Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

AE Pérez-Cobas, L Gomez-Valero… - Microbial …, 2020 - microbiologyresearch.org
Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …

Metagenomic tools in microbial ecology research

N Taş, AEE de Jong, Y Li, G Trubl, Y Xue… - Current Opinion in …, 2021 - Elsevier
Ability to directly sequence DNA from the environment permanently changed microbial
ecology. Here, we review the new insights to microbial life gleaned from the applications of …

Unraveling the functional dark matter through global metagenomics

GA Pavlopoulos, FA Baltoumas, S Liu, O Selvitopi… - Nature, 2023 - nature.com
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions
and activities,. Exploration of this vast sequence space has been limited to a comparative …

Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability

J Meng, W Li, C Diao, Z Li, J Zhao, G Haider… - Journal of Hazardous …, 2023 - Elsevier
Microplastics (MPs) have emerged as widely existing global environmental concerns in
terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes …

[HTML][HTML] Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

D Calderón-Franco, R Sarelse, S Christou, M Pronk… - Water Research, 2022 - Elsevier
Abstract In the One Health context, wastewater treatment plants (WWTPs) are central to
safeguarding water resources. Nonetheless, many questions remain about their …

COVID-19 pandemic reveals the peril of ignoring metadata standards

LM Schriml, M Chuvochina, N Davies… - Scientific data, 2020 - nature.com
Efficient response to the pandemic through the mobilization of the larger scientific
community is challenged by the limited reusability of the available primary genomic data …

Microbial dark matter: from discovery to applications

Y Zha, H Chong, P Yang, K Ning - Genomics, Proteomics and …, 2022 - academic.oup.com
With the rapid increase of the microbiome samples and sequencing data, more and more
knowledge about microbial communities has been gained. However, there is still much more …

NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes

FA Baltoumas, E Karatzas, S Liu… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of
metagenome-and metatranscriptome-derived protein families, whose members have no hits …

Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists

J Jo, J Oh, C Park - Journal of Microbiology, 2020 - Springer
Microbial communities present in diverse environments from deep seas to human body
niches play significant roles in the complex ecosystem and human health. Characterizing …

Comparison of the microbiome of artisanal homemade and industrial feta cheese through amplicon sequencing and shotgun metagenomics

K Papadimitriou, R Anastasiou, M Georgalaki… - Microorganisms, 2022 - mdpi.com
Feta is the most renowned protected designation of origin (PDO) white brined cheese
produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on …