Bacterial Genome Dynamics Research Articles

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.

The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux. rhea is open source and available at: https://github.com/treangenlab/rhea.

Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.

The complex architecture of DNA within living organisms is essential for maintaining the genetic information that dictates their functions and characteristics. Among the many complexities of genetic material organization, the folding and arrangement of DNA into chromosomes play a critical role in regulating gene expression, replication, and other essential cellular processes. Bacteria, despite their apparently simple cellular structure, exhibit a remarkable level of chromosomal organization that influences their adaptability and survival in diverse environments. Understanding the three-dimensional arrangement of bacterial chromosomes has long been a challenge due to technical limitations, but the development of Chromosome Conformation Capture (3C) methods revolutionized our ability to explore the hierarchical structure and the dynamics of bacterial genomes. Here, we review the major advances in the field of bacterial chromosome structure using 3C technology over the past decade.

Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

SummaryPlasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.

Microbial proteomics: how far have we come?

It is now over 15 years since the beginning of the microbial genome era. At that time, great interest was invested in the idea of understanding bacterial genome dynamics via the analysis of their protein components or 'proteomes'. As bacterial analysis had driven the early advances in genomic squencing, these organisms were amongst the first subjected to protein-based studies. it is fair to suggest in hindsight that the original hype did not match the outcomes. At that time the term proteome was coined, en masse protein analysis meant little more than two-dimensional electrophoresis gels and mainly Edman sequencing for protein identification. As such, only the most abundant cellular constituents could be analysed and interest soon turned for many researchers towards microarray-based transcriptomics where a much greater percentage of the genome could be surveyed. Despite this, substantial and continuing evidence has demonstrated that transcript and protein levels (and, of course, the associated substrates and products of the predicted protein functions) often do not correlate. Therefore, a truly ?systems biology? organism-wide approach is necessary, where genomics, transcriptomics, proteomics and metabolomics are integrated to understand how microbes respond to changes in their genetic or physiological environments, and thus generate new hypotheses for functional understanding. This article will examine how proteomics technology has evolved to the stage at which the total proteome can be elucidated, and provide a guide for ?best practice? for undertaking successful proteomics analyses.

Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales

BackgroundSpecies belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis.ResultsNon-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes.ConclusionsThe presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.

The Nature and Dynamics of Bacterial Genomes

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell.

Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics

Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.

Information Length: Spatial and Temporal Parameters among Stream Bacterial Assemblages

Bacteria, while known to be an integral part of all ecosystems, are seldom studied except as a single taxonomic unit. Few ecological studies even acknowledge the extraordinary functional and species diversity of bacteria. Recent research has elucidated some important facts about bacteria in stream ecosystems. For instance, the dynamics of bacterial genomes within a stream suggest that populations of these organisms are more stable temporally than spatially. We develop predictive models and testable hypotheses based on the information spiraling concept to describe the ecology of stream bacteria and to define 2 new terms: colonization distance and information length. Colonization distance (D_c) is the maximum distance downstream from original colony establishment at which a new colony of bacteria can be established. Information length (L_I) is defined as the maximum length over which a gene has an effect on an ecosystem process independent of a specific host. These terms are modeled relative to the average temporal energy load (joules/min) in the stream. Energy inputs that exceed biologically defined limits of use result in ecosystem energy leaks regardless of information length. Our models predict that information length should be shorter in montane streams than in Coastal Plain streams of southeastern USA. Furthermore, assuming equal average energy load between streams, the stream with the largest energy load variance will leak more energy downstream. Therefore, temperate streams should be less efficient than tropical streams at utilizing energy within a reach.

Genome evolution in enteric bacteria

For more than a decade, the study of bacterial evolution has been dominated by the comparative analysis of nucleotide sequences within and among species. This approach, combined with the characterization of extensive regions of the chromosome by pulsed-field gel electrophoresis, has led to new insights into the dynamics of bacterial genomes.

Dynamics of the Bacterial Genome: Deletions and Integrations as Mechanisms of Bacterial Virulence Modulation

Bacterial virulence is a multifactorial phenomenon, arising from the coordinate action of special abilities of the infectious agents, termed as virulence factors, which is crucial for the infectious process. The genetic determinants encoding those factors are termed virulence associated genes, which can be located on the bacterial chromosome or on extrachromosomal elements (plasmids). Various examples have repeatedly demonstrated that bacterial genome dynamics contributes to virulence modulation. Strikingly, a reduced in vivo virulence of the pathogens was shown to be due to the spontaneous loss of virulence associated genes. The deletion events can involve chromosomal as well as plasmid regions. Also integration of plasmids into the chromosome are considered as dynamic events. The new genetic location of the formerly plasmid encoded virulence associated genes can result in an alteration of virulence expression.