Nikos C. Kyrpides
Lawrence Berkeley National Laboratory
GeneGenomeMetagenomicsGenomicsType speciesPhylogenetic treePlasmidWhole genome sequencingStrain (biology)AlphaproteobacteriaBacteriaGeneticsArchaeaBiochemistryBotanyStrain (chemistry)Computational biologyEvolutionary biologyBiologyMicrobiology
Publications 710
#1Joana Fernandes Couceiro (IST: Instituto Superior Técnico)
#2Tina Keller-Costa (IST: Instituto Superior Técnico)H-Index: 10
Last. Rodrigo Costa (IST: Instituto Superior Técnico)H-Index: 31
view all 0 authors...
Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba) strains that were obtained from the octocoral Eunicella labiata. Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.
The substrates of the Brazilian campos rupestres have extremely low concentrations of key nutrients, mainly phosphorus, imposing severe restrictions to plant growth. Regardless, this ecosystem harbors enormous biodiversity which raises the question of how nutrients are cycled and acquired by the biosphere. To uncover the nutrient turnover potential of plant-associated microorganisms in the campos rupestres, we investigated the compositions and functions of microbiomes associated with two species...
#1Joan Carles Pons (UIB: University of the Balearic Islands)H-Index: 5
#2David Paez-Espino (JGI: Joint Genome Institute)H-Index: 22
Last. Mercè Llabrés (UIB: University of the Balearic Islands)H-Index: 11
view all 6 authors...
Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been ex...
3 CitationsSource
#1Lee Call (LBNL: Lawrence Berkeley National Laboratory)H-Index: 1
#2Stephen Nayfach (LBNL: Lawrence Berkeley National Laboratory)H-Index: 18
Last. Nikos C. Kyrpides (LBNL: Lawrence Berkeley National Laboratory)H-Index: 100
view all 3 authors...
Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery a...
#1David Danko (Cornell University)H-Index: 9
#2Daniela BezdanH-Index: 20
Last. Stas ZubenkoH-Index: 1
view all 670 authors...
Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246...
5 CitationsSource
#1Stephen Nayfach (LBNL: Lawrence Berkeley National Laboratory)H-Index: 18
#2David Paez-Espino (DOE: United States Department of Energy)H-Index: 22
Last. Philip Hugenholtz (UQ: University of Queensland)H-Index: 114
view all 11 authors...
Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of wh...
1 CitationsSource
#1Ryan D Ward (NMSU: New Mexico State University)
#2Jason E. Stajich (UCR: University of California, Riverside)H-Index: 62
Last. Nicole Pietrasiak (NMSU: New Mexico State University)H-Index: 16
view all 20 authors...
Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology relates to aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies of evolutionary relationships and gene content among these unique algae and their aquatic relatives.
#1Diego M. Roldán (University of the Republic)H-Index: 1
#2Nikos C. Kyrpides (JGI: Joint Genome Institute)H-Index: 100
Last. Rodolfo Javier Menes (University of the Republic)H-Index: 7
view all 9 authors...
A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-moti...
#1Alicia Clum (LBNL: Lawrence Berkeley National Laboratory)H-Index: 33
#2Marcel Huntemann (LBNL: Lawrence Berkeley National Laboratory)H-Index: 9
Last. Natalia Ivanova (LBNL: Lawrence Berkeley National Laboratory)H-Index: 82
view all 19 authors...
ABSTRACT 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 Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, comparative analysis system and provided for download via the ...
1 CitationsSource
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii ...