Results 81 to 90 of about 1,283,302 (227)

Brugia malayi gDNA metagenome assembly binned contigs

, 2023
We performed gDNA sequencing on Brugia malayi adult female samples containing the endosymbiotic bacterium Wolbachia. The reads were randomly downsampled to 10 million reads. Metagenome assembly was performed using metaSpades.
Lindsey Cantin (17513745)
core   +1 more source

Revolutionising Agricultural Sustainability: New ‘Furrow Tillage’ can Mitigate Short‐Term Soil‐to‐Atmosphere CO2 Flux and Promote Soil‐Plant‐Microbe Health

Advanced Science, EarlyView.
Furrow tillage resolves the conventional‐vs.‐no‐tillage trade‐off by simultaneously cutting CO2 efflux to 2.0–3.0 g C m−2 d−1 and unlocking high nutrient availability for the rice rhizosphere. This scalable agronomic solution strengthens soil health, enhances plant physiology, reshapes microbial metabolism, and shifts paddy systems toward a net ...
Arnab Majumdar, Munish Kumar Upadhyay, Argha Ghosh, Rakesh Biswas, Ioly Kotta Loizou, Martin Buck, Mark Tibbett, Biswajit Giri, Debojyoti Moulick, Manoj Kumar Jaiswal, Tarit Roychowdhury   +10 more
wiley   +1 more source

The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences [version 2; peer review: 2 approved, 1 approved with reservations]

Wellcome Open Research
We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases.
Jose Victor Lopez, Eerik Aunin, Ute Hentschel, Martha Alejandra Durán Canché, Rinat Bar-Shalom, Micha Ilan, Victoria McKenna, Laura Steindler, Elizabeth Sinclair, Graeme Oatley, Camilla Santos, Haoyu Niu, Noah Gettle, Michael Paulini, Rebecca O’Brien   +14 more
doaj   +1 more source

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

BMC Genomics, 2017
Background Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential.
Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards, Elizabeth A. Dinsdale   +11 more
doaj   +1 more source

Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities

Microorganisms, 2022
Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic ...
Zhao Chen, Jianghong Meng
doaj   +1 more source

Species assignments of metagenome assembly contigs

, 2014
Species assignments of metagenome assembly ...
Christopher Beitel (518618)
core   +1 more source

Unveiling the Taxonomic Diversity and Unprecedented Biosynthetic Treasure of the Phylum Myxococcota

Advanced Science, EarlyView.
Natural products remain vital sources of therapeutics, and the phylum Myxococcota constitutes an especially rich reservoir for them. Based on decades of microbiological efforts, we present 154 new Myxococcota genomes and revise taxonomy quadrupling the number of families and genera.
Amay Ajaykumar Agrawal, Ronald Garcia, Guangyi Chen, Chantal D. Bader, Peter Sullivan, Alexander Popoff, Daniel Krug, Maja Hunter, Sebastian Walesch, Emilia Oueis, Christine Frank, Haowen Zhao, Joachim J. Hug, Sebastian Keller, Pascal Hirsch, Azat Tagirdzhanov, Tatiana Malygina, Mary Victory E. Gutierrez, Alexey Gurevich, Judith Boldt, Boyke Bunk, Jörg Overmann, Ulrich Nübel, Andreas Keller, Olga V. Kalinina, Rolf Müller   +25 more
wiley   +1 more source

Reference-guided assembly of metagenomes with MetaCompass

Cell Reports Methods
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context.
Tu Luan, Victoria P. Cepeda-Espinoza, Bo Liu, Zac Bowen, Ujjwal Ayyangar, Mathieu Almeida, Sergey Koren, Todd J. Treangen, Adam Porter, Mihai Pop   +9 more
openaire   +2 more sources

Snowball: strain aware gene assembly of metagenomes [PDF]

Bioinformatics, 2016
Abstract Motivation Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require closely related reference genomes of the ...
I. Gregor, Alexander Schönhuth, Alice Carolyn McHardy   +2 more
openaire   +4 more sources

Rainfall Shapes the Diversity of Soil Nitrogen‐Fixing Microorganisms Worldwide

Advanced Science, EarlyView.
This study reveals the distinctive pattern and mechanism of rainfall driving the global biodiversity and biogeography of soil potential N‐fixing microorganisms, and constructs the theoretical framework. The results guide us on how to maintain ecosystem productivity under future climate changes (e.g., whether a specific region needs more N fertilizers ...
Bin Hua, Shuang Pang, Ang Li, Zonghao Hu, Honghui Wu, Shuhan Zhang, Yi Fan, Yi Wu, Wei Yang, Yachao Zhao, Yupeng Guan, Baoming Ji, Deliang Kong, Yong Zhao, Anton A. Goncharov, Anastasia Yu. Korotkevich, Rong Mao, Yang Zhang, Ximei Zhang   +18 more
wiley   +1 more source