EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights diversity, interactions, their roles health disease. However, complexity data processing need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, user‐friendly pipeline that supports multiple methods, including quality control host removal, read‐based, assembly‐based, binning, along with advanced genome analysis. The also features customizable settings, comprehensive visualizations, detailed parameter explanations, ensuring its adaptability across wide range scenarios. Looking forward, aim refine by addressing contamination issues, optimizing workflows third‐generation sequencing data, integrating emerging technologies like deep learning network analysis, further enhance accuracy. EasyMetageonome is freely available https://github.com/YongxinLiu/EasyMetagenome .

Language: Английский

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Factors Determining the Susceptibility of Fish to Effects of Human Pharmaceuticals

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(24), P. 8845 - 8862

Published: June 8, 2023

The increasing levels and frequencies at which active pharmaceutical ingredients (APIs) are being detected in the environment of significant concern, especially considering potential adverse effects they may have on nontarget species such as fish. With many pharmaceuticals lacking environmental risk assessments, there is a need to better define understand risks that APIs their biotransformation products pose fish, while still minimizing use experimental animals. There both extrinsic (environment- drug-related) intrinsic (fish-related) factors make fish potentially vulnerable human drugs, but not necessarily captured nonfish tests. This critical review explores these factors, particularly focusing distinctive physiological processes underlie drug absorption, distribution, metabolism, excretion toxicity (ADMET). Focal points include impact life stage absorption (A) via multiple routes; implications fish's unique blood pH plasma composition distribution (D) molecules throughout body; how endothermic nature varied expression activity drug-metabolizing enzymes tissues affect metabolism (M); physiologies relative contribution different excretory organs (E) metabolites. These discussions give insight into where existing data properties, pharmacokinetics pharmacodynamics from mammalian clinical studies or help inform

Language: Английский

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SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D777 - D783

Published: Oct. 28, 2023

Abstract Meta’omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to type, study or sampled environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived modalities across habitats, geography phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering wide array of environments augmented with manually-curated contextual data. Across total assembly 16 Tbp, comprises 35 billion predicted protein sequences 1.16 million newly constructed metagenome-assembled genomes (MAGs) medium high quality. Beyond mapping the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 species-level clusters, majority which are unclassified at species level using current tools. enables taxonomic profiling clusters via an updated, custom mOTUs database (https://motu-tool.org/) includes several layers functional annotation, as well crosslinks (micro-)biological databases. The resource accessible, searchable browsable http://spire.embl.de.

Language: Английский

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The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(D1), P. D1 - D8

Published: Jan. 6, 2023

The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 reporting on new databases 82 updates from resources previously published in the Issue. Six more most recently elsewhere. Major nucleic acid include Genbank, ENA, ChIPBase, JASPAR, mirDIP Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates BMRB RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING REBASE stand-out signalling enzymes section. Immunology-related CEDAR, second cancer epitopes receptors alongside returning IPD-IMGT/HLA PGG.MHC. Genomics-related Ensembl, GWAS Central UCSC Genome Browser. drugs their targets Open Targets, DrugCentral, CTD Pubchem. EMPIAR image archive appears time. entire database is freely available online website (https://academic.oup.com/nar). NAR Molecular Biology Collection has been updated, revisiting 463 entries, adding 92 eliminating 96 discontinued URLs so bringing current total to 1764 databases. It at http://www.oxfordjournals.org/nar/database/c/.

Language: Английский

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VOGDB—Database of Virus Orthologous Groups

Viruses, Journal Year: 2024, Volume and Issue: 16(8), P. 1191 - 1191

Published: July 25, 2024

Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution viruses, grouping sequences from virus genomes is particularly challenging. The low similarities genes viruses require specific approaches for sequence- structure-based clustering. Furthermore, annotation public databases not as consistent up date many cellular genomes. To tackle these problems, we have developed VOGDB, which a database orthologous groups. VOGDB multi-layer that progressively viral into connected by increasingly remote similarity. first layer based on pair-wise similarities, second profile alignments, third uses predicted structures find most allow more sensitive homology searches novel increase chance predicting annotations or inferring phylogeny. VOGD B all RefSeq partially reannotates them. updated with every release. unique feature inclusion both prokaryotic eukaryotic same clustering process, makes it possible explore old evolutionary relationships two freely available at vogdb.org under CC BY 4.0 license.

