Article
Biochemistry & Molecular Biology
Yann X. C. Bourgeois, Ben H. Warren
Summary: The continuous improvement of high-throughput sequencing techniques has enabled the production of whole genome data in various species, which in turn provides better tools for integrating selection into historical frameworks. However, the plethora of analytical tools may confuse users and hinder the dissemination of the latest methods.
Article
Plant Sciences
Christina Straub, Elena Colombi, Honour C. McCann
Summary: Population genomics plays a crucial role in reshaping our understanding of pathogen biology and evolution, especially in the field of plant pathology. Through this discipline, we can address key issues such as pathogen origins, transmission pathways, host specificity, virulence, and adaptation to changing agricultural practices.
Article
Parasitology
Jairo Alfonso Mendoza-Roldan, Giovanni Benelli, Marcos Antonio Bezerra-Santos, Viet-Linh Nguyen, Giuseppe Conte, Roberta Iatta, Tommaso Furlanello, Domenico Otranto
Summary: This study assessed the prevalence and distribution of tick-borne pathogens in clinically suspect dogs from three macro areas in Italy over a 15-year period. The results showed high seroprevalence and wide distribution of the four key pathogens, advocating for integrative control strategies for their prevention.
PARASITES & VECTORS
(2021)
Article
Multidisciplinary Sciences
Van Hai Khong, Philippe Carmona, Sylvain Gandon
Summary: Seasonality can have unpredictable effects on the persistence of vector-borne diseases, as it varies across different stages of the pathogen's life cycle. This study uses a general disease model to analyze the impact of periodic fluctuations on the basic reproduction ratio of the pathogen. The analysis reveals that seasonal variations in vector density or biting rate can either increase or decrease pathogen persistence, depending on the covariance between key compartments of the epidemiological model.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Agriculture, Dairy & Animal Science
Ingo Schaefer, Axel Peukert, Katharina Kerner, Elisabeth Mueller
Summary: Bacterial, protozoal, and viral vector-borne pathogens (VBPs) can cause infections in cats. There is little information on feline VBP prevalence in Germany. Stray cats are frequently exposed to vectors but receive no veterinary care. The aim of this study was to determine the prevalence of selected VBPs in stray cats. Overall, 11/50 (22%) and 32/50 (64%) cats tested positive for at least one VBP by direct and indirect detection methods, respectively.
Article
Evolutionary Biology
Parul Johri, Adam Eyre-Walker, Ryan N. Gutenkunst, Kirk E. Lohmueller, Jeffrey D. Jensen
Summary: This article discusses the challenges of disentangling the effects of natural selection and population history on genome-wide variation in population genetics. It highlights the theoretical and computational challenges that still need to be addressed, as well as the difficulties in dealing with model complexity and violations, and offers thoughts on potentially fruitful next steps.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Food Science & Technology
Xiayu Liu, Guangyu Liu, Yansha Wu, Xinxin Pang, Yajing Wu, Qinshu, Jianrui Niu, Qihe Chen, Xinglin Zhang
Summary: This article summarizes the common types and hazards of food-borne pathogens, the development of Tn-seq technology, and its applications in studying the physiology, pathogenesis, and environmental survival of food-borne pathogens.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Anastasia Diakou, Dimitra Sofroniou, Barbara Paoletti, Androniki Tamvakis, Stanislav Kolencik, Dimitris Dimzas, Simone Morelli, Marika Grillini, Donato Traversa
Summary: Ticks and fleas in dogs and cats from Cyprus were investigated in this study, and vector-borne pathogens were detected in these ectoparasites. The results emphasize the importance of systematic ectoparasite control in dogs and cats.
Review
Parasitology
Eric P. Caragata, Heverton L. C. Dutra, Pedro H. F. Sucupira, Alvaro G. A. Ferreira, Luciano A. Moreira
Summary: The review discusses the strategy of controlling arbovirus transmission by exploiting the Wolbachia-mosquito relationship, which has led to significant decreases in dengue virus incidence through releasing Wolbachia-infected mosquitoes. It also mentions that external factors can modulate Wolbachia density and transmission.
TRENDS IN PARASITOLOGY
(2021)
Article
Microbiology
Isabella Gruenberger, Amelie-Victoria Liebich, Temitayo Olabisi Ajibade, Oluwasola Olaiya Obebe, Nkiruka Fortunate Ogbonna, Licha N. N. Wortha, Maria S. S. Unterkoefler, Hans-Peter Fuehrer, Adekunle Bamidele Ayinmode
Summary: This study investigated the blood samples of 150 owned guard dogs in the southwest of Nigeria and found that 12% of samples tested positive for at least one pathogen. The prevalence of vector-borne pathogens in these dogs was lower than previous studies, possibly due to regular monitoring and treatment at veterinary clinics.
