Article
Genetics & Heredity
Diego A. A. Morais, Joao V. F. Cavalcante, Shenia S. Monteiro, Matheus A. B. Pasquali, Rodrigo J. S. Dalmolin
Summary: Metagenomic studies provide valuable insights into the taxonomic composition and functional characteristics of microbial communities. However, selecting and setting up the appropriate tools for comprehensive metagenomic analysis poses challenges. In this study, the researchers surveyed state-of-the-art tools, created simulated datasets, and performed benchmarks to develop an efficient and flexible metagenomic analysis pipeline called MEDUSA. Compared to existing tools, MEDUSA accurately identifies a greater number of species and is well-suited for functional analysis.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Tara N. Furstenau, Tsosie Schneider, Isaac Shaffer, Adam J. Vazquez, Jason Sahl, Viacheslav Fofanov
Summary: With the growth of sequence databases and sequencing datasets, traditional alignment methods are no longer suitable for taxonomic classification of metagenomic reads. Existing methods sacrifice either speed or accuracy. To address this issue, a flexible new method called MTSv has been designed to balance efficiency and accuracy.
Article
Biochemistry & Molecular Biology
Dalwinder Singh, Joy Roy
Summary: The identification of protein-coding and non-coding transcripts is crucial for understanding their biological roles. Computational approaches have been used for over a decade, but reliable and high-performance models are still lacking. This benchmark study evaluated the performance of 24 tools on diverse datasets and identified the key limitations affecting their performance.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Medicinal
Bailu Yan, Xinchun Ran, Anvita Gollu, Zihao Cheng, Xiang Zhou, Yiwen Chen, Zhongyue J. Yang
Summary: Data-driven modeling is crucial for biocatalyst design and discovery, and a biocatalytic database integrating enzyme structure and function data is urgently needed. In this study, we introduce IntEnzyDB as an integrated structure-kinetics database, which allows easy statistical modeling and machine learning. Using this database, we investigated the effects of mutations on enzyme efficiency, and found that efficiency-enhancing mutations are globally encoded. Furthermore, we provide a web interface for public access to enzymology data stored in IntEnzyDB.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Fernando Puente-Sanchez, Matthias Hoetzinger, Moritz Buck, Stefan Bertilsson
Summary: Microorganisms exhibit high adaptability at the genome level, with heritable traits emerging in response to environmental niches. The pangenome concept, which partitions genomes into core and accessory regions, is valuable for studying microbial ecology and evolution. In this study, SuperPang, an algorithm that generates pangenome assemblies from input genomes, is presented. SuperPang provides a modular view of the pangenome, allowing the analysis of allelic and gene content variation. The algorithm is demonstrated through an analysis of intra-species diversity in the Polynucleobacter genus.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Yujie Mao, Xiaohui Liu, Na Zhang, Zhi Wang, Maozhen Han
Summary: Antibiotic resistance genes (ARGs) are emerging pollutants found in various environments, and identifying these genes has become a growing concern. In this study, a non-redundant antibiotic resistance genes database (NRD) was constructed by consolidating sequences from existing databases. The advantages of NRD in detecting potential ARGs were demonstrated through comparisons with other databases using metagenome datasets.
Article
Engineering, Biomedical
Meryem Altin Karagoz, O. Ufuk Nalbantoglu
Summary: A CNN approach based on k-mer representation was proposed for metagenomic fragment classification, utilizing Relative Abundance Index to represent DNA and deep learning algorithm for classification. The comparison with existing spectral methods showed competitive performance across various metagenomic datasets, indicating the effectiveness of the proposed method.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2021)
Article
Microbiology
Michal Ziemski, Treepop Wisanwanichthan, Nicholas A. Bokulich, Benjamin D. Kaehler
Summary: The study found that, in some practical scenarios, naive Bayes classifiers excel in taxonomic classification of 16S rRNA gene sequences, making it difficult for other classification methods to further improve accuracy. Future improvements in taxonomy classification are unlikely to solely come from novel algorithms, but will also need to leverage other technological innovations such as ecological frequency information.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Spyros Tastsoglou, Giorgos Skoufos, Marios Miliotis, Dimitra Karagkouni, Ioannis Koutsoukos, Anna Karavangeli, Filippos S. Kardaras, Artemis G. Hatzigeorgiou
Summary: DIANA-miRPath is an online miRNA analysis platform that allows exploration of combined miRNA effects through predicted or experimentally supported miRNA interactions. Its latest version introduces a customizable target-based miRNA functional analysis engine, enriched with interaction, annotation, and parameterization options. The platform integrates various datasets and enables enrichment analysis on GO terms, pathways, and expression data for a wide range of states. Additionally, it provides a module for utilizing CRISPR knock-out screen datasets to identify miRNAs with potentially crucial roles.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Donovan H. Parks, Fabio Rigato, Patricia Vera-Wolf, Lutz Krause, Philip Hugenholtz, Gene W. Tyson, David L. A. Wood
Summary: A fundamental goal of microbial ecology is to accurately determine species composition in microbial ecosystems. Microba Community Profiler (MCP) was found to generate accurate relative abundance estimates and fewer false positive predictions compared to other classifiers, establishing it as the best-in-class tool for comprehensive and accurate species profiling of human gastrointestinal samples. Using the Microba Genome Database significantly increases the accuracy of species classification.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus, Todd J. Treangen
Summary: SeqScreen is a new approach that accurately characterizes short nucleotide sequences, helping us better understand pathogens. It can be used for detection and characterization of pathogens, and is important for epidemic monitoring and research.
