Review
Immunology
Damian Muszynski, Anna Kudra, Bartosz Kamil Sobocki, Marcin Folwarski, Ermanno Vitale, Veronica Filetti, Wojciech Dudzic, Karolina Kazmierczak-Siedlecka, Karol Polom
Summary: There is an urgent need to find new screening methods for the early detection of esophageal cancer, as this can lead to better clinical outcomes. The dysbiosis of the esophageal microbiome, as well as the oral microbiome, has been found to be associated with the development of esophageal cancer. Therefore, studying the changes in the oral microbiome can help identify markers for early detection of this cancer.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Yutao Chen, Hongchao Wang, Wenwei Lu, Tong Wu, Weiwei Yuan, Jinlin Zhu, Yuan Kun Lee, Jianxin Zhao, Hao Zhang, Wei Chen
Summary: In this study, a model was developed to predict the age of the host using gut microbiome metagenomics data. The model considered the influence of geographical factors and incorporated multiple omics data to improve accuracy. The study also identified potential biomarkers associated with the aging process, providing insights into the mechanisms of aging and potential interventions.
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
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
Daniel Hakim, Stephen Wandro, Karsten Zengler, Livia S. Zaramela, Brent Nowinski, Austin Swafford, Qiyun Zhu, Se Jin Song, Antonio Gonzalez, Daniel McDonald, Rob Knight
Summary: Assigning taxonomy in microbiome studies is challenging due to the ambiguity of reads overlapping multiple reference genomes. The introduction of genome cover as a metric helps distinguish artifacts from true contaminants. Saturated genome cover is essential for accurate interpretation, especially for low abundance bacteria, and the Zebra filter provides a method to compute and threshold genome cover for reproducible results.
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
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
Zhanshan (Sam) Ma
Summary: Analyzing 4,903 microbiome samples from 274 animal species and including 1,787 human gut microbiome samples, the study found a turning point in microbial neutrality levels from animals to humans, attributing it to human activities and social interactions.
Review
Biochemistry & Molecular Biology
Francesca De Filippis, Alessia Esposito, Danilo Ercolini
Summary: Currently available probiotics are limited in microbial species, but recent research suggests that the gut microbiome holds potential for beneficial microbes. Researchers are focusing on identifying and testing new gut-origin microbial strains for the development of next-generation probiotics. While some of these strains show promise for preventing and treating chronic diseases, human studies are lacking and regulatory approval is rare. Furthermore, challenges remain in cultivation and storage methods for oxygen-sensitive bacteria before wide market application.
CELLULAR AND MOLECULAR LIFE SCIENCES
(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
Microbiology
Pranvera Hiseni, Knut Rudi, Robert C. Wilson, Finn Terje Hegge, Lars Snipen
Summary: The study aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, including both MAGs and RefSeq genomes, to be used as a reference database. By screening over 5,700 healthy human gut metagenomes, a pool of over 381,000 genomes was obtained and clustered to form the HumGut collection, comprising 30,691 cluster representatives, demonstrating superior performance in metagenomic reads classification.
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
Biotechnology & Applied Microbiology
Evan Mann, Shahrokh Shekarriz, Michael G. Surette
Summary: The intestinal lining is protected by a mucous barrier primarily composed of complex carbohydrates. Gut microbes use a variety of glycoside hydrolases to break down mucosal sugars, facilitating host colonization, but excessive breakdown may lead to barrier erosion, pathogen invasion, and inflammation. Sialidases from the microbiome, specifically the GH156 family, play a crucial role in human microbiomes, with potential therapeutic applications in cancer therapy. However, the full extent of GH156 sialidases and their functions in the human gut environment are still being explored.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Editorial Material
Microbiology
Evelien M. Adriaenssens
Summary: The importance of bacteriophages has been increasingly recognized in the past 20 years, with research showing their significance in various environments globally. Genomic diversity surpasses morphological diversity, and the lack of a complete taxonomic framework results in the loss of crucial information.
Editorial Material
Microbiology
Jan Claesen, J. Mark Brown
Summary: This study comprehensively cataloged pathways involved in trimethylamine metabolism and identified key bacterial players in the process. It also discovered new TMA-reducing genera that have potential for probiotic strategies or targeted microbiome interventions.
Article
Biochemistry & Molecular Biology
Roberto Balbontin, Nelson Frazao, Isabel Gordo
Summary: The study reveals that the fitness cost of antibiotic resistance mutations in Escherichia coil is strongly correlated with DNA breaks, which are generated via transcription-translation uncoupling and increased formation of RNA-DNA hybrids. Targeting RNase HI enzyme can further increase DNA breaks and the cost of resistance. This research suggests a specific strategy to eliminate resistant bacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Massimo Amicone, Isabel Gordo
Summary: The study reveals that more intense clonal interference in large populations can promote diversification in eco-evolution dynamics, while the accumulation of deleterious and compensatory mutations in smaller populations may further drive the diversification process and initiate speciation.
Article
Microbiology
Catarina Pinto, Rita Melo-Miranda, Isabel Gordo, Ana Sousa
Summary: The lac operon is a well-known gene regulatory circuit in bacteria, providing a competitive advantage in the mouse gut by as much as 11%, contingent on diet and other gut microbiota. Despite lactose being absent in most mammals during adulthood, the selective pressure for maintaining the lac operon may be weak, explaining the polymorphism observed in E. coli.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tanja Dapa, Ricardo Serotte Ramiro, Miguel Filipe Pedro, Isabel Gordo, Karina Bivar Xavier
Summary: Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet can cause imbalances in the gut microbiota, leading to various pathological conditions. This study investigated the mutations in Bacteroides thetaiotaomicron in the gut under different dietary regimens and found that periodic dietary changes caused fluctuations in mutation frequency, accompanied by metabolic shifts.
