Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Food Science & Technology
Dimitra Dourou, Evgenia D. Spyrelli, Agapi Doulgeraki, Anthoula A. Argyri, Athena Grounta, George-John E. Nychas, Nikos G. Chorianopoulos, Chrysoula C. Tassou
Summary: Chicken meat is a widely consumed food globally, and understanding the bacterial diversity of different parts of chicken stored at various temperatures is crucial. This study utilized traditional culture methods and NGS analysis to explore the bacterial communities in chicken breast and thigh fillets, revealing a complex structure with different bacterial populations persisting during storage. The results suggest the necessity of combining classical microbiological methods with NGS technologies to fully characterize chicken meat spoilage microbiota.
Article
Respiratory System
Ya-Sian Chang, Siang-Jyun Tu, Yu-Chia Chen, Ting-Yuan Liu, Ya-Ting Lee, Ju-Chen Yen, Hsin-Yuan Fang, Jan-Gowth Chang
Summary: This study identified 19 known driver mutations and new variants in Taiwanese patients with non-small cell lung cancer. EGFR mutations were found at a higher frequency compared to Caucasians, while KRAS and TP53 mutations were less common. All ClinVar pathogenic variants were trunk mutations present in the tumor regions.
RESPIRATORY RESEARCH
(2021)
Article
Oncology
Christian Rolfo, Alexander Drilon, David Hong, Caroline McCoach, Afshin Dowlati, Jessica J. Lin, Alessandro Russo, Alison M. Schram, Stephen Liu, Jorge J. Nieva, Timmy Nguyen, Shahrooz Eshaghian, Michael Morse, Scott Gettinger, Mohammad Mobayed, Sarah Goldberg, Emilio Araujo-Mino, Neelima Vidula, Aditya Bardia, Janakiraman Subramanian, Deepa Sashital, Thomas Stinchcombe, Lesli Kiedrowski, Kristin Price, David R. Gandara
Summary: This study retrospectively reviewed a ctDNA database in advanced stage solid tumors to identify NTRK1 fusions, and found NTRK1 fusion events in 37 patients with nine unique fusion partners. 44% of cases had tissue testing for NTRK1 fusions, and the NTRK1 fusions detected by ctDNA were confirmed in tissue in 88% of cases. This study reports for the first time that minimally-invasive plasma NGS can detect NTRK fusions with a high positive predictive value.
BRITISH JOURNAL OF CANCER
(2022)
Article
Genetics & Heredity
Gang Liu, Shumiao Zhang, Xinsheng Zhao, Chao Li, Minghao Gong
Summary: Diet analysis is crucial in animal ecology, and the next generation sequencing (NGS) approach has been suggested as a promising tool to improve efficiency. However, challenges in generating NGS-based diet data and subsequent analyses have hindered its widespread application in the field. More developments and incorporation of additional perspectives are needed to encourage ecologists to gain novel insights in their work.
Article
Immunology
Jing Wang, Huan Xu, Xi Wang, Jian Lan
Summary: This study retrospectively analyzed the clinical data and treatment outcomes of 12 patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) using metagenomic next-generation sequencing (mNGS). The results showed that mNGS could rapidly and accurately diagnose NTM-PD and guide the selection of appropriate treatment, thereby improving the prognosis of patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Lingyue Zhu, Yan Chen, Ruibo Sun, Jiabao Zhang, Lauren Hale, Kenneth Dumack, Stefan Geisen, Ye Deng, Yinghua Duan, Bo Zhu, Yan Li, Wenzhao Liu, Xiaoyue Wang, Bryan S. Griffiths, Michael Bonkowski, Jizhong Zhou, Bo Sun
Summary: To achieve long-term sustainability of intensive agricultural practices, understanding belowground functional stability is crucial. This study investigated how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. The results showed that higher resource availability increased potential cross-trophic interactions, while low resource availability made stability more dependent on within trophic interactions and soil biodiversity.