Article
Computer Science, Artificial Intelligence
Mohammad Iqbal, Hsing-Kuo Pao
Summary: Trip destination forecasting has received attention in the context of intelligent transportation, with a proposed method outperforming other mining techniques in terms of accuracy and resource allocation efficiency.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Jillian Rumore, Matthew Walker, Franco Pagotto, Jessica D. Forbes, Christy-Lynn Peterson, Andrea D. Tyler, Morag Graham, Gary Van Domselaar, Celine Nadon, Aleisha Reimer, Natalie Knox
Summary: This study evaluated the performance of a foodborne pathogen-specific reference database compared to a universal reference database, and found that using a pathogen-specific database can achieve higher classification precision in complex food matrices, with lower computational resource requirements.
Article
Biochemistry & Molecular Biology
Robert D. Olson, Rida Assaf, Thomas Brettin, Neal Conrad, Clark Cucinell, James J. Davis, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce Parrello, Victoria Parrello, Jacob S. Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyunseung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens
Summary: This report introduces the Bioinformatics Resource Center program established by the National Institute of Allergy and Infectious Diseases (NIAID) to aid researchers in analyzing genome sequences and other omics-related data. The merger of PATRIC, IRD, and ViPR BRCs has resulted in the formation of BV-BRC, which offers a unified data model, enhanced visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools for the bacterial and viral research communities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Anna Abramova, Adriana Osinska, Haveela Kunche, Emil Burman, Johan Bengtsson-Palme
Summary: The software package CAFE-Coefficient can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these coefficients.
Article
Environmental Sciences
Emily K. Walker, Guy N. Brock, Ryan S. Arvidson, Reed M. Johnson
Summary: Beekeepers have reported significant honey bee deaths during and after almond bloom, and this study suggests that combining certain pesticides and fungicides during daylight hours could be a possible cause. Spray adjuvants were also found to increase the toxicity of pesticide mixtures. The findings highlight the need to protect bees from pesticides and consider alternative application methods.
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2022)
Article
Food Science & Technology
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: The EFSA collaborated with the EMA to assess specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals. The study aimed to understand the effects on bacterial resistance and growth promotion. New assessment models were recommended for addressing antimicrobial resistance, along with the need for further data to fill the gaps in calculations.
Article
Food Science & Technology
Ana Allende, Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: The European Food Safety Authority and the European Medicines Agency collaborated to assess the effects of antibiotic concentrations in feed on antimicrobial resistance and growth promotion. Due to data gaps, assessments for some antibiotics could not be completed, and further studies are recommended to fill these gaps.
Article
Food Science & Technology
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: EFSA collaborated with EMA to assess the specific concentrations of lincomycin in non-target feed for their effect on resistance and growth promotion. However, due to data gaps, the assessment could not be concluded. Further studies are recommended to fill the data gaps.
Article
Environmental Sciences
Gabriela M. Quinlan, Douglas Sponsler, Hannah R. Gaines-Day, Harper B. G. McMinn-Sauder, Clint R. Otto, Autumn H. Smart, Theotime Colin, Claudio Gratton, Rufus Isaacs, Reed Johnson, Meghan O. Milbrath, Christina M. Grozinger
Summary: The lack of seasonally sustained floral resources is a global threat to pollinator health. This study used hive scales to assess nectar intake and developed a random forest regression model to analyze the impact of climate, weather, and land cover on honey bee colony productivity. The results show that warm, wet regions and high growing degree day accumulation have detrimental effects on nectar intake, while grassy-herbaceous natural land has a positive effect. These findings highlight the potential of using hive scales to monitor the effects of climate change on pollinator floral resources.
