ORCID Profile
0000-0003-4484-7505
Current Organisation
E O Lawrence Berkeley National Laboratory
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Publisher: Springer Science and Business Media LLC
Date: 06-2012
DOI: 10.1038/NATURE11234
Publisher: Oxford University Press (OUP)
Date: 15-10-2006
Publisher: Springer Science and Business Media LLC
Date: 29-04-2011
DOI: 10.4056/SIGS.1553865
Publisher: Springer Science and Business Media LLC
Date: 09-11-2020
DOI: 10.1038/S41587-020-0718-6
Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to ,000 metagenomes collected from erse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic ersity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1093/NAR/GKW1030
Abstract: Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic s les. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (r/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from & ecologically erse metagenomic s les. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the s les, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2019
DOI: 10.1038/S41597-019-0141-3
Abstract: The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian c os rupestre s impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the c os rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of c os rupestres . We assessed the microbiomes of Vellozia epidendroides , which occupies shallow patches of soil, and Barbacenia macrantha , growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the c os rupestres , and to unravel new strategies for improved crop productivity in stressful environments.
Publisher: Springer Science and Business Media LLC
Date: 04-2021
DOI: 10.1038/S41587-021-00898-4
Abstract: A Correction to this paper has been published: 0.1038/s41587-021-00898-4.
Publisher: Springer Science and Business Media LLC
Date: 18-11-2020
DOI: 10.1038/S41587-020-00769-4
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Location: United States of America
No related grants have been discovered for Krishnaveni Palaniappan.