Language: Английский

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Gut microbiota strain richness is species specific and affects engraftment

Nature, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 27, 2024

Language: Английский

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BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(10), P. 5478 - 5495

Published: April 30, 2024

Abstract Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome of BGCFlow incorporates several and tools grouped into five common stages analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) mining, (v) comparative analysis. Furthermore, provides easy configuration different projects, parallel distribution, scheduled job monitoring, an interactive database visualize tables, exploratory Jupyter Notebooks, customized reports. demonstrate the application by investigating distribution various gene clusters detected 42 Saccharopolyspora genus, known produce industrially important secondary/specialized metabolites. BGCFlow-guided predicted more accurate dereplication BGCs guided targeted selected RiPPs. scalable, interoperable, adaptable, re-entrant, reproducible nature will provide effective way from ever-growing genomic datasets biotechnologically relevant species.

Language: Английский

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First report on comprehensive genomic analysis of a multidrug-resistant Enterobacter asburiae isolated from diabetic foot infection from Bangladesh

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 2, 2025

Enterobacter asburiae (E. asburiae) is a gram-negative rod-shaped bacterium which has emerging significance as an opportunistic pathogen having high virulence pattern and drug resistant properties. In this study, we present the detailed analysis of whole genome sequence multidrug-resistant (MDR) E. strain BDW1M3 from Bangladesh. The isolate was collected infected foot wound diabetic ulcer patient. Through sophisticated genomic techniques encompassing sequencing in-depth bioinformatic analyses, research unveils profound understanding isolate's antimicrobial resistance patterns, determinants, biosynthetic gene clusters, metabolic pathways pathogenic potential. displayed to Ampicillin, Fosfomycin, Cefoxitin, Tigecycline, Meropenem, Linezolid, Vancomycin antibiotics demonstrated capacity for biofilm formation. Several genes such blaACT−2,fosA2, baeR, qnrE2, vanA numbers including ybaJ, csrA, barA, uvrY, pgaD, hlyD, hlyC, terC, purD were detected. Metal investigation revealed presence cusCFBA operon system, many other zntA, zitB, czrB. Prophage region Myoviridae Comparative genomics with 47 (n = 47) shed light on genetic diversity strains diverse sources countries, notable observation that both human non-human origins exhibited significant pathogenicity potential, phylogenomic relations hinting at potential cross-species transmission. Pangenome indicated toward expanding pangenome asburiae. Further comprehensive studies are required investigate prevalence in Bangladesh emphasize towards unraveling bacterium's inherent intricate molecular mechanisms underlie its traits

Language: Английский

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PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Feb. 11, 2025

Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity understand how community profiles vary under different environmental conditions. Conventional approaches metaproteomic often treat protein functions as independent features, ignoring evolutionary relationships among taxa from which proteins originate. A more informative distance that incorporates relatedness needed better microbiome dissimilarities. Here, we introduce PhyloFunc, novel phylogeny inform on distance. Leveraging phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths weigh between-sample distances each taxon, rather than differences in taxonomic abundance UniFrac. Proof concept using simulated toy dataset and real mouse inoculated with synthetic gut fed diets show successfully captured compensatory effects phylogenetically related taxa. We further tested third complex human microbiomes treated five drugs compare PhyloFunc's performance other traditional methods. PCoA machine learning-based classification algorithms revealed higher sensitivity responses paracetamol. provide an open-source Python package (available at https://pypi.org/project/phylofunc/ ), enabling efficient calculation pair samples or generation matrix all within dataset. Unlike consider features unrelated, acknowledges role context shaping landscape metaproteomes. In particular, report accounts effect taxonomically species. Its effectiveness, relevance, enhanced distinguishing group variations are demonstrated through specific applications presented this study.

Language: Английский

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Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(11), P. 1828 - 1838

Published: Aug. 18, 2023

Abstract Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir methane on Earth. Yet, deep subsurface biosphere controls its contribution to production remain underexplored. Here, we use a multidisciplinary approach examine methanogenesis in (down 295 mbsf) from sites with varying degrees thermal alteration (none, past, current) at Guaymas Basin (Gulf California) for first time. Traditional (13C/12C D/H) multiply substituted (13CH3D 12CH2D2) isotope measurements reveal significant proportions all sites, signal site past alteration. With depth, relative decreases differing rates between sites. Gibbs energy calculations confirm is exergonic sediments, methylotrophic pathways consistently yielding more than canonical hydrogenotrophic acetoclastic pathways. metagenomic sequencing cultivation attempts indicate that methanogens present low abundance. We find only one methyl-coenzyme M (mcrA) sequence within entire dataset. Also, identify wide diversity methyltransferases (mtaB, mttB), but few sequences phylogenetically cluster methanogens. Our results suggest was produced over geologic time by relatively small methanogen populations, which have been variably influenced sediment Higher resolution sampling may clarify modern community. This study highlights importance using capture influences dynamic, settings like Basin.

Language: Английский

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