Tatajuba ― Exploring the distribution of homopolymer tracts

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialised bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source license GNU GPL version 3 from https://github.com/quadram-institute-bioscience/tatajuba.

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SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽

10.1186/s40168-021-01068-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

David Pellow ◽

Alvah Zorea ◽

Maraike Probst ◽

Ori Furman ◽

Arik Segal ◽

...

Keyword(s):

Bacterial Species ◽

Bacterial Genome ◽

Biological Knowledge ◽

Assessment Procedure ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Human Gut ◽

Double Stranded Dna ◽

Wide Range ◽

Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

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Metagenome of SARS-Cov2 patients in Shenzhen with travel to Wuhan shows a wide range of species - Lautropia, Cutibacterium, Haemophilus being most abundant - and Campylobacter explaining diarrhea

10.31219/osf.io/jegwq ◽

2020 ◽

Cited By ~ 7

Author(s):

Sandeep Chakraborty

Keyword(s):

Secondary Infection ◽

Bacterial Species ◽

Bacterial Load ◽

San Diego County ◽

Opportunistic Pathogens ◽

Sequencing Data ◽

Familial Cluster ◽

Chinese Study ◽

Wide Range ◽

Initial Results

The metagenome of patients infected with SARS-Cov2 [1] has shown Prevotella to be a key player in immune response [2] in one Chinese study [3], just starting in another [4] and a host of other opportunistic pathogens in a study from San Diego county [5]. The metagenome can also be queried to find host response genes [5], as was done in monkey cells infected with SARS-Cov2 [6]Nanopore sequencing data from a familial cluster in ShenzhenThe patients were tested for 4 bacterial species - Bordetella pertussis, Bordetella parapertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. The sequencing data (Accid:SRR10948474, Nanopore) from five patients in a family cluster from Shenzhen who presented with unexplained pneumonia after returning from Wuhan (Table 1) shows a wide range of bacterial species - Lautropia, Cutibacterium, Haemophilus being most abundant. The presence of Campylobacter explains diarrhea seen in the patient [7,8]. Also, their tests should have detected Mycoplasma, since it is there in the data.Significant bacterial load with some bacterial species predominatingThe bacterial reads are about 20% (95K out of 500K reads). The viral load is also significant here (70K reads) [2]. They are in SI.familial/allsequences.fa. The number of bacterial species (with at least two reads) is 876 (SI.familial/list.allbacteria.txt). Thus, it is important to consider secondary infection, a possible reason why azithromycin (in addition to hydroxychloroquine) has given good initial results in a clinical trial [9].

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Identification of Gradient Promoters of Gluconobacter oxydans and Their Applications in the Biosynthesis of 2-Keto-L-Gulonic Acid

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.673844 ◽

2021 ◽

Vol 9 ◽

Author(s):

Yue Chen ◽

Li Liu ◽

Shiqin Yu ◽

Jianghua Li ◽

Jingwen Zhou ◽

...

Keyword(s):

Gluconobacter Oxydans ◽

Acetic Acid Bacterium ◽

High Yield ◽

Transcriptional Level ◽

Molecular Tools ◽

Sequencing Data ◽

Strain Development ◽

Regulate Gene Expression ◽

Low Activity ◽

Regulate Gene

The acetic acid bacterium Gluconobacter oxydans is known for its unique incomplete oxidation and therefore widely applied in the industrial production of many compounds, e.g., 2-keto-L-gulonic acid (2-KLG), the direct precursor of vitamin C. However, few molecular tools are available for metabolically engineering G. oxydans, which greatly limit the strain development. Promoters are one of vital components to control and regulate gene expression at the transcriptional level for boosting production. In this study, the low activity of SDH was found to hamper the high yield of 2-KLG, and enhancing the expression of SDH was achieved by screening the suitable promoters based on RNA sequencing data. We obtained 97 promoters from G. oxydans’s genome, including two strong shuttle promoters and six strongest promoters. Among these promoters, P3022 and P0943 revealed strong activities in both Escherichia coli and G. oxydans, and the activity of the strongest promoter (P2703) was about threefold that of the other reported strong promoters of G. oxydans. These promoters were used to overexpress SDH in G. oxydans WSH-003. The titer of 2-KLG reached 3.7 g/L when SDH was under the control of strong promoters P2057 and P2703. This study obtained a series of gradient promoters, including two strong shuttle promoters, and expanded the toolbox of available promoters for the application in metabolic engineering of G. oxydans for high-value products.

