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
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
Engineering, Environmental
Qiaowen Tan, Weiying Li, Xiao Chen
Summary: This study investigated the importance of bacterial diversity in source tracking of fecal contamination, comparing the performances of different classification models. The results showed that the SVM model had the highest accuracy on local samples, indicating its efficiency and accuracy in fecal source tracking.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Ya Wang, Kelsey N. Thompson, Yan Yan, Meghan I. Short, Yancong Zhang, Eric A. Franzosa, Jiaxian Shen, Erica M. Hartmann, Curtis Huttenhower
Summary: Characterization of microbial activity is important for understanding the basic biology of microbial communities. Current sequence-based technologies can't differentiate microbial activity well, leading to incomplete understanding of microbial community structures and transmission mechanisms. 16S-RNA-seq has been proposed as a potential solution, but its efficacy has not been systematically evaluated. This study evaluated the viability assessment ability of 16S-RNA-seq in synthetic and complex microbial communities.
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
Hiroto Miura, Masayuki Takeda, Megumi Yamaguchi, Yoshihisa Ohtani, Go Endo, Yasuhisa Masuda, Kaede Ito, Yoshio Nagura, Kunihiro Iwashita, Tomohiro Mitani, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike
Summary: This study established a high-resolution and high-throughput rumen microbial profiling approach by combining the MinION platform and buccal swab samples, which could potentially be applied in large-scale studies for rumen microbial analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Gangding Huang, Yanning Mao, Weiwei Zhang, Qi Luo, Rong Xie, Dongmei Huang, Yumei Liang
Summary: Studies have shown that there are significant differences in the composition of intestinal flora between patients with COVID-19 and non-COVID-19 patients. This study analyzed alpha and beta diversity to compare species richness, diversity, and composition between COVID-19 and control groups. The study identified key Amplicon Sequence Variants (ASVs) that can be used for the diagnosis of COVID-19.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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
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
Biotechnology & Applied Microbiology
Dong Han, Hongmin Zhen, Xiaoyan Liu, Justyna Zulewska, Zhennai Yang
Summary: This study used both rRNA and gDNA sequencing on mouse cecal contents and found differences in microbial composition and functional predictions between the two methods. rRNA-derived sequencing improved identification capability of specific microorganisms and was more suitable for functional predictions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Richa Bharti, Dominik G. Grimm
Summary: Analyzing the microbiome using next-generation sequencing techniques has improved our understanding of environmental microorganisms. However, analysis is affected by experimental conditions and downstream analysis, and new sequencing technologies can impact results. This work aims to review important workflows for sequencing data and provide best-practice protocols.
BRIEFINGS IN BIOINFORMATICS
(2021)
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)
Article
Pharmacology & Pharmacy
Zhimin Miao, Yong Lai, Yingying Zhao, Lingmin Chen, Jianeng Zhou, Chunyan Li, Yan Wang
Summary: This study demonstrated the hepatoprotective effects of SCU in carbon tetrachloride-induced liver injury by regulating lipid metabolism, bile acid homeostasis, liver signaling pathways, and gut microbiota composition. SCU, originating from a functional food, showed promising potential as a protective agent against liver injury.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dattatray S. Mongad, Nikeeta S. Chavan, Nitin P. Narwade, Kunal Dixit, Yogesh S. Shouche, Dhiraj P. Dhotre
Summary: 16S rRNA gene amplicon sequencing accurately characterizes microbial taxonomic abundances but lacks functional information. MicFunPred, a new tool, uses core genes to predict metagenomes, showing low False Positive Rate and performing faster with lower computational requirements compared to other tools.
