Article
Microbiology
Andrew Oliver, Alexander B. Chase, Claudia Weihe, Stephanie B. Orchanian, Stefan F. Riedel, Clark L. Hendrickson, Mi Lay, Julia Massimelli Sewall, Jennifer B. H. Martiny, Katrine Whiteson
Summary: The study conducted a 2-week dietary fiber intervention, which showed that increasing fiber intake can significantly alter the composition of individual gut microbiomes, including increasing the abundance of known fiber-degrading microbes.
Article
Nutrition & Dietetics
Jacqueline Rehner, Georges P. Schmartz, Tabea Kramer, Verena Keller, Andreas Keller, Soeren L. Becker
Summary: Researchers conducted a study on the human gut microbiome of healthy volunteers following the Planetary Health diet and found a slight increase in probiotic-associated bacteria after 4 weeks.
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
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.
Article
Environmental Sciences
Thi Thuy Do, Stephen Nolan, Nicky Hayes, Vincent O'Flaherty, Catherine Burgess, Fiona Brennan, Fiona Walsh
Summary: The study compared the effects of storage, composting, and anaerobic digestion on pig slurry microbiome, resistome, and nutrient content. Each treatment method has advantages and disadvantages, with composting being the most effective at reducing risks to human health and the environment.
ENVIRONMENTAL POLLUTION
(2022)
Article
Medicine, Research & Experimental
Yaneth Citlalli Orbe-Orihuela, Elizabeth Ernestina Godoy-Lozano, Alfredo Lagunas-Martinez, Ana Cristina Castaneda-Marquez, Sofia Murga-Garrido, Cinthya Estefhany Diaz-Benitez, Adrian Ochoa-Leyva, Fernanda Cornejo-Granados, Miguel Cruz, Karel Estrada, Victor Hugo Bermudez-Morales, Alejandro Sanchez-Flores, AnaIsabel Burguete-Garcia
Summary: This study aimed to evaluate the taxonomic profile of gut microbiota using metagenomics and its association with diet-dependent childhood obesity. The results showed that children with an abundance of Holdemania spp. and high protein and complex carbohydrate consumption had lower z-BMI, waist circumference, and hip circumference. In contrast, Coprococcus catus showed a positive association with hip circumference and low intake of this dietary pattern. Additionally, the presence of Bilophila spp. and Paraprevotella xylaniphila with high saturated fat and simple carbohydrate consumption showed a positive association with z-BMI, hip circumference, and waist circumference.
ARCHIVES OF MEDICAL RESEARCH
(2022)
Article
Gastroenterology & Hepatology
Pajau Vangay, Tonya Ward, Sarah Lucas, Lalit K. Beura, Dominique Sabas, Max Abramson, Lisa Till, Susan L. Hoops, Purna Kashyap, Ryan C. Hunter, David Masopust, Dan Knights
Summary: In this study, the differential effects of human gut microbiota from the United States and rural Thailand on the murine gut mucosa and immune system were assessed. The results suggest that Western-associated human gut microbes contribute to a pro-inflammatory immune response.
Review
Microbiology
Jacob T. Nearing, Andre M. Comeau, Morgan G. I. Langille
Summary: Advances in DNA sequencing technology have improved researchers' ability to explore human microbiomes, but systemic biases introduced during the process can lead to inconsistent results. Biases begin with sample collection and persist throughout experiments, resulting in observed microbial communities that differ significantly from the true composition. efforts to reduce bias in sequence-based human microbiome studies are ongoing.
Article
Microbiology
Mary Hannah Swaney, Shelby Sandstrom, Lindsay R. Kalan
Summary: The skin microbiome plays a crucial role in maintaining skin health, and cobamide sharing may mediate dynamics within skin microbial communities.
Article
Biochemistry & Molecular Biology
So-Yun Jhang, Sung-Hyen Lee, Eun-Byeol Lee, Ji-Hye Choi, Sohyun Bang, Misun Jeong, Hwan-Hee Jang, Hyun-Ju Kim, Hae-Jeung Lee, Hyun-Cheol Jeong, Sung-Jin Lee
Summary: The study showed that Platycodon grandiflorum (PG) diets can increase the abundance of microorganisms in immunodeficient mice and are correlated with body weight, IgA, and IgM levels.
