scholarly journals The Second Chromosome Promotes the Adaptation of the Genus Flammeovirga to Complex Environments

2021 ◽  
Author(s):  
Zewei Feng ◽  
Zheng Zhang ◽  
Yu Liu ◽  
Jingyan Gu ◽  
Yuanyuan Cheng ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Symbiotic Bacteria ◽  
Human Pathogens ◽  
Complex Environments ◽  
Single Chromosome ◽  
Nonessential Genes

For decades, the typical bacterial genome has been thought to contain a single chromosome and a few small plasmids carrying nonessential genes. However, an increasing number of secondary chromosomes have been identified in various bacteria (e.g., plant symbiotic bacteria and human pathogens).

scholarly journals Campylobacter and helicobacter in the etiology of gastrointestinal diseases

2012 ◽  
Vol 64 (4) ◽  
pp. 1389-1404 ◽  
Author(s):  
Biljana Miljkovic-Selimovic ◽  
Branislava Kocic ◽  
Tatjana Babic
Keyword(s):  
Bacterial Genome ◽  
Optimal Growth ◽  
The Elderly ◽  
Distinct Species ◽  
Gastrointestinal Diseases ◽  
Human Pathogens ◽  
Endotoxin Activity ◽  
Clinical Presentations ◽  
Human Disorders ◽  
H Pylori

The order Campylobacterales comprises two genera: Campylobacter and Helicobacter, with a widespread distribution in both humans and animals. They are Gram-negative, spiral, helical and microaerophilic bacteria, with an optimal growth temperature of 37?C for H. pylori and 42?C for C. jejuni strains. While Helicobacter pylori are restricted to humans, other helicobacter species can be found in different mammals and occasionally in humans. Several Campylobacter species are recognized as human pathogens, while distinct species are pathogenic only occasionally, in children, the elderly and immunocompromised patients. Campylobacters and helicobacters are well adapted to the living conditions inside the gastrointestinal tract, where they can cause diseases as a consequence of inflammation. In addition, they are related to certain extraintestinal diseases, post-infectious sequels, malignancy and autoimmunity. Different clinical presentations of human disorders may be the consequences of the diversity in host immune response, bacterial genome, endotoxin activity as well as specific bacterial virulence factors.

scholarly journals A prospective role for the rumen in generating antibiotic resistance

2019 ◽  
Author(s):  
Cameron R. Strachan ◽  
Anna J. Mueller ◽  
Mahdi Ghanbari ◽  
Viktoria Neubauer ◽  
Benjamin Zwirzitz ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Single Gene ◽  
Bacterial Genome ◽  
Global Network ◽  
Farm Animals ◽  
Gene Trees ◽  
Human Pathogens ◽  
Genetic Determinants ◽  
Bacterial Genomes ◽  
Associated Bacteria

ABSTRACTAntibiotics were a revolutionary discovery of the 20th century, but the ability of bacteria to spread the genetic determinants of resistance via horizontal gene transfer (HGT) has quickly endangered their use1. Indeed, there is a global network of microbial gene exchange, the analysis of which has revealed particularly frequent transfer of resistance determinants between farm animals and human-associated bacteria2. Here, we leverage the recent release of a rumen microbial genome reference set and show that the wide-spread resistance gene cluster aadE-sat4-aphA-3 is harboured in ruminal Bacteroidetes. While this cluster appears to have been recently transferred between commensal bacteria in the rumen and many diverse animal and human pathogens, comparative analysis suggests that the cluster stabilized in the pathogens. Then, focusing on streptomycin resistance, it was found that homologues from the rumen span much of the known diversity of aminoglycoside O-nucleotidyltransferases (AadEs) and that distinct variants of the enzyme are present in a single rumen bacterial genome. Notably, a second variant of AadE has also been recently transferred, albeit more often as a single gene, throughout a different set of animal and human associated bacteria. By examining the synteny of AadE orthologues in various bacterial genomes and analyzing corresponding gene trees in an environmental context, we speculate that the ruminant associated microbiome has a salient role in the emergence of specific resistance variants and clusters. In light of the recent literature on the evolutionary origin of antibiotic resistance, we further suggest that the rumen provides a possible route of dissemination of resistance genes from soil resistomes, throughout the farm, and to human pathogens3.