Review
Genetics & Heredity
Manas Joshi, Adamandia Kapopoulou, Stefan Laurent
Summary: The study highlights the significant role of genetic variation within cis-regulatory elements (CREs) in influencing gene expression, phenotypic changes, and potentially speciation. Recent advancements in high-throughput sequencing technologies have furthered the understanding of the impact of such variation on local adaptation and evolution within natural populations.
FRONTIERS IN GENETICS
(2021)
Review
Biochemical Research Methods
Harshit Kumar, Manjit Panigrahi, Anuradha Panwar, Divya Rajawat, Sonali Sonejita Nayak, K. A. Saravanan, Kaiho Kaisa, Subhashree Parida, Bharat Bhushan, Triveni Dutt
Summary: This article explains how machine learning can be used to aid in detecting and studying natural selection patterns using population genomic data. The development of high-throughput genome sequencing technologies has made it easier to detect selective sweeps/selection signatures. By treating the problem of detecting selection signatures as a classification problem, machine learning can provide higher predictive accuracy and better resolution.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Simone Morelli, Francesca Gori, Mariasole Colombo, Donato Traversa, Giulia Sarrocco, Giulia Simonato, Chiara Nespeca, Angela Di Cesare, Antonio Frangipane di Regalbono, Fabrizia Veronesi, Ilaria Russi, Manuela Schnyder
Summary: The study revealed a risk of simultaneous infection with Angiostrongylus vasorum and major canine Vector-Borne Pathogens (VBPs) in dog populations in Italy. The occurrence of concurrent infections is significant and further research is needed to enhance control strategies.
Article
Parasitology
Juergen Kruecken, Gabor A. Czirjak, Sabrina Ramunke, Maria Serocki, Sonja K. Heinrich, Joerg Melzheimer, M. Carolina Costa, Heribert Hofer, Ortwin H. K. Aschenborn, Nancy A. Barker, Stefano Capodanno, Luis Madeira de Carvalho, Georg von Samson-Himmelstjerna, Marion L. East, Bettina Wachter
Summary: A study on brown and spotted hyenas in Namibia and Tanzania revealed high frequencies of various pathogens, with frequent co-infections observed in the samples. Ecological conditions were found to have a greater impact on pathogen diversity and frequency than host taxonomy.
PARASITES & VECTORS
(2021)
Article
Biochemistry & Molecular Biology
Wei Zhou, Michelle Spoto, Rachel Hardy, Changhui Guan, Elizabeth Fleming, Peter J. Larson, Joseph S. Brown, Julia Oh
Article
Genetics & Heredity
Min Li, Wei Zhou, Yilun Zhang, Lei Huang, Xinjie Wang, Jun Wu, Meng Meng, Hongran Wang, Chengtao Li, Yingnan Bian
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2020)
Correction
Ecology
Zhou Wei, Kin-hoe Chow, Elizabeth Fleming, Julia Oh
Article
Multidisciplinary Sciences
Akintunde Emiola, Wei Zhou, Julia Oh
Review
Microbiology
Michael Letko, Stephanie N. Seifert, Kevin J. Olival, Raina K. Plowright, Vincent J. Munster
NATURE REVIEWS MICROBIOLOGY
(2020)
Article
Virology
Stephanie N. Seifert, Jonathan E. Schulz, Stacy Ricklefs, Michael Letko, Elangeni Yabba, Zaidoun S. Hijazeen, Peter Holloway, Bilal Al-Omari, Hani A. Talafha, Markos Tibbo, Danielle R. Adney, Javier Guitian, Nadim Amarin, Juergen A. Richt, Chester McDowell, John Steel, Ehab A. Abu-Basha, Ahmad M. Al-Majali, Neeltje van Doremalen, Vincent J. Munster
Summary: The low genetic diversity of MERS-CoV genomes detected in Jordan camels suggests a lack of endemic circulation in these herds, contrasting with the diversity found in camel markets in KSA and UAE. The data indicate the transmission of MERS-CoV among camel herds in Jordan in 2016 following a single introduction event, similar to the nosocomial transmission observed during the 2015 MERS outbreak in South Korea.
Article
Microbiology
Elizabeth Fleming, Victor Pabst, Zoe Scholar, Ruoyun Xiong, Anita Y. Voigt, Wei Zhou, Amelia Hoyt, Rachel Hardy, Anna Peterson, Ryan Beach, Yvette Ondouah-Nzutchi, Jinhong Dong, Lucinda Bateman, Suzanne D. Vernon, Julia Oh
Summary: The researchers described and validated a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota. Through this method, they successfully recovered between 18.1-44.4% of total genera, which represented a significant proportion of the community composition reconstructed using metagenomic sequencing. Additionally, Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but less effective in estimating genetic distance.
