PICRUSt2 for prediction of metagenome functions

Nature Biotechnology, Год журнала: 2020, Номер 38(6), С. 685 - 688

Опубликована: Июнь 1, 2020

Язык: Английский

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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Bioinformatics, Год журнала: 2019, Номер 35(21), С. 4453 - 4455

Опубликована: Апрель 24, 2019

Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized scalable codes needed analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of established greedy search algorithm RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, usability compared with On taxon-rich datasets, typically finds higher-scoring trees than IQTree, an increasingly recent tool ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, introduces several new features, such as detection terraces space recently introduced transfer bootstrap support metric. Availability implementation The code available GNU GPL at https://github.com/amkozlov/raxml-ng. web service (maintained by Vital-IT) https://raxml-ng.vital-it.ch/. Supplementary information data Bioinformatics online.

Язык: Английский

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GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Bioinformatics, Год журнала: 2022, Номер 38(23), С. 5315 - 5316

Опубликована: Окт. 11, 2022

Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, growing size of GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts memory (∼320 GB) which limits its adoption ease use. Here, we present an update to that uses a divide-and-conquer approach where user genomes are initially placed into with family-level representatives followed placement appropriate class-level subtree comprising species representatives. This substantially reduces requirements while having minimal impact on classification. Availability implementation is implemented Python licenced under GNU General Public Licence v3.0. Source code documentation available at: https://github.com/ecogenomics/gtdbtk. Supplementary information data at Bioinformatics online.

Язык: Английский

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Год журнала: 2020, Номер 11(1)

Опубликована: Июль 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Язык: Английский

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Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Nature Genetics, Год журнала: 2021, Номер 53(6), С. 809 - 816

Опубликована: Май 10, 2021

Язык: Английский

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PICRUSt2: An improved and customizable approach for metagenome inference

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2019, Номер unknown

Опубликована: Июнь 15, 2019

One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition sampled communities. Here, we present PICRUSt2 ( https://github.com/picrust/picrust2 ), which expands capabilities original PICRUSt method 1 to predict potential a based profiles. This updated and implementation includes several improvements over previous algorithm: an expanded database families reference genomes, new approach now compatible with any OTU-picking or denoising algorithm, novel phenotype predictions. Upon evaluation, was more accurate than PICRUSt1 other current approaches overall. also flexible allows addition custom databases. We highlight these important caveats regarding use predicted metagenomes, are related inherent challenges analyzing metagenome data in general.

Язык: Английский

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Non‐specific amplification compromises environmental DNA metabarcoding with COI

Methods in Ecology and Evolution, Год журнала: 2019, Номер 10(11), С. 1985 - 2001

Опубликована: Авг. 2, 2019

Abstract Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, especially so developing community standards legislative frameworks, the choice of genetic marker primer set. Mitochondrial cytochrome c oxidase subunit I (COI), standard barcode for animals, with its extensive reference library, taxonomic discriminatory power predictable sequence variation, natural many metabarcoding applications. However, targeting specific groups samples, utility COI has yet to be fully scrutinized. Here, by using case study marine freshwater fishes British Isles, we quantify silico performance twelve pairs four mitochondrial loci – COI, b , 12S 16S terms library coverage, universality. We subsequently test vitro three one their specificity, reproducibility, congruence independent datasets derived traditional survey methods at five estuarine coastal sites around English Channel North Sea. Our results show that aqueous low template concentrations, both metazoan‐targeted fish‐targeted primers perform poorly comparison 12S, exhibiting levels reproducibility due non‐specific amplification prokaryotic non‐target eukaryotic DNAs. An ideal metabarcode would have an upon which custom could designed, either broad assessments biodiversity, or taxon surveys. Such database available but specificity hinders practical application, while conversely, offer high lack adequate references. The latter, however, can mitigated expanding concept barcodes include whole genomes generated genome‐skimming existing tissue collections.

Язык: Английский

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Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease

Movement Disorders, Год журнала: 2020, Номер 35(9), С. 1626 - 1635

Опубликована: Июнь 18, 2020

Abstract Background PD may begin with the intestinal accumulation of α‐synuclein fibrils, which can be causally associated gut dysbiosis. The variability microbiota across countries prevented us from identifying shared dysbiosis in PD. Objectives To identify countries. Methods We performed 16S ribosomal RNA gene sequencing analysis 223 patients and 137 controls, meta‐analyzed by combining our dataset four previously reported data sets United States, Finland, Russia, Germany. excluded uncommon taxa analyses. For pathway analysis, we developed Kyoto Encyclopedia Genes Genomes orthology set enrichment method. Results After adjusting for confounding factors (body mass index, constipation, sex, age, catechol‐O‐methyl transferase inhibitor), genera Akkermansia Catabacter , as well families Akkermansiaceae were increased, whereas Roseburia Faecalibacterium Lachnospiraceae ND3007 group decreased Catechol‐O‐methyl inhibitor intake markedly increased family Lactobacillaceae . Inspection these bacteria 12 datasets that not included meta‐analysis revealed genus frequently observed changes short‐chain fatty acid metabolisms dataset. Conclusions report mucin layer‐degrading is acid–producing are © 2020 International Parkinson Movement Disorder Society

Язык: Английский

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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

Bioinformatics, Год журнала: 2020, Номер 36(10), С. 3263 - 3265

Опубликована: Янв. 28, 2020

We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool conducting typical analyses on such data. The tools target trees placements, sequences, taxonomies other relevant data types, offer high-level simplicity as well low-level customizability, are computationally efficient, well-tested field-proven.

Язык: Английский

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Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Сен. 6, 2021

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that may produce legacy effects on soil microbial communities. However, it unclear whether precedent events lead to ecological memory formation, i.e., capacity past influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in mountain grassland central Austria with an experimental layout comparing 10 years recurrent single event ambient conditions. We show droughts increase dissimilarity communities compared control events, enhance multifunctionality during (calculated via measurements potential enzymatic activities, nutrients, biomass stoichiometry belowground net primary productivity). Our results indicate community composition changes concert its functioning, consequences for processes. The formation under resilience functioning against future

Язык: Английский

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