Article
Psychology, Biological
Jordi Merino, Hassan S. Dashti, Chloe Sarnowski, Jacqueline M. Lane, Petar Todorov, Miriam S. Udler, Yanwei Song, Heming Wang, Jaegil Kim, Chandler Tucker, John Campbell, Toshiko Tanaka, Audrey Y. Chu, Linus Tsai, Tune H. Pers, Daniel Chasman, Martin K. Rutter, Josee Dupuis, Jose C. Florez, Richa Saxena
Summary: In a multivariate genetic analysis, 26 genomic regions associated with carbohydrate, protein and fat intake were identified, implicating brain regions and neuronal subtypes in influencing eating behaviour. This research enhances understanding of individual differences in dietary intake by highlighting neural mechanisms and potentially offering new avenues for the prevention and treatment of complex metabolic diseases.
NATURE HUMAN BEHAVIOUR
(2022)
Article
Multidisciplinary Sciences
Evangelia Vayena, Anush Chiappino-Pepe, Homa MohammadiPeyhani, Yannick Francioli, Noushin Hadadi, Meric Ataman, Jasmin Hafner, Stavros Pavlou, Vassily Hatzimanikatis
Summary: This study introduces a workflow called NICEgame for identifying and curating nonannotated metabolic functions in genomes. By providing alternative reaction sets and candidate genes, NICEgame can resolve gaps in metabolic models and improve genome annotation accuracy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice, Kimberly A. Bishop-Lilly
Summary: Manual Annotation Studio (MAS) is a software tool designed to improve the efficiency of manual functional annotation for prokaryotic and viral genomes. It allows users to upload, edit, and track annotations, provides structure to projects, and reduces errors. MAS can interface with HPC clusters, support multiple users, and export data in various formats.
Article
Biochemical Research Methods
Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis
Summary: MicrobeAnnotator is a comprehensive pipeline for functional annotation of microbial genomes, combining results from multiple reference protein databases to provide functional annotations and metabolic summaries. Implemented in Python 3, it is freely available for download, demonstrating higher efficiency and accuracy compared to other tools for annotating genomes. Its output can be easily integrated into other analysis pipelines, offering a user-friendly interface for comparing and clustering genomes based on metabolic similarity.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou
Summary: The study introduces FusionGDB 2.0, a database with updated functional annotations of fusion genes, which is crucial for understanding genomic breakage context and developing therapeutic strategies. FusionGDB 2.0 provides comprehensive information on human fusion genes and their characteristics, making it a valuable resource for diverse human genomic studies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Environmental Sciences
Duantao Cao, Shuhong He, Xin Li, Lihong Shi, Feiyan Wang, Sumei Yu, Shiji Xu, Chao Ju, Hua Fang, Yunlong Yu
Summary: The bacterial strain Arthrobacter sp. C2 was isolated for atrazine degradation, showing degradation rates of 0.34, 1.94, and 18.64 mg/L/d at different concentrations. The optimal conditions for degradation were at 30°C and pH 7.0-9.0, and a metabolic pathway for atrazine degradation was proposed. The introduction of strain C2 into soil can enhance atrazine degradation and eliminate its toxic effects on wheat growth.
Article
Genetics & Heredity
Bryan Irvine M. Lopez, Narae An, Krishnamoorthy Srikanth, Seunghwan Lee, Jae-Don Oh, Dong-Hyun Shin, Woncheoul Park, Han-Ha Chai, Jong-Eun Park, Dajeong Lim
Summary: This study aimed to improve the predictive performance of a customized 50k SNP panel for four carcass traits in commercial Hanwoo cattle by adding highly predictive variants from sequence data. Results showed that adding 3000 pre-selected variants from each trait significantly improved prediction accuracy, with gains of up to 9.9% for backfat thickness, 9.2% for carcass weight, 6.4% for longissimus muscle area, and 4.7% for marbling score. The strategy used to select variants based on functional annotation did not show a clear advantage compared to using whole-genome data, indicating that using WGS data remained more accurate.
FRONTIERS IN GENETICS
(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
Multidisciplinary Sciences
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, Rene L. Warren, Inanc Birol
Summary: Long-read sequencing technologies have greatly improved, but there is little focus on reference-free transcriptome assembly methods. In this study, the authors introduce RNA-Bloom2, a reference-free method for long-read transcriptome sequencing data. They demonstrate its competitive assembly quality compared to reference-based methods, as well as its lower memory and runtime requirements. They also showcase its application in assembling a transcriptome sample of Sitka spruce, setting the groundwork for large-scale comparative transcriptomics without readily available genome assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Entomology
Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Hitomi Seike, Zhen Zhu, Yi Jun Zhou, Keisuke Fukumura, Shinji Nagata, Yasukazu Nakamura
Summary: We identified neuropeptides and their genomic loci in Gryllus bimaculatus, improving the draft genome annotation and facilitating research. Genome annotation is essential for supporting studies, but often lacks tissue-specific or low-expression genes. Through reference mapping, de novo transcriptome assembly, and manual curation, we annotated 41 neuropeptides in the cricket. These annotation methods can be applied to other insects and provide useful infrastructures for neuropeptide studies.
