Article
Biochemistry & Molecular Biology
Laurita Klimkaite, Ignas Ragaisis, Renatas Krasauskas, Modestas Ruzauskas, Edita Suziedeliene, Julija Armalyte
Summary: Soil, as a diverse habitat for microorganisms, contains both antibiotics and antibiotic resistance genes (ARGs). Bacteria naturally present in soil or water have innate ARGs to counteract the chemical compounds produced by competitors, making treatment difficult when these bacteria cause infections. By creating functional gene libraries using antibiotic-resistant bacteria from agricultural soils in Lithuania, we discovered novel variants of aminoglycoside and beta-lactam resistance genes. Our findings suggest that soil microorganisms possess a range of ARG variants that could potentially spread to clinical settings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shanzhou Huang, Zuyi Ma, Qi Zhou, Aimei Wang, Yuanfeng Gong, Zhenchong Li, Shujie Wang, Qian Yan, Dongping Wang, Baohua Hou, Chuanzhao Zhang
Summary: DUSP4 deficiency mediates Lenvatinib resistance by activating MAPK/ERK signaling, and combination therapy using Lenvatinib and MEK inhibitors may be a promising therapeutic strategy for overcoming Lenvatinib resistance.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvonen, Florian Hollfelder
Summary: The abundance of protein sequence data is not matched by the number of experimentally verified functional annotations. In this study, we used high-throughput microfluidic droplet screening to identify a new beta-glucuronidase enzyme with little homology to previously studied enzymes. This finding demonstrates the potential of functional metagenomics in uncovering the function of enzymes that cannot be predicted by bioinformatics.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Betulia de Morais Souto, Ana Carolina Bitencourt de Araujo, Pedro Ricardo Vieira Hamann, Andressa de Rezende Bastos, Isabel de Souza Cunha, Julianna Peixoto, Ricardo Henrique Kruger, Eliane Ferreira Noronha, Betania Ferraz Quirino
Summary: Functional screening of a metagenomic library from a Caatinga biome goat rumen led to the identification of a novel GH3 enzyme, BGL11, with multifunctional activities towards xylose-based substrates. This enzyme, BGL11, shows potential for industrial applications in plant biomass deconstruction for biofuel production.
Article
Cell Biology
Zhi Ruan, Kayo Takamatsu-Yukawa, Yuzhi Wang, Margaret L. Ushman, Adam Thomas Labadorf, Maria Ericsson, Seiko Ikezu, Tsuneya Ikezu
Summary: Activated microglia release extracellular vesicles (EVs) to modulate brain homeostasis and innate immunity. This study identifies Mcfd2, Sepp1, and Sdc1 as critical regulators of ATP-induced EV secretion from murine microglia and potential therapeutic targets for neuroinflammatory disorders.
Article
Infectious Diseases
Joao Vitor Wagner Ordine, Gabrielle Messias De Souza, Gustavo Tamasco, Stela Virgilio, Ana Flavia Tonelli Fernandes, Rafael Silva-Rocha, Maria-Eugenia Guazzaroni
Summary: Land-use conversion and antibiotic overuse promote the expansion of the soil resistome, which can be influenced by different land practices. This study profiled the resistome and microbiota of soils under different land practices in Sao Paulo, Brazil. The analysis revealed differences in community structures and dynamics correlated with land practices, as well as variations in the abundance and diversity of antibiotic resistance genes and virulence factors. Overall, this highlights the importance of monitoring antimicrobial resistance in the environment, particularly in soils undergoing land-use transformations.
Article
Cell Biology
Macus Hao-Ran Bao, Chunxue Yang, Aki Pui-Wah Tse, Lai Wei, Derek Lee, Misty Shuo Zhang, Chi Ching Goh, David Kung-Chun Chiu, Vincent Wai-Hin Yuen, Cheuk-Ting Law, Wai-Ching Chin, Noreen Nog-Qin Chui, Bowie Po-Yee Wong, Cerise Yuen-Ki Chan, Irene Oi-Lin Ng, Clive Yik-Sham Chung, Chun-Ming Wong, Carmen Chak-Lui Wong
Summary: The study reveals the crucial role of PTPMT1 in hypoxic survival of HCC, where its knockout impairs the assembly of ETC complexes, leading to further damage in HCC cells under hypoxic conditions.
