Identifying Bacterial Strains from Sequencing Data

Background: Oral cholera vaccines (OCVs) are an important tool for reduction of the worldwide cholera burden, but some individuals who receive an OCV do not develop protective immune responses. The gut microbiota is a potential explanation for these differences. Components of the gut microbiota associated with differences in OCV response have not been identified. Results: We used metagenomic sequencing to identify predicted protein-coding genes in the gut microbiota at the time of OCV administration, and then measured immune responses to vaccination. Vaccine recipients were classified as OCV 'responders' if they developed a post-vaccination increase in memory B cell populations that produce IgA or IgG specific for cholera toxin and the V. cholerae O-specific polysaccharide. We next analyzed microbial genes seen at similar abundances across individual samples and classified these into co-abundant gene groupings (CAGs), and correlated CAGs with OCV responses. Next, to identify specific bacterial strains associated with OCV responses, we mapped CAGs to bacterial genomes and generated a 'priority score' for each strain detected in the study population. This score reflects both the number of CAGs aligning to a specific bacterial genome and the strength of the association between the CAGs and the vaccine response. This strain-level analysis revealed relationships between the gut microbiota and immune response to OCV that were not detected at the genus or species level. Bacterial strains which produce short-chain fatty acids and those with sphingolipid-containing cell membranes were correlated with more robust immune responses to vaccination. Conclusion: Our study demonstrates a method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome. Using this approach, we identified strains for the study of bacterial-derived molecules or metabolites associated with immune responses; such agents might have potential utility as vaccine adjuvants.

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A high-resolution pipeline for 16S-sequencing identifies bacterial strains in human microbiome

10.1101/565572 ◽

2019 ◽

Cited By ~ 1

Author(s):

Igor Segota ◽

Tao Long

Keyword(s):

Bacterial Species ◽

Human Microbiome ◽

Amplicon Sequencing ◽

R Package ◽

Strain Level ◽

Sequencing Data ◽

Bacterial Strains ◽

16S Sequencing ◽

16S Amplicon Sequencing ◽

Sequencing Data Analysis

We developed a High-resolution Microbial Analysis Pipeline (HiMAP) for 16S amplicon sequencing data analysis, aiming at bacterial species or strain-level identification from human microbiome to enable experimental validation for causal effects of the associated bacterial strains on health and diseases. HiMAP achieved higher accuracy in identifying species in human microbiome mock community than other pipelines. HiMAP identified majority of the species, with strain-level resolution wherever possible, as detected by whole genome shotgun sequencing using MetaPhlAn2 and reported comparable relative abundances. HiMAP is an open-source R package available at https://github.com/taolonglab/himap.

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Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides

Frontiers in Microbiology ◽

10.3389/fmicb.2021.642829 ◽

2021 ◽

Vol 12 ◽

Author(s):

Joakim Bjerketorp ◽

Jolanta J. Levenfors ◽

Christina Nord ◽

Bengt Guss ◽

Bo Öberg ◽

...

Keyword(s):

Sequence Variation ◽

Hierarchical Cluster ◽

Multidrug Resistant ◽

Next Generation Sequencing Data ◽

Antibacterial Peptides ◽

Sequencing Data ◽

Bacterial Strains ◽

Separate Branch ◽

Selection For ◽

Generation Sequencing

Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3–30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700–960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.

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IDENTIFICATION AND MOLECULAR CHARACTERIZATION OF BACTERIA HAVING ANTIMICROBIAL AND ANTIBIOFILM ACTIVITY

International Journal of Pharmacy and Pharmaceutical Sciences ◽

10.22159/ijpps.2016v8i10.12338 ◽

2016 ◽

Vol 8 (10) ◽

pp. 111

Author(s):

Garima Sharma ◽

Shweta Dang ◽

Sanjay Gupta ◽

Reema Gabrani

Keyword(s):

