Article
Biochemistry & Molecular Biology
Nelson Frazao, Isabel Gordo
Summary: The amount of bacterial evolution in our intestines and the factors that control it are currently unknown. It is highly likely that new strains capable of coexisting for long periods of time are formed in our guts. Horizontal gene transfer mediated by temperate phages is also common in mammalian intestines. However, the roles of mutation and especially lysogeny in driving gut bacterial adaptation are still poorly understood.
Review
Microbiology
Logan C. C. Ott, Melha Mellata
Summary: This review discusses key studies on current models for bacterial conjugation in the gut, including in silico, in vitro, and in vivo models. The importance of studying plasmid transfer in the gut is emphasized, as it plays a significant role in the emergence and spread of antimicrobial resistance and virulence genes. The review highlights the need for alternate models that accurately represent the gut environment and provides directions for future research.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Anne Chevallereau, Benoit J. Pons, Stineke van Houte, Edze R. Westra
Summary: This review explores the composition and evolution of phage communities and their roles in controlling the population and evolutionary dynamics of bacterial communities. The study emphasizes the need for greater ecological realism in laboratory studies to better understand the complexity of microbial communities thriving in natural environments.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biology
Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel, Fabian Staubach
Summary: The study reveals the significant impact of microbial genomic variation on host fitness, with the thiamine biosynthesis pathway playing a role in the variation of offspring production in Drosophila. Horizontal gene transfer can enhance microbiome flexibility and potentially contribute to host adaptation.
Article
Virology
Steven G. Sutcliffe, Michael Shamash, Alexander P. Hynes, Corinne F. Maurice
Summary: The study revealed that common medications at gut-predicted concentrations can induce phages in human gut bacteria, potentially altering the human gut microbiome. Unlike antibiotics, host-targeted medications led to species-specific induction effects.
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
Multidisciplinary Sciences
Darka Labavi, Claude Loverdo, Anne-Florence Bitbol
Summary: The gut microbiota has important genetic diversity, and the spatial features of the gut can shape evolution within this environment. The fixation probability of neutral bacterial mutants in a minimal model of the gut is found to be substantially increased compared to a well-mixed system when there are strong spatial dependencies in the profiles of food and bacterial concentration. The fixation probability then becomes independent of total population size, and can be explained by introducing an active population concept.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Jeffrey J. Power, Fernanda Pinheiro, Simone Pompei, Viera Kovacova, Melih Yueksel, Isabel Rathmann, Mona Foerster, Michael Laessig, Berenike Maier
Summary: Horizontal gene transfer is an important factor in bacterial evolution, allowing for rapid evolution and increased adaptation in recipient organisms. Adaptive evolution mainly occurs in populations with increased fitness, with HGT selection having a broad genetic basis and showing different types of selection in functional gene networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Brandon H. Schlomann, Raghuveer Parthasarathy
Summary: By studying the formation of three-dimensional bacterial clusters experimentally and theoretically, it was found that the distribution of gut bacterial cluster sizes follows a power law decay, with the decay trend of larger clusters being strain-dependent.
Article
Biology
Michael Sheinman, Ksenia Arkhipova, Peter F. Arndt, Bas E. Dutilh, Rutger Hermsen, Florian Massip
Summary: Horizontal gene transfer (HGT) is a key force in microbial evolution, with long-distance HGT being frequent. The function of sequences strongly impacts their transfer rate, varying significantly between different functional categories. This study provides a comprehensive view of HGT and its role in driving bacterial evolution.
Review
Pharmacology & Pharmacy
Qingquan Chen, Tejas Dharmaraj, Pamela C. Cai, Elizabeth B. Burgener, Naomi L. Haddock, Andy J. Spakowitz, Paul L. Bollyky
Summary: Bacteriophages can have complex effects on bacterial responses to antibiotics, promoting susceptibility to antibiotics or contributing to antimicrobial resistance and tolerance. Some bacteriophages facilitate the transfer of antibiotic resistance genes between bacteria, while chronic infection by filamentous phages can promote bacterial tolerance and hinder the effectiveness of antibiotics.
Review
Microbiology
Andrey N. Shkoporov, Christopher J. Turkington, Colin Hill
Summary: Bacteriophages are obligate predators of bacteria, controlling their population and distribution. They efficiently kill bacteria and have applications in phage therapy and food preservation. However, in complex environments like the human gut, the interaction between phages and bacteria is best characterized as a mutualistic relationship, rather than a fight to the death.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Parasitology
Ying Li, Shumin Wang, Kexin Zhang, Yansong Yin, Xinyu Zhang, Qian Zhang, Xinxin Kong, Luyao Tang, Ruiling Zhang, Zhong Zhang
Summary: In this study, the effects of Serratia marcescens on the growth and development of housefly larvae were analyzed using phage technology. The results showed that S. marcescens inhibits the growth and development of housefly larvae and leads to changes in the intestinal bacterial composition. Furthermore, the use of phages to reduce the abundance of S. marcescens promoted the reproduction of beneficial bacteria. This study revealed the mechanism by which S. marcescens inhibits the growth and development of housefly larvae, and highlighted the importance of intestinal flora for larval development.
PARASITES & VECTORS
(2023)
Article
Ecology
Alan Emanuel Silva Cerqueira, Tobin J. Hammer, Nancy A. Moran, Weyder Cristiano Santana, Maria Catarina Megumi Kasuya, Cynthia Canedo da Silva
Summary: A study on Brazilian stingless bees revealed that they lack common bacterial symbionts Snodgrassella and Gilliamella found in other social corbiculate bees, instead harboring more environmental bacteria and bee-specific Starmerella yeasts. This indicates ecological shifts or acquisition of new symbionts as functional replacements in the stingless bees.
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
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
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
Respiratory System
Sara Melo-Dias, Miguel Cabral, Andreia Furtado, Sara Souto-Miranda, Maria Aurora Mendes, Joao Cravo, Catarina Rodrigues Almeida, Alda Marques, Ana Sousa
Summary: Pulmonary rehabilitation (PR) can alter the composition of oral microbiota, which is associated with the effectiveness of PR for COPD management. It increases the abundance of beneficial bacteria Prevotella melaninogenica and decreases harmful bacteria Streptococcus and Lautropia.
RESPIRATORY RESEARCH
(2023)
Correction
Respiratory System
Sara Melo-Dias, Carla Valente, Lilia Andrade, Alda Marques, Ana Sousa
RESPIRATORY RESEARCH
(2022)
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)
Article
Respiratory System
Sara Melo-Dias, Carla Valente, Lilia Andrade, Alda Marques, Ana Sousa
Summary: Individuals with COPD have been found to have a distinct oral microbiota composition, with differences in bacterial profiles compared to healthy individuals. Salivary bacteria show associations with COPD, particularly in relation to severe exacerbations, suggesting the potential use of saliva as a non-invasive specimen for future studies on respiratory diseases like COPD.
RESPIRATORY RESEARCH
(2022)