scholarly journals Automated strain separation in low-complexity metagenomes using long reads

2021 ◽  
Author(s):  
R. Vicedomini ◽  
C. Quince ◽  
A. E. Darling ◽  
R. Chikhi
Keyword(s):  
Large Scale ◽  
Functional Characterization ◽  
Low Complexity ◽  
Complete Separation ◽  
Metagenomic Sequencing ◽  
Assembly Method ◽  
Starting Point ◽  
Long Read ◽  
Different Strains ◽  
Strain Separation

AbstractHigh-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Despite this, strain-level resolution from metagenomic sequencing remains challenging. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly method that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities and showed it consistently produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 27-89% additional genomic material than conventional metagenome assemblies on individual strain genomes. Our results hence demonstrate that strain separation is possible in low-complexity microbiomes using a single regular long read dataset. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements aiming to provide better strain-resolved metagenome assemblies in environments of higher complexities.

scholarly journals Strainberry: automated strain separation in low-complexity metagenomes using long reads

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Riccardo Vicedomini ◽  
Christopher Quince ◽  
Aaron E. Darling ◽  
Rayan Chikhi
Keyword(s):  
Large Scale ◽  
Functional Characterization ◽  
Low Complexity ◽  
Complete Separation ◽  
Starting Point ◽  
Long Read ◽  
Metagenome Assembly ◽  
Different Strains ◽  
Multiple Strains ◽  
Strain Separation

AbstractHigh-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.

scholarly journals Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

2021 ◽  
Author(s):  
Marc W. Van Goethem ◽  
Andrew R. Osborn ◽  
Benjamin P. Bowen ◽  
Peter F. Andeer ◽  
Tami L. Swenson ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Temporal Dynamics ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Metagenomic Sequencing ◽  
Pronounced Increase ◽  
Environmental Processes ◽  
Soil Communities ◽  
Functional Dynamics ◽  
Long Read

AbstractMicrobial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 695 novel, full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night in cyanobacteria but not in other phyla, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

scholarly journals Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marc W. Van Goethem ◽  
Andrew R. Osborn ◽  
Benjamin P. Bowen ◽  
Peter F. Andeer ◽  
Tami L. Swenson ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Temporal Dynamics ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Metagenomic Sequencing ◽  
Pronounced Increase ◽  
Environmental Processes ◽  
Soil Communities ◽  
Functional Dynamics ◽  
Long Read

AbstractMicrobial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform

2019 ◽  
Vol 22 (5) ◽  
pp. 346-354
Author(s):  
Yan A. Ivanenkov ◽  
Renat S. Yamidanov ◽  
Ilya A. Osterman ◽  
Petr V. Sergiev ◽  
Vladimir A. Aladinskiy ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Large Scale ◽  
Underlying Mechanism ◽  
Luciferase Assay ◽  
Reporter System ◽  
E Coli ◽  
Starting Point ◽  
High Concentrations ◽  
Mic Value

Aim and Objective: Antibiotic resistance is a serious constraint to the development of new effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with antibacterial activity. Materials and Methods: Using our unique double-reporter system, in-house large-scale HTS campaign was conducted for the identification of antibacterial potency of small-molecule compounds. The construction allows us to visually assess the underlying mechanism of action. After the initial HTS and rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were carried out. Results: HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the same strain. In contrast to the parent hit, this compound was more active and selective, and provided a robust IP position. Conclusion: N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the development of novel active and selective antibacterial compounds.

scholarly journals Urban Policies and Large Projects in Central City Areas: The Example of Madrid (Spain)

Urban Science ◽  
2021 ◽  
Vol 5 (2) ◽  
pp. 42
Author(s):  
Dolores Brandis García
Keyword(s):  
Urban Planning ◽  
20Th Century ◽  
Large Scale ◽  
Central City ◽  
Global Market ◽  
Late 20Th Century ◽  
Public And Private ◽  
Urban Policies ◽  
Starting Point ◽  
The City

Since the late 20th century major, European cities have exhibited large projects driven by neoliberal urban planning policies whose aim is to enhance their position on the global market. By locating these projects in central city areas, they also heighten and reinforce their privileged situation within the city as a whole, thus contributing to deepening the centre–periphery rift. The starting point for this study is the significance and scope of large projects in metropolitan cities’ urban planning agendas since the final decade of the 20th century. The aim of this article is to demonstrate the correlation between the various opposing conservative and progressive urban policies, and the projects put forward, for the city of Madrid. A study of documentary sources and the strategies deployed by public and private agents are interpreted in the light of a process during which the city has had a succession of alternating governments defending opposing urban development models. This analysis allows us to conclude that the predominant large-scale projects proposed under conservative policies have contributed to deepening the centre–periphery rift appreciated in the city.

scholarly journals FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanping Long ◽  
Zhijian Liu ◽  
Jinbu Jia ◽  
Weipeng Mo ◽  
Liang Fang ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Walls ◽  
Large Scale ◽  
Full Length ◽  
Cell Level ◽  
Root Cells ◽  
Rna Profiling ◽  
Different Types ◽  
Long Read ◽  
Single Nucleus

AbstractThe broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.

scholarly journals Low-complexity sparse-aware multiuser detection for large-scale MIMO systems

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Rong Ran ◽  
Hayoung Oh
Keyword(s):  
Large Scale ◽  
Mimo Systems ◽  
Minimum Mean Square Error ◽  
Multiple Input Multiple Output ◽  
Low Complexity ◽  
Finite Alphabet ◽  
Multiuser Detectors ◽  
Input Multiple Output ◽  
Error Detector ◽  
Significant Performance

AbstractSparse-aware (SA) detectors have attracted a lot attention due to its significant performance and low-complexity, in particular for large-scale multiple-input multiple-output (MIMO) systems. Similar to the conventional multiuser detectors, the nonlinear or compressive sensing based SA detectors provide the better performance but are not appropriate for the overdetermined multiuser MIMO systems in sense of power and time consumption. The linear SA detector provides a more elegant tradeoff between performance and complexity compared to the nonlinear ones. However, the major limitation of the linear SA detector is that, as the zero-forcing or minimum mean square error detector, it was derived by relaxing the finite-alphabet constraints, and therefore its performance is still sub-optimal. In this paper, we propose a novel SA detector, named single-dimensional search-based SA (SDSB-SA) detector, for overdetermined uplink MIMO systems. The proposed SDSB-SA detector adheres to the finite-alphabet constraints so that it outperforms the conventional linear SA detector, in particular, in high SNR regime. Meanwhile, the proposed detector follows a single-dimensional search manner, so it has a very low computational complexity which is feasible for light-ware Internet of Thing devices for ultra-reliable low-latency communication. Numerical results show that the the proposed SDSB-SA detector provides a relatively better tradeoff between the performance and complexity compared with several existing detectors.

scholarly journals Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

2021 ◽  
Author(s):  
Valentin Waschulin ◽  
Chiara Borsetto ◽  
Robert James ◽  
Kevin K. Newsham ◽  
Stefano Donadio ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Full Length ◽  
Metagenomic Sequencing ◽  
Short Read ◽  
Short Read Sequencing ◽  
Rich Diversity ◽  
Long Read ◽  
The Rich

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.

scholarly journals Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Regional Scale ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

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