Article
Biotechnology & Applied Microbiology
Anna Cusco, Daniel Perez, Joaquim Vines, Norma Fabregas, Olga Francino
Summary: Long-read sequencing in metagenomics allows for the assembly of complete genomes from complex microbial communities, providing important biological information that is often missed by short-read sequencing. In this study, long-read metagenomics with Nanopore sequencing successfully retrieved eight high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample, including crucial ribosomal genes and tRNAs. Additionally, high-molecular-weight DNA extraction improved assembly contiguity and recovery of rRNA operons, demonstrating the significance of long reads in metagenomics research.
Article
Microbiology
Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Gabrielle Potocki-Veronese
Summary: Transport is a crucial step in the metabolism of glycosides by bacteria, which is key for microbiota function and equilibrium. However, our understanding of how bacteria utilize glycosides is limited by the lack of knowledge about transport proteins. In this study, an activity-based screening method was used to identify functional glycoside transporters from microbiomes. The results provide new insights into how glycosides are selectively metabolized by bacteria and offer a new approach to screening for glycoside-transporter specificity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Ellen E. Higginson, M. Abu Sayeed, Joana Pereira Dias, Vignesh Shetty, Mamatha Ballal, Sunil Kumar Srivastava, Ian Willis, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Summary: Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. The gut microbiome may play a role in the resistance or progression to ETEC infection. In this study, the researchers analyzed the gut microbiomes of individuals in Bangladesh infected with ETEC, both symptomatically and asymptomatically. Symptomatic patients had higher bacterial burden, were more likely to be coinfected with other pathogenic bacteria, and had a higher prevalence of antimicrobial resistance genes. The composition of the gut microbiome was different between symptomatic and asymptomatic individuals, providing insight into the impact of the gut microbiome in intestinal infections.
Article
Microbiology
Richard Wolff, William Shoemaker, Nandita Garud
Summary: The human gut microbiome exhibits substantial ecological diversity at both the species and strain levels. The majority of species maintain stable genetic diversity over time, and strain abundances can be predicted by a stochastic logistic model, suggesting dynamic stability. Additionally, strain abundances follow macroecological laws known to hold at the species level. These findings highlight the importance of strains as an ecological unit in the human gut microbiome.
Article
Biochemistry & Molecular Biology
Shaqed Carasso, Bettina Fishman, Liel Stelmach Lask, Tamar Shochat, Naama Geva-Zatorsky, Eran Tauber
Summary: Each individual's chronotype, whether an early riser or a late sleeper, has a significant impact on the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. By analyzing the gut microbiome, distinct microbial signatures associated with different chronotypes were identified, suggesting the potential for developing dietary interventions to improve the health outcomes of late chronotypes.
Article
Cardiac & Cardiovascular Systems
Ellen G. Avery, Hendrik Bartolomaeus, Ariana Rauch, Chia-Yu Chen, Gabriele N'Diaye, Ulrike Loeber, Theda U. P. Bartolomaeus, Raphaela Fritsche-Guenther, Andre F. Rodrigues, Alex Yarritu, Cheng Zhong, Lingyan Fei, Dmitry Tsvetkov, Mihail Todiras, Joon-Keun Park, Lajos Marko, Andras Maifeld, Andreas Patzak, Michael Bader, Stefan Kempa, Jennifer A. Kirwan, Sofia K. Forslund, Dominik N. Mueller, Nicola Wilck
Summary: This study investigated the impact of microbial colonization on organ damage in hypertension using germ-free and colonized mice models. The results showed that the kidney is more sensitive to microbial influence, and the colonization status is associated with circulating metabolites and inflammatory cells relevant to hypertension.
