Unraveling metagenomics through long-read sequencing: a comprehensive review

Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)

Published: Jan. 28, 2024

Abstract The study of microbial communities has undergone significant advancements, starting from the initial use 16S rRNA sequencing to adoption shotgun metagenomics. However, a new era emerged with advent long-read (LRS), which offers substantial improvements over its predecessor, short-read (SRS). LRS produces reads that are several kilobases long, enabling researchers obtain more complete and contiguous genomic information, characterize structural variations, epigenetic modifications. current leaders in technologies Pacific Biotechnologies (PacBio) Oxford Nanopore Technologies (ONT), each offering distinct set advantages. This review covers workflow metagenomics sequencing, including sample preparation (sample collection, extraction, library preparation), processing (quality control, assembly, binning), analysis (taxonomic annotation functional annotation). Each section provides concise outline key concept methodology, presenting original as well how it is challenged or modified context LRS. Additionally, introduces range tools compatible can be utilized execute process. aims present metagenomics, highlight transformative impact LRS, provide selection suitable for this task.

Language: Английский

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Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

Frontiers in Science, Journal Year: 2024, Volume and Issue: 2

Published: April 25, 2024

This article advocates for mobilizing pathogen genomic surveillance to contain and mitigate health threats from infectious diseases antimicrobial resistance (AMR), building upon successes achieved by large-scale genome sequencing analysis of SARS-CoV-2 variants in guiding COVID-19 monitoring public responses adopting a One Health approach. Capabilities laboratory-based epidemic alert systems should be enhanced fostering (i) universal access real-time whole sequence (WGS) data pathogens inform clinical practice, infection control, policies, vaccine drug research development; (ii) integration diagnostic microbiology data, testing asymptomatic individuals, epidemiological into programs; (iii) stronger cross-sectorial collaborations between healthcare, health, animal environmental using approaches, toward understanding the ecology transmission pathways AMR across ecosystems; (iv) international collaboration interconnection networks, harmonization laboratory methods, standardization methods global reporting, including on variant or strain nomenclature; (v) responsible sharing databases, platforms according FAIR (findability, accessibility, interoperability, reusability) principles; (vi) system implementation its cost-effectiveness different settings. Regional policies governance initiatives foster concerted development efficient utilization protect humans, animals, environment.

Language: Английский

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Microbial diagnostics in periodontal diseases

Periodontology 2000, Journal Year: 2024, Volume and Issue: 95(1), P. 176 - 193

Published: May 26, 2024

Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding subgingival community dynamics. Certain pathobionts can orchestrate establishment dysbiotic communities that subvert host immune system, triggering inflammation and tissue destruction. Yet, diagnosis management conditions still rely on clinical radiographic examinations, overlooking well-established etiology. This review summarizes chronological emergence etiological models co-evolution with technological advances detection. We additionally approaches currently accessible to clinicians, highlighting their value broadening assessment. The epidemiological importance obtaining culture-based antimicrobial susceptibility profiles taxa for antibiotic resistance surveillance is also underscored, together clinically relevant guide antibiotherapy choices, when necessary. Furthermore, 16S-based shotgun metagenomic profiling discussed outlining signatures. Because dysbiosis precedes damage, biomarker identification offers early diagnostic possibilities forestall disease relapses during maintenance. Altogether, this highlights underutilized potential microbiology periodontology, spotlighting areas most conductive its implementation enhancing prevention, treatment predictability, addressing global resistance.

Language: Английский

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The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications

Molecular Cancer, Journal Year: 2025, Volume and Issue: 24(1)

Published: Jan. 15, 2025

The polymorphic microbiome is considered a new hallmark of cancer. Advances in High-Throughput Sequencing have fostered rapid developments research. interaction between cancer cells, immune and microbiota defined as the immuno-oncology (IOM) axis. Fungal microbes (the mycobiome), although representing only ∼ 0.1-1% microbiome, are critical immunologically active component tumor microbiome. Accumulating evidence suggests possible involvement commensal pathogenic fungi initiation, progression, treatment responsiveness. tumor-associated mycobiome mainly consists gut mycobiome, oral intratumoral mycobiome. However, role remains poorly understood, diversity complexity analytical methods make it challenging to access this field. This review aims elucidate causal complicit roles development progression while highlighting issues that need be addressed executing such We systematically summarize advantages limitations current fungal detection analysis methods. enumerate integrate these recent findings into our understanding accompanied by prospect novel exhilarating clinical implications.