Article
Biochemistry & Molecular Biology
Tiago Pedreira, Christoph Elfmann, Neil Singh, Joerg Stuelke
Summary: The new field of synthetic biology focuses on creating artificially designed organisms, with a major breakthrough being the development of the minimal genome bacterium JCVI-syn3A. To better understand the functions of the genes and proteins of artificial bacteria, the SynWiki database was established, providing interactive protein-protein interaction information.
Article
Endocrinology & Metabolism
L. R. Dillard, N. Wase, G. Ramakrishnan, J. J. Park, N. E. Sherman, R. Carpenter, M. Young, A. N. Donlan, W. Petri, J. A. Papin
Summary: This study investigates the metabolic signatures of non-acute and severe COVID-19 samples and finds that non-acute infection is associated with inhibited inflammatory response, while severe infection is linked to musculoskeletal degeneration and hijacked host metabolism. The findings highlight the metabolic transition from innate immune response to inflammatory and metabolic dysfunction in severe COVID-19.
Article
Microbiology
Christoph Elfmann, Bingyao Zhu, Tiago Pedreira, Ben Hossbach, Maria Lluch-Senar, Luis Serrano, Joerg Stuelke
Summary: The article introduces the significance of Mycoplasma pneumoniae and its database MycoWiki. As a minimal organism, M. pneumoniae can provide insights into the basic requirements for cellular life. MycoWiki integrates various data sources to facilitate the analysis of protein functions.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Alban Mathieu, Mickael Leclercq, Melissa Sanabria, Olivier Perin, Arnaud Droit
Summary: Shotgun sequencing of environmental DNA has greatly advanced the field of environmental microbiology, but current alignment methods have limitations. Deep learning models show promise in improving annotation efficiency, but their robustness needs further validation in different environmental samples and genome databases.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Neelakantan Thulasi Devika, Ashok Kumar Jangam, Vinaya Kumar Katneni, Prasanna Kumar Patil, Suganya Nathamuni, Mudagandur Shashi Shekhar
Summary: The study utilized constraint-based genome-scale metabolic modeling approach to screen and identify six candidate bacterial strains with growth enhancement and pathogen suppression capabilities, including three novel strains, for probiotic applications. This is the first study to apply genomic-scale metabolic models for aquaculture purposes and detect bacterial species limiting Vibrio harveyi growth.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, Jose P. Faria, Janaka N. Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E. Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
Summary: ModelSEED has been a primary resource for building draft genome-scale metabolic models based on annotated microbial or plant genomes for over 10 years. The biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase, distinguished by various properties and designed to facilitate comparison and integration of annotations from different tools and databases.
NUCLEIC ACIDS RESEARCH
(2021)
Correction
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
NATURE BIOTECHNOLOGY
(2021)
Correction
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I- Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
NATURE BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Carol L. Ecale Zhou, Jeffrey Kimbrel, Robert Edwards, Katelyn McNair, Brian A. Souza, Stephanie Malfatti
Summary: multiPhATE2 is a tool for annotation and comparative genomics of bacteriophage genomes, which performs gene finding, comparison, functional annotation, and extends the search space. It supports gene matching among related genomes, accelerates computations with multiprocessing, and has flexibility and the ability to be restarted at multiple points within the workflow.
G3-GENES GENOMES GENETICS
(2021)
Article
Ecology
Hyungseok Kim, Jeffrey A. Kimbrel, Christopher A. Vaiana, Jessica R. Wollard, Xavier Mayali, Cullen R. Buie
Summary: Photosynthetic microalgae are important for fixing CO2 and have potential as a renewable bioenergy source. By studying the metabolic interactions between microorganisms, this research explores the factors influencing community development. The novel system provides a useful tool for investigating metabolic interactions between microbes in aquatic ecosystems.
Article
Microbiology
Gareth Trubl, Jeffrey A. Kimbrel, Jose Liquet-Gonzalez, Erin E. Nuccio, Peter K. Weber, Jennifer Pett-Ridge, Janet K. Jansson, Mark P. Waldrop, Steven J. Blazewicz
Summary: Using stable isotope probing and targeted metagenomics, it was discovered that active bacterial and viral populations play crucial roles in carbon cycling and host interactions in Arctic peat soils under simulated winter conditions. These active populations demonstrate significant differences in identity and function compared to the unlabeled community, highlighting viruses as a major community-structuring agent in sub-freezing anoxic conditions.
Article
Microbiology
Megan M. Morris, Jeffrey A. Kimbrel, Haifeng Geng, Mary Bao Tran-Gyamfi, Eizadora T. Yu, Kenneth L. Sale, Todd W. Lane, Xavier Mayali
Summary: Bacteria play important roles in nutrient-rich aquatic environments, such as engineered algal biofuel systems, but our knowledge about the microbial ecology of algal cultivation systems remains limited. In this study, we used metagenomics to characterize the metabolic capacities of bacteria associated with the biofuel-relevant microalga Microchloropsis salina and predicted metabolic interactions between algae and manipulated communities of bacteria. These findings provide insights into the scalability of lab-based algal-bacterial interactions and offer a framework for empirical testing of genome-based metabolic predictions.