Antimicrobial Activity ◽

Antibacterial Activity ◽

Micrococcus Luteus ◽

Antibiofilm Activity ◽

Potential Candidate ◽

Indicator Organisms ◽

Sequencing Data ◽

Bacterial Strains ◽

Rdna Sequencing ◽

Animal Farm

Objective: The aim of the current study was to isolate and identify the bacteriocinogenic strain exhibiting broad range antimicrobial activity and antibiofilm activity from soil of animal farms.Methods: In the current study, bacterial strains were isolated from soil of twelve different regions of animal farm all over India and screened for antimicrobial activity against Staphylococcus epidermidis, Micrococcus luteus, Pseudomonas fluorescence and Escherichia coli. Antibiofilm ability of these selected strains was checked on preformed biofilm of S. epidermidis and in addition biofilm disruption potential was also determined. The potent bacterial strain was identified at molecular level by 16S ribosomal DNA (rDNA) sequencing.Results: 30 out of 231 strains isolated from soil were selected on the basis of antibacterial activity against S. epidermidis. One potential candidate (GAS 101) exhibited ≥99% inhibition against S. epidermidis, M. luteus, P. fluorescence and E. coli and also showed antibiofilm activity. GAS 101 16S rDNA sequencing data identified it as Bacillus subtilis. The sequence of B. subtilis was submitted to genbank under accession no. KJ564301.Conclusion: B. subtilis GAS 101 isolated from soil of animal farm showed the antibacterial activity against all indicator organisms and also displayed antibiofilm activity against preformed biofilm and inhibited biofilm formation of S. epidermidis.

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PaPrBaG: A random forest approach for the detection of novel pathogens from NGS data

10.7287/peerj.preprints.2379v1 ◽

2016 ◽

Author(s):

Carlus Deneke ◽

Robert Rentzsch ◽

Bernhard Y Renard

Keyword(s):

Random Forest ◽

Sequence Similarity ◽

Next Generation Sequencing Data ◽

Reference Database ◽

Sequencing Data ◽

Bacterial Strains ◽

Bacterial Genomes ◽

Pathogenicity Prediction ◽

Ngs Data ◽

Reference Genomes

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from reference database used. Here, we present the random forest based approach PaPrBaG (Pathogenicity Prediction for Bacterial Genomes). PaPrBaG overcomes genetic divergence by training on a wide set of species with known pathogenicity phenotype. To that end we generated a novel label source of pathogenic and non-pathogenic bacterial strains, using a rule-based protocol to annotate pathogenicity based on genome metadata. A detailed comparative study reveals that PaPrBaG has several advantages over sequence similarity approaches. Most importantly, it always provides a prediction whereas other approaches discard a large number of sequencing reads that are far away from currently known reference genomes. Furthermore, PaPrBaG remains reliable even at very low genomic coverages. Combining PaPrBaG with existing approaches further improves prediction results.

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Iron Bacterial Phylogeny and their Execution Towards Iron Availability in Equatorial Indian Ocean and Coastal Arabian Sea

Polish Journal of Microbiology ◽

10.33073/pjm-2013-054 ◽

2013 ◽

Vol 62 (4) ◽

pp. 391-400 ◽

Cited By ~ 2

Author(s):

RAJU RAJASABAPATHY ◽

CHELLANDI MOHANDASS ◽

AJAKKALAMOOLE SRINIVAS VIJAYARAJ ◽

VARSHA VINAYAK MADIVAL ◽

RAM MURTI MEENA

Keyword(s):