Article
Immunology
Shilei Wang, Lihua Xing
Summary: Metagenomics next-generation sequencing (mNGS) is a promising method for detecting pathogenic infections, especially Non-Tuberculous Mycobacterial (NTM) and tuberculosis (TB). In this study, mNGS analysis successfully identified six distinct NTM species, primarily Mycobacterium avium complex (MAC). Conventional culture methods faced challenges, resulting in negative results, while qPCR testing showed positive results for the NTM infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Ecology
Daniel Montoya
Summary: This study integrates empirical aquatic food webs with a multitrophic model to show that ecosystem function variability generally follows a hump-shaped pattern along the species richness gradient. The dependence of ecosystem function on species diversity is driven by both bottom-up and top-down control, which regulate taxa composition and dominance. An important implication of this study is that biodiversity loss may not only reduce the average levels of ecosystem functioning but also increase unpredictability by generating greater function variability.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Review
Cell Biology
Wenjuan Zhang, Jian Cao, Ke Liu, Ziwei Qu, Ying Zheng, Jun Yu, Yishan Yu, Yongsheng Wang, Wendy Wu
Summary: Immunotherapy has become the main systemic therapy for cancer patients, but current biomarkers are limited by tumor tissue accessibility. Rare mutations in CD274 gene's UTR region have been suggested as potential biomarkers for immunotherapy efficacy. This study explores the multi-omics analysis of CD274 UTR region using cSMART 2.0 technology and finds that rare structural variants exist in different Chinese cancer populations, which can predict response to immune checkpoint inhibitors. Liquid biopsy-based cSMART 2.0 technology offers a more sensitive and accurate detection method when tissue samples are unavailable.
CELL DEATH DISCOVERY
(2023)
Article
Engineering, Environmental
Zexin Tao, Xiaojuan Lin, Yao Liu, Feng Ji, Suting Wang, Ping Xiong, Li Zhang, Qing Xu, Aiqiang Xu, Ning Cui
Summary: This study collected sewage samples from Jinan, China from 2018 to 2019, and analyzed classic and novel HAstVs using real-time quantitative PCR and next generation sequencing. The results showed that sewage contains a high diversity of astroviruses, and there are multiple co-circulating lineages within each local HAstV genotype.
Article
Soil Science
Kurt O. Reinhart, Matthew J. Rinella, Hilaire S. Sanni Worogo, Richard C. Waterman, Lance T. Vermeire
Summary: Identifying grazing practices that maximize food production and soil carbon sequestration is globally important. This study tested the effects of five grazing treatments on soil organic carbon (SOC) stocks using a randomized controlled trial (RCT) and found that new grazing practices can increase SOC accrual. The results indicate that SOC accrual is mainly associated with factors related to decreased SOC mineralization. Additionally, the study highlights the importance of pre-treatment data for reliable results in little-replicated RCTs.
Article
Engineering, Multidisciplinary
Mourad Elloumi, Mostafa A. Ahmad, Ahmed H. Samak, Ali M. Al-Sharafi, Daisuke Kihara, Ahmed Taloba
Summary: Non-null tests are versatile and efficient for measuring aspheric surfaces with deviations from a reference sphere. Complex system modeling and simulations are required to correct retracing errors and replicate aspheric fabrication imperfections. A ray-tracing-based technique is proposed for simulating the non-null interferometer, effectively rectifying the retracing error and providing fast and generic tests with sufficient performance.
ALEXANDRIA ENGINEERING JOURNAL
(2022)
Article
Gastroenterology & Hepatology
Marta Magaz, Alberto Alvarez-Larran, Dolors Colomer, Monica Lopez-Guerra, M. Angeles Garcia-Criado, Gabriel Mezzano, Ernest Belmonte, Pol Olivas, Guillem Soy, Francisco Cervantes, Anna Darnell, Jose Ferrusquia-Acosta, Anna Baiges, Fanny Turon, Virginia Hernandez-Gea, Juan Carlos Garcia-Pagan
Summary: The study showed that NGS can identify JAK2-exon 12 mutations in NC-SVT patients that were not previously detected by conventional techniques, and it also detected High Molecular Risk (HMR) variants in approximately one-third of patients with NC-SVT, who seem to have a higher risk of splanchnic rethrombosis. These findings support the potential usefulness of NGS as a diagnostic tool in the management of NC-SVT.