Article
Ecology
Rachel Hestrin, Megan Kan, Marissa Lafler, Jessica Wollard, Jeffrey A. Kimbrel, Prasun Ray, Steven J. Blazewicz, Rhona Stuart, Kelly Craven, Mary Firestone, Erin E. Nuccio, Jennifer Pett-Ridge
Summary: Drought can disrupt soil microbial activity and biogeochemical processes. This study found that certain plant-associated fungi can protect soil microbial communities from the effects of drought. In soils inoculated with these fungi, bacterial growth potential and diversity were not affected by water limitation. These results suggest that fungal-bacterial synergies may contribute to bacterial resilience to moisture limitation.
Article
Virology
Jenna McGowan, Monica Borucki, Hicham Omairi, Merina Varghese, Shahnaz Vellani, Sukanya Chakravarty, Shumin Fan, Srestha Chattopadhyay, Mashuk Siddiquee, James B. Thissen, Nisha Mulakken, Joseph Moon, Jeffrey Kimbrel, Amit K. Tiwari, Roger Travis Taylor, Dae-Wook Kang, Crystal Jaing, Ritu Chakravarti, Saurabh Chattopadhyay
Summary: Wastewater-based epidemiology (WBE) is an effective tool for predicting the community spread of infectious diseases, especially during the COVID-19 pandemic. Through analyzing the correlation between viral gene copies and clinical cases, as well as sequencing RNA from wastewater to identify viral mutants, WBE can be used to predict the spread of COVID-19 and the emergence of new variants of concern. Furthermore, significant changes in the microbial community of wastewater, particularly in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae, show a strong correlation with the presence of SARS-CoV-2. These microbial biomarkers could serve as prediction tools for future infectious disease surveillance and outbreak responses.
Article
Microbiology
Alex Greenlon, Ella Sieradzki, Olivier Zablocki, Benjamin J. Koch, Megan M. Foley, Jeffrey A. Kimbrel, Bruce A. Hungate, Steven J. Blazewicz, Erin E. Nuccio, Christine L. Sun, Aaron Chew, Cynthia-Jeanette Mancilla, Matthew B. Sullivan, Mary Firestone, Jennifer Pett-Ridge, Jillian F. Banfield
Summary: The growth and physiology of soil microorganisms are influenced by both current and historical soil environmental conditions. By using genome-resolved metagenomics, we found that precipitation levels have a significant impact on the activity and growth rates of soil microorganisms. In addition, the activity of bacteriophages in the soil is correlated with the activity of their hosts. Contrary to expectations, the ability to decompose organic matter and oxidize carbon compounds is broadly distributed among active and inactive bacteria.
Article
Soil Science
Megan M. Foley, Steven J. Blazewicz, Karis J. McFarlane, Alex Greenlon, Michaela Hayer, Jeffrey A. Kimbrel, Benjamin J. Koch, Victoria L. Monsaint-Queeney, Keith Morrison, Ember Morrissey, Bruce A. Hungate, Jennifer Pett-Ridge
Summary: The structure of both total and growing microbial communities differed across sites, reflecting the influence of climate history and environmental filtering. The growth rates of bacterial taxa were consistently lower in the site with the lowest mean annual precipitation, indicating adaptation to water stress. Additionally, the growth rate coherence across taxa suggests genetically determined physiological traits and evolutionary constraints.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Virology
Jeffrey Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Marti, James Thissen, Nisha Mulakken, Sarah H. Sandholtz, Tyshawn Ferrell, Chris Daum, Sara Hall, Brent Segelke, Kathryn T. Arrildt, Sharon Messenger, Debra A. Wadford, Crystal Jaing, Jonathan E. Allen, Monica K. Borucki
Summary: Genetic analysis of SARS-CoV-2 positive clinical samples collected in California during the early months of the pandemic revealed insights into the emergence and spread of viral mutations. Many mutations associated with global variants were present at varying frequencies even in samples collected during the initial detection of the virus in the US. Subconsensus mutations emerged later in the consensus sequences. Spike protein mutations and mutations in the furin cleavage site, nucleocapsid, and envelope genes were detected prior to their emergence in variant genotypes. A bioinformatics pipeline enabled detection of low-frequency variants, including a spike protein deletion associated with a variant of concern.
Article
Microbiology
Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone, Jennifer Pett-Ridge
Summary: The study introduced a semi-automated, high-throughput SIP pipeline to support well-replicated experiments in soil microhabitats, showcasing how this approach can improve operational efficiency and reproducibility in studying actively growing microbes within AMF hyphosphere. This method generated a series of metagenome-assembled genomes (MAGs) from C-13-labeled AMF hyphosphere DNA, revealing insights into key processes involved in nutrient cycling within the hyphosphere.
Correction
Biochemistry & Molecular Biology
Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, Jose P. Faria, Janaka N. Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E. Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)