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A structural perspective on the mechanisms of quorum sensing activation in bacteria

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765201520140482 ◽

2015 ◽

Vol 87 (4) ◽

pp. 2189-2203 ◽

Cited By ~ 5

Author(s):

CAROLINA LIXA ◽

AMANDA MUJO ◽

CRISTIANE D. ANOBOM ◽

ANDERSON S. PINHEIRO

Keyword(s):

Gene Expression ◽

Quorum Sensing ◽

Rational Design ◽

Three Dimensional ◽

Cell Communication ◽

Dependent Manner ◽

Regulate Gene Expression ◽

Wide Range ◽

A Cell ◽

Regulate Gene

Bacteria are able to synchronize the population behavior in order to regulate gene expression through a cell-to-cell communication mechanism called quorum sensing. This phenomenon involves the production, detection and the response to extracellular signaling molecules named autoinducers, which directly or indirectly regulate gene expression in a cell density-dependent manner. Quorum sensing may control a wide range of biological processes in bacteria, such as bioluminescence, virulence factor production, biofilm formation and antibiotic resistance. The autoinducers are recognized by specific receptors that can either be membrane-bound histidine kinase receptors, which work by activating cognate cytoplasmic response regulators, or cytoplasmic receptors acting as transcription factors. In this review, we focused on the cytosolic quorum sensing regulators whose three-dimensional structures helped elucidate their mechanisms of action. Structural studies of quorum sensing receptors may enable the rational design of inhibitor molecules. Ultimately, this approach may represent an effective alternative to treat infections where classical antimicrobial therapy fails to overcome the microorganism virulence.

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Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution

10.1101/2021.08.03.454900 ◽

2021 ◽

Author(s):

Boas CL van der Putten ◽

Niek AH Huijsmans ◽

Daniel R Mende ◽

Constance Schultsz

Keyword(s):

De Novo ◽

Phylogenetic Analyses ◽

Bacterial Species ◽

Phylogenetic Reconstruction ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

De Novo Genome Assembly ◽

Relevant Alternatives ◽

Wide Range ◽

Similar Accuracy

Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95% average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked seventeen distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and SKA achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or SKESA outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction k-mer alignment methods are relevant alternatives to reference mapping at species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.

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SCAPP: An algorithm for improved plasmid assembly in metagenomes

10.1101/2020.01.12.903252 ◽

2020 ◽

Cited By ~ 1

Author(s):

David Pellow ◽

Alvah Zorea ◽

Maraike Probst ◽

Ori Furman ◽

Arik Segal ◽

...

Keyword(s):

Bacterial Species ◽

Bacterial Genome ◽

Biological Knowledge ◽

Assessment Procedure ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Human Gut ◽

Double Stranded Dna ◽

Wide Range ◽

Python Package

Background: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

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Ribo-attenuators: novel elements for reliable and modular riboswitch engineering

10.1101/086199 ◽

2016 ◽

Author(s):

Thomas Folliard ◽

Barbara Mertins ◽

Thomas P Prescott ◽

Harrison Steel ◽

Thomas Newport ◽

...

Keyword(s):

Gene Expression ◽

Small Molecules ◽

Regulatory Elements ◽

Genetic Element ◽

Regulate Gene Expression ◽

Considerable Potential ◽

Expression Variation ◽

Wide Range ◽

Genetic Context ◽

Regulate Gene

AbstractRiboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a Ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, and thus increases their reliability for a wide range of applications.

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