Article
Multidisciplinary Sciences
Yunxi Liu, R. A. Leo Elworth, Michael D. Jochum, Kjersti M. Aagaard, Todd J. Treangen
Summary: Contaminant sequences in metagenomic samples can impact interpretation of microbiome studies, especially in low biomass environments. The authors propose a computational approach called Squeegee, which can detect microbial contamination and identify contaminants in publicly available datasets lacking negative controls.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Byunghan Lee, Hyeyoung Min, Sungroh Yoon, Inanc Birol
Summary: This study proposes an efficient method for error correction in metagenomic sequencing, reducing denoising time demands and overestimation of OTUs. By utilizing data-level parallelism and multiple processing units, the approach significantly improves the efficiency of denoising efforts and provides web-based visualization of results.
Article
Multidisciplinary Sciences
Hyunmin Koo, Casey D. Morrow
Summary: This study developed an analytic method to detect indicators of microbial strain dysbiosis and found shared gut commensal microbes in both healthy individuals and COVID-19 patients, suggesting a potential dysbiosis in the microbial strain community.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Samuel Zimmerman, Braden T. Tierney, Chirag J. Patel, Aleksandar D. Kostic
Summary: This study quantified the heterogeneity in microbial gene content across different ecological environments. The researchers identified a large number of nonredundant genes, with the majority occurring in only one sample. They also discovered sets of genes associated with specific ecological environments and highlighted the incompleteness and inaccuracy of previous microbiome gene catalogs.
Article
Chemistry, Physical
Maxime Blatter, Louis Delabays, Clement Furrer, Gerald Huguenin, Christian Pierre Cachelin, Fabian Fischer
Summary: The construction and long-term reliability of large microbial fuel cells (MFCs) are current challenges. Research has shown that MFCs can effectively remove pollutants such as COD, ammonia, and phosphorus from wastewater under specific conditions, while also achieving energy self-sufficiency.
JOURNAL OF POWER SOURCES
(2021)
Article
Microbiology
Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Richard Bonneau, Elodie Ghedin
Summary: Based on the analysis of household samples, we found that metagenomic-type analyses of the microbiome can track the transmission of airway bacteria. Microbial communities were more similar between individuals who cohabit in the same household than between individuals from different households. Sharing of bacteria from the airways increased in households with influenza infections compared to control households. However, due to the limited number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.
Review
Microbiology
Karrie K. K. Ko, Kern Rei Chng, Niranjan Nagarajan
Summary: Lessons learnt from the COVID-19 pandemic emphasize the importance of awareness and surveillance for zoonoses, emerging infectious diseases, and antimicrobial resistance. Metagenomics-based surveillance methods offer a promising solution for improving early detection of pathogens.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Huebner, Zandra Fagernaes, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche, Kirsten Kuesel
Summary: By adapting methods from microbial archaeology and paleogenomics, we recovered sufficient DNA from seven rock specimens for metagenomic analysis. Limestones serve as archives for genetic records of past microbial communities, including those sensitive to environmental stress, due to specific conditions facilitating long-term DNA preservation.
Article
Microbiology
Joanna Coker, Kateryna Zhalnina, Clarisse Marotz, Deepan Thiruppathy, Megan Tjuanta, Gavin D'Elia, Rodas Hailu, Talon Mahosky, Meagan Rowan, Trent R. Northen, Karsten Zengler
Summary: Microbes and plants form beneficial associations in soil communities, contributing to the growth and health of both. This study develops a model synthetic community of 16 soil microorganisms to advance research on plant-microbe interactions. The optimized preservation and dissemination methods of this microbial community will enhance soil microbe research.
Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Review
Engineering, Marine
Cora Hoerstmann, Sylke Wohlrab, Uwe John
Summary: High-throughput sequencing technologies have advanced our understanding of microbial diversity in the oceans, but research on microbial eukaryotes (protists) lags behind. This review discusses the challenges and opportunities of high-throughput sequencing methods for studying the evolutionary, ecological, and functional aspects of oceanic protists. These approaches allow for a deeper understanding of the functional role of protists and the changes in marine ecosystems.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Microbiology
Siew Herng Chan, Muhammad Hafiz Ismail, Chuan Hao Tan, Scott A. Rice, Diane McDougald
Summary: The study found that predation by protozoa and bacteriophage positively correlated with the formation of aerobic granules. The increase in abundance of filamentous phages may promote the structural formation of granules, while the absence of protozoa after chemical treatment delayed the initiation of granules formation.
