Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities DOI Creative Commons
Alexander Van Uffelen,

Andrés Posadas,

Nancy H. C. Roosens

и другие.

Scientific Data, Год журнала: 2024, Номер 11(1)

Опубликована: Авг. 10, 2024

Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore promises improved through longer reads. However, extensive benchmarking studies on data are lacking. We systematically evaluated performance of bacterial taxonomic for several commonly used classifiers, standardized reference sequence databases, the largest collection publicly available defined mock thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, high recall. Most fall first group, although precision can be without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, selection depends scope practical requirements. Although few designed long reads exist, they generally exhibit better performance. comprehensive provides concrete recommendations, supported by code reassessment fine-tuning other scientists.

Язык: Английский

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools DOI Creative Commons
Robyn Wright, A. Comeau, Morgan G. I. Langille

и другие.

Microbial Genomics, Год журнала: 2023, Номер 9(3)

Опубликована: Март 3, 2023

In metagenomic analyses of microbiomes, one the first steps is usually taxonomic classification reads by comparison to a database previously taxonomically classified genomes. While different studies comparing methods have determined that tools are 'best', there two been used most to-date: Kraken (

Язык: Английский

Процитировано

31
The Skin Microbiome: Current Techniques, Challenges, and Future Directions DOI Creative Commons

Tasha M. Santiago-Rodríguez,

Brice Le François,

Jean M. Macklaim

и другие.

Microorganisms, Год журнала: 2023, Номер 11(5), С. 1222 - 1222

Опубликована: Май 6, 2023

Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership function may differ depending on various specialized niches or micro-environments skin. The group microorganisms inhabiting skin, also known skin microbiome, offers protection against pathogens while actively interacting with host's immune system. Some members microbiome can act opportunistic pathogens. is influenced by factors such site, birth mode, genetics, environment, products, conditions. association(s) health disease has (have) been identified characterized via culture-dependent culture-independent methods. Culture-independent methods (such high-throughput sequencing), in particular, have expanded our understanding microbiome's role maintaining promoting disease. However, intrinsic challenges associated low microbial biomass high host content samples hindered advancements field. In addition, limitations current collection extraction biases derived from sample preparation analysis significantly results conclusions many studies. Therefore, present review discusses technical processing samples, advantages disadvantages sequencing approaches, potential future areas focus for

Язык: Английский

Процитировано

28
Phage-inclusive profiling of human gut microbiomes with Phanta DOI
Yishay Pinto, Meenakshi Chakraborty,

Navami Jain

и другие.

Nature Biotechnology, Год журнала: 2023, Номер 42(4), С. 651 - 662

Опубликована: Май 25, 2023

Язык: Английский

Процитировано

28
Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere DOI Creative Commons
Vinko Zadjelovic, Robyn Wright, Chiara Borsetto

и другие.

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Ноя. 1, 2023

The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity these materials serve as vectors for pathogenic bacteria reservoirs Antimicrobial Resistance Genes (ARG). In- ex-situ incubations were used characterise riverine plastisphere taxonomically functionally in order determine whether antibiotics within water influenced ARG profiles microbiomes how compared those on natural surfaces such wood their planktonic counterparts.We show that plastics support a distinct microbiome containing potential pathogens ARGs. While was similar biofilms grew wood, they from surrounding microbiome. Hence, whilst opportunistic (i.e. Pseudomonas aeruginosa, Acinetobacter Aeromonas) subtypes confer resistance macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents glycopeptides) predominant all surface-related microbiomes, especially weathered plastics, completely different set Escherichia, Salmonella, Klebsiella Streptococcus) ARGs aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone fosfomycin) dominated compartment. Our genome-centric analysis allowed assembly 215 Metagenome Assembled Genomes (MAGs), linking other virulence-related genes host. Interestingly, MAG belonging Escherichia -that clearly predominated water- harboured more virulence factors than any MAG, emphasising virulent pathogenic-related groups. Finally, using environmentally-relevant concentrations increased prevalence corresponding ARGs, but compartments -including plastispheres- affected differently by each antibiotic.Our results provide insights into harbour potentially function reservoir environmental impact pose if act either or is aggravated persistence environment due recalcitrance buoyancy. Nevertheless, high similarities with growing co-occurring even worrisome observed highlights urgent need integrate when assessing risks exposure anthropogenically-impacted ecosystems. Video Abstract.

Язык: Английский

Процитировано

28
Ten common issues with reference sequence databases and how to mitigate them DOI Creative Commons
Samuel D. Chorlton

Frontiers in Bioinformatics, Год журнала: 2024, Номер 4

Опубликована: Март 15, 2024

Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated benchmarked, far less attention given to the reference sequence database used in classification. Issues with databases are pervasive. Database contamination is most recognized issue literature; however, it remains relatively unmitigated analyses. Other common issues include taxonomic errors, inappropriate inclusion exclusion criteria, content errors. This review covers ten potential downstream consequences these issues. Mitigation measures discussed for each issue, including bioinformatic curation strategies. Together, strategies present a path towards more accurate, reproducible translatable sequencing.

