Review
Biochemistry & Molecular Biology
Chiao-Juno Chiu, Miao-Tzu Huang
Summary: Asthma is a major global health issue affecting over 300 million people worldwide. The main goals of asthma management are to alleviate symptoms, reduce the risk of exacerbations, and minimize long-term medicinal adverse effects. Personalized precision therapy according to individualized clinical characteristics and laboratory biomarkers is the future prospect.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Sara Mousa, Muhammad Sarfraz, Walaa K. Mousa
Summary: Trillions of diverse microbes in the gut have significant impacts on drug metabolism and can lead to variation in drug response. The gut microbiome encodes millions of unique genes, greatly expanding the traditional drug metabolic reactions that occur in the liver. Recent findings also suggest that drugs can shape the gut microbial community, making it difficult to predict drug-microbiota interactions. This review discusses the multidirectional interaction between the host, oral medications, and gut microbiota and explores the potential of personalized medicine in drug metabolism.
Review
Oncology
Martina Di Modica, Valeria Arlotta, Lucia Sfondrini, Elda Tagliabue, Tiziana Triulzi
Summary: Microbiota plays a key role in cancer by influencing various host physiological functions and affecting the efficacy of anticancer treatments. The involvement of the breast microbiota in breast cancer has been extensively studied. This review focuses on the impact of gut and breast microbiota on HER2+ breast cancer subtype and discusses the potential of defining microbial signatures associated with disease aggressiveness, treatment response, and therapy toxicity. The mechanisms of microorganism-host interactions and the possibility of microbiota editing in breast cancer prevention and treatment optimization are also explored.
FRONTIERS IN ONCOLOGY
(2022)
Review
Cell Biology
Laura Kuehl, Pauline Graichen, Nele von Daacke, Anne Mende, Malgorzata Wygrecka, Daniel P. Potaczek, Sarah Miethe, Holger Garn
Summary: The global burden of respiratory diseases is heavy and increasing, necessitating accurate models for research. Human lung organoids have become a highly transferrable three-dimensional in vitro model system, offering possibilities for precise research and understanding of lung injury and regeneration. With the use of state-of-the-art technologies and protocols, the full potential of human lung organoids can be realized in the fields of drug development, gene therapy, and organoid transplantation.
Review
Pathology
Daniel Andersson, Helena Kristiansson, Mikael Kubista, Anders Stahlberg
Summary: ctDNA analysis has become a relevant biomarker in cancer management, but biological and technical challenges need to be addressed before widespread clinical implementation. Analysis of multiple mutations combined with simultaneous assessment of other analytes may be a solution to improve sensitivity. Improved standardization and guidelines will facilitate the introduction of ctDNA analysis into clinical routine.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2021)
Review
Medicine, General & Internal
Theodoros Karampitsakos, Brenda M. Juan-Guardela, Argyris Tzouvelekis, Jose D. Herazo-Maya
Summary: Idiopathic pulmonary fibrosis (IPF) is a highly heterogeneous and lethal chronic lung disease. Precision medicine approaches have not been effectively implemented in IPF clinical practice, despite the existence of numerous diagnostic, prognostic, and theragnostic biomarker candidates.
Article
Engineering, Biomedical
I. De Falco, A. Della Cioppa, T. Koutny, U. Scafuri, E. Tarantino
Summary: This paper proposes an innovative framework for Federated Learning that tackles the issues of data privacy and communication security by using machine learning algorithms. It also provides explicit knowledge for domain experts using an Evolutionary Algorithm.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2024)
Article
Multidisciplinary Sciences
Itay Daybog, Oren Kolodny
Summary: Recent empirical studies contradict each other regarding the relationship between host fitness and the composition of its microbiome. While the microbiome is crucial for host wellbeing, the composition of the microbiome can vary significantly among individuals of the same population. Gnotobiotic individuals exhibit harmful phenotypes, but introducing arbitrary microbiota into the system often rescues these phenotypes, even when the microbiota comes from soil or phylogenetically distant host species.
NATURE COMMUNICATIONS
(2023)
Review
Gastroenterology & Hepatology
Sophie Vieujean, Edouard Louis
Summary: Inflammatory bowel diseases (IBD) consist of ulcerative colitis and Crohn's disease, with significant interindividual heterogeneity. Precision medicine could improve disease management by identifying patients likely to respond to specific drugs and tailoring interventions accordingly, reducing side effects and expenses. However, applying precision medicine in IBD is challenging due to the complex biology, clinical heterogeneity, and variabilities in temporal and therapeutic factors.
