scholarly journals Reconstruction of Bacterial Metagenome-Assembled Genome Sequences from Alpine Bog Vegetation

2020 ◽  
Vol 9 (35) ◽  
Author(s):  
Wisnu Adi Wicaksono ◽  
Tomislav Cernava ◽  
Christian Berg ◽  
Gabriele Berg
Keyword(s):  
Plant Species ◽  
Bacterial Genome ◽  
Genome Sequences ◽  
Bog Ecosystems ◽  
Genetic Potential ◽  
Plant Hosts ◽  
Ecological Roles

ABSTRACT Bacteria are essential constituents of bog ecosystems. Here, we report 44 bacterial genome sequences reconstructed from metagenomes sampled across 12 plant species representing Alpine bog vegetation. This resource will facilitate further exploration of the genetic potential of these bacteria and allow researchers to refine their ecological roles in association with their plant hosts.

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals Towards a better understanding of the bacterial pan-genome

2021 ◽  
Vol 17 ◽  
pp. 84-96
Author(s):  
Dawid Gmiter ◽  
Sylwia Nawrot ◽  
Ilona Pacak ◽  
Katarzyna Zegadło ◽  
Wiesław Kaca
Keyword(s):  
Population Structure ◽  
Bacterial Genome ◽  
Species Level ◽  
Genome Sequences ◽  
Pan Genome ◽  
Multiple Genes ◽  
Number Of Genes ◽  
Structure Diversity

The bacterial pan-genome is a relatively new concept that refers to the number of genes observed in a given set of bacterial genome sequences, either at the intra- or inter-species level. Determining the pan-genome of a given species of bacteria using a large number of strains allows one to compare multiple genes and to determine evolutionary links between isolates. This information can help to determine population structure, diversity in terms of prevalence in a given environment and pathogenicity of microorganisms. Within this review, we explain the most important issues related to pan-genome studies. We also include a brief description of some selected bacterial pan-genomes. Finally, we propose an easy-toperform workflow to study bacterial pan-genomes that will facilitate nonexperts in a pan-genome-based investigation.

scholarly journals PlasClass improves plasmid sequence classification

2019 ◽  
Author(s):  
David Pellow ◽  
Itzik Mizrahi ◽  
Ron Shamir
Keyword(s):  
State Of The Art ◽  
Bacterial Genome ◽  
Unknown Origin ◽  
The State ◽  
Sequence Classification ◽  
Genome Sequences ◽  
Plasmid Sequence ◽  
Link Type ◽  
Classification Tool ◽  
Metagenomic Assembly

AbstractBackgroundMany bacteria contain plasmids, but separating between contigs that originate on the plasmid and those that are part of the bacterial genome can be difficult. This is especially true in metagenomic assembly, which yields many contigs of unknown origin. Existing tools for classifying sequences of plasmid origin give less reliable results for shorter sequences, are trained using a fraction of the known plasmids, and can be difficult to use in practice.ResultsWe present PlasClass, a new plasmid classifier. It uses a set of standard classifiers trained on the most current set of known plasmid sequences for different sequence lengths. PlasClass outperforms the state-of-the-art plasmid classification tool on shorter sequences, which constitute the majority of assembly contigs, while using less time and memory.ConclusionsPlasClass can be used to easily classify plasmid and bacterial genome sequences in metagenomic or isolate assemblies. It is available from: https://github.com/Shamir-Lab/PlasClass

scholarly journals The extent of carbapenemase-encoding genes in public genome sequences

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11000
Author(s):  
Ingmar Janse ◽  
Rick Beeloo ◽  
Arno Swart ◽  
Michael Visser ◽  
Leo Schouls ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Host Species ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Bacterial Genome ◽  
Companion Animals ◽  
Health Concern ◽  
Genome Sequences ◽  
Genetic Elements ◽  
Encoding Genes

