Article
Agronomy
Ko-Hsuan Chen, Reid Longley, Gregory Bonito, Hui-Ling Liao
Summary: The improved two-step PCR approach significantly enhances sequence quantity and recovery rate, while maintaining high read quality. By incorporating synthetic barcodes independently, this method can be broadly adapted to different genomic regions and organisms of scientific interest.
Article
Biochemical Research Methods
Josip Rudar, Teresita M. Porter, Michael Wright, G. Brian Golding, Mehrdad Hajibabaei
Summary: Our work introduces LANDMark, a meta-classifier that combines characteristics of several machine learning models into a decision tree and ensemble learning framework. Leveraging contemporary machine learning approaches, LANDMark is able to create highly predictive and consistent models when analyzing amplicon sequencing data, outperforming other models like Random Forest, Linear Support Vector Machine, and Logistic Regression.
BMC BIOINFORMATICS
(2022)
Article
Ecology
Lisa Prudnikow, Birgit Pannicke, Roebbe Wuenschiers
Summary: The possibility of identifying plants based on the taxonomic information from their pollen grains has various applications in biology. In the past, pollen origin was analyzed using microscopy and chemical treatment, which is time-consuming and requires expert knowledge. Now, DNA analysis provides advantages and challenges compared to traditional methods. This article presents a practical guide for genetic pollen analysis using nanopore sequencing, with a focus on pollen collected by pollinating insects.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Bilgenur Baloglu, Zhewei Chen, Vasco Elbrecht, Thomas Braukmann, Shanna MacDonald, Dirk Steinke
Summary: Metabarcoding using Oxford Nanopore MinION™ with rolling circle amplification (RCA) successfully generated full-length consensus DNA barcodes for a bulk mock sample of 50 aquatic invertebrate species, achieving median accuracies of up to 99.3% for long concatemeric reads. The study demonstrated the potential of Nanopore sequencing for metabarcoding, but suggested exploration of other isothermal amplification procedures to improve consensus accuracy.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Mycology
Petr Baldrian, Tomas Vetrovsky, Clementine Lepinay, Petr Kohout
Summary: High-throughput DNA sequencing has revolutionized biodiversity research in mycology, with over 200 studies generating 250 million sequences of the mycological marker ITS2. The total estimated extant fungal diversity is 6.28 million taxa, with Ascomycota and Basidiomycota dominating. Soil and litter have the highest alpha diversity of fungi, while lichens and plant tissues have the highest proportion of unknown species.
Article
Veterinary Sciences
Raquel Rios-Castro, Alejandro Romero, Raquel Aranguren, Alberto Pallavicini, Elisa Banchi, Beatriz Novoa, Antonio Figueras
Summary: This study utilized DNA metabarcoding to investigate putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia, Spain. It found distinct eukaryotic community compositions between sediment and water fractions, with protists being the most diverse group. The presence of harmful algae, invasive species, and potential pathogens impacting aquaculture and marine ecosystems was detected, highlighting the importance of assessing marine ecosystem health with metabarcoding.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Environmental Sciences
Ah Ran Kim, Tae-Ho Yoon, Chung Il Lee, Chang-Keun Kang, Hyun-Woo Kim
Summary: The metabarcoding analysis using the newly designed FishU primers provides a more accurate and diverse representation of fish larvae diversity compared to the MiFish primers. This approach offers useful data for understanding fish reproduction.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Virology
Izabela Fabianska, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, Dietmar Mayer
Summary: High-throughput sequencing (HTS) is effective in detecting both known and unknown viruses in samples, providing support for determining the safety of biological products such as vaccines. Due to the complexity of bioinformatics, standardized and reliable methods are necessary for managing HTS data. The LABRADOR analysis pipeline demonstrates reliable detection of viruses in mixtures of model viruses, vaccines, and clinical samples.
Article
Entomology
Xiao-Man Zhang, Zhi-Yong Shi, Shao-Qian Zhang, Peng Zhang, John-James Wilson, Chungkun Shih, Jing Li, Xue-Dong Li, Guo-Yue Yu, Ai-Bing Zhang
Summary: The study presents a fast and effective sequencing strategy for identifying larvae of Lepidoptera and their diets, with high-quality sequences obtained through long-multiplex-metabarcoding. The SHMMT approach is shown to be reliable and cost-effective, with accurate identification of larvae diets. This new method will facilitate research on insect-plant networks.
