio Andreelli, Matthias Blueher, Rima Chakaroun, Julien Chilloux, Luis Pedro Coelho, Maria Carlota Dao, Promi Das, Soraya Fellahi, Sofia Forslund, Nathalie Galleron, Tue H. Hansen, Bridget Holmes, Boyang Ji, Helle Krogh Pedersen, Phuong Le, Emmanuelle Le Chatelier, Christian Lewinter, Louise Manneras-Holm, Florian Marquet, Antonis Myridakis, Veronique Pelloux, Nicolas Pons, Benoit Quinquis, Christine Rouault, Hugo Roume, Joe-Elie Salem, Nataliya Sokolovska, Nadja B. Sondertoft, Sothea Touch, Sara Vieira-Silva, Pilar Galan, Jens Holst, Jens Peter Gotze, Lars Kober, Henrik Vestergaard, Torben Hansen, Serge Hercberg, Jean-Michel Oppert, Jens Nielsen, Ivica Letunic, Marc-Emmanuel Dumas, Michael Stumvoll, Oluf Borbye Pedersen, Peer Bork, Stanislav Dusko Ehrlich, Jean-Daniel Zucker, Fredrik Baeckhed, Jeroen Raes, Karine Clement
Summary: This study investigated the functional composition of the gut microbiome in healthy individuals, as well as those with severe obesity and type 2 diabetes. The results revealed a deficiency in bacterial biotin producers and transporters in severe obesity, which was associated with metabolic and inflammatory phenotypes. However, strategies involving biotin and prebiotic supplementation, as well as bariatric surgery, were found to improve the gut microbiome diversity and increase bacterial biotin production, leading to better metabolic outcomes.
Article
Cell Biology
Celine Henry, Ariane Bassignani, Magali Berland, Olivier Langella, Harry Sokol, Catherine Juste
Summary: Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis, such as in the case of intestinal bowel diseases (IBDs). By analyzing gut metaproteomes, the study found differences in the microbial taxonomy and functionality among different IBD phenotypes, providing a promising additional diagnostic tool for IBDs.
Article
Multidisciplinary Sciences
Sandra Plancade, Magali Berland, Melisande Blein-Nicolas, Olivier Langella, Ariane Bassignani, Catherine Juste
Summary: A univariate selection method was proposed to handle missing values in metaproteomics data, which combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. The method showed good performance in comparison to imputation-based methods, especially in simulated scenarios.
Article
Multidisciplinary Sciences
Nathalie Coutry, Julie Nguyen, Salima Soualhi, Francois Gerbe, Victoria Meslier, Valerie Dardalhon, Mathieu Almeida, Benoit Quinquis, Florence Thirion, Fabien Herbert, Imene Gasmi, Ali Lamrani, Alicia Giordano, Pierre Cesses, Laure Garnier, Steeve Thirard, Denis Greuet, Chantal Cazevieille, Florence Bernex, Christelle Bressuire, Douglas Winton, Ichiro Matsumoto, Herve M. Naomi And, Naomi Taylor, Philippe Jay
Summary: Imbalance of gut microbiota is associated with pathological conditions. We propose a three-step mechanism for dysbiosis initiation, involving Paneth cell dysfunction, activation of epithelial tuft cells, and chronic inflammation. Paneth cells play an essential role in maintaining a balanced microbiota and preventing dysbiosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Lucie Etienne-Mesmin, Victoria Meslier, Ophelie Uriot, Elora Fournier, Charlotte Deschamps, Sylvain Denis, Aymeric David, Sarah Jegou, Christian Morabito, Benoit Quinquis, Florence Thirion, Florian Plaza Onate, Emmanuelle Le Chatelier, S. Dusko Ehrlich, Stephanie Blanquet-Diot, Mathieu Almeida
Summary: Recent advances in human microbiome characterization have discovered significant oral microbial detection in stools of dysbiotic patients. In this study, a new model of oral-to-gut invasion was proposed and demonstrated using an in vitro colon model, salivary enrichment protocol, and whole-metagenome shotgun sequencing. The study revealed the preference of oral microorganisms for the mucosal microenvironment and suggested potential oral-to-intestinal mucosal competitions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Petros Andrikopoulos, Judith Aron-Wisnewsky, Rima Chakaroun, Antonis Myridakis, Sofia K. Forslund, Trine Nielsen, Solia Adriouch, Bridget Holmes, Julien Chilloux, Sara Vieira-Silva, Gwen Falony, Joe-Elie Salem, Fabrizio Andreelli, Eugeni Belda, Julius Kieswich, Kanta Chechi, Francesc Puig-Castellvi, Mickael Chevalier, Emmanuelle Le Chatelier, Michael T. Olanipekun, Lesley Hoyles, Renato Alves, Gerard Helft, Richard Isnard, Lars Kober, Luis Pedro Coelho, Christine Rouault, Dominique Gauguier, Jens Peter Gotze, Edi Prifti, Philippe Froguel, Jean-Daniel Zucker, Fredrik Backhed, Henrik Vestergaard, Torben Hansen, Jean-Michel Oppert, Matthias Bluher, Jens Nielsen, Jeroen Raes, Peer Bork, Muhammad M. Yaqoob, Michael Stumvoll, Oluf Pedersen, S. Dusko Ehrlich, Karine Clement, Marc-Emmanuel Dumas
Summary: The study reveals that kidney function is the main determinant of circulating TMAO levels, while microbiota composition and diet play minor but significant roles. Mediation analysis suggests a causal relationship between TMAO and kidney function, which is supported by preclinical models. The study also finds that anti-diabetic drugs with reno-protective properties can lower TMAO levels.