Indian Ocean ◽

16S Rrna ◽

16S Rrna Gene ◽

Arabian Sea ◽

Sequence Data ◽

Restriction Analysis ◽

Equatorial Indian Ocean ◽

Rrna Gene ◽

Sequencing Data ◽

Bacterial Strains

Based on distinct colony morphology, color, size, shape and certain other traits, 92 bacterial isolates were investigated to understand their managerial ability on iron from the Arabian Sea and Equatorial Indian Ocean samples. The ARDRA (amplified rDNA restriction analysis) applied to eliminate the duplication of the bacterial strains, resulted 39 different banding patterns. The 16S rRNA gene sequencing data indicate the dominancy of three phylogenetic groups, alpha-Proteobacteria (10.25%), gamma-Proteobacteria (35.89%) and Bacilli (53.84%) in these waters. Marinobacter and Bacillus were the only common genera from both of the regions. Pseudoalteromonas, Halomonas, Rheinheimera, Staphylococcus and Idiomarina were some of the other genera obtained from the Arabian Sea. Erythrobacter, Roseovarius, Sagittula and Nitratireductor were found mostly in Equatorial Indian Ocean. In addition, 16S rRNA gene sequence data of some of our iron bacterial strains belong to novel species and one isolate ASS2A could form a new genus. Close to 23% of the isolates were able to produce high affinity sets of ligands like siderophores to mediate iron transport into the cell. The current study indicated that the Equatorial Indian Ocean species were well adapted to oxidize iron as an electron acceptor and the Arabian Sea species preferably go through siderophore production.

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2-kupl: mapping-free variant detection from DNA-seq data of matched samples

BMC Bioinformatics ◽

10.1186/s12859-021-04185-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yunfeng Wang ◽

Haoliang Xue ◽

Christine Pourcel ◽

Yang Du ◽

Daniel Gautheret

Keyword(s):

Dna Sequences ◽

Reference Genome ◽

Point Mutations ◽

Variant Calling ◽

Low Complexity ◽

Structural Variants ◽

Sequencing Data ◽

Bacterial Strains ◽

Two Samples ◽

Variant Detection

Abstract Background The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats. Results We introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves higher accuracy than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome sequencing data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease. Conclusions We developed a mapping-free protocol for variant calling between matched DNA-seq samples. Our protocol is suitable for variant detection in unmappable genome regions or in the absence of a reference genome.

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Genetic Diversity among 3-Chloroaniline- and Aniline-Degrading Strains of theComamonadaceae

Applied and Environmental Microbiology ◽

10.1128/aem.67.3.1107-1115.2001 ◽

2001 ◽

Vol 67 (3) ◽

pp. 1107-1115 ◽

Cited By ~ 112

Author(s):

Nico Boon ◽

Johan Goris ◽

Paul De Vos ◽

Willy Verstraete ◽

Eva M. Top

Keyword(s):

Insertion Sequence ◽

Denaturing Gradient Gel Electrophoresis ◽

Treatment Plant ◽

Sole Source ◽

Northern Hybridization ◽

Comamonas Testosteroni ◽

Sequencing Data ◽

Bacterial Strains ◽

Oxidative Deamination ◽

Sequence Element

ABSTRACT We examined the diversity of the plasmids and of the genetdnQ, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-CA). Three strains have been described and identified previously, i.e., Comamonas testosteroni I2 and Delftia acidovorans CA28 and BN3.1. Strains LME1 and B8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified asD. acidovorans. Both Delftia andComamonas belong to the familyComamonadaceae. All five strains possess a large plasmid of ca. 100 kb, but the plasmids from only four strains could be transferred to a recipient strain by selection on aniline or 3-CA as a sole source of carbon and/or nitrogen. Plasmid transfer experiments and Southern hybridization revealed that the plasmid of strain I2 was responsible for total aniline but not 3-CA degradation, while the plasmids of strains LME1 and B8c were responsible only for the oxidative deamination of aniline. Several transconjugant clones that had received the plasmid from strain CA28 showed different degradative capacities: all transconjugants could use aniline as a nitrogen source, while only some of the transconjugants could deaminate 3-CA. For all four plasmids, the IS1071 insertion sequence of Tn5271 was found to be located on a 1.4-kb restriction fragment, which also hybridized with the tdnQ probe. This result suggests the involvement of this insertion sequence element in the dissemination of aniline degradation genes in the environment. By use of specific primers for the tdnQ gene fromPseudomonas putida UCC22, the diversity of the PCR-amplified fragments in the five strains was examined by denaturing gradient gel electrophoresis (DGGE). With DGGE, three different clusters of the tdnQ fragment could be distinguished. Sequencing data showed that the tdnQ sequences of I2, LME1, B8c, and CA28 were very closely related, while thetdnQ sequences of BN3.1 and P. putidaUCC22 were only about 83% identical to the other sequences. Northern hybridization revealed that the tdnQ gene is transcribed only in the presence of aniline and not when only 3-CA is present.