scholarly journals Deep genome annotation of the opportunistic human pathogenStreptococcus pneumoniaeD39

2018 ◽  
Author(s):  
Jelle Slager ◽  
Rieza Aprianto ◽  
Jan-Willem Veening
Keyword(s):  
Single Molecule ◽  
Genome Annotation ◽  
Antigenic Variation ◽  
Current Knowledge ◽  
Bacterial Genome ◽  
Treatment Strategies ◽  
Human Pathogens ◽  
Genome Data ◽  
Manual Curation ◽  
Automated Tools

ABSTRACTA precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence ofStreptococcus pneumoniaestrain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor. We generated a new genome annotation using automated tools, followed by manual curation, reflecting the current knowledge in the field. By combining sequence-driven terminator prediction, deep paired-end transcriptome sequencing and enrichment of primary transcripts by Cappable-Seq, we mapped 1,015 transcriptional start sites and 748 termination sites. Using this new genomic map, we identified several new small RNAs (sRNAs), riboswitches (including twelve previously misidentified as sRNAs), and antisense RNAs. In total, we annotated 92 new protein-encoding genes, 39 sRNAs and 165 pseudogenes, bringing theS. pneumoniaeD39 repertoire to 2,151 genetic elements. We report operon structures and observed that 9% of operons lack a 5’-UTR. The genome data is accessible in an online resource called PneumoBrowse (https://veeninglab.com/pneumobrowse) providing one of the most complete inventories of a bacterial genome to date. PneumoBrowse will accelerate pneumococcal research and the development of new prevention and treatment strategies.

scholarly journals Genome announcement of Steinernema khuongi and its associated symbiont from Florida

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Anil Baniya ◽  
Peter DiGennaro
Keyword(s):  
Biological Control ◽  
Comparative Genomics ◽  
Genome Sequence ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Control Measures ◽  
Symbiotic Bacteria ◽  
Total Length ◽  
Central Ridge ◽  
Promising Source

Abstract Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.

scholarly journals Correcting index databases improves metagenomic studies

2019 ◽  
Author(s):  
Guillaume Méric ◽  
Ryan R. Wick ◽  
Stephen C. Watts ◽  
Kathryn E. Holt ◽  
Michael Inouye
Keyword(s):  
Meta Analysis ◽  
Fold Increase ◽  
Taxonomic Composition ◽  
Human Pathogens ◽  
Complex Environments ◽  
Accessible Information ◽  
Two Factors ◽  
Ncbi Refseq ◽  
Reference Index ◽  
Microbiome Data

AbstractAssessing the taxonomic composition of metagenomic samples is an important first step in understanding the biology and ecology of microbial communities in complex environments. Despite a wealth of algorithms and tools for metagenomic classification, relatively little effort has been put into the critical task of improving the quality of reference indices to which metagenomic reads are assigned. Here, we inferred the taxonomic composition of 404 publicly available metagenomes from human, marine and soil environments, using custom index databases modified according to two factors: the number of reference genomes used to build the databases, and the monophyletic strictness of species definitions. Index databases built following the NCBI taxonomic system were also compared to others using Genome Taxonomy Database (GTDB) taxonomic redefinitions. We observed a considerable increase in the rate of read classification using modified reference index databases as compared to a default NCBI RefSeq database, with up to a 4.4-, 6.4- and 2.2-fold increase in classified reads per sample for human, marine and soil metagenomes, respectively. Importantly, targeted correction for 70 common human pathogens and bacterial genera in the index database increased their specific detection levels in human metagenomes. We also show the choice of index database can influence downstream diversity and distance estimates for microbiome data. Overall, the study shows a large amount of accessible information in metagenomes remains unexploited using current methods, and that the same data analysed using different index databases could potentially lead to different conclusions. These results have implications for the power and design of individual microbiome studies, and for comparison and meta-analysis of microbiome datasets.

scholarly journals Screening for highly transduced genes in Staphylococcus aureus reveals both lateral and specialized transduction