Article
Soil Science
Adrian Langarica-Fuentes, Marta Manrubia, Madeline E. Giles, Susan Mitchell, Tim J. Daniell
SOIL BIOLOGY & BIOCHEMISTRY
(2018)
Article
Multidisciplinary Sciences
Alexander Peltzer, Alissa Mittnik, Chuan-Chao Wang, Tristan Begg, Cosimo Posth, Kay Nieselt, Johannes Krause
SCIENTIFIC REPORTS
(2018)
Correction
Agricultural Engineering
Urooj Zafar, Petrus Nzerem, Adrian Langarica-Fuentes, Ashley Houlden, Alan Heyworth, Alberto Saiani, Geoff D. Robson
BIORESOURCE TECHNOLOGY
(2019)
Article
Biochemical Research Methods
Sven Fillinger, Luis de la Garza, Alexander Peltzer, Oliver Kohlbacher, Sven Nahnsen
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2019)
Article
Biochemical Research Methods
Leon Bichmann, Annika Nelde, Michael Ghosh, Lukas Heumos, Christopher Mohr, Alexander Peltzer, Leon Kuchenbecker, Timo Sachsenberg, Juliane S. Walz, Stefan Stevanovic, Hans-Georg Rammensee, Oliver Kohlbacher
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Oncology
Zulrahman Erlangga, Katharina Wolff, Tanja Poth, Alexander Peltzer, Sven Nahnsen, Steffi Spielberg, Kai Timrott, Norman Woller, Florian Kuehnel, Michael P. Manns, Anna Saborowski, Arndt Vogel, Michael Saborowski
Letter
Biotechnology & Applied Microbiology
Philip A. Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen
NATURE BIOTECHNOLOGY
(2020)
Editorial Material
Biochemical Research Methods
Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Ecology
Xin Shu, Tim J. Daniell, Paul D. Hallett, Elizabeth M. Baggs, Susan Mitchell, Adrian Langarica-Fuentes, Bryan S. Griffiths
Summary: This study compared the resistance and resilience of carbon mineralization, ammonia oxidation, and denitrification in two managed soils after being subjected to persistent and transient stresses. Results showed that different stresses had varying impacts on soil functions, leading to changes in bacterial community structures and gene abundances. The study highlights the complex interactions between soil physiochemical properties, stressors, and microbial life history traits in determining functional resistance and resilience.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtuena, Zandra Fagernaes, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer
Summary: The advancement of ancient DNA applications has led to the development of a redesigned and extended version of the EAGER pipeline, aiming to ensure accessibility, reproducibility, and alignment with the latest practices. Developed within the nf-core initiative, nfcore/eager provides high-quality software development and maintenance support to facilitate a wider range of ancient DNA analyses across diverse research groups and fields.
Article
Multidisciplinary Sciences
Cosimo Posth, Valentina Zaro, Maria A. Spyrou, Stefania Vai, Guido A. Gnecchi-Ruscone, Alessandra Modi, Alexander Peltzer, Angela Motsch, Kathrin Nagele, Ashild J. Vagene, Elizabeth A. Nelson, Rita Radzeviciute, Cacilia Freund, Lorenzo M. Bondioli, Luca Cappuccini, Hannah Frenzel, Elsa Pacciani, Francesco Boschin, Giulia Capecchi, Ivan Martini, Adriana Moroni, Stefano Ricci, Alessandra Sperduti, Maria Angela Turchetti, Alessandro Riga, Monica Zavattaro, Andrea Zifferero, Henrike O. Heyne, Eva Fernandez-Dominguez, Guus J. Kroonen, Michael McCormick, Wolfgang Haak, Martina Lari, Guido Barbujani, Luca Bondioli, Kirsten Bos, David Caramelli, Johannes Krause
Summary: The study found that during the Iron Age, the Etruscans had a component of Indo-European-associated steppe ancestry, but lacked recent Anatolian-related admixture. However, during the Roman Imperial period, there was an abrupt population-wide shift to eastern Mediterranean ancestry. Northern European components appeared in central Italy during the Early Middle Ages, shaping the genetic landscape of present-day Italian populations.
Meeting Abstract
Biochemistry & Molecular Biology
J. Alneberg, M. U. Garcia, A. Peltzer, T. Koch, M. Proks, A. Wilm, P. A. Ewels
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Meeting Abstract
Anthropology
Verena J. Schuenemann, Alexander Peltzer, Wolfgang Haak, Stephan Schiffels, Johannes Krause
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2017)