Genome sequences provide information on the genetic elements present in an organism, and currently there are databases containing hundreds of thousands of bacterial genome sequences. These repositories allow for mining patterns concerning antibiotic resistance gene occurrence in both pathogenic and non-pathogenic bacteria in e.g. natural or animal environments, and link these to relevant metadata such as bacterial host species, country and year of isolation, and co-occurrence with other resistance genes. In addition, the advances in the prediction of mobile genetic elements, and discerning chromosomal from plasmid DNA, broadens our view on the mechanism mediating dissemination. In this study we utilize the vast amount of data in the public database PATRIC to investigate the dissemination of carbapenemase-encoding genes (CEGs), the emergence and spread of which is considered a grave public health concern. Based on publicly available genome sequences from PATRIC and manually curated CEG sequences from the beta lactam database, we found 7,964 bacterial genomes, belonging to at least 70 distinct species, that carry in total 9,892 CEGs, amongst which blaNDM, blaOXA, blaVIM, blaIMP and blaKPC. We were able to distinguish between chromosomally located resistance genes (4,137; 42%) and plasmid-located resistance genes (5,753; 58%). We found that a large proportion of the identified CEGs were identical, i.e. displayed 100% nucleotide similarity in multiple bacterial species (8,361 out of 9,892 genes; 85%). For example, the New Delhi metallo-beta-lactamase NDM-1 was found in 42 distinct bacterial species, and present in seven different environments. Our data show the extent of carbapenem-resistance far beyond the canonical species Acetinobacter baumannii, Klebsiella pneumoniae or Pseudomonas aeruginosa. These types of data complement previous systematic reviews, in which carbapenem-resistant Enterobacteriaceae were found in wildlife, livestock and companion animals. Considering the widespread distribution of CEGs, we see a need for comprehensive surveillance and transmission studies covering more host species and environments, akin to previous extensive surveys that focused on extended spectrum beta-lactamases. This may help to fully appreciate the spread of CEGs and improve the understanding of mechanisms underlying transmission, which could lead to interventions minimizing transmission to humans.

scholarly journals Analysis of bifidobacterial evolution using a multilocus approach

2006 ◽  
Vol 56 (12) ◽  
pp. 2783-2792 ◽  
Author(s):  
Marco Ventura ◽  
Carlos Canchaya ◽  
Antonio Del Casale ◽  
Franco Dellaglio ◽  
Erasmo Neviani ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Evolutionary Process ◽  
Housekeeping Gene ◽  
Pharmaceutical Products ◽  
Gene Sequences ◽  
Genome Sequences ◽  
Functional Ingredients ◽  
Conserved Genes ◽  
Multilocus Approach ◽  
Type Strains

Bifidobacteria represent one of the most numerous groups of bacteria found in the gastrointestinal tract of humans and animals. In man, gastrointestinal bifidobacteria are associated with health effects and for this reason they are often used as functional ingredients in food and pharmaceutical products. Such applications may benefit from or require a clear and reliable bifidobacterial species identification. The increasing number of available bacterial genome sequences has provided a large amount of housekeeping gene sequences that can be used both for identification of bifidobacterial species as well as for understanding bifidobacterial evolution. In order to assess their relative positions in the evolutionary process, fragments from seven conserved genes, clpC, dnaB, dnaG, dnaJ1, purF, rpoC and xfp, were sequenced from each of the currently described type strains of the genus Bifidobacterium. The results demonstrate that the concatenation of these seven gene sequences for phylogenetic purposes allows a significant increase in the discriminatory power between taxa.

scholarly journals Detection of phytopathogens of the genusDickeyausing a PCR primer prediction pipeline for draft bacterial genome sequences

2012 ◽  
Vol 62 (3) ◽  
pp. 587-596 ◽  
Author(s):  
L. Pritchard ◽  
S. Humphris ◽  
G. S. Saddler ◽  
N. M. Parkinson ◽  
V. Bertrand ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Genome Sequences ◽  
Pcr Primer

scholarly journals Isolation and Characterization of a Novel Lipase from a Metagenomic Library of Tidal Flat Sediments: Evidence for a New Family of Bacterial Lipases

2006 ◽  
Vol 72 (11) ◽  
pp. 7406-7409 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh ◽  
Jae Kwang Song ◽  
Jung-Hoon Yoon
Keyword(s):  
Experimental Data ◽  
Tidal Flat ◽  
Bacterial Genome ◽  
Metagenomic Library ◽  
Lipolytic Enzyme ◽  
Genome Sequences ◽  
New Family ◽  
Isolation And Characterization ◽  
Tidal Flat Sediments

ABSTRACT We cloned lipG, which encoded a lipolytic enzyme, from a Korean tidal flat metagenomic library. LipG was related to six putative lipases previously identified only in bacterial genome sequences. These enzymes comprise a new family. We partially characterized LipG, providing the first experimental data for a member of this family.

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