Publications by authors named "Nikos Kyrpides"

618 Publications

Frigoriflavimonas asaccharolytica gen. nov., sp. nov., a novel psychrophilic esterase and protease producing bacterium isolated from Antarctica.

Antonie Van Leeuwenhoek 2021 Dec 20;114(12):1991-2002. Epub 2021 Sep 20.

Institut Für Mikrobiologie, Veterinärmedizinische Universität Wien, Wien, Austria.

The rod-shaped and Gram-stain-negative bacterial strain 16F, isolated from an air sample collected at King George Island, maritime Antarctica, was investigated to determine its taxonomic status. Strain 16F is strictly aerobic, catalase positive, oxidase positive and non-motile. Strain 16F hydrolyses casein, lecithin, Tween 20, 60 and 80, but not aesculin, gelatin and starch. Growth of strain 16F is observed at 0-20 °C (optimum 10 °C), pH 5.0-8.0 (optimum pH 6.0), and in the presence of 0-2.0% NaCl (optimum 0.5%). The predominant menaquinone is MK-6, and the major fatty acids comprise anteiso-C and iso-C. The major polar lipids are phosphatidylethanolamine, ornithine lipid OL2, unidentified phospholipid PL1 and the unidentified lipids L3 and L6 lacking functional groups. The DNA G + C content based on the draft genome sequence is 32.3 mol%. Sequence analysis of the 16S rRNA gene indicates the highest similarity to Kaistella palustris 3A10 (95.4%), Kaistella chaponensis Sa 1147-06 (95.2%), Kaistella antarctica AT1013 (95.1%), Kaistella carnis NCTC 13525 (95.1%) and below 95.0% to other species with validly published names. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences places strain 16F in a distinct branch, indicating a separate lineage within the family Weeksellaceae. Based on the data from our polyphasic approach, 16F represents a novel species of a new genus, for which the name Frigoriflavimonas asaccharolytica gen. nov, sp. nov. is proposed. The type strain is 16F (= CCM 8975 = CGMCC No.1.16844).
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http://dx.doi.org/10.1007/s10482-021-01656-xDOI Listing
December 2021

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.

Nat Commun 2021 09 16;12(1):5483. Epub 2021 Sep 16.

U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
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http://dx.doi.org/10.1038/s41467-021-25646-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8446083PMC
September 2021

Illuminating the Virosphere Through Global Metagenomics.

Annu Rev Biomed Data Sci 2021 07;4:369-391

Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; email:

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 and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.
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http://dx.doi.org/10.1146/annurev-biodatasci-012221-095114DOI Listing
July 2021

The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos.

Microbiol Resour Announc 2021 Aug 26;10(34):e0032021. Epub 2021 Aug 26.

Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.

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.
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http://dx.doi.org/10.1128/MRA.00320-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388533PMC
August 2021

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.

Nat Microbiol 2021 07 24;6(7):960-970. Epub 2021 Jun 24.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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 which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
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http://dx.doi.org/10.1038/s41564-021-00928-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8241571PMC
July 2021

sp. nov., an airborne bacterium isolated from King George Island, Antarctica.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.

A rod-shaped and Gram-stain-negative bacterial strain 9A, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9A belongs to the genus and shows the highest similarity to CCM 8649 (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9A is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9A is MK-7 and the major fatty acids comprise Summed Feature 3 (C c and/or C c; 25.2 %), iso-C (23.2 %), C c (11.6 %), Summed Feature 4 (anteiso-C B/iso-C I) (9.6 %) and anteiso-C (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern -homospermidine is predominant. On the basis of the results obtained, strain 9A is proposed as a novel species of the genus , for which the name sp. nov. is suggested. The type strain is 9A (=CCM 8971=LMG 32109=DSM 111653).
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http://dx.doi.org/10.1099/ijsem.0.004838DOI Listing
June 2021

Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria.

Microbiol Resour Announc 2021 Jun 3;10(22):e0025821. Epub 2021 Jun 3.

Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, New Mexico, USA.

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.
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http://dx.doi.org/10.1128/MRA.00258-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354539PMC
June 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance.

Cell 2021 Jun 26;184(13):3376-3393.e17. Epub 2021 May 26.

Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.

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 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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http://dx.doi.org/10.1016/j.cell.2021.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238498PMC
June 2021

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of and Three Candidate Species From China and Japan.

Front Microbiol 2021 3;12:632731. Epub 2021 May 3.

Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States.

JAD2, the only cultured representative of the order , is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for JAD2 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 JAD2 and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing " Thermoflexus japonica," " Thermoflexus tengchongensis," and " Thermoflexus sinensis." Genomics was integrated with targeted exometabolomics and C metabolic probing of . The genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The JAD2 exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms . Metabolic probing of JAD2 using C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms .
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http://dx.doi.org/10.3389/fmicb.2021.632731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8129789PMC
May 2021

DOE JGI Metagenome Workflow.

mSystems 2021 May 18;6(3). Epub 2021 May 18.

Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723-D733, 2021, https://doi.org/10.1093/nar/gkaa983). The DOE JGI Metagenome Workflow is designed for processing metagenomic data sets starting from Illumina fastq files. It performs data preprocessing, error correction, assembly, structural and functional annotation, and binning. The results of processing are provided in several standard formats, such as fasta and gff, and can be used for subsequent integration into the Integrated Microbial Genomes and Microbiomes (IMG/M) system where they can be compared to a comprehensive set of publicly available metagenomes. As of 30 July 2020, 7,155 JGI metagenomes have been processed by the DOE JGI Metagenome Workflow. Here, we present a metagenome workflow developed at the JGI that generates rich data in standard formats and has been optimized for downstream analyses ranging from assessment of the functional and taxonomic composition of microbial communities to genome-resolved metagenomics and the identification and characterization of novel taxa. This workflow is currently being used to analyze thousands of metagenomic data sets in a consistent and standardized manner.
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http://dx.doi.org/10.1128/mSystems.00804-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269246PMC
May 2021

VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.

Bioinformatics 2021 Jan 20. Epub 2021 Jan 20.

Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain.

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 explored for determining viral taxonomy and host targets.

Results: In this work we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified.

Availability: The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools.

Supplementary Information: http://bioinfo.uib.es/~recerca/VPF-Class/.
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http://dx.doi.org/10.1093/bioinformatics/btab026DOI Listing
January 2021

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion.

mBio 2021 01 19;12(1). Epub 2021 Jan 19.

Biological Computation and Process Laboratory, Chemical Process and Energy Resources Institute, Centre for Research and Technology Hellas, Thessalonica, Greece

Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent "paralog" gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a. Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, including SARS-CoV-2. Using sophisticated sequence comparisons, we confirm its origins from Orf7a, another gene in the lineage that appears as more conserved, compared to Orf8. Orf7a is a potential immune antagonist of known structure, while a deletion of Orf8 was shown to decrease the severity of the infection in a cohort study. The subtle sequence similarities imply that Orf8 has the same immunoglobulin-like fold as Orf7a, confirmed by structure determination. We characterize the subgroups of this superfamily and demonstrate the highly idiosyncratic divergence patterns during the evolution of the virus.
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http://dx.doi.org/10.1128/mBio.03014-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7845636PMC
January 2021

CheckV assesses the quality and completeness of metagenome-assembled viral genomes.

Nat Biotechnol 2021 05 21;39(5):578-585. Epub 2020 Dec 21.

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.
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http://dx.doi.org/10.1038/s41587-020-00774-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8116208PMC
May 2021

A genomic catalog of Earth's microbiomes.

Nat Biotechnol 2021 04 9;39(4):499-509. Epub 2020 Nov 9.

DOE Joint Genome Institute, Berkeley, CA, USA.

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 >10,000 metagenomes collected from diverse 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 diversity 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.
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http://dx.doi.org/10.1038/s41587-020-0718-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041624PMC
April 2021

Genomes OnLine Database (GOLD) v.8: overview and updates.

Nucleic Acids Res 2021 01;49(D1):D723-D733

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. The current status of the database, along with recent updates and improvements are described in this manuscript.
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http://dx.doi.org/10.1093/nar/gkaa983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778979PMC
January 2021

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.

Nucleic Acids Res 2021 01;49(D1):D764-D775

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
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http://dx.doi.org/10.1093/nar/gkaa946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778971PMC
January 2021

Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.

Microbiol Resour Announc 2020 Oct 29;9(44). Epub 2020 Oct 29.

Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA.

The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.
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http://dx.doi.org/10.1128/MRA.00895-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595945PMC
October 2020

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.

Nucleic Acids Res 2021 01;49(D1):D751-D763

Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE's Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments.
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http://dx.doi.org/10.1093/nar/gkaa939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778900PMC
January 2021

Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina).

Microbiol Resour Announc 2020 Oct 8;9(41). Epub 2020 Oct 8.

Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.
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http://dx.doi.org/10.1128/MRA.00882-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545284PMC
October 2020

High-quality draft genome sequences of DSM 14164, DSM 17497, DSM 15088, DSM 21245 and DSM 16006: taxonomic considerations.

Access Microbiol 2019 29;1(10):e000067. Epub 2019 Oct 29.

Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.

is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: (DSM 14164), (DSM 17497), (DSM 15088) (DSM 21245) and (DSM 16006). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the phylogenetic group of species.
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http://dx.doi.org/10.1099/acmi.0.000067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7491935PMC
October 2019

Recombination should not be an afterthought.

