Article
Biology
Gerardo A. Stoppiello, Claudia Coleine, Ralf Moeller, Caterina Ripa, Daniela Billi, Laura Selbmann
Summary: This study investigated microbial diversity on the snow surface of the Antarctic Polar Plateau and found that seasonality was the main driver of bacterial and fungal assemblages. The fungal component was dominated by Basidiomycota and Ascomycota, while the bacterial component was mainly represented by Bacteroidota. The study highlighted the impact of human activity on microbial composition in this environment.
Review
Biotechnology & Applied Microbiology
Lakshmi Kasirajan, Julie A. Maupin-Furlow
Summary: Lignocellulosic biofuels and chemicals hold promise in reducing fossil fuel dependence and mitigating air pollution. Haloarchaea and their enzymes, capable of sustaining catalytic activity under extreme conditions, are being explored as ideal resources for biofuel production and value-added products.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Multidisciplinary Sciences
Zhidong Zhang, Guilin Liu, Yao Chen, Weizhen Xue, Qianyue Ji, Qiwu Xu, He Zhang, Guangyi Fan, He Huang, Ling Jiang, Jianwei Chen
Summary: This study compared hybrid assembly strategies for genome assembly of six bacterial isolates using different sequencing platforms, and found that stLFR sequencing data yielded more contiguity and gene function integrity compared to NGS. The research provides a cost-effective chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.
Article
Biotechnology & Applied Microbiology
Daichi Morimoto, Naohiro Yoshida, Aya Sasaki, Satoshi Nakagawa, Yoshihiko Sako, Takashi Yoshida
Summary: The bloom-forming toxic cyanobacterium Microcystis aeruginosa interacts with diverse broad- and narrow-host-range viruses. However, the dynamics of the Microcystis population (at the intraspecies level) and viruses with different host ranges remain unknown.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Maria Robles, Ines Garbayo, Jacek Wierzchos, Carlos Vilchez, Maria Cuaresma
Summary: The efficacy of low-frequency ultrasound pulses in cell disaggregation of Chroococcidiopsis sp. aggregates was studied, and it was found that the ultrasound pulses were effective in disaggregating the aggregates, improving photosynthetic efficiency and nutrient availability while maintaining cellular viability. This is significant for large-scale production.
JOURNAL OF APPLIED PHYCOLOGY
(2022)
Article
Microbiology
Can Akpolat, Ana Beatriz Fernandez, Pinar Caglayan, Baris Calli, Meral Birbir, Antonio Ventosa
Summary: The study analyzed 30 brine samples from various salt lakes and salterns in Turkey, finding that archaea dominated these habitats while bacteria were present in lower amounts. Various archaeal and bacterial genera were detected, with Haloquadratum and Halorhabdus being the most abundant genera found in all sampling sites.
Article
Immunology
Gregory L. Damhorst, Max W. Adelman, Michael H. Woodworth, Colleen S. Kraft
Summary: There is increasing recognition of the significance of the gut microbiome in human health and disease. Traditional and modern technologies have advanced our knowledge in this field, but standardizing the language and metrics for characterizing the microbiome is still a work in progress. The capabilities of gut microbiome-based diagnostics are promising for clinical applications, with selected examples demonstrating their potential impact.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Plant Sciences
Joanne Mackie, Wycliff M. Kinoti, Sumit Chahal, David A. Lovelock, Paul R. Campbell, Lucy T. T. Tran-Nguyen, Brendan C. Rodoni, Fiona E. Constable
Summary: A targeted whole genome sequencing method has been developed for detecting cucumber green mottle mosaic virus, which can effectively address the challenges in genomic sequencing of plant viruses by enriching target nucleic acid and using Oxford Nanopore MinION sequencing technology. The results of the study show that this method can efficiently and accurately detect the virus, and also yield good results in degraded samples.
