Results 51 to 60 of about 1,840,918 (247)

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes [PDF]

Frontiers in Microbiology, 2018
Contigs for all MAGs are available on figshare and NCBI BioProject PRJNA432584. The raw sequence FASTA files for the ten metagenomes are available at JGI (Supplementary Table S1).
Marie E. Kroeger, Tom O. Delmont, A. M. Eren, A. M. Eren, Kyle M. Meyer, Jiarong Guo, Kiran Khan, Jorge L. M. Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clovis D. Borges, James M. Tiedje, Siu M. Tsai, Klaus Nüsslein   +13 more
openaire   +5 more sources

Analysis of novel bacterial metagenome-assembled genomes from lignin-degrading microbial consortia [PDF]

Current Research in Microbial Sciences
Despite recent progress, bacterial degradation of lignin is not completely understood. To address the mechanisms that bacteria from unknown taxonomic groups use to perform lignin-monomer degradation, functional analysis of bacterial metagenome-assembled genomes from soil-derived consortia enriched for microorganisms capable of degrading lignin was ...
Vitória Pinheiro Balestrini, Otávio Henrique Bezerra Pinto, Blake A. Simmons, John M. Gladden, Ricardo Henrique Krüger, Betania Ferraz Quirino   +5 more
openaire   +4 more sources

DOE JGI Metagenome Workflow [PDF]

, 2021
The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated ...
Reddy, TBK, Clum, Alicia, Yoshinaga, Yuko, Seshadri, Rekha, Bushnell, Brian, Varghese, Neha, Daum, Chris, Foster, Bryce, Ivanova, Natalia N, Mukherjee, Supratim, Chen, I-Min A, O’Malley, Ronan, Kyrpides, Nikos C, Huntemann, Marcel, Foster, Brian, Hajek, Patrick P, Eloe-Fadrosh, Emiley A, Copeland, Alex, Roux, Simon   +18 more
core   +1 more source

Noncanonical Peloruside A Biosynthesis by an Uncultivated Verrucomicrobiota Symbiont

Angewandte Chemie, EarlyView.
Noncanonical biochemistry of the peloruside PKS characterized in this work, comprising double bond generation by a noncanonical tridomain (blue), acetyl‐CoA recycling (orange), and proofreading systems (purple and yellow). The Z‐double bond is installed by TEB1 through O‐acetylation and acetate elimination. The acyl ligase PelB (AL, orange) selectively
Amy E. Fraley, Michael Rust, Moritz Wagner, Ida R. Hipfinger, Paul J. N. Böhm, Cora L. Dieterich, Christopher M. Field, Michael J. Page, Jeremy G. Owen, Robert A. Keyzers, Shinichi Sunagawa, Jörn Piel   +11 more
wiley   +2 more sources

KEMET – A python tool for KEGG Module evaluation and microbial genome annotation expansion

Computational and Structural Biotechnology Journal, 2022
Background: The rapid accumulation of sequencing data from metagenomic studies is enabling the generation of huge collections of microbial genomes, with new challenges for mapping their functional potential.
Matteo Palù, Arianna Basile, Guido Zampieri, Laura Treu, Alessandro Rossi, Maria Silvia Morlino, Stefano Campanaro   +6 more
doaj   +1 more source

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. [PDF]

, 2013
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing
Niranjan Nagarajan, Eliza Xin Pei Ho, Andreas Wilm (7951), Hibberd, Martin Lloyd, Louie Low (400408), Nagarajan, Niranjan, Eliza Xin Pei Ho (400407), Ong, Swee Hoe, Christophe Lay (400406), Martin Lloyd Hibberd (259920), Low, Louie, Kukkillaya, Vinutha Uppoor, Andreas Wilm, Martin Lloyd Hibberd, Lay, Christophe, Niranjan Nagarajan (131213), Wilm, Andreas, Ho, Eliza Xin Pei, Vinutha Uppoor Kukkillaya (400405), Swee Hoe Ong, Louie Low, Swee Hoe Ong (400404), Vinutha Uppoor Kukkillaya, Christophe Lay   +23 more
core   +1 more source

Metagenomic assembly unravel microbial response to redox fluctuation in acid sulfate soil [PDF]

Soil Biology and Biochemistry, 2017
Abstract Acid sulfate soil (ASS) is sensitive to redox fluctuations induced by climate change and human activities. Oxidation of sulfur and sulfide in ASS leads to the release of acid and consequently metals, posing severe hazards to coastal environment, while microbial contribution and response to oxidation is poorly understood.
Su, Jianqiang, Xia, Yu, Yao, Huaiying, Li, Yaying, An, Xinli, Singh, Brajesh K. (R15253), Zhang, Tong, Zhu, Yongguan   +7 more
openaire   +2 more sources

CAMISIM: simulating metagenomes and microbial communities

Microbiome, 2019
Background Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing ...
Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R. Lesker, Peter Belmann, Matthew Z. DeMaere, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges, Alice C. McHardy   +12 more
doaj   +1 more source

Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities [PDF]

, 2014
Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology.
Daniel eLaughlin, Fierer, Noah, Laughlin, Daniel C., Noah Fierer, Noah eFierer, Albert eBarberan, Daniel C. Laughlin, Barberán, Albert, Albert Barberán   +8 more
core   +1 more source

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome

Environmental Microbiome, 2023
Background Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective ...
Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Edis Sepo, Ruth Gómez Expósito, Alisson Fernando Chiorato, Rodrigo Mendes, Siu Mui Tsai, Victor J Carrión   +8 more
doaj   +1 more source