Nat Rev Microbiol 2020 11;18(11):606

DOE Joint Genome Institute, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41579-020-00451-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503439PMC
November 2020

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism.

mBio 2020 09 8;11(5). Epub 2020 Sep 8.

School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA

Fungal-bacterial symbioses range from antagonisms to mutualisms and remain one of the least understood interdomain interactions despite their ubiquity as well as ecological and medical importance. To build a predictive conceptual framework for understanding interactions between fungi and bacteria in different types of symbioses, we surveyed fungal and bacterial transcriptional responses in the mutualism between () (ATCC 52813, host) and its (formerly ) endobacteria versus the antagonism between a nonhost (ATCC 11559) and isolated from the host, at two time points, before and after partner physical contact. We found that bacteria and fungi sensed each other before contact and altered gene expression patterns accordingly. did not discriminate between the host and nonhost and engaged a common set of genes encoding known as well as novel symbiosis factors. In contrast, responses of the host versus nonhost to endobacteria were dramatically different, converging on the altered expression of genes involved in cell wall biosynthesis and reactive oxygen species (ROS) metabolism. On the basis of the observed patterns, we formulated a set of hypotheses describing fungal-bacterial interactions and tested some of them. By conducting ROS measurements, we confirmed that nonhost fungi increased production of ROS in response to endobacteria, whereas host fungi quenched their ROS output, suggesting that ROS metabolism contributes to the nonhost resistance to bacterial infection and the host ability to form a mutualism. Overall, our study offers a testable framework of predictions describing interactions of early divergent Mucoromycotina fungi with bacteria. Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.
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http://dx.doi.org/10.1128/mBio.02088-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482071PMC
September 2020

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.

Microbiome 2020 08 9;8(1):116. Epub 2020 Aug 9.

School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.

Background: Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.

Results: The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.

Conclusion: Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.
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http://dx.doi.org/10.1186/s40168-020-00889-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416419PMC
August 2020

sp. nov., isolated from air sampling in maritime Antarctica.

Int J Syst Evol Microbiol 2020 Sep;70(9):4935-4941

Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química y Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay.

A rod-shaped and Gram-stain-negative bacterial strain, 1B, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1B is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1B is observed at 0-20 °C (optimum, 10 °C), pH 6.0-8.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1B within the genus and shows the highest similarity to VUG-A42aa (97.5 %). The predominant menaquinone of strain 1B is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C 7 and/or C 6; 32.5 %), iso-C (17.6 %) and anteiso C (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1B represents a novel species of the genus , for which the name sp. nov. is suggested. The type strain is 1B (=CCM 8970=CGMCC 1.16843).
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http://dx.doi.org/10.1099/ijsem.0.004362DOI Listing
September 2020

A unified catalog of 204,938 reference genomes from the human gut microbiome.

Nat Biotechnol 2021 01 20;39(1):105-114. Epub 2020 Jul 20.

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.
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http://dx.doi.org/10.1038/s41587-020-0603-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801254PMC
January 2021

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.

ISME J 2020 10 13;14(10):2527-2541. Epub 2020 Jul 13.

Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Our current knowledge of host-virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host-virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus-host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host-virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed "Piggyback-the-Winner" theory.
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http://dx.doi.org/10.1038/s41396-020-0705-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490370PMC
October 2020

A scoutRNA Is Required for Some Type V CRISPR-Cas Systems.

Mol Cell 2020 08 8;79(3):416-424.e5. Epub 2020 Jul 8.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94114, USA. Electronic address:

CRISPR-Cas12c/d proteins share limited homology with Cas12a and Cas9 bacterial CRISPR RNA (crRNA)-guided nucleases used widely for genome editing and DNA detection. However, Cas12c (C2c3)- and Cas12d (CasY)-catalyzed DNA cleavage and genome editing activities have not been directly observed. We show here that a short-complementarity untranslated RNA (scoutRNA), together with crRNA, is required for Cas12d-catalyzed DNA cutting. The scoutRNA differs in secondary structure from previously described tracrRNAs used by CRISPR-Cas9 and some Cas12 enzymes, and in Cas12d-containing systems, scoutRNA includes a conserved five-nucleotide sequence that is essential for activity. In addition to supporting crRNA-directed DNA recognition, biochemical and cell-based experiments establish scoutRNA as an essential cofactor for Cas12c-catalyzed pre-crRNA maturation. These results define scoutRNA as a third type of transcript encoded by a subset of CRISPR-Cas genomic loci and explain how Cas12c/d systems avoid requirements for host factors including ribonuclease III for bacterial RNA-mediated adaptive immunity.
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http://dx.doi.org/10.1016/j.molcel.2020.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196889PMC
August 2020

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation.

Commun Biol 2020 06 19;3(1):320. Epub 2020 Jun 19.

Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA.

Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling Hg, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature.
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http://dx.doi.org/10.1038/s42003-020-1047-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305189PMC
June 2020
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