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Articles by Gilbert JA
Effects of different cultivation methods on the rhizosphere microbial community and secondary metabolites of Houttuynia cordata Thunb.
Effects of different cultivation methods on the rhizosphere microbial community and secondary metabolites of Houttuynia cordata Thunb.
The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more
The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more 1Department of Biology and Environmental Science, Linnéuniversitetet, Kalmar, Kalmar, Sweden 2Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI, United States of America DOI 10.7717/peerj.20328 Academic Editor Daniel Fischer Subject Areas Bioinformatics, Computational Biology, Ecology, Microbiology Keywords Metatranscriptomics, Denovoassembly,...
Comparative analysis of tensiomyographic and isokinetic assessments of the rectus abdominis and erector spinae in bodybuilding trainees with nonspecific low back pain
1Department of Physical Education, Inha University, Incheon, Republic of South Korea 2Department of Physical Therapy, Sahmyook University, Seoul, Republic of South Korea 3Research Institute of Sports and Industry Science, Hanseo University, Seosan, Chungcheongnamdo, Republic of South Korea 4Department of Physical Education, KyungDong University, Yangju, Republic of South Korea DOI 10.7717/peerj.20309 Academic Editor Yumeng Li Subject Areas Rehabilitation, Sports Medicine Keywords Nonspecific...
Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
Xuemei Han performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft. Huan Liu performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft. Xue Bai analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, xue Bai performed the sample collection and processing, and approved the final draft.
Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool
Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Quitandinha, Petrópolis, Rio de Janeiro, Brazil DOI 10.7717/peerj.20232 Academic Editor Liang Wang Subject Areas Bioinformatics, Genomics, Microbiology Keywords Bacteria sporulation, Metagenome-assembled genomes, Firmicutes, Machine learning, Spore-forming bacteria Copyright © Licence This is an open access...
Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term
Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term Sydney Institute of Agriculture, The University of Sydney, NSW, Australia DOI 10.7717/peerj.20162 Academic Editor Charles Okpala Subject Areas Agricultural Science, Biodiversity, Bioinformatics, Ecology, Microbiology Keywords Soil bacteria, Soil storage, Abundant and rare species Copyright © Licence This is an open access article distributed under the terms of the Creative Commons Attribution...
Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park
Sally Kong conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft. Eliana Abrams performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft. Yehuda Binik performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.
Effects of irrigation and nitrogen management on phyllosphere microbial communities of silage maize
The field experiment was conducted from Apr. 2022 to Nov. 2022 at the Experimental Field of Zhaotong University (27°36′65′N, 103°74′63′E, altitude 1,912 m; Guoxue Road, Zhaoyang district, Yunnan province, China).
Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes
Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes 1Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Veracruz, Mexico 2Red de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Xalapa, Veracruz, Mexico 3Instituto de Ciencias Básicas, Universidad Veracruzana, Xalapa, Veracruz, Mexico 4Facultad de Biología and Museo de Zoología, Universidad Veracruzana, Xalapa, Veracruz, Mexico DOI 10.7717/peerj.19376 Academic...
Impact of seasonal flooding and hydrological connectivity loss on microbial community dynamics in mangrove sediments of the southern Gulf of Mexico
Mirna Vázquez-Rosas-Landa conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft. Rosela Pérez-Ceballos conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the article, and approved the final draft.
PyBootNet: a python package for bootstrapping and network construction
PyBootNet: a python package for bootstrapping and network construction 1Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America 2Department of Biology, San Diego State University, San Diego, CA, United States of America DOI 10.7717/peerj.18915 Academic Editor Elliot Lefkowitz Subject Areas Bioinformatics, Microbiology Keywords Microbial communities, Computational biology, Built environment, Gut microbiome, Network metrics, Software...
Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region
Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region 1Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia 2Biodiversity Genomics Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia 3Department of Biological Sciences, University Collage of Haqel, University of Tabuk, Tabuk, Saudi Arabia 4Department of Statistics, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia 5Department of...
Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama‘ehuakanaloa Seamount
Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama‘ehuakanaloa Seamount 1Department of Biology, Western Washington University, Bellingham, WA, United States 2Department of Biology, College of Charleston, Charleston, SC, United States DOI 10.7717/peerj.18099 Academic Editor Peter Girguis Subject Areas Ecology, Microbiology, Computational Science, Biogeochemistry, Biological Oceanography Keywords Hydrothermal vents,...
Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students
Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students 1Physical Education Department, Zhengzhou Shengda University, Zhengzhou, Henan, China 2School of Physical Education, Shanghai University of Sport, Shanghai, Shanghai, China 3Department of Movement Sciences, KU Leuven, Leuven, Belgium 4School of Psychology, Shenzhen University, Shenzhen, Guangdong, China 5Centre for Mental Health, Shenzhen University, Shenzhen, Guangdong, China DOI...
Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora
Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora 1Yunnan Urban Agricultural Engineering & Technological Research Centre, Kunming University, Kunming, Yunnan Province, China 2School of Agriculture and Biotechnology, Kunming University, Kunming, Yunnan, China 3Microbiology Department, La Trobe University, Melbourne, Vic, Australia 4Kunming Key Laboratory of Hydro-ecology Restoration of Dianchi Lake, Kunming University, Kunming,...
Raised water temperature enhances benthopelagic links via intensified bioturbation and benthos-mediated nutrient cycling
Raised water temperature enhances benthopelagic links via intensified bioturbation and benthos-mediated nutrient cycling 1Benthic Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Bremen, Germany 2Aquatic Nutrient Cycles, Helmholtz Centre Hereon, Geesthacht, Hamburg, Germany 3Shelf Sea System Ecology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Helgoland, Germany DOI 10.7717/peerj.17047 Academic Editor Konstantinos...
Effects of nanoplastics on the gut microbiota of Pacific white shrimp Litopenaeus vannamei
Effects of nanoplastics on the gut microbiota of Pacific white shrimp Litopenaeus vannamei 1Geography, School of Humanities, Universiti Sains Malaysia, Penang, Malaysia 2Fishery Machinery and Instrument Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, China 3Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China 4Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial...
Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods
Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods 1Skolkovo Institute of Science and Technology, Moscow, Russia 2Moscow State University, Moscow, Russia 3Artificial Intelligence Research Institute (AIRI), Moscow, Russia 4Institute for Information Transmission Problems, Moscow, Russia DOI 10.7717/peerj.15838 Academic Editor Alexander Bolshoy Subject Areas Bioinformatics, Genomics, Microbiology, Gastroenterology and Hepatology, Data...
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome
Additional Information and Declarations Competing Interests The authors declare that they have no competing interests. Author Contributions J. Eduardo Martinez-Hernandez conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.
Comparing quantile regression spline analyses and supervised machine learning for environmental quality assessment at coastal marine aquaculture installations
Performance of the QRS- and RF-inferred molecular biotic index When comparing mol-IQIQRS and mol-IQIRF in terms of accuracy in the EQ classification, their performance can be considered equally good, since they both reached to “almost perfect” agreement with the IQIMA according to Cohen’s kappa statistics.
Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird
Introduction For some herbivorous vertebrates, leaves are an abundant and accessible food; however, animals do not have enzymes to degrade the complex carbohydrates of plant cell walls. As a result, microorganisms of their digestive tract are responsible for degrading these components through fermentation in specialized chambers in the gastrointestinal tract (GIT) (Parra, 1978; Stevens & Hume, 1998).
Comparative transcriptome analysis of Armillaria gallica 012m in response to ethephon treatment
Author Contributions Haiying Yang conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft. Kaixiang He performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft. Yapu Cao conceived and designed the experiments, performed the experiments, prepared figures and/or tables, and approved the final draft.
Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N
Data analysis The raw read sequences were processed by QIIME2 (Fung et al., 2021), and the DADA2 plugin was used to identify amplicon sequence variants (ASVs; (Callahan et al., 2016). Taxonomic assignments of ASV representative sequences were performed with a confidence threshold of 0.8 by a naïve Bayes classifier that was trained on the Ribosomal Database Project (RDP) (version 11.5) (http://rdp.cme.msu.edu/). Then, the spike-in sequences were identified, and the total reads were counted.
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Discussion This study demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. By applying Hi-C to a synthetic microbial community we showed that genomic DNA was associated by Hi-C read pairs within strains orders of magnitude more frequently than between strains. Hi-C reads associated genomic regions at distances not achievable with mate-pair or long-read sequencing technologies.
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