The Skin Microbiome: Current Landscape and Future Opportunities

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3950 - 3950

Published: Feb. 16, 2023

Our skin is the largest organ of body, serving as an important barrier against harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this protects body from invading pathogens through a sophisticated innate immune response co-adapted consortium commensal microorganisms, collectively termed microbiota. These microorganisms inhabit distinct biogeographical regions dictated by physiology. Thus, it follows that perturbations to normal homeostasis, occurs with ageing, diabetes disease, can cause microbial dysbiosis increase infection risk. In review, we discuss emerging concepts in microbiome research, highlighting pertinent links between cutaneous repair. Moreover, address gaps current knowledge highlight key areas requiring further exploration. Future advances field could revolutionise way treat associated ageing other pathologies.

Language: Английский

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Nanopore sequencing: flourishing in its teenage years

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence

Neural Regeneration Research, Journal Year: 2023, Volume and Issue: 19(4), P. 833 - 845

Published: Aug. 14, 2023

A growing body of evidence suggests that the gut microbiota contributes to development neurodegenerative diseases via microbiota-gut-brain axis. As a contributing factor, dysbiosis always occurs in pathological changes diseases, such as Alzheimer's disease, Parkinson's and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped reveal bidirectional communication between central nervous system enteric is facilitated by microbiota's diverse microorganisms, for both neuroimmune neuroendocrine systems. Here, we summarize bioinformatics analysis wet-biology validation metagenomics with an emphasis on multi-omics studies virome. The pathogen-associated signaling biomarkers identifying brain disorders potential therapeutic targets are also elucidated. Finally, discuss role diet, prebiotics, probiotics, postbiotics exercise interventions remodeling microbiome reducing symptoms diseases.

Language: Английский

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Strategies and tools in illumina and nanopore‐integrated metagenomic analysis of microbiome data

iMeta, Journal Year: 2023, Volume and Issue: 2(1)

Published: Jan. 9, 2023

Abstract Metagenomic strategy serves as the foundation for ecological exploration of novel bioresources (e.g., industrial enzymes and bioactive molecules) biohazards pathogens antibiotic resistance genes) in natural engineered microbial systems across multiple disciplines. Recent advancements sequencing technology have fostered rapid development field microbiome research where an increasing number studies applied both illumina short reads (SRs) nanopore long (LRs) their metagenomic workflow. However, given high complexity environmental data set bioinformatic challenges caused by unique features these technologies, integrating SRs LRs is not straightforward one might assume. The fast renewal existing tools growing diversity new algorithms make access to this even more difficult. Therefore, here we systematically summarized complete workflow from DNA extraction processing strategies applying nanopore‐integrated metagenomics investigation microbiomes. Overall, review aims provide a timely knowledge framework researchers that are interested or struggling with integration analysis. discussions presented will facilitate improved understanding community functionalities assembly natural, engineered, human microbiomes, benefiting

Language: Английский

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Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: May 6, 2024

Abstract Background Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green brown thriving submerged plant litter within Sungai Klah hot Malaysia, characterised by temperatures 58–74 °C. Using Illumina shotgun metagenomics Nanopore ligation sequencing, we investigated diversity functional metagenome-assembled genomes (MAGs) with specific focus biofilm formation, heat stress response, carbohydrate catabolism. Results Leveraging power both short-reads long-reads, employed an Illumina-Nanopore hybrid assembly approach to construct MAGs enhanced quality. The dereplication process, facilitated dRep tool, validated efficiency assembly, yielding that reflected intricate these ecosystems. comprehensive analysis uncovered intriguing insights thermophilic taxa biofilms. Moreover, examined degradation biofilms, shedding light participation diverse breakdown starch, cellulose, hemicellulose. We highlight Chloroflexota Armatimonadota exhibited wide array glycosyl hydrolases targeting various substrates, underscoring their metabolic versatility utilisation carbohydrates at elevated temperatures. Conclusions advances understanding ecology under temperature revealing adaptation from In addition, our findings biotechnology application through identification lignocellulose-degrading enzymes. By demonstrating utilising reads, value combining multiple sequencing methods more thorough exploration complex communities.

Language: Английский

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Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis

Bioresource Technology, Journal Year: 2024, Volume and Issue: 401, P. 130740 - 130740

Published: April 25, 2024

Language: Английский

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Revisiting diagnostics: Practical application of Next-Generation Sequencing technologies for infectious diseases

Clinical Microbiology and Infection, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

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Nanopore Environmental Analysis

JACS Au, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

As global pollution continues to escalate, timely and accurate monitoring is essential for guiding governance safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge instrumental analysis methods, which often require labor-intensive time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents promising solution by enabling the rapid identification multiple targets within complex mixtures with minimal preparation. A wide range have been characterized using natural biological nanopores or artificial solid-state nanopores, their distinct advantages include simple preparation, high sensitivity, onsite analysis. In particular, long-read nanopore sequencing has led dramatic improvements in analyses microbial communities, allows species-level taxonomic assignment amplicon sequencing, simplifies assembly metagenomes. this Perspective, we review latest advancements analyzing chemical through sensing techniques. We also explore challenges that remain rapidly evolving field provide outlook on potential transform monitoring, risk assessment, health protection.

Language: Английский

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Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 3, 2025

The gut microbiota actually shares the host's physical space and affects physiological functions health indicators through a complex network of interactions with host. However, its role as determinant host disease is often underestimated. With emergence new technologies including next-generation sequencing (NGS) advanced techniques such microbial community sequencing, people have begun to explore interaction mechanisms between microorganisms hosts at various omics levels genomics, transcriptomics, metabolomics, proteomics. enrichment multi-omics integrated analysis methods based on microbiome, an increasing number statistical also been proposed. In this review, we summarized research currently used study microbiome We analyzed advantages limitations briefly introduced their application progress.

Language: Английский

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Benchmarking of analysis tools and pipeline development for nanopore long-read metagenomics

Science Bulletin, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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