2020 ◽  
Author(s):  
Janine Zara Bowring ◽  
Yue Su ◽  
Ahlam Alsaadi ◽  
Sine L. Svenningsen ◽  
Julian Parkhill ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Integration Site ◽  
Direct Sequencing ◽  
Bacterial Genome ◽  
Bacterial Cells ◽  
Mutant Library ◽  
Human Pathogens ◽  
Bacterial Dna

AbstractBacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer in the human pathogen, Staphylococcus aureus. Transduction involves packaging of bacterial DNA by viruses and enables transmission of virulence and resistance genes between cells. To learn more about transduction in S. aureus, we searched a transposon mutant library for genes and mutations that enhanced transfer mediated by the temperate phage, φ11. Using a novel screening strategy, we performed multiple rounds of transduction of transposon mutant pools selecting for an antibiotic resistance marker within the transposon element. When determining the locations of transferred mutations, we found that, within each pool of 96 mutants the screen had selected for just 1 or 2 transposon mutant(s). Subsequent analysis showed that the position of the transposon, rather than inactivation of bacterial genes, was responsible for the phenotype. Interestingly, from multiple rounds we identified a pattern of transduction that encompassed mobile genetic elements, as well as chromosomal regions both upstream and downstream of the phage integration site. The latter was confirmed by DNA sequencing of purified phage lysates. Importantly, transduction frequencies were lower for phage lysates obtained by phage infection rather than induction. Our results confirm previous reports of lateral transduction of bacterial DNA downstream of the integrated phage, but also indicate specialized transduction of DNA upstream of the phage, likely involving imprecise excision of the phage from the bacterial genome. These findings illustrate the complexity of transduction processes and increase our understanding of the mechanisms by which phages transfer bacterial DNA.ImportanceHorizontal transfer of DNA between bacterial cells contributes to the spread of virulence and antibiotic resistance genes in human pathogens. For Staphylococcus aureus, bacterial viruses are particularly important. These viruses, termed bacteriophages, can transfer bacterial DNA between cells by a process known as transduction, which despite of its importance is only poorly characterized. Here, we employed a transposon mutant library to investigate transduction in S. aureus. We show that the location of bacterial DNA in relation to bacteriophages integrated in the bacterial genome is a key decider of how frequently that DNA is transduced. Based on serial transduction of transposon mutant pools and direct sequencing of bacterial DNA in bacteriophage particles, we demonstrate both lateral and specialized transduction. The use of mutant libraries to investigate the patterns of bacterial DNA transfer between cells could help understand how bacteria evolve virulence and resistance and may ultimately lead to new intervention strategies.

scholarly journals Nascent Genomic Evolution and Allopatric Speciation ofMyroides profundiD25 in Its Transition from Land to Ocean

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yu-Zhong Zhang ◽  
Yi Li ◽  
Bin-Bin Xie ◽  
Xiu-Lan Chen ◽  
Qiong-Qiong Yao ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Marine Environment ◽  
High Salinity ◽  
Genomic Sequence ◽  
Bacterial Genome ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Expression Levels ◽  
Unique Genes

ABSTRACTA large amount of bacterial biomass is transferred from land to ocean annually. Most transferred bacteria should not survive, but undoubtedly some do. It is unclear what mechanisms these bacteria use in order to survive and even thrive in a new marine environment.Myroides profundiD25T, a member of theBacteroidetesphylum, was isolated from deep-sea sediment of the southern Okinawa Trough near the China mainland and had high genomic sequence identity to and synteny with the human opportunistic pathogenMyroides odoratimimus. Phylogenetic and physiological analyses suggested thatM. profundirecently transitioned from land to the ocean. This provided an opportunity to explore how a bacterial genome evolved to survive in a novel environment. Changes in the transcriptome were evaluated when both species were cultured under low-salinity conditions and then transferred to high-salinity conditions. Comparative genomic and transcriptomic analyses showed thatM. profundialtered transcription regulation in the early stages of survival. In these stages, vertically inherited genes played a key role in the survival ofM. profundi. The contribution ofM. profundiunique genes, some possibly acquired by horizontal gene transfer (HGT), appeared relatively small, and expression levels of unique genes were diminished under the high-salinity conditions. We postulate that HGT genes might play an important role in longer-term adaptation. These results suggested that some human pathogens might have the ability to survive in and adapt to the marine environment, which may have important implications for public health control in coastal regions.IMPORTANCEHorizontal gene transfer (HGT) is considered to be important for bacteria to adapt to a different microhabitat. However, our results showed that vertically inherited genes might play more important roles than HGT genes in the nascent adaptation to the marine environment in the bacteriumMyroides profundi, which has recently been transferred from land to ocean.M. profundiunique genes had low expression levels and were less regulated under high-salinity conditions, indicating that the contribution of HGT genes to survival of this bacterium under marine high-salinity conditions was limited. In the early adaptation stages,M. profundiapparently survived and adapted mainly by regulating the expression of inherited core genes. These results may explain in part why human pathogens can easily be detected in marine environments.