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Isolation of thermophilic Actinobacteria from compost and identification of bioactive compounds with antimicrobial properties

Access Microbiology ◽

10.1099/acmi.ac2020.po0835 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Gillian Halket ◽

Paul Herron ◽

Carol Munro

Keyword(s):

Aspergillus Fumigatus ◽

Bioactive Compounds ◽

Pathogenic Fungus ◽

Antimicrobial Properties ◽

Gene Clusters ◽

Whole Genome Sequencing Data ◽

Antimicrobial Compounds ◽

Sequencing Data ◽

Bacterial Strains ◽

Rdna Sequencing

To combat the problem of antimicrobial resistance, we are testing the hypothesis that thermophilic Actinobacteria produce novel antimicrobials at higher temperatures, with potential activity against life-threatening infections like invasive aspergillosis caused by the fungus Aspergillus fumigatus. Samples from “windrows” at a green waste processing facility yielded 36 potential thermophilic Actinobacterial strains isolated at 50oC, as well as strains of A. fumigatus. The phylogeny and identities of the bacterial strains were determined by 16S rDNA sequencing. Three strains - DJT 15 Streptomyces thermoviolaceus subsp. apingens, DJT 32 Saccharomonospora viridis and DJT 36 Saccharomonospora glauca - have shown inhibitory activity in bioassays against the ESKAPE pathogens, two of which (DJT 32 and 36) also inhibited the growth of the fungal pathogen Aspergillus fumigatus isolated from the same compost. Strain DJT 32 has also been shown to have an inhibitory effect against azole resistant human pathogenic strains of A. fumigatus. Whole genome Sequencing data of DJT 15 and 32 have been used to identify possible biosynthetic gene clusters for antimicrobial compounds (novel or otherwise) through AntiSmash analysis. Alongside this, bioactive compounds have been extracted from broth cultures of each strain using HP-20 Resin method, and the metabolites will be identified using LC:MS combined with metabolic profiling. Extraction and identification of novel metabolites will provide a path for the development of new antimicrobials for clinical use. This study has shown that thermophilic Actinobacteria produce antimicrobial compounds at higher temperatures, against Staphylococcus aureus and against the highly pathogenic fungus, A. fumigatus.

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Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

10.1101/2020.03.05.978866 ◽

2020 ◽

Cited By ~ 1

Author(s):

Yu Hu ◽

Li Fang ◽

Christopher Nicholson ◽

Kai Wang

Keyword(s):

Human Microbiome ◽

Human Microbiome Project ◽

Error Rates ◽

Tool Development ◽

Sequencing Data ◽

Bacterial Strains ◽

Microbial Genomes ◽

Oxford Nanopore ◽

Long Read ◽

Adequate Coverage

SummaryLong-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length, and are therefore particularly relevant for microbiome studies. However, due to the higher per-base error rates than typical short-read sequencing, the application of long-read sequencing on microbiomes remains largely unexplored. Here we deeply sequenced two human microbiota mock community samples (HM-276D and HM-277D) from the Human Microbiome Project. We showed that assembly programs consistently achieved high accuracy (~99%) and completeness (~99%) for bacterial strains with adequate coverage. We also found that long-read sequencing provides accurate estimates of species-level abundance (R=0.94 for 20 bacteria with abundance ranging from 0.005% to 64%). Our results demonstrate the feasibility to characterize complete microbial genomes and populations from error-prone Nanopore sequencing data, but also highlight necessary bioinformatics improvements for future metagenomics tool development.

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