CARDIOVASCULAR RESEARCH
(2023)
Review
Cardiac & Cardiovascular Systems
Zeinab Ghorbani, Asma Kazemi, Theda U. P. Bartolomaeus, Fahimeh Martami, Morvarid Noormohammadi, Arsalan Salari, Ulrike Loeber, Heydar Ali Balou, Sofia K. Forslund, Marjan Mahdavi-Roshan
Summary: This study conducted a systematic literature search and meta-analysis to determine the effect sizes of probiotics on blood lipid parameters. The results showed that probiotic/synbiotic supplements can significantly decrease triglyceride, total cholesterol, and LDL-C levels, and increase HDL-C levels. These effects are more pronounced in individuals with hyperlipidemia, diabetes, and metabolic syndrome. However, further large and well-conducted randomized controlled trials are needed to provide more convincing evidence.
CARDIOVASCULAR RESEARCH
(2023)
Review
Medicine, General & Internal
Sofia K. Forslund
Summary: Experimental trials have shown that reducing food intake can increase lifespan and delay the onset of disease. The gut microbiota plays a role in regulating host health and imbalances in the microbiome can contribute to various diseases. Fasting, combined with dietary improvements, can reduce inflammation and improve metabolic health, with the gut microbiota mediating some of these effects.
JOURNAL OF INTERNAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Katherine M. Kennedy, Marcus C. de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Backhed, Peer Bork, Thorsten Braun, Frederic D. Bushman, Joel Dore, Willem M. de Vos, Ashlee M. Earl, Jonathan A. Eisen, Michal A. Elovitz, Stephanie C. Ganal-Vonarburg, Michael G. Ganzle, Wendy S. Garrett, Lindsay J. Hall, Mathias W. Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J. Macpherson, Ruth C. Massey, Alice Carolyn McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O'Mahony, Paul W. O'Toole, Eric G. Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M. Sloboda, Gordon C. S. Smith, Harry Sokol, Tim D. Spector, Michael G. Surette, Gerald W. Tannock, Alan W. Walker, Moran Yassour, Jens Walter
Summary: The colonization of microbial communities in the human fetus and the prenatal intrauterine environment is still controversial. Recent studies analyzing microbial populations in human fetuses indicate that the detected signals might be due to contamination during sample collection or DNA sequencing processes. The presence of live and replicating microbial populations in healthy fetal tissues contradicts fundamental concepts in immunology and clinical microbiology. This has significant implications for our understanding of human immune development and highlights the challenges in studying microbial communities in low-biomass environments.
Article
Biochemistry & Molecular Biology
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lazaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun P. Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
Summary: The InterPro database has been updated with new data content and website features, providing a more user-friendly access to protein sequence classification and functional domain identification. It has also integrated features from the retiring Pfam website and developed a card game to engage the non-scientific community. Furthermore, the database explores the benefits and challenges of using artificial intelligence for protein structure prediction.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Pharmacology & Pharmacy
Morvarid Noormohammadi, Zeinab Ghorbani, Ulrike Lober, Marjan Mahdavi-Roshan, Theda U. P. Bartolomaeus, Asma Kazemi, Nargeskhatoon Shoaibinobarian, Sofia K. Forslund
Summary: Recent studies have shown that probiotics, prebiotics, and synbiotics can affect the levels of adiponectin and leptin, although these findings are still being debated. This study conducted a systematic review and meta-analysis of randomized controlled trials to explore the impact of probiotic/synbiotic supplementation on appetite-regulating hormones and the desire to eat. The results showed that probiotic/synbiotic supplementation led to a significant decrease in leptin concentration and a slight increase in adiponectin levels, while also slightly increasing the desire to eat.
PHARMACOLOGICAL RESEARCH
(2023)
Article
Microbiology
Rebecca L. Knoll, Victor Hugo Jarquin-Diaz, Jonas Klopp, Alissa Kemper, Katja Hilbert, Barlo Hillen, Daniel Pfirrmann, Perikles Simon, Viola Baehner, Oliver Nitsche, Stephan Gehring, Lajos Marko, Sofia K. Forslund, Krystyna Poplawska
Summary: This study investigated whether regular and monitored exercise and nutritional support promotes CF microbiome health. The results showed that the respiratory and intestinal microbiome composition remained stable and highly specific to each patient during the study period, and disease-associated pathogens dominated the composition and functionality of the microbiome.
