Genome-resolved metagenomics: a game changer for microbiome medicine

N Kim, J Ma, W Kim, J Kim, P Belenky… - Experimental & Molecular …, 2024 - nature.com
Recent substantial evidence implicating commensal bacteria in human diseases has given
rise to a new domain in biomedical research: microbiome medicine. This emerging field …

[HTML][HTML] Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review

J Sadurski, M Polak-Berecka, A Staniszewski, A Waśko - Foods, 2024 - mdpi.com
This review article offers a comprehensive overview of the current understanding of using
metagenomic tools in food microbiome research. It covers the scientific foundation and …

SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing

S Pan, XM Zhao, LP Coelho - Bioinformatics, 2023 - academic.oup.com
Motivation Metagenomic binning methods to reconstruct metagenome-assembled genomes
(MAGs) from environmental samples have been widely used in large-scale metagenomic …

Map** the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

G Michoud, H Peter, SB Busi, M Bourquin… - Nature …, 2025 - nature.com
Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked
by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize …

Effective binning of metagenomic contigs using contrastive multi-view representation learning

Z Wang, R You, H Han, W Liu, F Sun, S Zhu - Nature Communications, 2024 - nature.com
Contig binning plays a crucial role in metagenomic data analysis by grou** contigs from
the same or closely related genomes. However, existing binning methods face challenges in …

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

M Sereika, F Petriglieri, TBN Jensen… - The ISME …, 2023 - academic.oup.com
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria,
which are capable of conducting long-distance electron transfer. Currently, all cable bacteria …

Weak magnetic field promotes denitrification by stimulating ferromagnetic ion-containing metalloprotein expression

Y Lin, Y Chen, H Wang, Y Yu, Y Wang, S Ma, L Wang… - Water Research, 2024 - Elsevier
Weak magnetic field (WMF) has been recognized to promote biological denitrification
processes; however, the underlying mechanisms remain largely unexplored, hindering the …

Adverse environmental perturbations may threaten kelp farming sustainability by exacerbating Enterobacterales diseases

Y Zhang, S Nair, Z Zhang, J Zhao, H Zhao… - Environmental …, 2024 - ACS Publications
Globally kelp farming is gaining attention to mitigate land-use pressures and achieve carbon
neutrality. However, the influence of environmental perturbations on kelp farming remains …

Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution

K Wang, G Hua, J Li, Y Yang, C Zhang, L Yang, X Hu… - Imeta, 2024 - Wiley Online Library
Structural variations (SVs) are a major source of domestication and improvement traits. We
present the first duck pan‐genome constructed using five genome assemblies capturing∼ …

Predicting climate-change impacts on the global glacier-fed stream microbiome

M Bourquin, H Peter, G Michoud, SB Busi… - Nature …, 2025 - nature.com
The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of
climate change. However, forecasts of how GFS microbiome structure and function will …