ENVIRONMENTAL RESEARCH LETTERS
(2022)
Article
Ecology
Rodney T. Richardson
Summary: The study found that mistagging rates were consistent across taxa within the datasets analyzed, and modeling mistagging as a binomial process with uniform distribution across dual-index combinations helped control mistag-associated false discoveries.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Entomology
Chia-Hua Lin, Sreelakshmi Suresh, Emma Matcham, Paityn Monagan, Hailey Curtis, Rodney T. Richardson, Reed M. Johnson
Summary: This study demonstrated that honey bees regularly forage on soybeans in Ohio, as shown through microscopic and molecular pollen analysis of honey samples combined with waggle dance inference of foraging patterns. The abundance of soybean pollen in honey increased with the number of surrounding soybean fields, and honey bees preferred foraging in soybean fields during soybean bloom.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Karen L. Bell, Katherine J. Turo, Abigail Lowe, Kevin Nota, Alexander Keller, Francisco Encinas-Viso, Laura Parducci, Rodney T. Richardson, Richard M. Leggett, Berry J. Brosi, Kevin S. Burgess, Yoshihisa Suyama, Natasha de Vere
Summary: Anthropogenic activities are causing global changes in the environment, leading to restructuring and decline of plant-pollinator communities. To understand and manage these impacts, it is necessary to characterize plant-pollinator communities across different habitats using rapid and high-throughput methods like pollen DNA metabarcoding. This technique is advantageous for understanding complex ecological networks and can be used to assess plant-pollinator interactions, monitor ecosystem change, and model the distribution of allergenic pollen.
Article
Oncology
Tove Wikstrom, Sanna Abrahamsson, Johan Bengtsson-Palme, Joakim Ek, Pihla Kuusela, Elham Rekabdar, Peter Lindgren, Ulla-Britt Wennerholm, Bo Jacobsson, Lil Valentin, Henrik Hagberg
Summary: This study used a transcriptomic approach to investigate the differences in the active vaginal microbiome and human transcriptome at midgestation between women delivering spontaneously preterm and those delivering at term. The study found that primarily bacterial species of low occurrence were differentially expressed at midgestation in women who delivered preterm. However, specific human transcripts, such as KLK2, KLK3, and several isoforms of MT1s, were found to be expressed at higher levels in preterm cases, indicating their potential involvement in critical inflammatory pathways associated with spontaneous preterm delivery.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Environmental Sciences
Anna Abramova, Thomas U. Berendonk, Johan Bengtsson-Palme
Summary: The environment plays a crucial role in the emergence and spread of antimicrobial resistance (AMR), yet monitoring efforts outside of clinical and veterinary settings have been limited. This is partly due to a lack of comprehensive reference data for most environments. To establish a baseline of AMR in various settings, a literature survey was conducted, identifying 150 papers with relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data, spanning from 2001 to 2020 and representing 1594 samples from 30 countries and 12 sample types, revealed that the abundances of most ARGs in human impacted environments fell within a range of 10-5 to 10-3 copies per 16S rRNA, approximately one ARG copy in a thousand bacteria. Overall, these findings provide a comprehensive overview of ARG occurrence and levels in different environments, contributing to the development of risk assessment models in AMR monitoring frameworks.
ENVIRONMENT INTERNATIONAL
(2023)
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
Entomology
Brandon Shannon, Emily Walker, Reed M. Johnson
Summary: Commercial beekeepers transporting honey bees for almond pollination have observed honey bee deaths possibly caused by pesticide applications during crop bloom. This study examined the toxicity of adjuvants and adjuvant-pesticide mixtures on adult worker honey bees. The results showed that some adjuvants caused acute mortality to honey bees at application rates, both alone and when combined with pesticides, while others demonstrated decreased toxicity. Understanding the toxicity of adjuvants to honey bees will help inform the best practices for pesticide applicators during bloom.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2023)
Review
Entomology
Brandon Shannon, Hongyoung Jeon, Reed M. Johnson
Summary: Adjuvant products in pesticide tank mixtures can enhance pesticidal activities, but they pose potential risks to beneficial insects, such as honey bees. It is necessary to better understand the toxicity of adjuvants in order to reduce the risks they pose to honey bees and other beneficial insects.
JOURNAL OF INSECT SCIENCE
(2023)
Article
Food Science & Technology
Harper McMinn-Sauder, Chia-Hua Lin, Tyler Eaton, Reed Johnson
Summary: The study found that honey bees in both agricultural and urban environments exhibit similar foraging patterns during the spring, primarily focusing on flowering trees and shrubs until the beginning of clover bloom. Furthermore, there were differences in pollen and nectar foraging within colonies, which is significant for understanding bee foraging behavior.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2022)
