Article
Ecology
Sydney B. Wizenberg, Laura R. Newburn, Rodney T. Richardson, Mateus Pepinelli, Ida M. Conflitti, Mashaba Moubony, Daniel Borges, M. Marta Guarna, Ernesto Guzman-Novoa, Leonard J. Foster, Amro Zayed
Summary: Honey bees, traditionally known as pollinators of flowering plants, may also play a role in dispersing non-flowering plant taxa. The study sheds light on the broad impact of honey bees on plant-pollinator interactions and suggests their potential role as vectors of gene flow.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(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
Biology
Schuyler D. Smith, Jinlyung Choi, Nicole Ricker, Fan Yang, Shannon Hinsa-Leasure, Michelle L. Soupir, Heather K. Allen, Adina Howe
Summary: The study presents a high-throughput sequencing method called DARTE-QM for screening antibiotic resistance genes in environmental DNA samples. It demonstrates the effectiveness of this method in soil, manure, and livestock fecal samples, as well as a synthetic mock-community reference.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
Matthew Y. Cho, Marc Oliva, Anna Spreafico, Bo Chen, Xu Wei, Yoojin Choi, Rupert Kaul, Lillian L. Siu, Bryan Coburn, Pierre H. H. Schneeberger
Summary: In this study, a quantitative PCR-based assay was used to predict host-to-microbe ratios before sequencing, validated on two sample types, and showed accurate prediction across a range of sample compositions. This easy-to-use assay can help researchers plan their shotgun sequencing experiments more efficiently by predicting human-to-microbe ratios.
Article
Medicine, Legal
Yanlei Liu, Chao Xu, Wenpan Dong, Xueying Yang, Shiliang Zhou
Summary: This study demonstrates how environmental plant DNA metabarcoding technology was used to determine a criminal suspect. By extracting DNA, amplifying genes, sequencing, and bioinformatics analysis, the suspect was successfully identified. This indicates that plant DNA in environmental soil can be a new source of evidence with high potentials for applications in criminal cases.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Review
Biodiversity Conservation
Abigail Lowe, Laura Jones, Lucy Witter, Simon Creer, Natasha de Vere
Summary: The identification of floral visitation by pollinators is crucial for understanding the ecological interactions between plants and pollinators on a fine-scale, and has implications for biodiversity conservation and ecosystem health. This review examines the use of DNA metabarcoding in studying plant-pollinator interactions, providing detailed methodological considerations for each step of the workflow and emphasizing the importance of method standardization. The review also discusses future opportunities and directions for using molecular methods to analyze plant-pollinator interactions.
Article
Pharmacology & Pharmacy
Jinxin Liu, Weishan Mu, Mengmeng Shi, Qing Zhao, Weijun Kong, Hongbo Xie, Linchun Shi
Summary: This study utilized shotgun metabarcoding to identify the biological ingredients in traditional herbal patent medicine Wuhu San. The results showed that this technology could effectively complement traditional methods in identifying prescribed ingredients.
FRONTIERS IN PHARMACOLOGY
(2021)
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)
Review
Microbiology
Lu Zhang, FengXin Chen, Zhan Zeng, Mengjiao Xu, Fangfang Sun, Liu Yang, Xiaoyue Bi, Yanjie Lin, YuanJiao Gao, HongXiao Hao, Wei Yi, Minghui Li, Yao Xie
Summary: Metagenomics is a new approach to studying microorganisms from a specific environment, focusing on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, as well as interactions and relationships with the environment. Sequencing technologies have evolved to high-throughput next-generation sequencing (NGS) and third-generation sequencing (TGS), showing advantages in rapid detection of pathogenic microorganisms. With the help of new algorithms, taxonomic profiling and gene prediction of microbial species can be better performed. Functional metagenomics is helpful for screening new bioactive substances and functional genes from microorganisms and their metabolites.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Conny P. Serite, Arsalan Emami-Khoyi, Ofentse K. Ntshudisane, Nicola C. James, Bettine Jansen van Vuuren, Taryn Bodill, Paul D. Cowley, Alan K. Whitfield, Peter R. Teske
Summary: Understanding the dietary preferences of endangered species is important for conservation strategies. The study compared metabarcoding and metagenomics to analyze the diets of endangered pipefish species. Metabarcoding showed a difference in prey preference between the two species, while metagenomics identified additional copepod species in one species' diet. Metagenomics was found to be a useful complementary method for dietary analysis, although it is more affected by a lack of reference sequences.
