Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

Y Li, C Zhang, W Zheng, X Zhou… - Proteins: Structure …, 2021 - Wiley Online Library
This article reports and analyzes the results of protein contact and distance prediction by our
methods in the 14th Critical Assessment of techniques for protein Structure Prediction …

Marine sponge and octocoral-associated bacteria show versatile secondary metabolite biosynthesis potential and antimicrobial activities against human pathogens

JF Almeida, M Marques, V Oliveira, C Egas… - Marine Drugs, 2022 - mdpi.com
Marine microbiomes are prolific sources of bioactive natural products of potential
pharmaceutical value. This study inspected two culture collections comprising 919 host …

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

Y Liu, T Brinkhoff, M Berger, A Poehlein, S Voget… - Microbiome, 2023 - Springer
Abstract Background The RCA (Roseobacter clade affiliated) cluster belongs to the family
Roseobacteracea and represents a major Roseobacter lineage in temperate to polar …

Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4

S Ghimire-Kafle, ME Weaver Jr… - Applied and …, 2023 - Am Soc Microbiol
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic
bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here …

Plant N-glycan breakdown by human gut Bacteroides

LI Crouch, PA Urbanowicz, A Baslé… - Proceedings of the …, 2022 - National Acad Sciences
The major nutrients available to the human colonic microbiota are complex glycans derived
from the diet. To degrade this highly variable mix of sugar structures, gut microbes have …

Structural foundations of potassium selectivity in channelrhodopsins

EG Govorunova, OA Sineshchekov, LS Brown… - Mbio, 2022 - Am Soc Microbiol
Potassium-selective channelrhodopsins (KCRs) are light-gated K+ channels recently found
in the stramenopile protist Hyphochytrium catenoides. When expressed in neurons, KCRs …

Characterization of genomic, physiological, and probiotic features Lactiplantibacillus plantarum DY46 strain isolated from traditional lactic acid fermented shalgam …

AE Yetiman, A Keskin, BN Darendeli, SE Kotil… - Food Bioscience, 2022 - Elsevier
Lactiplantibacillus plantarum is a significant probiotic where it could be found in ubiquitous
niches. In this study, a new Lb. plantarum strain DY46 was isolated from a traditional lactic …

Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid …

A Yetiman, M Horzum, D Bahar, M Akbulut - Probiotics and Antimicrobial …, 2024 - Springer
This study aimed to characterize the genomic and metabolic properties of a novel Lb.
fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called …

[HTML][HTML] Viroid-like colonists of human microbiomes

IN Zheludev, RC Edgar, MJ Lopez-Galiano… - BioRxiv, 2024 - ncbi.nlm.nih.gov
Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements
that we first identified in human gut metatranscriptomic data.“Obelisks” share several …

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

C Coclet, PO Sorensen, U Karaoz, S Wang, EL Brodie… - Microbiome, 2023 - Springer
Background Viruses impact nearly all organisms on Earth, including microbial communities
and their associated biogeochemical processes. In soils, highly diverse viral communities …