Язык: Английский

Процитировано

15
A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass DOI Creative Commons
Joana Pereira‐Marques, Rui M. Ferreira, Céu Figueiredo

и другие.

Gut Microbes, Год журнала: 2024, Номер 16(1)

Опубликована: Фев. 29, 2024

The high background of host RNA poses a major challenge to metatranscriptome analysis human samples. Hence, metatranscriptomics has been mainly applied microbe-rich samples, while its application in tissues with low ratio microbial cells yet be explored. Since there is no computational workflow specifically designed for the taxonomic and functional this type we propose an effective strategy accurately characterize microbiome content. We experimentally generated synthetic samples well-characterized bacterial cell compositions, mimicking loads. These were used optimizing establishing controlled setting. Our results show that integration optimized Kraken 2/Bracken HUMAnN 3 content, enables accurate identification large number species false-positive rate, improving detection functions. effectiveness our was demonstrated simulated datasets, most importantly, gastric tissue specimens, thus providing proof concept applicability on mucosal gastrointestinal tract. use reliable approach content will expand understanding activity microbiome, uncovering critical interactions between health disease.

Язык: Английский

Процитировано

6
Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines DOI Creative Commons
Vadim Puller, Florian Plaza Oñate, Edi Prifti

и другие.

Microbial Genomics, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 13, 2025

Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not customize databases but translate results common use the with environment. Specifically, conducted two realistic simulations of gut microbiome samples, each based specific taxonomic profiler, and used different references project results, namely Genome Taxonomy Database Unified Human Gastrointestinal Genome. To demonstrate importance using framework, evaluated four established profilers as well impact perceived performance these profilers. Finally, provide guidelines enhance future profiler for human ecosystems: (i) or create tailored your biological context (BC), (ii) identify feature space suited BC independent catalogues by (iii) apply comprehensive set metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) quantification (UniFrac and/or Aitchison distance).

Язык: Английский

Процитировано

0
NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis DOI Creative Commons
Emmy Wesdorp,

Laura G.Y. Rotte,

Li‐Ting Chen

и другие.

npj Genomic Medicine, Год журнала: 2025, Номер 10(1)

Опубликована: Март 17, 2025

Abstract In immunocompromised pediatric patients, diagnosing invasive pulmonary aspergillosis (IPA) poses a significant challenge. Next-Generation Sequencing (NGS) shows promise for detecting fungal DNA but lacks standardization. This study aims to advance towards clinical evaluation of liquid biopsy NGS Aspergillus detection, through an wet-lab procedures and computational analysis. Our findings support using both CHM13v2.0 GRCh38.p14 in host-read mapping reduce false-positives. We demonstrate the sensitivity our custom kraken2 database, cRE.21, species. Additionally, cell-free sequencing superior performance whole-cell by recovering higher fractions lung fluid (bronchoalveolar lavage [BAL] fluid) plasma samples from patients with probable IPA. proof-of-principle, A. fumigatus was identified 5 out 7 BAL 3 samples. optimized workflow can fungal-NGS research represents step enhancing diagnostic certainty enabling more sensitive accurate species-level diagnosis IPA patients.

Язык: Английский

Процитировано

0
Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika DOI Open Access
Charlotte E. T. Huyghe, Antoine Fages, Fabrizia Ronco

и другие.

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Март 28, 2025

Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items essential to characterise trophic specialisations and understand the dynamics dietary adaptations. In this study, we explored niches 56 species from radiation cichlid fishes Lake Tanganyika, encompassing all major phylogenetic lineages feeding specialisations. We employed metagenomic sequencing approach identify food sources investigated at high taxonomic resolution, over 400 digestive content samples wild-caught individuals around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta Streptophyta as primary phyla Tanganyikan cichlids. Moreover, confirmed presence other identified taxa not previously documented be part cichlids' diet. Based on their compositions, cichlids can grouped into herbivores, invertivores, piscivores mixed feeders. Further, showed that disparity shaped by rapid divergence cases niche convergence. composition correlated with carbon nitrogen stable isotope values, gut length, body morphology. Differences diet-such consumption diatoms, streptophytes chlorophytes versus fish arthropods-were associated changes body, upper oral jaw lower pharyngeal shape. Collectively, study presents comprehensive detailed classification cichlids, highlighting power approaches delineating

Язык: Английский

Процитировано

0
Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut DOI Creative Commons
Matthias Schmitz, Nicholas J. Dimonaco, Thomas Clavel

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 3, 2025

Язык: Английский

Процитировано

0