FRONTIERS IN MARINE SCIENCE
(2023)
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
Biochemistry & Molecular Biology
Karen L. Bell, Katherine J. Turo, Abigail Lowe, Kevin Nota, Alexander Keller, Francisco Encinas-Viso, Laura Parducci, Rodney T. Richardson, Richard M. Leggett, Berry J. Brosi, Kevin S. Burgess, Yoshihisa Suyama, Natasha de Vere
Summary: Anthropogenic activities are causing global changes in the environment, leading to restructuring and decline of plant-pollinator communities. To understand and manage these impacts, it is necessary to characterize plant-pollinator communities across different habitats using rapid and high-throughput methods like pollen DNA metabarcoding. This technique is advantageous for understanding complex ecological networks and can be used to assess plant-pollinator interactions, monitor ecosystem change, and model the distribution of allergenic pollen.
Review
Biochemical Research Methods
Minerva Fatimae Ventolero, Saidi Wang, Haiyan Hu, Xiaoman Li
Summary: The study investigated 20 computational tools and identified BHap, mixtureS, and StrainFinder as the best performing tools for inferring bacterial strain genomes from shotgun sequencing reads. The study also discussed future directions to address the limitations of these tools.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Nicola Tommasi, Paolo Biella, Davide Maggioni, Luca Fallati, Giulia Agostinetto, Massimo Labra, Paolo Galli, Andrea Galimberti
Summary: This study found that moderate landscape fragmentation of green areas shapes many aspects of the pollination ecosystem service, where despite interactions being less complex and mediated by pollinator body size, pollinator insect biodiversity and potential plant reproduction are supported.
Article
Zoology
Brian D. Inouye, Berry J. Brosi, Emily H. Le Sage, Manuel T. Lerdau
Summary: Biological systems are constrained by trade-offs among robustness, resilience, and performance. Redundancy and plasticity are important mechanisms governing these trade-offs. Identifying common themes requires similar approaches to quantify these trade-offs.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2022)
Article
Biology
Laura Avila, Elizabeth Dunne, David Hofmann, Berry J. Brosi
Summary: In the past decade, the use of antibiotics in US crops has dramatically increased, but little is known about the effects on beneficial organisms. This study found that dietary exposure to streptomycin, a commonly used antibiotic, negatively affected the learning, foraging, and behavior of bumblebees. The results highlight the need for further research on the impacts of antibiotic use on beneficial insects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Vishnu Raghuram, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit, Joanna B. Goldberg, Timothy D. Read
Summary: This study investigates the mutations in the agr operon of Staphylococcus aureus and their impact on strain characteristics. The study shows a close association between agr type and S. aureus clonal complex, and a strong linkage between agrBDC alleles. More than 5% of the genomes analyzed have frameshift mutations in the agr operon. The recurring mutations in different clonal lineages suggest that strains with agr frameshifts are short-lived in evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
Samantha J. Worthy, Kylie Bucalo, Erin Perry, Alex Reynolds, Jennifer Cruse-Sanders, Alvaro J. Perez, Kevin S. Burgess
Summary: Orchidaceae is a large plant family that is difficult to identify using traditional taxonomic methods. This study investigates the utility of rbcL and matK DNA barcode markers to discriminate between orchid species from an Andean forest in Ecuador. The results show that the matK gene region is more effective for species and genus discrimination compared to the rbcL gene region, highlighting the importance of incorporating genetic methods in plant species identification.
PLANT SYSTEMATICS AND EVOLUTION
(2022)
Article
Ecology
Jia-Jia Liu, Kevin S. Burgess, Xue-Jun Ge
Summary: The strength of the relationship between biodiversity and biomass production is influenced by environmental stress and time. Factors such as species pool size and rainfall play an important role in this relationship.
ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Lu Liu, Yu-Qu Zhang, Liscely Tumi, Mery L. Suni, Monica Arakaki, Kevin S. Burgess, Xue-Jun Ge
Summary: The study analyzed a large number of plastomes of Puya plants, finding that they are highly conserved in genomic structure and organization, and provide distinct species discrimination features. Additionally, the study revealed that the diversification of Puya is related to the changes in the Andean mountains and Pleistocene climatic oscillations.