Article
Environmental Sciences
Felipe A. S. Barbosa, Leonardo A. S. Brait, Felipe Hernandes Coutinho, Camilo M. Ferreira, Eduardo Freitas Moreira, Lucas de Queiroz Salles, Pedro Milet Meirelles
Summary: Aquifers are of great importance for society, economy, and ecology as they provide a significant portion of the world's freshwater supply. Analyzing microbial communities in different aquifers can help detect and predict environmental impacts. It was found that aquifer categories and low-abundant candidate taxa are strong predictors of microbial community structure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Amanda Pacholak, Agnieszka Zgola-Grzeskowiak, Ewa Kaczorek
Summary: The purpose of this research was to investigate the biodegradation of nitrofurantoin (NFT), a potential carcinogenic nitrofuran antibiotic, by two microbial communities from different environmental niches. The study found that NFT significantly altered the community structure and increased biodiversity in the aquatic systems. The research also discovered new transformation products of NFT.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
TzeHau Lam, Dillon Chew, Helen Zhao, Pengfei Zhu, Lili Zhang, Yajie Dai, Jiquan Liu, Jian Xu
Summary: Microbiomes on surfaces in kindergartens have a significant impact on the hygiene and wellbeing of young children. Good hand hygiene practices are crucial for managing hygiene levels and minimizing the spread of harmful microbes in susceptible indoor environments.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Cell Biology
Meenakshi Agarwal, Ashish Pathak, Rajesh Singh Rathore, Om Prakash, Rakesh Singh, Rajneesh Jaswal, John Seaman, Ashvini Chauhan
Article
Genetics & Heredity
Rajneesh Jaswal, Ashish Pathak, Bobby Edwards, Robert Lewis, John C. Seaman, Paul Stothard, Kirill Krivushin, Jochen Blom, Oliver Rupp, Ashvini Chauhan
Article
Cell Biology
Meenakshi Agarwal, Rajesh Singh Rathore, Charles Jagoe, Ashvini Chauhan
Article
Microbiology
Ashish Pathak, Paul Stothard, Ashvini Chauhan
Summary: Eastern oysters in the United States play a crucial role as keystone species in Gulf of Mexico estuarine waters, providing important economic, ecological, environmental, and cultural services. Recent research has highlighted the ability of oysters to sequester impurities and nutrients through their filtration mechanism and microbially-mediated denitrification processes. Pseudomonads, a type of bacteria interplaying with oyster host species, show significant metabolic and ecological potential, deserving further assessment.
Article
Microbiology
Ashvini Chauhan, Rajesh Singh Rathore, Meenakshi Agarwal, Adi J. Chauhan, Aryan Taywade
Summary: We report the genomic features of Bradyrhizobium sp. strain SRS-191, isolated from a former nuclear legacy site in Aiken, South Carolina, USA. The strain has a genome size of 7,621,400 bp and carries genes for environmentally beneficial traits like heavy metal resistance, nitrogen fixation, and aromatic biodegradation, as well as genes for antimicrobial resistance.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Review
Microbiology
Jake M. Robinson, Nicole Redvers, Araceli Camargo, Christina A. Bosch, Martin F. Breed, Lisa A. Brenner, Megan A. Carney, Ashvini Chauhan, Mauna Dasari, Leslie G. Dietz, Michael Friedman, Laura Grieneisen, Andrew J. Hoisington, Patrick F. Horve, Ally Hunter, Sierra Jech, Anna Jorgensen, Christopher A. Lowry, Ioana Man, Gwynne Mhuireach, Edauri Navarro-Perez, Euan G. Ritchie, Justin D. Stewart, Harry Watkins, Philip Weinstein, Suzanne L. Ishaq
Summary: This study aims to summarize and stimulate research on microbial exposure and social equity, providing focus for funders and policymakers.
Article
Microbiology
Meenakshi Agarwal, Rajesh Singh Rathore, Allen Black, Xiaoyu Xu, John Seaman, Ashvini Chauhan
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Biochemical Research Methods
Meenakshi Agarwal, Rajesh Singh Rathore, Ashvini Chauhan
METHODS AND PROTOCOLS
(2020)
Article
Genetics & Heredity
Ashish Pathak, Ashvini Chauhan, Paul Stothard, Stefan Green, Mark Maienschein-Cline, Rajneesh Jaswal, John Seaman
Article
Genetics & Heredity
Ashvini Chauhan, Ashish Pathak, Ayman Y. I. Ewida, Zabrenna Griffiths, Paul Stothard