ArticleJournal of microbiological methods2017
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica.
Article in Journal of microbiological methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 62 citations in OpenAlex.
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- Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms.Microorganisms · 2021Article
- Bacterial diversity changes in agricultural soils influenced by poultry litter fertilization.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2021Article
- Bacterial diversity and predicted enzymatic function in a multipurpose surface water system - from wastewater effluent discharges to drinking water production.Environmental microbiome · 2021Article
- Shifts of microbiota during cheese production: impact on production and quality.Applied microbiology and biotechnology · 2021Review
- Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes.Frontiers in microbiology · 2021Article
- Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage.PloS one · 2021Article
- Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern.Scientific reports · 2020Article
- Effects of Chitosan-Gentamicin Conjugate Supplement on Non-Specific Immunity, Aquaculture Water, Intestinal Histology and Microbiota of Pacific White Shrimp (Marine drugs · 2020Article
- Age- and Sex-Linked Bacterial Community Variation and Function Prediction from Insoles of Healthy Chinese Population.Indian journal of microbiology · 2020Article
- Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences.Environmental microbiome · 2020Article
- Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis.Scientific reports · 2020Article
- Source Environments of the Microbiome in Perennially Ice-Covered Lake Untersee, Antarctica.Frontiers in microbiology · 2019Article
- Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos.AMB Express · 2018Article
- Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin.FEMS microbiology letters · 2018Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.
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