CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: July 11, 2022

Advances in DNA sequencing and bioinformatics have dramatically increased the rate of recovery microbial genomes from metagenomic data. Assessing quality metagenome-assembled (MAGs) is a critical step prior to downstream analysis. Here, we present CheckM2, an improved method predicting completeness contamination MAGs using machine learning. We demonstrate effectiveness CheckM2 on synthetic experimental data, show that it outperforms original version CheckM MAG quality. substantially faster than its database can be rapidly updated with new high-quality reference genomes. accurately predicts genome for novel lineages, even those sparse genomic representation, or reduced size (e.g. symbionts) such as found Patescibacteria DPANN superphylum. provides accurate predictions across tree life, giving confidence when inferring biological conclusions MAGs.

Language: Английский

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Inferring microbiota functions from taxonomic genes: a review

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Deciphering microbiota functions is crucial to predict ecosystem sustainability in response global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading big data era and improving ability link diversity with functions. Recent advances bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding using taxonomic gene information. This cheaper approach every aspect serves as an alternative shotgun sequencing. Although these are increasingly used by ecologists, objective evaluation their modularity, portability, robustness lacking. Here, we reviewed 100 scientific papers inference ecological trait assignment rank advantages, specificities, drawbacks tools, a benchmarking. To date, mainly devoted bacterial functions, fungal A major limitation lack reference genomes-compared human microbiota-especially complex ecosystems such soils. Finally, explore applied research prospects. These promising already provide relevant information functioning, but standardized indicators corresponding repositories still lacking that would enable them be operational diagnosis.

Language: Английский

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A high-quality genome compendium of the human gut microbiome of Inner Mongolians

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(1), P. 150 - 161

Published: Jan. 5, 2023

Language: Английский

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Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Aug. 26, 2023

Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part gene for 16S rRNA subunit, which serves as a biomarker identifying and quantifying various taxa present in microbiome sample. Several computational methods exist analyzing amplicon sequencing. However, most-used bioinformatics tools cannot produce high quality genus-level species-level taxonomic calls may underestimate potential accuracy these calls. We used sequencing data from mock communities to evaluate sensitivity specificity several pipelines genomic reference libraries analyses, concentrating measuring assignments reads. evaluated DADA2, QIIME 2, Mothur, PathoScope Kraken 2 conjunction with Greengenes, SILVA, RefSeq. Profiling were compared using publicly available community sources, comprising 136 samples varied species richness evenness, different amplified regions within gene, both DNA spike-ins cDNA collections plated cells. designed whole-genome metagenomics, outperformed DADA2 plugin, are theoretically specialized analyses. Evaluations identified SILVA RefSeq/Kraken Standard superior Greengenes. These findings support fully capable, competitive options genus- analysis, whole genome sequencing, metagenomics tools.

Language: Английский

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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(2)

Published: Feb. 29, 2024

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation function. To mitigate this, tools PICRUSt2, Tax4Fun2, PanFP MetGEM infer profiles from sequencing data using different algorithms. Prior studies have cast doubts on quality these predictions, motivating us systematically evaluate matched metagenomic datasets, simulated data. Our contribution is threefold: (i) data, we investigate if technical biases could explain discordance between inferred expected results; (ii) considering human cohorts type two diabetes, colorectal cancer obesity, test health-related differential abundance measures categories are concordant gene-inferred metagenome-derived and; (iii) since copy number an confounder in inference, customised normalisation with rrnDB database improve results. results show that gene-based inference generally do not necessary sensitivity delineate changes microbiome should thus be used care. Furthermore, outline differences individual tested recommendations tool selection.

Language: Английский

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Massively parallel single-cell sequencing of diverse microbial populations

Nature Methods, Journal Year: 2024, Volume and Issue: 21(2), P. 228 - 235

Published: Jan. 17, 2024

Language: Английский

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Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by oligonucleotides used. We performed a systemic evaluation probes/primers known polyphosphate-accumulating organisms (PAOs) glycogen-accumulating (GAOs). Most FISH probes showed blind spots covered nontarget bacterial groups. Ca. Competibacter promising coverage specificity. Those Accumulibacter desirable but targeted out-group bacteria, including Competibacter, Thauera, Dechlorosoma, some Cyanobacteria. Defluviicoccus good specificity poor coverage. Probes targeting Tetrasphaera or Dechloromonas low Specifically, DEMEF455, Bet135, Dech453 Accumulibacter. Special attentions needed when using these to resolve PAO/GAO phenotype Dechloromonas. species-specific Accumulibacter, Lutibacillus, Phosphoribacter, highly specific. Overall, 1.4% 9.6% 43.3% Defluviicoccus, 54.0% MiDAS database were not existing probes. Different primer sets distinct PAOs GAOs. None them all members. 520F-802R 515F-926R most balanced All primers extremely Microlunatus (<36.0%), implying their probably overlooked roles EBPR systems. A clear understanding strength weaknesses each probe set is premise rational interpretation obtained community results.

Language: Английский

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Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 431 - 455

Published: Aug. 17, 2018

Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen samples-has applications across a variety fields. While basic species-level using standard barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities mixes (qualitative matching) and (b) generates sequence reads proportionally their relative abundance in sample (quantitative unclear, as these have not been assessed known standards. We tested quantitative qualitative robustness constructed mixtures varying richness (1-9 species), taxonomic relatedness (within genera class) rarity (5%-100% grains), Illumina MiSeq with rbcL ITS2. Qualitatively, composition determinations were largely correct, but false positives negatives occurred. False typically driven by lack gap or sample. Species relatedness, however, did strongly impact correct determinations. likely contamination, chimeric sequences and/or misidentification bioinformatics pipeline. Quantitatively, proportion for each was only weakly correlated its abundance, contrast suggestions from some other studies. Quantitative mismatches are correctable consistent scaling factors, instead context-dependent on present Together, our results show that robust determining presence/absence should be used infer grains.

Language: Английский

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Macroecology to Unite All Life, Large and Small

Trends in Ecology & Evolution, Journal Year: 2018, Volume and Issue: 33(10), P. 731 - 744

Published: Sept. 9, 2018

Language: Английский

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Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

Trends in Microbiology, Journal Year: 2020, Volume and Issue: 29(1), P. 19 - 27

Published: June 24, 2020

Amplicon sequencing of partial regions the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, rDNA dynamic and can exhibit substantial interspecific intraspecific variation in copy number prokaryotes and, especially, eukaryotes. As change a common response environmental change, not necessarily property species. Variation number, especially capacity for large changes driven by external cues, complicates analyses amplicon sequence data. We highlight need (i) interpret data light possible variation, (ii) examine potential plasticity as an important ecological factor better understand how communities are structured heterogeneous environments.

Language: Английский

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