SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

Frontiers in Microbiology, Journal Year: 2019, Volume and Issue: 9

Published: Jan. 24, 2019

The improvement of sequencing technologies has facilitated generalization metagenomic sequencing, which become a standard procedure for analyzing the structure and functionality microbiomes. Bioinformatic analysis results poses challenge because it involves many different complex steps. SqueezeMeta is fully automatic pipeline metagenomics/metatranscriptomics, covering all steps analysis. includes multi-metagenome support that enables co-assembly related metagenomes retrieval individual genomes via binning procedures. features several unique characteristics: or unlimited number merging assembled metagenomes, both with read mapping estimation abundances genes in each metagenome. It also bin checking retrieving genomes. Internal checks assembly provide information about consistency contigs bins. Moreover, are stored MySQL database, where they can be easily exported shared, inspected anywhere using flexible web interface allows simple creation queries. We illustrate potential by 32 gut way, enabling million hundreds genomic One motivations development was producing software capable running small desktop computers thus amenable to users settings. were able co-assemble two these complete full less than one day laptop computer. This reveals capacity run without high-performance computing infrastructure absence any network connectivity. therefore adequate situ, real time produced nanopore sequencing. downloaded from https://github.com/jtamames/SqueezeMeta.

Language: Английский

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Accurate and complete genomes from metagenomes

Genome Research, Journal Year: 2020, Volume and Issue: 30(3), P. 315 - 333

Published: March 1, 2020

Genomes are an integral component of the biological information about organism; thus, more complete genome, informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, first reported sequences manually curated to completion. However, bottleneck imposed by requirement for isolates precluded genomic insights vast majority microbial life. Shotgun sequencing communities, referred initially as community genomics subsequently genome-resolved metagenomics, can circumvent this limitation obtaining metagenome-assembled (MAGs); but gaps, local assembly errors, chimeras, contamination fragments other limit value these genomes. Here, we discuss genome curation improve and, in some cases, achieve (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably very complex systems such soil sediment. Through analysis 7000 published isolate genomes, verify cumulative GC skew combination with metrics establish sequence accuracy. The identified potential misassemblies reference isolated bacteria repeat that likely gave rise them. We methods could be implemented bioinformatic approaches ensure metabolic evolutionary analyses based on high-quality

Language: Английский

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Globally Consistent Quantitative Observations of Planktonic Ecosystems

Frontiers in Marine Science, Journal Year: 2019, Volume and Issue: 6

Published: April 25, 2019

In this paper we review on the technologies available to make globally quantitative observations of particles, in general, and plankton, particular, world oceans, for sizes varying from sub-micron centimeters. Some these have been years while others only recently emerged. Use is critical improve understanding processes that control abundances, distributions composition provide data necessary constrain ecosystem biogeochemical models, forecast changes marine ecosystems light climate change. begin by providing motivation plankton observations, quantification diversity qualification a global scale. We then expand state-of-the-art, detailing variety relevant (mostly) mature measurements, including bulk measurements pigment composition, uses genomic, optical, acoustical methods analysis using particles counters, flow cytometers imaging devices. follow highlighting requirements observing system, approach achieve it associated challenges. conclude with ranked action-item recommendations next ten move towards our vision holistic ocean-wide system. Particularly, suggest demonstration project GO-SHIP line and/or long-term observation site there ensuring issues methods, tools, analysis, quality assessment curation are addressed early implementation. Global coordination key success will bring new insights nutrient regeneration, ocean production, fisheries, carbon sequestration.

Language: Английский

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FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Jan. 31, 2020