Article
Engineering, Environmental
Zishu Liu, Yuxiang Zhao, Baofeng Zhang, Jiaqi Wang, Lizhong Zhu, Baolan Hu
Summary: Soil is the major reservoir of antibiotic resistance genes (ARGs), particularly multidrug efflux pump genes, which have raised concerns due to their high prevalence in natural soil ecosystems. This study examined the influence of soil pH on the selection and composition of multidrug efflux pump genes in soil resistomes. The findings indicate that acidic soil environments significantly enrich multidrug efflux pump genes, reflecting the benefits of high soil proton activity on these genes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Virology
Xiang Lu, Rong Zhu, Ziyuan Dai
Summary: A novel whale papillomavirus (wPV) was discovered in a whale pharyngeal metagenomic library. The complete genome of wPV has a typical papillomavirus organization pattern and shows similarities to Dyodeltapapillomavirus genus. This discovery contributes to our knowledge of viral ecology in marine mammals and offers insights into potential future infectious diseases.
Article
Microbiology
Madangchanok Imchen, V. T. Anju, Siddhardha Busi, Mahima S. Mohan, Pattnaik Subhaswaraj, Madhu Dyavaiah, Ranjith Kumavath
Summary: Biofilms formed by microbial cells on surfaces serve as a breeding ground for drug-resistant pathogens and ARG enrichment, but they also play beneficial roles in promoting plant growth and wastewater treatment. Inhibiting biofilm formation through quorum quenching is a feasible approach. Surveillance of biofilm microbiome is crucial for assessing risks and harnessing bioactive potential. Metagenomics is a preferred method for studying biofilm microbiome and discovering new species.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Microbiology
Yueyang Yan, Hao Li, Amna Fayyaz, Yunpeng Gai
Summary: The study investigated the diversity and abundance of antibiotic resistance genes in the gut microbiota of cynomolgus monkeys using metagenomic analysis. It was found that dietary changes significantly affect the composition and abundance of ARGs in the gut microbiota of cynomolgus monkeys. Furthermore, all ARG types carried by humans were also present in cynomolgus monkeys, indicating potential conservation and homology in tetracycline resistance genes.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biology
Akil Akhtar, Madhu Lata, Sonali Sunsunwal, Amit Yadav, Kajal Lnu, Srikrishna Subramanian, T. N. C. Ramya
Summary: Uncultured microbes are a valuable source of novel genes and gene products. Functional metagenomics can be used to identify and annotate these novel gene products. In this study, a metagenomic phage display library was constructed and screened to identify previously unannotated carbohydrate binding domains. Several new carbohydrate binding domains were discovered, including a levan binding domain and four complex N-glycan binding domains.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Christopher A. Gaulke, Emily R. Schmeltzer, Mark Dasenko, Brett M. Tyler, Rebecca Vega Thurber, Thomas J. Sharpton
Summary: This study evaluated five different metagenomic library preparation methods across a range of microbial communities, finding that community type and input DNA amount influence the performance of each method. Careful consideration of sample properties is necessary when selecting the most appropriate metagenomic library preparation method.
Article
Microbiology
Samuel E. Barnett, Rob Egan, Brian Foster, Emiley A. Eloe-Fadrosh, Daniel H. Buckley
Summary: Soil microbes play a crucial role in the global carbon cycle, but our understanding of how the carbon cycle operates in soil communities is limited. This is mainly due to the lack of functional genes that define carbon transformations. Through metagenomic stable isotope probing, we linked genomic features of bacteria to their carbon acquisition and growth dynamics in soil. We identified genomic traits that can predict bacterial ecological strategies, providing insights into bacterial interactions with soil carbon.
Article
Cell Biology
Jennifer M. Pfaff-Kilgore, Edgar Davidson, Kathryn Kadash-Edmondson, Mayda Hernandez, Erin Rosenberg, Ross Chambers, Matteo Castelli, Nicola Clementi, Nicasio Mancini, Justin R. Bailey, James E. Crowe, Mansun Law, Benjamin J. Doranz
Summary: The E1 and E2 envelope proteins of hepatitis C virus (HCV) form a surprisingly fragile complex where even a single alanine mutation at 92% of positions disrupts its function. The identified amino-acid-level targets are highly conserved and functionally critical, providing potential opportunities for improved therapies and vaccines against hepatitis C.