THERAPEUTIC ADVANCES IN GASTROENTEROLOGY
(2023)
Review
Health Care Sciences & Services
Angelo Michele Inchingolo, Giuseppina Malcangi, Fabio Piras, Giulia Palmieri, Vito Settanni, Lilla Riccaldo, Roberta Morolla, Silvio Buongiorno, Elisabetta de Ruvo, Alessio Danilo Inchingolo, Antonio Mancini, Francesco Inchingolo, Gianna Dipalma, Stefania Benagiano, Gianluca Martino Tartaglia, Assunta Patano
Summary: Precision medicine, utilizing highly precise technologies and big data, has enabled personalized medicine with rapid and reliable diagnoses and targeted therapies. Recent studies have focused on applying precision medicine to the study of tumors. In the field of dentistry, precision medicine in the oral microbiota can be utilized for prevention and treatment. This article evaluates the interaction between microbiota and oral cancer, as well as the use of biomarkers as risk predictors. Through a literature search and analysis, the correlation between oral diseases/cancers and changes in the microbiota is explained, highlighting the increasing utility of precision medicine in enhancing diagnosis and treatment.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Chemistry, Analytical
Zhijun Chen, Shunchang Hu, Shengfei Zhang, Qingdong Zhang, Zhen Zhang, Wuyi Ming
Summary: This study established a numerical model to analyze the main factors affecting the molding of large glass components and found the optimal solution using an optimization algorithm. The accuracy of the model was verified through experimentation, providing guidance for subsequent precision molding.
Article
Engineering, Biomedical
David Caballero, Catarina M. Abreu, Ana C. Lima, Nuno N. Neves, Rui L. Reis, Subhas C. Kundu
Summary: Traditional cancer treatment approaches are becoming obsolete, leading to more patients failing to respond to treatments. Personalized genetic profiling offers a more accurate method of treatment, but still faces issues like low local drug efficacy. Efforts are now focused on developing precision medicine-based strategies to improve cancer treatment efficiency.
Article
Plant Sciences
Hanqing Li, Lin Ling, Changkai Wen, Huaiyu Liu, Guangwei Wu, Xiaofei An, Zhijun Meng, Bingxin Yan
Summary: A structure optimization method of direct seeding device based on a multi-index orthogonal experiment was proposed in this study. The optimal structural parameters were obtained through optimization analysis, and the corresponding performance indicators were validated through tests.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Oncology
Catalina M. Perello-Reus, Teresa Rubio-Tomas, Eugenia Cisneros-Barroso, Lesly Ibarguen-Gonzalez, Juan Jose Segura-Sampedro, Rafael Morales-Soriano, Carles Barcelo
Summary: Pancreatic cancer adenocarcinoma (PDAC) is a highly lethal disease with a low survival rate. Molecular-guided therapy decisions in PDAC are currently not commonly used. PDAC cancer stem cells (PDAC-SC) rely on the microanatomical structures of the tumor microenvironment, and the altered microbiome in PDAC patients affects treatment responses and patient survival.
FRONTIERS IN ONCOLOGY
(2022)
Article
Health Care Sciences & Services
Ranjan Sinha, Dashyanng Kachru, Roshni Ray Ricchetti, Simitha Singh-Rambiritch, Karthik Marimuthu Muthukumar, Vidhya Singaravel, Carmel Irudayanathan, Chandana Reddy-Sinha, Imran Junaid, Garima Sharma, Patricia Alice Francis-Lyon
Summary: The study analyzed weight loss outcomes of 393 participants in a personalized digital care program and found that incorporating genomic data significantly improved the accuracy of weight loss models. Coaching informed by genetic risk and active engagement of participants were found to enhance intervention efficacy.
JOURNAL OF MEDICAL INTERNET RESEARCH
(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
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)
Article
Agronomy
Manisha Sanjay Sirsat, Paula Rodrigues Oblessuc, Ricardo S. Ramiro
Summary: Genomic Prediction is a powerful approach for predicting grain yield, and the choice of prediction algorithm is more important than the choice of feature selection method. Random forests and gradient boosting algorithms generate highly predictive and robust models for wheat grain yield.
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
Microbiology
Marta Lourenco, Lisa Osbelt, Virginie Passet, Francois Gravey, Daniela Megrian, Till Strowig, Carla Rodrigues, Sylvain Brisse
Summary: Klebsiella pneumoniae (Kp) is a major contributor to global antimicrobial resistance. This study presents a new strategy for isolating anti-Kp phages using capsule-deficient Kp mutants as hosts. This strategy offers promise for therapeutic development by circumventing the Kp capsule host restriction barrier.
MICROBIOLOGY SPECTRUM
(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)