Article
Microbiology
Elaine Haddock, Julie Callison, Stephanie N. Seifert, Atsushi Okumura, Tsing-Lee Tang-Huau, Shanna S. Leventhal, Matthew C. Lewis, Jamie Lovaglio, Patrick W. Hanley, Carl Shaia, David W. Hawman, Vincent J. Munster, Michael A. Jarvis, Juergen A. Richt, Heinz Feldmann
Summary: Despite being intermediate hosts for many viruses, pigs are not susceptible to productive SARS-CoV-2 infection and do not serve as a reservoir for zoonotic transmission.
Article
Ecology
Hannelore MacDonald, Erol Akcay, Dustin Brisson
Summary: The traditional trade-off between transmission and virulence cannot explain the intermediate levels of parasite virulence observed in nature. Host phenology, the timing of seasonal activity, can act as an alternative driver of virulence evolution, selecting for intermediate parasite virulence strategies.
Article
Dermatology
Anita Y. Voigt, Akintunde Emiola, Jethro S. Johnson, Elizabeth S. Fleming, Hoan Nguyen, Wei Zhou, Kenneth Y. Tsai, Christine Fink, Julia Oh
Summary: The skin microbiome plays an important role in skin health and diseases. This study found that pathobiont Staphylococcus aureus was increased in squamous cell carcinoma (SCC) compared with healthy skin, while commensal Cutibacterium acnes was decreased. This transitional microbial dysbiosis from healthy skin to actinic keratosis to SCC suggests the potential of the skin microbiome as a biomarker and warrants further investigation on how these microbes influence skin cancer progression.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Ecology
Hannelore MacDonald, Dustin Brisson
Summary: Parasite-host interactions can drive periodic population dynamics, and host phenology plays a crucial role in determining the frequency and impact of these interactions. This study used a mathematical model to analyze a parasite system with seasonal host activity and found that parasites can reach densities necessary to destabilize host dynamics and drive population cycles in certain phenological scenarios.
ECOLOGY AND EVOLUTION
(2022)
Article
Infectious Diseases
Stephanie N. Seifert, Robert J. Fischer, Eeva Kuisma, Cynthia Badzi Nkoua, Gerard Bounga, Marc-Joël Akongo, Jonathan E. Schulz, Beatriz Escudero-Perez, Beal-Junior Akoundzie, Vishnou Reize Bani Ampiri, Ankara Dieudonne, Ghislain Dzeret Indolo, Serge D. Kaba, Igor Louzolo, Lucette Nathalie Macosso, Yanne Mavoungou, Valchy Bel-Bebi Miegakanda, Rock Aime Nina, Kevin Tolovou Samabide, Alain I. Ondzie, Francine Ntoumi, Cesar Munoz-Fontela, Jean-Vivien Mombouli, Sarah H. Olson, Chris Walzer, Fabien Roch Niama, Vincent J. Munster
Summary: This study investigated the presence of Ebola virus infection in bats near an Ebola outbreak in the Bikoro region of the Democratic Republic of the Congo. The results showed that although EBOV genomic material was not detected in bat-derived samples, serological data suggested recent exposure to EBOV in bats in the region.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Review
Microbiology
Ryan Caldwell, Wei Zhou, Julia Oh
Summary: There is a diverse microbial community on the human skin, including bacteria, fungi, viruses, and small multicellular eukaryotes. The genetic diversity of the skin microbiome at the species and strain levels contributes to its functional impact on cutaneous immunity, barrier integrity, aging, and other skin processes. Further research on strain diversity, spatial distribution, and metabolic diversity will enhance our understanding of the essentiality of the microbiome to the skin ecosystem and facilitate the development of targeted topical therapeutics.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Jane Dwivedi-Yu, Zachary Oppler, Matthew Mitchell, Yun Song, Dustin Brisson
Summary: Population genomics plays a crucial role in addressing important questions in microbial evolution and pathogenesis. However, the practical limitations of obtaining sufficient quantities of pure microbial genomic DNA for next-generation sequencing currently hinder microbial population genomics research. In this study, we present swga2.0, an optimized and parallelized pipeline for designing selective whole genome amplification (SWGA) primer sets, which incorporates active and machine learning methods to evaluate amplification efficacy and significantly decreases program runtime.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Cell Biology
Peter J. Larson, Wei Zhou, Alba Santiago, Sarah Driscoll, Elizabeth Fleming, Anita Y. Voigt, Ock K. Chun, James J. Grady, George A. Kuchel, Julie T. Robison, Julia Oh
Summary: A study on the gut, oral, and skin microbiota reveals microbial dysbiosis in institutionalized older adults and identifies the skin as a major reservoir for pathogens. This research suggests that the skin microbiome plays a significant role in disease risk and the spread of multidrug resistant pathogens.
