Article
Microbiology
Chelsea L. Murphy, Andriy Sheremet, Peter F. Dun, John R. Spear, Ramunas Stepanauskas, Tanja Woyke, Mostafa S. Elshahed, Noha H. Youssef
Summary: The study conducted a thorough comparative genomic analysis of 108 genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum, revealing their specialization in methylotrophy and identification of an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds. The occurrence of multiple alkane hydroxylases and monooxygenases was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Members of Binatota were found to prefer terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
Article
Microbiology
Tatiana Dvorkina, Anton Bankevich, Alexei Sorokin, Fan Yang, Boahemaa Adu-Oppong, Ryan Williams, Keith Turner, Pavel A. Pevzner
Summary: The study introduces a gene prediction tool called ORFograph that can predict IPGs in assembly graphs and has discovered numerous novel IPGs from (meta)genomic datasets. Analysis of assembly graphs reveals potential candidate IPGs, including known genes hidden in assembly graphs and potential new IPGs. ORFograph is a fast tool that could potentially identify even more novel IPGs for phenotypic testing from (meta)genomic assembly graphs than traditional gene-finding methods.
Review
Infectious Diseases
Irene Bianconi, Richard Aschbacher, Elisabetta Pagani
Summary: Recent advancements in sequencing technology and data analytics have revolutionized pathogen detection and typing, making the process faster and more cost-effective. Genomic analysis is becoming the standard for pathogen analysis and control, providing insights into pathogen epidemiology and antimicrobial resistance. Integrated genomic data can accurately predict resistance phenotypes and aid in the investigation and control of hospital outbreaks. When combined with epidemiological data, genomic data can provide profound insights into the evolution and genetic relationships of antimicrobial resistance in pathogens, hosts, and the environment.
Article
Health Care Sciences & Services
Silvia Llorente, Jaime Delgado
Summary: Genomic information is highly sensitive and requires privacy protection. However, most current genomic information formats lack security mechanisms. To address this issue, we proposed the modular architecture GIPAMS based on ISO/IEC 23092 and GA4GH initiatives, aiming to provide management and privacy protection for different formats of genomic information.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Review
Microbiology
Paton Vuong, Michael J. Wise, Andrew S. Whiteley, Parwinder Kaur
Summary: Microorganisms and their natural products play a significant role in ecological processes and industrial applications. Microbial bioprospecting, through culture-independent methods and genome mining, allows the exploration and discovery of microbial bioproducts. Next generation sequencing has enabled the creation of extensive sequence databases, which, combined with bioinformatic tools, provide valuable information on the metabolic capacity and ecological distribution of microorganisms.
CRITICAL REVIEWS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Julianne M. O'Daniel, Sara Ackerman, Lauren R. Desrosiers, Shannon Rego, Sara J. Knight, Lonna Mollison, Grace Byfield, Katherine P. Anderson, Maria Danila, Carol R. Horowitz, Galen Joseph, Grace Lamoure, Nangel M. Lindberg, Carmit K. McMullen, Kathleen F. Mittendorf, Michelle A. Ramos, Mimsie Robinson, Catherine Sillari, Ebony B. Madden
Summary: There is a critical need for genomic medicine research that reflects and benefits diverse populations, but disparities and challenges in research populations persist. New approaches through stakeholder engagement can enhance outcomes. Tailored strategies and early engagement efforts across stakeholder groups contribute to improved research outcomes and relevance.
GENETICS IN MEDICINE
(2022)
Review
Microbiology
Nsa Dada, Natapong Jupatanakul, Guillaume Minard, Sarah M. Short, Jewelna Akorli, Luis Martinez Villegas
Summary: This article introduces the motivation and goals of establishing the Mosquito Microbiome Consortium, highlighting current issues in mosquito microbiome research and proposing guidelines and methods. The initiative aims to advance mosquito microbiome research to better understand the role of the mosquito microbiome in mosquito biology and disease vector control.
Article
Microbiology
Liang Shen, Yongqin Liu, Michelle A. Allen, Baiqing Xu, Ninglian Wang, Timothy J. Williams, Feng Wang, Yuguang Zhou, Qing Liu, Ricardo Cavicchioli
Summary: The study revealed a new bacterial clade, Group C, with superior ability to grow at -1 degrees C and distinct genomic traits in comparison to non-polar or alpine Group A. Metagenomic analysis showed an over-representation of Group C in Canadian permafrost communities and an under-representation of Group A in polar and alpine samples, indicating niche adaptation and environmental temperature responses. The findings suggest the potential value of defining genomic markers for specific taxa in monitoring cold environments and understanding environmental changes.
