Metagenomics: An effective approach for exploring microbial diversity and functions

NN Nam, HDK Do, KT Loan Trinh, NY Lee - Foods, 2023 - mdpi.com
Various fields have been identified in the “omics” era, such as genomics, proteomics,
transcriptomics, metabolomics, phenomics, and metagenomics. Among these …

The skin microbiome: current techniques, challenges, and future directions

TM Santiago-Rodriguez, B Le François, JM Macklaim… - Microorganisms, 2023 - mdpi.com
Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses
whose membership and function may differ depending on the various specialized niches or …

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples

NJ Wu-Woods, JT Barlow, F Trigodet, DG Shaw… - Nature …, 2023 - nature.com
Host–microbe interactions have been linked to health and disease states through the use of
microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However …

[HTML][HTML] The application of metagenomics to study microbial communities and develop desirable traits in fermented foods

M Srinivas, O O'Sullivan, PD Cotter, D Sinderen… - Foods, 2022 - mdpi.com
The microbial communities present within fermented foods are diverse and dynamic,
producing a variety of metabolites responsible for the fermentation processes, imparting …

Effect of diet on the gut mycobiome and potential implications in inflammatory bowel disease

J Buttar, E Kon, A Lee, G Kaur, G Lunken - Gut Microbes, 2024 - Taylor & Francis
The gut microbiome is a complex, unique entity implicated in the prevention, pathogenesis,
and progression of common gastrointestinal diseases. While largely dominated by bacterial …

Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies

C Brennan, P Belda-Ferre, S Zuffa… - …, 2024 - journals.asm.org
Large-scale studies are essential to answer questions about complex microbial communities
that can be extremely dynamic across hosts, environments, and time points. However …

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

IB Slizovskiy, M Oliva, JK Settle, LV Zyskina, M Prosperi… - Microbiome, 2022 - Springer
Background Metagenomic data can be used to profile high-importance genes within
microbiomes. However, current metagenomic workflows produce data that suffer from low …

[HTML][HTML] Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater

J Akter, WJM Smith, Y Liu, I Kim, SL Simpson… - Science of The Total …, 2024 - Elsevier
The lack of standardized methods and large differences in virus concentration and extraction
workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater …

Identifying eukaryotes and factors influencing their biogeography in drinking water metagenomes

M Gabrielli, Z Dai, V Delafont… - Environmental …, 2023 - ACS Publications
The biogeography of eukaryotes in drinking water systems is poorly understood relative to
that of prokaryotes or viruses, limiting the understanding of their role and management. A …