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and acceptor by iron-oxidizing iron-reducing microorganisms in variety of biological processes, including photosynthesis respiration. While it the fourth most abundant metal Earth's crust, iron often limiting growth oxic environments because readily oxidized precipitated. Much our understanding how compete utilize based laboratory experiments. However, advent next-generation sequencing surge publicly available sequence data has made possible to probe structure function microbial communities environment. To bridge gap between acquisition, redox cycling, storage, magnetosome formation model plethora from environmental studies, we have created comprehensive database hidden Markov models (HMMs) genes related reduction/oxidation Bacteria Archaea. Along with this database, present FeGenie, bioinformatics tool that accepts genome metagenome assemblies input uses HMM annotate provided datasets respect iron-related gene neighborhood. An important contribution efficient identification involved oxidation dissimilatory reduction, which been largely overlooked standard annotation pipelines. We validated FeGenie against selected set 28 isolate genomes showcase its utility exploring 27 metagenomes, 4 human oral biofilms, 17 candidate organisms, members phyla radiation. show accurately identifies isolates. Furthermore, analysis metagenomes using demonstrates repertoire abundance each environment correlated richness. will not replace reliability culture-dependent analyses physiology, provides reliable predictions derived up-to-date genetic markers. FeGenie's maintained continually updated new are discovered. freely available: https://github.com/Arkadiy-Garber/FeGenie.

Language: Английский

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Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria

ISME Communications, Journal Year: 2021, Volume and Issue: 1(1)

Published: May 20, 2021

The study of microbial communities is hampered by the large fraction still unknown bacteria. However, many these species have been isolated, yet lack a validly published name or description. validation names for novel bacteria requires that uniqueness those taxa demonstrated and their properties are described. accepted format this protologue, which can be time-consuming to create. Hence, research fields in microbiology biotechnology will greatly benefit from new approaches reduce workload harmonise generation protologues.We developed Protologger, bioinformatic tool automatically generates all necessary readouts writing detailed protologue. By producing multiple taxonomic outputs, functional features ecological analysis using 16S rRNA gene genome sequences single species, time needed gather information describing substantially reduced. usefulness Protologger was three isolate collections describe 34 taxa, encompassing 17 genera, including automatic ecologically functionally relevant names. We also highlight need utilise delineation methods, as while inconsistencies between each method occur, combined approach provides robust placement. open source; scripts datasets available, along with webserver at www.protologger.de.

Language: Английский

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The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Cell Host & Microbe, Journal Year: 2019, Volume and Issue: 26(2), P. 283 - 295.e8

Published: Aug. 1, 2019

Language: Английский

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Biosynthetic potential of the global ocean microbiome

Nature, Journal Year: 2022, Volume and Issue: 607(7917), P. 111 - 118

Published: June 22, 2022

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically biotechnologically relevant enzymes biochemical compounds2,3. However, studying identify genomic pathways the synthesis of such compounds4 assigning them their respective hosts remains challenging. The biosynthetic microorganisms in open ocean largely uncharted owing limitations analysis genome-resolved data at global scale. Here we investigated novelty gene clusters by integrating around 10,000 genomes from cultivated single cells with more than 25,000 newly reconstructed draft 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new clusters, several which were found previously unsuspected phylogenetic groups. Among these groups, identified lineage ('Candidatus Eudoremicrobiaceae') that belongs an uncultivated bacterial phylum includes some most biosynthetically diverse environment. From these, characterized phospeptin pythonamide pathways, revealing cases unusual bioactive compound structure enzymology, respectively. Together, research demonstrates how microbiomics-driven strategies can enable investigation undescribed natural products groups environments.

Language: Английский

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Potential for primary productivity in a globally-distributed bacterial phototroph

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(7), P. 1861 - 1866

Published: March 5, 2018

Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified surface ocean. Using Tara Oceans metagenomic dataset, we draft genomes of nine bacteria genomic phototrophy, via Calvin-Benson-Bassham cycle, oxidation sulfite thiosulfate. Forming a monophyletic clade within Alphaproteobacteria lacking cultured representatives, organisms compose minor constituents local microbial communities (0.1-1.0%), but globally distributed, present multiple samples from North Pacific, Mediterranean Sea, East Africa Coastal Province, Atlantic. This discovery may require re-examination oceans to understand constrain role this group play global cycle.

Language: Английский

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A genomic view of the reef-building coral Porites lutea and its microbial symbionts

Nature Microbiology, Journal Year: 2019, Volume and Issue: 4(12), P. 2090 - 2100

Published: Sept. 23, 2019

Language: Английский

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The fate of organic carbon in marine sediments - New insights from recent data and analysis

Earth-Science Reviews, Journal Year: 2020, Volume and Issue: 204, P. 103146 - 103146

Published: Feb. 29, 2020

Language: Английский

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