NATURE COMMUNICATIONS
(2023)
Review
Microbiology
Georgios Papoutsoglou, Sonia Tarazona, Marta B. Lopes, Thomas Klammsteiner, Eliana Ibrahimi, Julia Eckenberger, Pierfrancesco Novielli, Alberto Tonda, Andrea Simeon, Rajesh Shigdel, Stephane Bereux, Giacomo Vitali, Sabina Tangaro, Leo Lahti, Andriy Temko, Marcus J. Claesson, Magali Berland
Summary: Predictive analysis of microbiome data within a machine learning workflow presents challenges in preprocessing, feature selection, and model interpretation. This study offers recommendations on algorithm selection and pipeline creation based on a multi-cohort dataset of colorectal cancer patients. It is found that compositional transformations and filtering methods do not always improve predictive performance, but multivariate feature selection algorithms reduce classification errors. Linear modeling combined with visualization techniques can yield interpretable results and provide biological insights.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Domenica D'Elia, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, Marta B. Lopes, Eliana Ibrahimi, Aleksandra Gruca, Alina Nechyporenko, Marcus Frohme, Thomas Klammsteiner, Enrique Carrillo-de Santa Pau, Laura Judith Marcos-Zambrano, Karel Hron, Gianvito Pio, Andrea Simeon, Ramona Suharoschi, Isabel Moreno-Indias, Andriy Temko, Miroslava Nedyalkova, Elena-Simona Apostol, Ciprian-Octavian Truica, Rajesh Shigdel, Jasminka Hasic Telalovic, Erik Bongcam-Rudloff, Piotr Przymus, Naida Babic Jordamovic, Laurent Falquet, Sonia Tarazona, Alexia Sampri, Gaetano Isola, David Perez-Serrano, Vladimir Trajkovik, Lubos Klucar, Tatjana Loncar-Turukalo, Aki S. Havulinna, Christian Jansen, Randi J. Bertelsen, Marcus Joakim Claesson
Summary: The rapid development of machine learning techniques has opened up new applications in the field of microbiome research, improving healthcare practices in the era of precision medicine. ML4Microbiome is a European network that aims to promote collaboration between microbiome researchers and ML experts to optimize and standardize ML approaches for microbiome analysis.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Victoria Meslier, Elisa Menozzi, Aymeric David, Christian Morabito, Sara Lucas Del Pozo, Alexandre Famechon, Janet North, Benoit Quinquis, Sofia Koletsi, Jane Macnaughtan, Roxana Mezabrovschi, S. Dusko Ehrlich, Anthony H. V. Schapira, Mathieu Almeida
Summary: Recent attention has highlighted the importance of oral microbiota in human health and disease, especially in Parkinson's disease. It has been found that a semi-automated DNA extraction protocol can improve sample processing efficiency without compromising the structure of the oral microbiome.
Article
Cell Biology
Qian Xu, Chunyan Wu, Qi Zhu, Renyuan Gao, Jianquan Lu, Mireia Valles-Colomer, Jian Zhu, Fang Yin, Linsheng Huang, Lulu Ding, Xiaohui Zhang, Yonghui Zhang, Xiao Xiong, Miaomiao Bi, Xiang Chen, Yefei Zhu, Lin Liu, Yongqiang Liu, Yongshen Chen, Jian Fan, Yan Sun, Jun Wang, Zhan Cao, Chunsun Fan, S. Dusko Ehrlich, Nicola Segata, Nan Qin, Huanlong Qin
Summary: A comparison of the gut microbiome and blood metabolome between long-lived individuals and their children reveals extensive remodeling in advanced age and a generational divergence in correlations with socioeconomic factors. Genetic associations with metagenomic and metabolomic features are largely generation-specific, but cross-generational associations are found for plasma metabolic quantitative traits.
