Let me upgrade you: impact of mobile genetic elements on enterococcal adaptation and evolution

CN Johnson, EK Sheriff, BA Duerkop… - Journal of …, 2021 - Am Soc Microbiol
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and
pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene …

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

HK Shrestha, MR Appidi, MI Villalobos Solis, J Wang… - BMC microbiology, 2021 - Springer
Background Microbe-microbe interactions between members of the plant rhizosphere are
important but remain poorly understood. A more comprehensive understanding of the …

Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction

P Yang, W Zheng, K Ning… - Proceedings of the …, 2021 - National Acad Sciences
Information derived from metagenome sequences through deep-learning techniques has
significantly improved the accuracy of template free protein structure modeling. However …

MetaDecoder: a novel method for clustering metagenomic contigs

CC Liu, SS Dong, JB Chen, C Wang, P Ning, Y Guo… - Microbiome, 2022 - Springer
Background Clustering the metagenomic contigs into potential genomes is a key step to
investigate the functional roles of microbial populations. Existing algorithms have achieved …

PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria

S Patz, A Gautam, M Becker, S Ruppel… - Biorxiv, 2021 - biorxiv.org
Plant-beneficial microorganisms are gaining importance for sustainable plant production
and phytosanitary practices. Yet there is a lack of computational approaches targeting …

Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting

J Wei, P Lotfy, K Faizi, S Baungaard, E Gibson, E Wang… - Cell Systems, 2023 - cell.com
Effective and precise mammalian transcriptome engineering technologies are needed to
accelerate biological discovery and RNA therapeutics. Despite the promise of …

The notable achievements and the prospects of bacterial pathogen genomics

GD Amoutzias, M Nikolaidis, A Hesketh - Microorganisms, 2022 - mdpi.com
Throughout the entirety of human history, bacterial pathogens have played an important role
and even shaped the fate of civilizations. The application of genomics within the last 27 …

Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate …

N Ghimire, B Kim, CM Lee, TJ Oh - BMC genomics, 2022 - Springer
Abstract Background While the genus Variovorax is known for its aromatic compound
metabolism, no detailed study of the peripheral and central pathways of aromatic compound …

[HTML][HTML] High potential for biomass-degrading enzymes revealed by hot spring metagenomics

NJ Reichart, RM Bowers, T Woyke… - Frontiers in …, 2021 - frontiersin.org
Enzyme stability and activity at elevated temperatures are important aspects in
biotechnological industries, such as the conversion of plant biomass into biofuels. In order to …

Biochemistry of methanol‐dependent acetogenesis in Eubacterium callanderi KIST612

HM Dietrich, F Kremp, C Öppinger… - Environmental …, 2021 - Wiley Online Library
Methanol is the simplest of all alcohols, is universally distributed in anoxic sediments as a
result of plant material decomposition and is constantly attracting attention as an interesting …