Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity

Microbiology Spectrum, Год журнала: 2023, Номер 11(3)

Опубликована: Май 18, 2023

Anelloviruses represent the major and most diverse component of healthy human virome, referred to as anellome. In this study, we determined anellome 50 blood donors, forming two sex- age-matched groups. were detected in 86% donors. The number anelloviruses increased with age was approximately twice high men women. A total 349 complete or nearly genomes classified belonging torque teno virus (TTV), mini (TTMV), midi (TTMDV) anellovirus genera (197, 88, 64 sequences, respectively). Most donors had intergenus (69.8%) intragenus (72.1%) coinfections. Despite limited intradonor recombination analysis showed 6 events ORF1. As thousands sequences have been described recently, finally analyzed global diversity anelloviruses. Species richness close saturation each genus. Recombination found be main factor promoting diversity, although its effect significantly lower TTV than TTMV TTMDV. Overall, our results suggest that differences between may caused by variations relative contribution recombination.

Язык: Английский

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Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii

AMB Express, Год журнала: 2024, Номер 14(1)

Опубликована: Май 4, 2024

Abstract Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those natural origin. In this context, we aimed to use metagenomic nanopore sequence analysis soil microbiota coupled with conventional phenotypic screening and genomic identifying antimicrobial metabolites produced by promising isolate(s). study, whole metagenome sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning sequences probable secondary metabolite gene clusters were extracted analyzed antiSMASH version 2 DeepBGC. Results showed most abundant taxa Bifidobacterium, Burkholderia , Nocardiaceae (99.21%, followed Sphingomonadaceae (82.03%) B. haynesii (34%). Phenotypic respective samples has resulted in Bacillus isolate exhibited broad-spectrum antibacterial activities against various MDR pathogens. It identified microscopical, cultural, molecular methods as (B.) MZ922052. The revealed conservation seven biosynthetic namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes bacteriocin Lasso peptide (95%) bacillibactin (53%). conclusion, helped identify MZ922052 harboring metabolites. This is first report bacteriocin, lichenysin,

Язык: Английский

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Clinical metagenomics for infectious corneal ulcers: Rags to riches?

The Ocular Surface, Год журнала: 2019, Номер 18(1), С. 1 - 12

Опубликована: Окт. 25, 2019

Язык: Английский

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Microbiome Diagnostics

Clinical Chemistry, Год журнала: 2019, Номер 66(1), С. 68 - 76

Опубликована: Дек. 16, 2019

During the past decade, breakthroughs in sequencing technology and computational biology have provided basis for studies of myriad ways which microbial communities ("microbiota") on human body influence health disease. In almost every medical specialty, there is now a growing interest accurate replicable profiling microbiota use diagnostic therapeutic application.This review provides an overview approaches, challenges, considerations applications borrowing from other areas molecular diagnostics, including clinical metagenomics. Methodological evolving approaches mitochondrially encoded 16S rRNA-based amplicon to metagenomics metatranscriptomics are discussed. To improve replicability, at least most vulnerable steps testing workflows will need be standardized continuous efforts needed define QC standards. Challenges such as purity reagents consumables, improvement reference databases, availability diagnostic-grade data analysis solutions require joint across disciplines with manufacturers.The literature supporting important links between different anatomic sites disease expanding rapidly manipulation intestinal becoming routine. The next decade likely see implementation microbiome diagnostics laboratories fully capitalize technological scientific advances apply them routine practice.

Язык: Английский

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Toward Accurate and Robust Environmental Surveillance Using Metagenomics

Frontiers in Genetics, Год журнала: 2021, Номер 12

Опубликована: Март 5, 2021

Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out addressing need. However, several hurdles remain be overcome order generate actionable interpretations from metagenomic sequencing data infection prevention. Conceptually technically, we focus on viability assessment, taxonomic resolution, quantitative metagenomics, discuss their current advancements, necessary precautions directions further development. We highlight importance building solid conceptual frameworks identifying rational limits facilitate application techniques. also propose usage internal standards as promising approach analytical bottlenecks introduced low biomass samples inherent lack quantitation metagenomics. Taken together, hope this perspective will contribute bringing accurate consistent environmental ground.