Article
Cardiac & Cardiovascular Systems
Anne-Maj Samuelsson, Theda Ulrike Patricia Bartolomaeus, Harithaa Anandakumar, Irene Thowsen, Elham Nikpey, Jianhua Han, Lajos Marko, Kenneth Finne, Olav Tenstad, Johannes Eckstein, Nikolaus Berndt, Titus Kuehne, Sarah Kedziora, Ibrahim Sultan, Trude Skogstrand, Tine Karlsen, Harri Nurmi, Sofia K. Forslund, Entela Bollano, Kari Alitalo, Dominik N. Muller, Helge Wiig
Summary: This study investigates the role of VEGF-B in cardiac proteomic and metabolic adaptation in heart failure, and finds that VEGF-B TG accelerates metabolic maladaptation, leading to structural cardiomyopathy and systolic heart failure.
CARDIOVASCULAR RESEARCH
(2023)
Article
Biochemical Research Methods
Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho
Summary: This study proposes a new semi-supervised binning method, SemiBin2, which utilizes self-supervised learning to learn feature embeddings from contigs. The results show that self-supervised learning achieves better performance than semi-supervised learning used in SemiBin1, and SemiBin2 outperforms other state-of-the-art binners. The proposed method also shows improved performance in handling long-read data.
Review
Environmental Sciences
Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, Luis Pedro Coelho, Sofia K. Forslund, Remi Gschwind, Annamari Heikinheimo, Victor Hugo Jarquin-Diaz, Ayaz Ali Khan, Uli Kluemper, Ulrike Loeber, Marmar Nekoro, Adriana D. Osinska, Svetlana Ugarcina Perovic, Tarja Pitkanen, Ernst Kristian Rodland, Etienne Ruppe, Yngvild Wasteson, Astrid Louise Wester, Rabaab Zahra
Summary: Antimicrobial resistance (AMR) poses a global threat to human and animal health, and monitoring resistant bacteria and genes is crucial. However, monitoring of AMR in the environment is lacking, hindering our understanding of how resistant microorganisms are disseminated and the human health risks. This lack of knowledge includes the "normal" background levels of environmental AMR, high-risk environments for transmission, antibiotic concentration effects, and detecting non-circulating resistance genes. We need to address these knowledge gaps before implementing large-scale AMR monitoring in the environment.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Thomas S. B. Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M. Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel R. Mende, Robert D. Finn, Michael Kuhn, Luis Pedro Coelho, Peer Bork
Summary: SPIRE is a searchable planetary-scale microbiome resource that integrates various metagenome-derived microbial data modalities. It includes a large number of metagenomic samples and newly constructed high-quality genomes, as well as functional annotation and taxonomic classification information.
NUCLEIC ACIDS RESEARCH
(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)
Article
Rheumatology
Morgan Essex, Valeria Rios Rodriguez, Judith Rademacher, Fabian Proft, Ulrike Loeber, Lajos Marko, Uwe Pleyer, Till Strowig, Jeremy Marchand, Jennifer A. Kirwan, Britta Siegmund, Sofia K. Forslund, Denis Poddubnyy
Summary: This study identified shared and disease-specific microbial associations in spondyloarthritis (SpA) and related inflammatory pathologies using 16S ribosomal RNA sequencing on stool samples.
ARTHRITIS & RHEUMATOLOGY
(2023)
Article
Neurosciences
Florence Thirion, Helene Speyer, Tue Haldor Hansen, Trine Nielsen, Yong Fan, Emmanuelle Le Chatelier, Sebastien Fromentin, Magali Berland, Florian Plaza Onate, Nicolas Pons, Nathalie Galleron, Florence Levenez, Lajos Marko, Till Birkner, Torben Jorgensen, Sofia K. Forslund, Henrik Vestergaard, Torben Hansen, Merete Nordentoft, Ole Mors, Michael E. Benros, Oluf Pedersen, Stanislav D. Ehrlich
Summary: This study found significant differences in the gut microbiota between patients with schizophrenia, healthy individuals, and individuals with metabolic syndrome. The functional potential of the gut microbiota was associated with cognitive function in patients with schizophrenia, suggesting the gut microbiota could be a target for intervention to alleviate cognitive dysfunction.
BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE
(2023)