ECOLOGY AND EVOLUTION
(2022)
Article
Entomology
Douglas Chesters, Xiuwei Liu, Karen L. Bell, Michael C. Orr, Tingting Xie, Qingsong Zhou, Chaodong Zhu
Summary: Microbiomes associated with bee nests have an impact on colony health through various mechanisms. This study investigates how different honeybee species differ in microbiome assembly processes and the contributions of floral visitations and the environment to diversity. The results show that microbiome composition is primarily driven by pollen composition and human disturbance negatively affects microbiome diversity. This research contributes to understanding microbiome diversity of key pollinators in biodiversity hotspots.
Article
Biochemistry & Molecular Biology
Karen L. Bell, Katherine J. Turo, Abigail Lowe, Kevin Nota, Alexander Keller, Francisco Encinas-Viso, Laura Parducci, Rodney T. Richardson, Richard M. Leggett, Berry J. Brosi, Kevin S. Burgess, Yoshihisa Suyama, Natasha de Vere
Summary: Anthropogenic activities are causing global changes in the environment, leading to restructuring and decline of plant-pollinator communities. To understand and manage these impacts, it is necessary to characterize plant-pollinator communities across different habitats using rapid and high-throughput methods like pollen DNA metabarcoding. This technique is advantageous for understanding complex ecological networks and can be used to assess plant-pollinator interactions, monitor ecosystem change, and model the distribution of allergenic pollen.
Article
Ecology
Connor Morozumi, Xingwen Loy, Victoria Reynolds, Annie Schiffer, Beth Morrison, Jade Savage, Berry Brosi
Summary: Global climate change poses a threat to species interactions, but we lack clear predictions on how these changes will impact communities. Perturbations associated with climate change, such as droughts, can change resource levels and thus affect species interactions and ecological network structure. Our study found that drought can restructure plant-pollinator networks, resulting in increased generalization in terms of link presence-absence, but increased specialization when considering quantitative network intensities.
Article
Plant Sciences
Annie Schiffer, Xingwen Loy, Connor Morozumi, Berry J. Brosi
Summary: Changes in flowering time caused by climate change can impact plant fecundity. This study compared the individual-level responses of three montane species with different seasonal flowering times and found that variation in individual phenology affects fecundity, with species-specific effects. Pollen limitation may be more influential than conspecific density in determining seed set. Understanding individual-level changes in phenology is crucial for understanding plant reproductive success.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Microbiology
Abraham G. Moller, Robert A. Petit III, Michelle H. Davis, Timothy D. Read
Summary: This study developed a method for rapid detection of vancomycin-intermediate resistance in Staphylococcus aureus through long-read genomic sequencing. The method can identify VISA genotypes and incorporate a comprehensive database of VISA genetic determinants.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biodiversity Conservation
Amanda M. Emmett, John K. Scott, Bruce L. Webber, Anita A. Severn-Ellis, Karen L. Bell
Summary: Understanding the historical context of biological invasions can improve weed management outcomes. In this study, we identified the introduction pathway and biogeographical origin of bitou bush in Australia through genomic tools and historical records. The genomic diversity analysis supported the previous findings that all Australian material originated from the southern part of South Africa. Historical records suggested the introduction of bitou bush in eastern Australia through dry shipping ballast in around 1900. The chloroplast genome variation revealed a single source population introduction to eastern Australia and a likely pathway connecting Newcastle or Port Kembla to Kwinana in Western Australia.
BIOLOGICAL INVASIONS
(2023)
Article
Microbiology
Concerta L. L. Holley, Vijaya Dhulipala, Stavaros A. A. Maurakis, Ashley Nicole Greenawalt, Timothy D. D. Read, Cynthia N. N. Cornelissen, William M. M. Shafer
Summary: The expression of the vaccine candidate gene ompA in Neisseria gonorrhoeae is regulated by iron ions and a new transcription factor called NceR. This study reveals the complexity of gene regulation for vaccine candidates and improves our understanding of their availability during infection.
Article
Genetics & Heredity
Kevin G. Libuit, Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, Michelle R. Scribner, Robert A. Petit, Catarina Ines Mendes, Marcela Huergo, Gregory Legacki, Christine Loreth, Daniel J. Park, Joel R. Sevinsky
Summary: We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories. By using the Terra data analysis platform and specific bioinformatics workflows, we are able to perform standardized analysis and generate reproducible, validated, and auditable results that meet the needs of public health practitioners.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Abraham G. Moller, Robert A. Petit, Timothy D. Read
Summary: Phage therapy is a potential alternative treatment for Staphylococcus aureus infections. The study found that phage adsorption genes are highly conserved in the S. aureus species, but horizontal gene transfer may play an important role in the strain-specific evolution of host range patterns.