scholarly journals The Divided Bacterial Genome: Structure, Function, and Evolution

2017 ◽  
Vol 81 (3) ◽  
Author(s):  
George C. diCenzo ◽  
Turlough M. Finan
Keyword(s):  
Meta Analysis ◽  
Bacterial Genome ◽  
Genome Structure ◽  
Dna Molecules ◽  
Human Pathogens ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Content Type ◽  
A Genome ◽  
And Function

SUMMARY Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.

Legionellaand non-Legionellabacteria in a biological treatment plant

2013 ◽  
Vol 59 (2) ◽  
pp. 102-109 ◽  
Author(s):  
Else Marie Fykse ◽  
Tone Aarskaug ◽  
Ingjerd Thrane ◽  
Janet Martha Blatny
Keyword(s):  
Bacterial Community ◽  
Legionella Pneumophila ◽  
Biological Treatment ◽  
Bacterial Population ◽  
Treatment Plant ◽  
Human Pathogens ◽  
Complex Environments ◽  
Pseudomonas Spp ◽  
Rdna Sequencing ◽  
Legionnaires Disease

Legionella pneumophila were previously identified in the aeration ponds (up to 1010CFU/L) of a biological wastewater treatment plant at Borregaard Ind. Ltd., Sarpsborg, Norway, and in air samples (up to 3300 CFU/m3) collected above the aeration ponds. After 3 outbreaks of Legionnaires’ disease reported in this area in 2005 and 2008, the aeration ponds of the plant were shut down by the Norwegian authorities in September 2008. The aim of the present work was to analyze the Legionella and non-Legionella bacterial communities in the aeration ponds before and during the shutdown process and to identify potential human pathogens. The non-Legionella bacterial community was investigated in selected samples during the shutdown process by 16S rDNA sequencing of clone libraries (400 clones) and growth analysis. The concentration of L. pneumophila and Pseudomonas spp. DNA were monitored by quantitative PCR. Results showed a decrease in the concentration of L. pneumophila and Pseudomonas spp. during the shutdown. This was accompanied by a significant change in the composition of the bacterial community in the aeration ponds. This study demonstrated that several advanced analytical methods are necessary to characterize the bacterial population in complex environments, such as the industrial aeration ponds.

scholarly journals Complete Genome Sequence of the African Strain AXO1947 of Xanthomonas oryzae pv. oryzae

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
J. C. Huguet-Tapia ◽  
Z. Peng ◽  
B. Yang ◽  
Z. Yin ◽  
S. Liu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Bacterial Genome ◽  
Xanthomonas Oryzae ◽  
Sequencing Technology ◽  
Tal Effectors ◽  
Single Chromosome ◽  
Long Read ◽  
Target Characterization ◽  
African Clade

Xanthomonas oryzae pv. oryzae is the etiological agent of bacterial rice blight. Three distinct clades of X. oryzae pv. oryzae are known. We present the complete annotated genome of the African clade strain AXO194 using long-read single-molecule PacBio sequencing technology. The genome comprises a single chromosome of 4,674,975 bp and encodes for nine transcriptional activator-like (TAL) effectors. The approach and data presented in this announcement provide information for complex bacterial genome organization and the discovery of new virulence effectors, and they facilitate target characterization of TAL effectors.

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