Review
Plant Sciences
Jakob Petereit, Jacob Marsh, Philipp E. Bayer, Monica F. Danilevicz, William J. W. Thomas, Jacqueline Batley, David Edwards
Summary: Soybean, a legume of economic and nutritional value, has seen increasing yields due to the breeding of improved varieties and the application of genetic and genomic approaches. With advancements in genome technologies, studying variations between individuals and populations has become more accessible. The development of soybean pangenomes has revealed significant structural variations between individuals and provided valuable information for breeding improved cultivars.
Article
Microbiology
Xiang Li, Changming Lu, Yumeng Dai, Zhixiong Yu, Wu Gu, Tingting Li, Xinyu Li, Xu Li, Xiujuan Wang, Zhencheng Su, Mingkai Xu, Huiwen Zhang
Summary: Researchers have enriched a microbial consortium called L1 from soil contaminated with the herbicide chlorimuron-ethyl (CE) using a top-down synthetic biology strategy. The consortium was able to degrade 98.04% of 100 mg L-1 CE within 6 days. Through metagenome and 16S rDNA sequencing, the researchers identified the dominant genera in consortium L1 and predicted the degradation pathway of CE. They also found close interactions and co-metabolic relationships between strains in the consortium. This study provides important insights for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia, as well as a new route for pollution control and biodegradation of sulfonylurea herbicides.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Wenjing Zhang, Yantao Liang, Kaiyang Zheng, Chengxiang Gu, Yundan Liu, Ziyue Wang, Xinran Zhang, Hongbing Shao, Yong Jiang, Cui Guo, Hui He, Hualong Wang, Yeong Yik Sung, Wen Jye Mok, Yuzhong Zhang, Andrew McMinn, Min Wang
Summary: This study reported the first Oceanospirillum phage, vB_OliS_GJ44, with novel genetic features and homology with other uncultured phages, proposing a new viral genus Oceanospirivirus within the Siphoviridae family.
Article
Genetics & Heredity
Natalie J. Kane, Ana S. A. Cohen, Courtney Berrios, Bridgette Jones, Tomi Pastinen, Mark A. Hoffman
Summary: This analysis evaluates enrollment patterns for the GA4K study using an equity-focused strategy. The study finds underrepresentation of racial and ethnic minority populations with low-income in the cohort, as well as geographic inequities in enrollment. The authors suggest using high-resolution, place-based data to identify and characterize inequities and target community engagement.
GENETICS IN MEDICINE
(2023)
Article
Green & Sustainable Science & Technology
Ran Du, Chong Li, Weichao Lin, Carol Sze Ki Lin, Jianbin Yan
Summary: This study constructed an artificial consortium with improved biomass conversion capability and good operation stability for consolidated bioprocessing (CBP) in biomass biorefinery. The diversity of microbial community structure and gene functions of the domesticated consortium was analyzed, showing a simplified microbial structure and aggregation of functional genes related to conversion of cellulosic materials for biofuel production. CBP of wheat straw using the domesticated consortium achieved the highest yield ever reported for ethanol and solvent production. These results highlight the potential of the domesticated consortium in lignocellulosic biomass biorefinery.
Review
Food Science & Technology
Anastasios Tsoungos, Violeta Pemaj, Aleksandra Slavko, John Kapolos, Marina Papadelli, Konstantinos Papadimitriou
Summary: This review explores recent advances in table olive research through omics and meta-omics approaches, offering insights into the genomic, metagenomic, and metabolomic analysis of the microbial community in table olives. These methods hold the promise of groundbreaking advances in table olive processing technology.
Article
Microbiology
Xinyang Huang, David L. Erickson, Jianghong Meng
Summary: There has been a surge of interest in the impact of microbial diversity on human health, food safety, and environmental functions. Accurately measuring the diversity and structure of these communities is crucial for understanding their effects. PhyloPlus, a web portal developed in this study, allows users to generate customized phylogenies for bacterial or archaeal communities, enabling more accurate descriptions and preventing misleading conclusions.