Review
Microbiology
Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan F. Kreuze, Marie Lefebvre, Goncalo Silva, Martha Malapi-Wight, Paolo Margaria, Irena Mavriric Plesko, Sam McGreig, Laura Miozzi, Benoit Remenant, Jean-Sebastien Reynard, Johan Rollin, Mike Rott, Olivier Schumpp, Sebastien Massart, Annelies Haegeman
Summary: High-throughput sequencing (HTS) technologies are essential for plant virus diagnostics and research, as they can detect any plant virus in a sample without prior knowledge. Efficient and reliable bioinformatic tools are crucial for analyzing the huge amount of generated sequences. This paper provides a critical overview of the steps involved in HTS for plant virus detection, including sample preparation, data analysis, and viral sequence classification, aiming to assist researchers in conducting well-structured HTS data analysis.
Article
Biochemistry & Molecular Biology
Filipa M. S. Martins, Miguel Porto, Maria J. Feio, Bastian Egeter, Aurelie Bonin, Sonia R. Q. Serra, Pierre Taberlet, Pedro Beja
Summary: DNA metabarcoding from ethanol-preserved macroinvertebrate samples is a convenient method for biodiversity assessment and biomonitoring of aquatic ecosystems. However, errors and biases need to be quantified before mainstreaming into monitoring programmes. COI marker showed best performance, but a multimarker approach is recommended for detecting a wider range of taxa in freshwater macroinvertebrate samples.
Review
Biochemistry & Molecular Biology
Paula Arribas, Carmelo Andujar, Martin I. Bidartondo, Kristine Bohmann, Eric Coissac, Simon Creer, Jeremy R. deWaard, Vasco Elbrecht, Gentile F. Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson
Summary: High-throughput sequencing technology is increasingly used for biodiversity characterization and monitoring, offering a deeper understanding of global biodiversity when applied across broad geographical scales. International collaborative efforts are needed to maximize the potential of HTS data for global integration and synthesis, particularly in establishing an effective Genomic Observatories network for terrestrial biodiversity integration.
Article
Biochemistry & Molecular Biology
Marie-Pierre Chapuis, Laure Benoit, Maxime Galan
Summary: Obtaining high-quality nucleic acids is crucial for studying bacterial communities associated with animal hosts. This study compared five DNA extraction protocols for animal samples using different methods, including mechanical or enzymatic lysis. The results showed that none of the methods fully eliminated bias, but one method with enzymatic lysis had lower bias. Standardization of DNA extraction is important for comparing microbiome results across different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Tania N. Kim, Yury V. Bukhman, Michelle A. Jusino, Erin D. Scully, Brian J. Spiesman, Claudio Gratton
Summary: Determining feeding relationships of lady beetles is important for understanding the potential of biological control in the field. In this study, DNA metabarcoding was used to characterize the actual feeding relationships of lady beetles and validate the methods. The results showed that DNA metabarcoding accurately assessed diet composition and breadth in lady beetle populations. The study also found differences in diet composition and richness between different habitat types. Prey detection rates varied with diet composition and habitat type, and lower detection rates suggest the need for analyzing a larger number of individuals to fully assess diet diversity.
BIOLOGICAL CONTROL
(2022)
Article
Multidisciplinary Sciences
Vasco Elbrecht, Ecaterina Edith Vamos, Dirk Steinke, Florian Leese
Article
Multidisciplinary Sciences
Vasco Elbrecht, Paul D. N. Hebert, Dirk Steinke
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Thomas W. A. Braukmann, Natalia Ivanova, Sean W. J. Prosser, Vasco Elbrecht, Dirk Steinke, Sujeevan Ratnasingham, Jeremy R. de Waard, Jayme E. Sones, Evgeny Zakharov, Paul D. N. Hebert
MOLECULAR ECOLOGY RESOURCES
(2019)
Article
Biochemistry & Molecular Biology
Vera M. A. Zizka, Vasco Elbrecht, Jan-Niklas Macher, Florian Leese
MOLECULAR ECOLOGY RESOURCES
(2019)
Article
Biochemistry & Molecular Biology
Mailys Gauthier, Lara Konecny-Dupre, Agnes Nguyen, Vasco Elbrecht, Thibault Datry, Christophe Douady, Tristan Lefebure
MOLECULAR ECOLOGY RESOURCES
(2020)
Article
Multidisciplinary Sciences
Vasco Elbrecht, Thomas W. A. Braukrnann, Natalia Ivanova, Sean W. J. Prosser, Mehrdad Hajibabaei, Michael Wright, Evgeny Zakharov, Paul D. N. Hebert, Dirk Steinke
Review
Biochemistry & Molecular Biology
Paula Arribas, Carmelo Andujar, Martin I. Bidartondo, Kristine Bohmann, Eric Coissac, Simon Creer, Jeremy R. deWaard, Vasco Elbrecht, Gentile F. Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson
Summary: High-throughput sequencing technology is increasingly used for biodiversity characterization and monitoring, offering a deeper understanding of global biodiversity when applied across broad geographical scales. International collaborative efforts are needed to maximize the potential of HTS data for global integration and synthesis, particularly in establishing an effective Genomic Observatories network for terrestrial biodiversity integration.
