Article
Microbiology
Wenke Zhang, Xiaoquan Fan, Haobo Shi, Jian Li, Mingqian Zhang, Jin Zhao, Xiaoquan Su
Summary: In this study, a comprehensive method called Qscore was proposed to evaluate the performance of 16S rRNA amplicons in microbial profiling. The method integrated factors such as amplification rate, taxonomic annotation, sequence type, and length. Evaluation of a wide range of microbe species and microbiomes showed that the Qscore-suggested parameters resulted in high precision in microbiome profiling. This study has significant implications for guiding future microbiome studies and enabling the reuse of massive sequence data.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Kayla M. Williamson, Brandie D. Wagner, Charles E. Robertson, Mark J. Stevens, Marci K. Sontag, Peter M. Mourani, J. Kirk Harris
Summary: The study aimed to increase the sensitivity of bacterial community analysis without impacting community composition or interfering with cluster formation during sequencing. The modified PCR protocol showed increased sensitivity in detecting bacterial communities in airway samples, crucial for studying the highly variable human airway microbiome.
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Marcel Suleiman, Francesca Demaria, Cristina Zimmardi, Boris Alexander Kolvenbach, Philippe Francois-Xavier Corvini
Summary: Pharmaceuticals accumulation in the environment is a concern for our planet and health. Little is known about the biodegradation capacity of microbial communities for multiple micropollutants. This study demonstrates the feasibility of cultivating stable microbial communities capable of degrading a mixture of highly concentrated pharmaceuticals.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Shu Li, Bao Qi, Wan Wang, Xueyan Peng, Andrey A. Gontcharov, Bao Liu, Qi Wang, Yu Li
Summary: The study identified the bacterial communities associated with the plasmodia of six myxomycetes species and found that while the bacterial composition varied among species, there was a high similarity in the functional composition of the bacterial communities. The enrichment for gram-negative and aerobic bacteria in plasmodia suggests that myxomycetes may selectively recruit certain bacteria from the environment.
Article
Immunology
Vitor Heidrich, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, Anamaria A. Camargo
Summary: Accessibility to next-generation sequencing (NGS) has enabled the profiling of microbial communities. Choosing the right 16S rRNA hypervariable region for sequencing is critical. This study evaluated the performance of different hypervariable regions in male urinary microbiota profiling and found that V1V2 region is more suitable.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Agriculture, Dairy & Animal Science
Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramirez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Summary: Microbiome studies in animal science using 16S rRNA gene sequencing are becoming more common. This review serves as a guide for animal scientists less familiar with this method, discussing common issues and considerations in planning such studies.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Microbiology
Ezgi Ozkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Summary: LotuS2 is a lightweight and user-friendly pipeline for amplicon sequence analysis, offering high speed and precision, as well as improved data quality through extensive pre- and post-processing steps.
Article
Microbiology
Laura E. Tibbs-Cortes, Bienvenido W. Tibbs-Cortes, Stephan Schmitz-Esser
Summary: This study analyzed the microbiota of tardigrades from apple orchards in central Iowa, United States, and found that tardigrades have a distinct microbiota from their environment. They also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens. This suggests the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Wisnu Adi Wicaksono, Christina Morauf, Henry Mueller, Ahmed Abdelfattah, Christina Donat, Gabriele Berg
Summary: The study aimed to investigate the relationship between grapevine cultivars susceptibility to Plasmopara viticola and the phyllosphere microbiota. Through analyzing the 16S rRNA gene library of the dominant phyllosphere bacterial phyla Alphaproteobacteria in seven Vitis genotypes at different developmental stages, it was found that young leaves had higher Alphaproteobacterial richness and diversity, while the microbial communities of mature leaves were structurally distinct according to P. viticola resistance levels. The study also revealed that plants recruit specific bacterial taxa that mediate microbe-microbe interactions and structure mature communities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Microbiology
Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Summary: A high-throughput sequencing method was developed for profiling Pseudomonas species in soil microbiomes, identifying more species than 16S rRNA gene sequencing or cultivation. This method allows for tracing specific species of Pseudomonas and screening environmental samples for further isolation and exploitation.
Article
Biodiversity Conservation
Anais Chanson, Corrie S. Moreau, Christophe Duplais
Summary: This study examines the impact of host ecology and evolutionary history on the microbial communities of Amazonian ants. The research shows that habitat does not play a role in structuring ant microbial communities, but ant diet and nesting mode do influence bacterial communities. Additionally, nesting mode is the determining factor for microbial eukaryote communities, while microbial diversity is not correlated with host phylogeny.
Article
Environmental Sciences
Tilak Nayak, Debjit De, Parimal Karmakar, Argha Deb, Paltu Kumar Dhal
Summary: This study examined the microbial dynamics of drinking water with different radon gradients and found that sites with radon contamination had lower microbial diversity. The dominant microbial families varied between sites with different radon gradients, highlighting the potential for utilizing microbial communities for biostimulation-based in situ bioremediation.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2021)
Article
Agronomy
Svetlana B. Lysko, Olga A. Baturina, Natalia B. Naumova, Nadezhda A. Lescheva, Valentina I. Pleshakova, Marsel R. Kabilov
Summary: This study examined the effect of pectin prebiotics on the gut microbiota of chickens. The results showed that the prebiotic supplementation increased the abundance of Enterococcus and improved feed use efficiency and growth performance. The response of the microbiota to antibiotics showed more sex-related differential OTUs compared to the pectin prebiotic. Therefore, sex should be taken into account in interventional studies of gut microbiota.