JOURNAL OF HEPATOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Carl Simon Strittmatter, Anja Poehlein, Axel Himmelbach, Rolf Daniel, Alexander Steinbuchel
Summary: The number of genes encoding beta-oxidation enzymes in Cupriavidus necator H16 is high, but only two operons, A0459-A0464 and A1526-A1531, were expressed during growth with long-chain-length fatty acids (LCFAs). The deletion of these operons had a negative effect on growth with longer chain fatty acids. RNA-Seq analysis revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biodiversity Conservation
Sebastian Koethe, Florian D. Schneider, Nikita Bakanov, Carsten A. Bruehl, Lisa Eichler, Thomas Fickel, Birgit Gemeinholzer, Thomas Hoerren, Alexandra Lux, Gotthard Meinel, Livia Schaeffler, Christoph Scherber, Martin Sorg, Stephanie J. Swenson, Wiltrud Terlau, Angela Turck, Vera M. A. Zizka, Gerlind U. C. Lehmann, Roland Muehlethaler
Summary: In recent years, there has been increasing public attention and demand for political action regarding the decline of insect biodiversity and its consequences on ecosystem functions and services. To address the complex causes of insect decline, the DINA project in Germany assesses insect communities in nature reserves and investigates their interactions with various factors such as plant diversity, pesticide exposure, and climate. The project involves obtaining scientific data and engaging stakeholders to identify opportunities and challenges in insect conservation. Results show a positive association between insect richness and biomass, while also highlighting the negative impacts of pesticides and agricultural production on insect diversity. Stakeholders expressed support for insect conservation but emphasized the need for more information, data, and flexible policy options.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Biodiversity Conservation
Joerdis F. Terlau, Ulrich Brose, Nico Eisenhauer, Angelos Amyntas, Thomas Boy, Alexander Dyer, Alban Gebler, Christian Hof, Tao Liu, Christoph Scherber, Ulrike E. Schlaegel, Anja Schmidt, Myriam R. Hirt
Summary: Anthropogenic global warming affects mobile terrestrial insects by changing their activity levels and distribution patterns. Heat extremes induce physiological responses in insects, causing them to either decrease activity or seek out favorable microhabitats. The availability of these microhabitats is affected by anthropogenic land transformation, which reduces habitat heterogeneity. It is important to understand the combined effects of these global change drivers on insect activity.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Microbiology
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kaempfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon- Wo Kwon
Summary: In this study, two strains of bacteria were isolated from wasps in Germany and Korea. Molecular and phenotypic analysis showed that these strains are closely related to known species but also have distinct characteristics. Therefore, it is proposed to name these strains Aristophania vespae.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Juan Guzman, Anja Poehlein, Rolf Daniel, Peter Kaempfer, Andreas Vilcinskas
Summary: Strain G314FT, isolated from Lucilia sericata in Germany, belongs to the genus Vagococcus. It shows high sequence identity with Vagococcus bubulae, Vagococcus martis, and Vagococcus teuberi, indicating that it represents a new species of the genus. The genome of G314FT is the smallest among the closely related species and has differences in amino acid biosynthesis and carbohydrate metabolism.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Delphine Clara Zemp, Nathaly Guerrero-Ramirez, Fabian Brambach, Kevin Darras, Ingo Grass, Anton Potapov, Alexander Roell, Isabelle Arimond, Johannes Ballauff, Hermann Behling, Dirk Berkelmann, Siria Biagioni, Damayanti Buchori, Dylan Craven, Rolf Daniel, Oliver Gailing, Florian Ellsaesser, Riko Fardiansah, Nina Hennings, Bambang Irawan, Watit Khokthong, Valentyna Krashevska, Alena Krause, Johanna Kueckes, Kevin Li, Hendrik Lorenz, Mark Maraun, Miryam Sarah Merk, Carina C. M. Moura, Yeni A. Mulyani, Gustavo B. Paterno, Herni Dwinta Pebrianti, Andrea Polle, Di Ajeng Prameswari, Lena Sachsenmaier, Stefan Scheu, Dominik Schneider, Fitta Setiajiati, Christina Ani Setyaningsih, Leti Sundawati, Teja Tscharntke, Meike Wollni, Dirk Hoelscher, Holger Kreft
Summary: There are still knowledge gaps in how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes in the United Nations Decade on Ecosystem Restoration. This study presents findings from a 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, showing higher indicators of biodiversity and ecosystem functioning in tree islands compared to conventionally managed oil palm. Enriching oil palm-dominated landscapes with tree islands is a promising ecological restoration strategy that does not decrease oil palm yield.