CELL HOST & MICROBE
(2022)
Article
Ecology
Paulo Durao, Massimo Amicone, Lilia Perfeito, Isabel Gordo
Summary: In this study, genotypic and phenotypic characteristics of laboratory and natural strains of the yeast Schizosaccharomyces pombe were described. It was found that competitive fitness with a focal strain was a better predictor of long-term community composition compared to maximum growth rate. Additionally, maladaptation to the abiotic environment was observed in communities with more than three members by the end of the experiment.
ECOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Dragan Stajic, Claudia Bank, Isabel Gordo
Summary: Epigenetic regulation of gene expression allows for the emergence of distinct phenotypic states within the clonal population, and these states can switch in a stochastic manner between generations. This study shows that under fluctuating environmental conditions, rapid epigenetic switching provides an advantage, while genetic mutations are favored in stable environments.
GENOME BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Ecology
Isabel Gordo
Summary: The rate of fixation of different antibiotic-resistance mutation types demonstrates a trade-off influenced by population size.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Debanjan Mukherjee, Angelo Ferreira Chora, Jean-Christophe Lone, Ricardo S. Ramiro, Birte Blankenhaus, Karine Serre, Mario Ramirez, Isabel Gordo, Marc Veldhoen, Patrick Varga-Weisz, Maria M. Mota
Summary: This study reveals that the microbiota colonizing the lung can promote respiratory distress syndrome and mortality during malaria infections. Parasite sequestration in the lung results in sustained immune activation and production of anti-inflammatory cytokine compromises microbial control, leading to severe lung disease. Clearance of bacteria prevents MA-ARDS-associated lethality. Hence, the balance between the host's anti-inflammatory response and microbial control should be considered when intervening against respiratory complications.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
N. Frazao, A. Konrad, M. Amicone, E. Seixas, D. Guleresi, M. Laessig, I Gordo
Summary: By monitoring evolution for more than six thousand generations in the mouse gut, the authors show that a colonizing bacterial strain evolves through two modes: one involving metabolic mutations and the other involving the domestication of bacteriophages. The study demonstrates the importance of the microbiota diversity and the presence of related strains in the colonization success of Escherichia coli. The research also highlights the rapid formation of ecotypes and phage domestication in the mammalian gut.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Jorge Moura de Sousa, Marta Lourenco, Isabel Gordo
Summary: Horizontal gene transfer is a crucial driver of bacterial diversity and the rapid spread of antibiotic resistance in host-associated microbiomes. Recent studies have greatly enhanced our understanding of horizontal gene transfer mechanisms, the ecological complexities of bacterial interactions and mobile elements, and the impact of host physiology on genetic exchanges. Detecting and quantifying genetic exchanges in vivo pose fundamental challenges, but novel computational approaches and theoretical models combined with experimental methods are helping to overcome these challenges. Integration of these approaches with studies on multiple strains and transfer elements in both in vivo and controlled host-associated environments is essential.
CELL HOST & MICROBE
(2023)
Review
Microbiology
Hugo C. Barreto, Isabel Gordo
Summary: A large number of microorganisms continuously divide in the guts of animals and humans, allowing for real-time observation of microbial evolution. Recent studies have revealed that natural selection shapes within-host evolution in the intestines of mice and humans, with the gut microbiota being highly dynamic and influenced by species diversity. Genetic and bioinformatics tools can help quantify the selection strength on mutations and transfer events in gut ecosystems, providing insights into the drivers and functional consequences of gut evolution. Understanding the rules of intrahost microbiota evolution is crucial for the development of effective microbiota therapies.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biology
Ana-Hermina Ghenu, Andre Amado, Isabel Gordo, Claudia Bank
Summary: Predicting mutational effects is crucial for antibiotic resistance control, but it becomes difficult due to G x E, G x G, or G x G x E interactions. This study quantified G x G x E effects in Escherichia coli and assessed the predictability of fitness landscapes across different environments. The results showed the dominance of ABR genotypes over gene knock-outs in the presence of antibiotics, indicating the predictability of evolution in adverse environments.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nelson Frazao, Isabel Gordo
Summary: Social networks can shape the species composition of the gut microbiome by influencing the ecology of gut bacteria. In an experimental evolution study in mice, it was found that there is a transmission rate of 7% (& PLUSMN;3% 2SE) of E. coli cells per day between hosts living in the same household. The results also showed that hosts with similar diets and habits are expected to have similar microbiome species compositions and evolutionary dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Medicine, Research & Experimental
Vitor Borges, Joana Isidro, Nidia Sequeira Trovao, Silvia Duarte, Helena Cortes-Martins, Hugo Martiniano, Isabel Gordo, Ricardo Leite, Luis Vieira, Raquel Guiomar, Joao Paulo Gomes
Summary: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented in collaboration with over 50 laboratories distributed nationwide. The study detected at least 277 independent introductions of SARS-CoV-2, mostly from European countries, highlighting the importance of early measures in minimizing the spread of the virus.
COMMUNICATIONS MEDICINE
(2022)
Article
Evolutionary Biology
Massimo Amicone, Vitor Borges, Maria Joao Alves, Joana Isidro, Libia Ze-Ze, Silvia Duarte, Luis Vieira, Raquel Guiomar, Joao Paulo Gomes, Isabel Gordo
Summary: By conducting experimental evolution with two strains of SARS-CoV-2 in Vero cells, researchers estimated a high rate of mutation accumulation, particularly in the strain carrying the D614G mutation.
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2022)