Article
Ecology
Jarno Turunen, Vasco Elbrecht, Dirk Steinke, Jukka Aroviita
Summary: The study found that riparian forests in agricultural headwater streams can improve ecosystem functions, mitigate adverse impacts of agriculture on biota, and have a significant effect on water temperatures.
FRESHWATER BIOLOGY
(2021)
Article
Ecology
Bilgenur Baloglu, Zhewei Chen, Vasco Elbrecht, Thomas Braukmann, Shanna MacDonald, Dirk Steinke
Summary: Metabarcoding using Oxford Nanopore MinION™ with rolling circle amplification (RCA) successfully generated full-length consensus DNA barcodes for a bulk mock sample of 50 aquatic invertebrate species, achieving median accuracies of up to 99.3% for long concatemeric reads. The study demonstrated the potential of Nanopore sequencing for metabarcoding, but suggested exploration of other isothermal amplification procedures to improve consensus accuracy.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Kristine Bohmann, Vasco Elbrecht, Christian Caroe, Iliana Bista, Florian Leese, Michael Bunce, Douglas W. Yu, Mathew Seymour, Alex J. Dumbrell, Simon Creer
Summary: Metabarcoding of DNA from environmental or bulk samples is a valuable tool for biodiversity research, but different experimental strategies have their own advantages, challenges, and limitations. Ensuring data reliability is crucial for practitioners using this method.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Vasco Elbrecht, Angie Lindner, Laura Manerus, Dirk Steinke
Summary: This study explores arthropod diversity in indoor environments by collecting dead specimens from light fixtures, finding that factors such as type of fixture, lightbulb used, cleanliness, and specimen size can affect diversity. Differences in arthropod diversity were observed between different buildings, indicating that individual samples may not fully represent the overall diversity.
Article
Multidisciplinary Sciences
Vasco Elbrecht, Sarah J. Bourlat, Thomas Horren, Angie Lindner, Adriana Mordente, Niklas W. Noll, Livia Schaffler, Martin Sorg, Vera M. A. Zizka
Summary: Size fractionation of Malaise trap bulk samples can increase taxon recovery, especially for small specimens. Mixing samples in different proportions can further enhance the detection rate of small size fractions. Therefore, considering size sorting and mixing proportions of samples is crucial for optimizing metabarcoding protocols.
Article
Biotechnology & Applied Microbiology
Marie V. Brasseur, Arne J. Beermann, Vasco Elbrecht, Daniel Grabner, Bianca Peinert-Voss, Romana Salis, Martina Weiss, Christoph Mayer, Florian Leese
Summary: This study used transcriptome-wide sequencing data to quantify the effects of multiple anthropogenic stressors on gene expression in the freshwater amphipod Gammarus fossarum. The results showed that stressor exposure led to the suppression of genes involved in metabolic and energy consuming cellular processes. The strongest transcriptional response was induced by increased salinity, which contradicted the observed abundance patterns. The interactions between stressors were mainly antagonistic.
Review
Biology
Paula Arribas, Carmelo Andujar, Kristine Bohmann, Jeremy R. DeWaard, Evan P. Economo, Vasco Elbrecht, Stefan Geisen, Marta Goberna, Henrik Krehenwinkel, Vojtech Novotny, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Anna Papadopoulou, Alfried P. Vogler, Brent C. Emerson
Summary: Metazoan metabarcoding is an important strategy for biodiversity inventorying, but differences in workflows might compromise data integration. To address this issue, a modular framework for harmonized data generation was proposed, focusing on terrestrial arthropods. Key points for harmonization were identified and guidelines were provided to reduce methodological options and promote best practice.