Language: Английский

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Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk

Cells, Journal Year: 2024, Volume and Issue: 13(23), P. 1987 - 1987

Published: Dec. 1, 2024

The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It crucial preserve a healthy microbiome since pathogenic bacteria, such as

Language: Английский

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Progress in the Study of Intratumoral Microorganisms in Hepatocellular Carcinoma

Journal of Hepatocellular Carcinoma, Journal Year: 2025, Volume and Issue: Volume 12, P. 59 - 76

Published: Jan. 1, 2025

The intratumoral microbiota, an integral part of liver tumors, has garnered significant attention from researchers due to its role in tumor development regulation and impact on cancer treatment. Intratumoral microorganism not only influences tumorigenesis progression, but also serves as potential biomarkers targets for therapy. Targeted manipulation these microorganisms holds great promise personalized However, there is a lack systematic summaries reports the study hepatocellular carcinoma. This comprehensive review aims address this gap by summarizing research progress related field carcinoma bacteria, including their sources, types, distribution characteristics within development, underlying mechanisms, application prospects. Through analysis, it proposed that intratumor organisms can be used markers diagnosis treatment, drug carrier materials targeting tissues, prospects developing new combination therapies based in-depth understanding interactions between microenvironment, immune cells, etc. well exploring interactions. It hoped perspective theoretical support provided future targeted therapy insights ideas points methods research.

Language: Английский

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The Swiss Pathogen Surveillance Platform – towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata

Microbial Genomics, Journal Year: 2023, Volume and Issue: 9(5)

Published: May 12, 2023

The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental foodborne isolates. It enables rapid detailed transmission monitoring outbreak of pathogens using whole genome sequencing data associated metadata. features controlled access, complex dynamic queries, dedicated dashboards automated sharing with international repositories, providing actionable results for public health the vision improve societal well-being health.

Language: Английский

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Advance computational tools for multiomics data learning

Biotechnology Advances, Journal Year: 2024, Volume and Issue: 77, P. 108447 - 108447

Published: Sept. 7, 2024

Language: Английский

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Ribotyping Staphylococcus epidermidis Using Probabilistic Sequence Analysis and Levenshtein Distance Algorithm

Current Microbiology, Journal Year: 2025, Volume and Issue: 82(2)

Published: Jan. 10, 2025

Staphylococcus epidermidis (S. epidermidis) live in different human locations and natural environments. For ribotyping S. sub-species, 2507 PCR-amplified reads of 16S rRNA genes a public dataset were used for probabilistic sequence analysis. A probability logo (sequence pLogo) as reference was constructed. Through implementation Levenshtein Distance algorithm, two 20-base pairs (bp) motifs, commonly present reads, identified. The top 38 isolates, which carried nucleotide domains that made sequences but have high similarity scores to 20-bp found from 11 human, 8 animal, 9 plant 10 environmental samples, indicating these motifs broadly diverse isolates. Thirty-one genes, currently not the dataset, utilized verify feasibility using sub-species. S1, S3, S2, isolates on scalp domain with similarities motif pLogo. phylogenetic tree showed S2 S3 single common ancestor. Two newly identified here, thus, provided residues epidermidis.

Language: Английский

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Hepatic Steatosis and Microbiota: A Regional Study on Patients from Western Romania

Gastrointestinal Disorders, Journal Year: 2025, Volume and Issue: 7(1), P. 9 - 9

Published: Jan. 18, 2025

Background/Objectives: The gut–liver axis is bidirectional and influences the body’s homeostasis. Pathologies such as metabolic dysfunction-associated steatotic liver (MASL) can have detrimental effects on human microbiome, with multiple systemic effects. Furthermore, geographical particularities of intestinal microbiome may influence disease. study’s outcome was to identify dysbiosis in a group patients MASL from western region Romania. Methods: NGS shotgun genomic sequencing (WGS metagenomics) method used bacteria fecal samples. data were analyzed using IBM SPSS Statistics software [version 29.0.2.0 (20)]. Results: Out 122 included study, 43 (35.24%) exhibited low alpha diversity. In subgroup normal biodiversity index, approximately half identified Firmicutes/Bacteroidetes ratio below lower reference value, while remaining presented based decreased concentrations Proteobacteria Prevotella, considered among most relevant species supporting dysbiosis. A higher prevalence Prevotella (15.99 ± 13.65%) study cohort. Conclusions: present demonstrates that Romania exhibit criteria for dysbiosis, namely reduced bacterial diversity, along significant alterations populations Firmicutes, Bacteroidetes, Proteobacteria, Prevotella. Together, these findings suggest possible geo-cultural factors highlighting need regionally adapted therapeutic interventions support health.

Language: Английский

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