Article
Food Science & Technology
Gabriel A. Rivas, Liliana Semorile, Lucrecia Delfederico
Summary: The microbial communities in Malbec vineyards in Argentina were characterized with a predominance of Proteobacteria and Actinobacteria in the soil and rhizosphere. The order Rhizobiales stood out with its plant-growth promotion properties. Ascomycota and Basidiomycota were the most abundant phyla in fungal communities. The wine samples showed low levels of lactic acid bacteria and the presence of acetic acid bacteria throughout fermentation without affecting the wine acidity.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemical Research Methods
Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe Elie Gozlan, Marine Combe
Summary: This article introduces an amplicon-based nanopore sequencing pipeline for analyzing the genetic diversity of SARS-CoV-2 and other pathogens. The pipeline integrates multiple bioinformatics tools, allowing users with minimal bioinformatics skills to perform downstream analysis steps with a simple command line and configuration file.
Article
Biology
Alessandro Napoli, Claudia Coleine, Nikea J. Ulrich, Ralf Moeller, Daniela Billi, Laura Selbmann
Summary: The Concordia Research Station is an important location for preparing for future human missions to Mars and studying microbial diversity in extreme environments. DNA sequencing techniques were used to analyze surface snow samples collected over a two-year period, revealing a low but diverse microbiome. The results have implications for planetary protection and the search for life in astrobiology.
Article
Microbiology
Benjamin J. Callahan, Dmitry Grinevich, Siddhartha Thakur, Michael A. Balamotis, Tuval Ben Yehezkel
Summary: LoopSeq is a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads, enabling direct identification of microbial genes and species in complex samples. Compared to standard Illumina amplicon sequencing, LoopSeq offers an order-of-magnitude improvement in length and accuracy, allowing accurate identification of species and strains from complex to low-biomass microbiome samples.
Article
Environmental Sciences
Hidetoshi Urakawa, Michael A. Kratz, Taylor L. Hancock, Rick A. Armstrong
Summary: This study developed a new method (QT-AMP) for the identification and quantification of Enterococcus using a high-throughput sequencing platform. The method detected 11 Enterococcus species, including three rare species and eight commonly found species, in water samples from three rivers in southwest Florida. QT-AMP showed a higher detection level compared to regular sequencing methods.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Agronomy
Jiamin Gao, Shi Chen, Yang Wang, Jiejun Qi, Xiaomeng Li, Gehong Wei, Shuo Jiao
Summary: This study revealed the differences in microbial communities in the lateral roots with/without nodules and identified a keystone ecological cluster positively linking with multiple functional cycling.
Article
Immunology
Jill M. C. Hakim, Andreea Waltmann, Freddy Tinajeros, Oksana Kharabora, Edith Malaga Machaca, Maritza Calderon, Maria del Carmen Menduina, Jeremy Wang, Daniel Rueda, Mirko Zimic, Manuela Verastegui, Jonathan J. Juliano, Robert H. Gilman, Monica R. Mugnier, Natalie M. Bowman
Summary: Investigating the diversity of parasite strains in congenital Chagas infection, amplicon sequencing of a T. cruzi gene was conducted on clinical samples from Chagas positive mothers and their infected infants. The study found that multiple parasite strains are involved in initiating congenital infection, and the diversity of parasite strains is higher in infants than in mothers. These findings suggest that the probability of vertical transmission is influenced by parasite factors.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Marine & Freshwater Biology
Janina C. Vogt, Dirk C. Albach, Katarzyna A. Palinska
Article
Ecology
Janina C. Vogt, Raeid M. M. Abed, Dirk C. Albach, Katarzyna A. Palinska
Article
Biodiversity Conservation
K. A. Palinska, T. Schneider, W. Surosz
Article
Environmental Sciences
Raeid M. M. Abed, Katarzyna A. Palinska, Juergen Koester
GEOMICROBIOLOGY JOURNAL
(2018)
Article
Marine & Freshwater Biology
Katarzyna A. Palinska, Waldemar Surosz
OCEANOLOGICAL AND HYDROBIOLOGICAL STUDIES
(2018)
Article
Marine & Freshwater Biology
Katarzyna A. Palinska, Waldemar Surosz
Article
Marine & Freshwater Biology
Mayalen Zubia, Christophe Vieira, Katarzyna A. Palinska, Melanie Roue, Jean-Claude Gaertner, Ilona Zloch, Mathieu Grellier, Stjepko Golubic