Язык: Английский

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De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Ноя. 10, 2022

Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant human health and disease. However, contaminant sequences in metagenomic samples can potentially impact interpretation findings reported microbiome studies, especially low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing microbial contaminants when negative controls are unavailable. On samples, compare Squeegee predictions experimental control data show accurately recovers putative contaminants. We analyze varying biomass Human Microbiome Project identify likely, previously unreported kit contamination. Collectively, our results highlight with high precision thus represents computational approach for

Язык: Английский

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Soil Metatranscriptomics: An Improved RNA Extraction Method Toward Functional Analysis Using Nanopore Direct RNA Sequencing

Phytobiomes Journal, Год журнала: 2023, Номер 7(1), С. 42 - 54

Опубликована: Янв. 24, 2023

Soil microbes play an undeniable role in sustainable agriculture, plant health, and soil management. A deeper understanding of microbial composition function has been gained through next-generation sequencing. Although metagenomics provided valuable information about diversity, issues stemming from RNA extraction, low abundance some populations (e.g., viruses), messenger enrichment have slowed the progress metatranscriptomics. variety extraction methods developed thus far yet none available protocols can obtain with high quality, purity, yield for third-generation The latter requires quality large quantities (with no or contamination such as humic acids). Also, use commercial kits in-batch is quite expensive, these lack buffer details, which prevents optimization different types. An improved cost-effective method extracting RNAs mineral organic soils presented this article. acidic sodium acetate phosphate modifications to bead beating nucleic acid precipitation lead higher yields quality. Using method, we obtained almost DNA-free RNA. By using nanopore's direct sequencing, extracted contamination-free were successfully sequenced. Finally, taxonomic groups bacteria, fungi, archaea, viruses classified profiled, functional annotation datasets was carried out in-house customized bioinformatics workflow.

Язык: Английский

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Future potential of metagenomics in microbiology laboratories

Expert Review of Molecular Diagnostics, Год журнала: 2021, Номер 21(12), С. 1273 - 1285

Опубликована: Ноя. 10, 2021

Rapid and sensitive diagnostic strategies are necessary for patient care public health. Most of the current conventional microbiological assays detect only a restricted panel pathogens at time or require microbe to be successfully cultured from sample. Clinical metagenomics next-generation sequencing (mNGS) has potential unbiasedly all in sample, increasing sensitivity detection enabling discovery unknown infectious agents. High expectations have been built around mNGS; however, this technique is far widely available. This review highlights advances currently available options terms costs, turnaround time, sensitivity, specificity, validation, reproducibility mNGS as tool clinical microbiology laboratories. The need novel increase microbial diagnostics clear. revolutionize microbiology. However, its role yet established, which crucial implementing technique. A clear definition algorithms that include vital show utility. Similarly real-time PCR, will one day become any testing algorithm.

Язык: Английский

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Exploring the Diversity of the Human Blood Virome

Viruses, Год журнала: 2021, Номер 13(11), С. 2322 - 2322

Опубликована: Ноя. 21, 2021

Metagenomics is greatly improving our ability to discover new viruses, as well their possible associations with disease. However, metagenomics has also changed understanding of viruses in general. The vast expansion currently known viral diversity revealed a large fraction non-pathogenic and offers perspective which function important components many ecosystems. In this vein, studies the human blood virome are often motivated by search for diseases, especially those associated transfusions. these have common presence apparently blood, particularly anelloviruses and, lower extent, pegiviruses (HPgV). To shed light on virome, we subjected pooled plasma samples from 587 healthy donors Spain enrichment protocol, followed massive parallel sequencing. This showed that were clearly major component remarkable diversity. total, assembled 332 complete or near-complete anellovirus genomes, 50 could be considered species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates subsequently used characterizing virus. In-depth investigation should help elucidate ecology unveil potentially diseases.

Язык: Английский

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Metagenomic analysis of dental calculus in ancient Egyptian baboons

Scientific Reports, Год журнала: 2019, Номер 9(1)

Опубликована: Дек. 23, 2019

Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, metagenomics made it possible to unlock the wealth microbial dietary information dental calculus reconstruct oral microbiomes lifestyle humans from past. Although most studies have so far focused on humans, is known form in wide range animals, potentially informing how human-animal interactions changed animals' ecology. Here, we characterise microbiome six Egyptian baboons held captivity during late Pharaonic era (9th-6th centuries BC) two historical zoo via shotgun metagenomics. We demonstrate that these captive possessed distinctive when compared modern Neanderthals wild chimpanzee. These results may reflect omnivorous behaviour baboons, even though health, provisioning other factors associated with human management, baboons' microbiome. anticipate our study be starting point for more extensive animal examine extent which domestication management past affected diet, health target animals.

Язык: Английский

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