Article
Environmental Sciences
Jimyung Moon, Anja Schubert, Anja Poehlein, Rolf Daniel, Volker Mueller
Summary: To inactivate the Wood-Ljungdahl pathway in Acetobacterium woodii, two subunits of the methylene-tetrahydrofolate reductase were genetically deleted. The mutant was unable to grow on C1 compounds, lactate, ethanol, or butanediol, but could grow on fructose with lower rates and yields compared to the wild-type. Growth on fructose was restored by the addition of an external electron sink, such as glycine betaine + CO2 or caffeate. Transcriptome analyses revealed enzymes potentially involved in mixed acid fermentation (MAF) from fructose in A. woodii.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Ines Friedrich, Hannes Neubauer, Alisa Kuritsyn, Bernhard Bodenberger, Faina Tskhay, Sara Hartmann, Anja Poehlein, Mechthild Boemeke, Michael Hoppert, Dominik Schneider, Robert Hertel, Rolf Daniel
Summary: By investigating host-associated metaviromes, we found that the classical isolation technique may miss the diversity of non-plaque forming phages. Through direct plaque-based isolation using new hosts, we discovered a higher phage diversity in Brevundimonas and Serratia. This study demonstrates the potential of combining metavirome analysis with traditional isolation techniques to reveal further phage diversity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Green & Sustainable Science & Technology
Najeeb Al-Amin Iddris, Greta Formaglio, Carola Paul, Volker von Gross, Guantao Chen, Andres Angulo-Rubiano, Dirk Berkelmann, Fabian Brambach, Kevin F. A. Darras, Valentyna Krashevska, Anton Potapov, Arne Wenzel, Bambang Irawan, Muhammad Damris, Rolf Daniel, Ingo Grass, Holger Kreft, Stefan Scheu, Teja Tscharntke, Aiyen Tjoa, Edzo Veldkamp, Marife D. Corre
Summary: This full factorial experiment conducted in an Indonesian state-owned industrial oil palm plantation evaluated the effects of reduced management practices on ecosystem functions and biodiversity. The results showed that mechanical weeding exhibited higher multifunctionality and increased plant species diversity compared to herbicide treatment. Furthermore, reduced fertilization and mechanical weeding increased profit and gross margin while achieving similar yields.
NATURE SUSTAINABILITY
(2023)
Article
Microbiology
Dominik Schneider, Aygun Ganbarzade, Sina Post, Daniela Zuehlke, Tjorven Hinzke, Jacqueline Hollensteiner, Anja Poehlein, Katharina Riedel, Rolf Daniel
Summary: The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was found in a hospital wastewater sample in Greifswald, Germany. Its genome consists of one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome contains 5,322 coding sequences, shows high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Lydia Alberti, Patricia Koenig, Sabine Zeidler, Anja Poehlein, Rolf Daniel, Beate Averhoff, Volker Mueller
Summary: Acinetobacter baumannii, a nosocomial pathogen, exhibits significant metabolic diversity. Growth on L-arabinose was found, and transcriptome analyses identified two gene clusters responsible for the oxidation of pentonates to a-ketoglutarate. These clusters also encode an uptake system and a regulator for specific pentonate oxidation pathways. Despite a cross-talk between these pathways, growth on pentoses was observed in pathogenic Acinetobacter species, while growth on L-arabinose provided benefits for long-term survival and desiccation resistance in A. baumannii ATCC 19606.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tim Boeer, Frank R. Bengelsdorf, Mechthild Boemeke, Rolf Daniel, Anja Poehlein
Summary: This study reports the complete genome sequences of acetogenic strains from the genus Terrisporobacter, along with functional annotation and pathway reconstruction analysis. The study also identifies species-specific nutrient requirements and constructs a model for acetogenesis in Terrisporobacter.
Editorial Material
Biology
Christoph Scherber
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Microbiology
Simone Anza, Dominik Schneider, Rolf Daniel, Michael Heistermann, Somboon Sangmaneedet, Julia Ostner, Oliver Schuelke
Summary: Maternal glucocorticoids (GCs) can have detrimental effects on offspring development, particularly during early gestation. This study found that high maternal GC levels during early gestation were associated with reduced bacterial richness in the offspring's gut microbiota. The effect of maternal GCs on the gut microbiota worsened with offspring age and was 10 times stronger than the effect of exposure during late prenatal or postnatal periods.
Article
Microbiology
Miriam Antonia Schueler, Rolf Daniel, Anja Poehlein
Summary: This study presents the complete genome of a non-toxigenic Clostridioides difficile strain isolated from horse feces. The genome consists of one chromosome and one plasmid, and encodes 3,798 putative genes. The strain represents a sub-cluster in the cryptic clade C-III.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)