Geomicrobiology in Hot Spring Hydrothermal Systems

Published: Jan. 1, 2025

Language: Английский

---

Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources

Current Microbiology, Journal Year: 2025, Volume and Issue: 82(6)

Published: April 22, 2025

Language: Английский

---

Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG

F1000Research, Journal Year: 2024, Volume and Issue: 13, P. 640 - 640

Published: June 17, 2024

Background Building Metagenome–Assembled Genomes (MAGs) from highly complex metagenomics datasets encompasses a series of steps covering cleaning the sequences, assembling them to finally group into bins. Along process, multiple tools aimed assess quality and integrity each MAG are implemented. Nonetheless, even when incorporated within end–to–end pipelines, outputs these pieces software must be visualized analyzed manually lacking integration in complete framework. Methods We developed Nextflow pipeline (MAGFlow) for estimating MAGs through wide variety approaches (BUSCO, CheckM2, GUNC QUAST), as well annotating taxonomically metagenomes using GTDB-Tk2. MAGFlow is coupled Python–Dash application (BIgMAG) that displays concatenated outcomes included by MAGFlow, highlighting most important metrics single interactive environment along with comparison/clustering input data. Results By MAGFlow/BIgMAG, user will able benchmark obtained different workflows or establish belonging samples following the divide rule methodology. Conclusions MAGFlow/BIgMAG represents unique tool integrates state-of-the-art study extract visually much information possible range genome features.

Language: Английский

---

Dataset of 313 metagenome-assemble genomes from streamer hot spring water

Data in Brief, Journal Year: 2024, Volume and Issue: 56, P. 110829 - 110829

Published: Aug. 10, 2024

This data report presents prokaryotic metagenome-assembled genomes (MAGs) from a hot spring stream with temperatures between 64 and 100°C. The water was filtered the extracted total DNA sequenced using Illumina HiSeq 2500 platform. Approximately 80 Gb of raw were generated, which subsequently assembled MEGAHIT v1.2.9. MAGs generated MetaWRAP binning approaches MetaBAT2, CONCOCT MaxBin2. We constructed 25 medium-quality 24 high-quality archaeal MAGs, 152 112 bacterial MAGs. fasta files these are available in NCBI database as well Mendeley Data. Major phyla identified include Bacteroidota, Chloroflexota, Desulfobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, Verrucomicrobiota, Armatimonadota, Nitrospirota, Acidobacteriota, Elusimicrobiota, Planctomycetota, Candidate division WOR-3, Aquificota, Thermoproteota, Micrarchaeota. dataset is valuable for studies on thermophilic genomes, reconstruction biochemical pathways gene discovery.

Language: Английский

---

Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG

F1000Research, Journal Year: 2024, Volume and Issue: 13, P. 640 - 640

Published: Sept. 23, 2024

Background Building Metagenome–Assembled Genomes (MAGs) from highly complex metagenomics datasets encompasses a series of steps covering cleaning the sequences, assembling them to finally group into bins. Along process, multiple tools aimed assess quality and integrity each MAG are implemented. Nonetheless, even when incorporated within end–to–end pipelines, outputs these pieces software must be visualized analyzed manually lacking integration in complete framework. Methods We developed Nextflow pipeline (MAGFlow) for estimating MAGs through wide variety approaches (BUSCO, CheckM2, GUNC QUAST), as well annotating taxonomically metagenomes using GTDB-Tk2. MAGFlow is coupled Python–Dash application (BIgMAG) that displays concatenated outcomes included by MAGFlow, highlighting most important metrics single interactive environment along with comparison/clustering input data. Results By MAGFlow/BIgMAG, user will able benchmark obtained different workflows or establish belonging samples following the divide rule methodology. Conclusions MAGFlow/BIgMAG represents unique tool integrates state-of-the-art study extract visually much information possible range genome features.

Language: Английский

---

Enhancing Photosynthetic Carbon Transport in Rice Plant Optimizes Rhizosphere Bacterial Community in Saline Soil

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(22), P. 12184 - 12184

Published: Nov. 13, 2024

Saline soils exert persistent salt stress on plants that inhibits their ability to carry out photosynthesis and leads photosynthetic carbon (C) scarcity in plant roots the rhizosphere. However, it remains unclear how a rhizosphere environment is shaped by C partitioning under saline conditions. Given sucrose primary form of transport, we, respectively, created transport distorted (STD) enhanced (STE) rice lines through targeted mutation overexpression transporter gene

Language: Английский

---