Bacterial Species Concept Research Articles

Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems.

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.

Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.

One More Decade of Agrobacterium Taxonomy.

This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species as ecological species because the genomovar G3 genomic cluster, which initially includes clinical strains, now also includes plant-associated and cave isolates.

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

The lack of a consensus bacterial species concept greatly hampers our ability to understand and organize bacterial diversity. Operational taxonomic units (OTUs), which are clustered on the basis of DNA sequence identity alone, are the most commonly used microbial diversity unit. Although it is understood that OTUs can be phylogenetically incoherent, the degree and the extent of the phylogenetic inconsistency have not been explicitly studied. Here, we tested the phylogenetic signal of OTUs in a broad range of bacterial genera from various phyla. Strikingly, we found that very few OTUs were monophyletic, and many showed evidence of multiple independent origins. Using previously established bacterial habitats as benchmarks, we showed that OTUs frequently spanned multiple ecological habitats. We demonstrated that ecological heterogeneity within OTUs is caused by their phylogenetic inconsistency, and not merely due to ‘lumping’ of taxa resulting from using relaxed identity cut-offs. We argue that ecotypes, as described by the Stable Ecotype Model, are phylogenetically and ecologically more consistent than OTUs and therefore could serve as an alternative unit for bacterial diversity studies. In addition, we introduce QuickES, a new wrapper program for the Ecotype Simulation algorithm, which is capable of demarcating ecotypes in data sets with tens of thousands of sequences.

Comparative Genomics of Wolbachia and the Bacterial Species Concept

The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.

The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories

Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation

BackgroundThe criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.ResultsThe bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.ConclusionThe presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.

The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella

A key issue troubling bacterial taxonomy and systematics is the lack of a biological species definition. Criteria to be used for defining bacterial species on genetic and biological bases should be able to reveal clear-cut boundaries among clusters of bacteria. To date, DNA-DNA re-association assays and ribosomal RNA sequence comparison have been useful in determining relative evolutionary distances among bacteria but the data are continuous and thus cannot define bacterial clusters as taxonomic units to be called species. Using Salmonella as models, we have looked for definite genetic and biologic uniqueness of clusters of bacteria. Based on our findings that each Salmonella lineage has a unique genome structure shared by strains of the same lineage but not overlapping with strains of other Salmonella lineages, we conclude that this is a result of genetic isolation following divergence of the bacteria. We propose that there should be genetic boundaries between different species of bacteria at the genomic level, which awaits further genomic information for validation.

Bacteriology as a Cultural System: Analysis and its Discontents

A cultural system in two senses, bacteriology is underrepresented in the history and philosophy of science (significantly, however, it was the home science of the great prophet of underdetermination, Ludwik Fleck).1 Pasteur and Koch garner attention, but more as founders than practitioners.2 A quarter century ago, in 1987, Olga Amsterdamska called attention to the peculiarity of the enterprise, a biomedical praxis tied only loosely to natural history, to biology, or even to science.3 In this paper I shall examine the bacteriology presented in American textbooks between 1935 and 1950 in the terms of John Pickstone's Ways of knowing: A new history of science, technology, and medicine (2000), and supporting work (2007, 2009).4 In the book, Pickstone identified world-reading (natural philosophy), natural history, analysis, and experimental synthesis as distinct modes of knowing, which had arisen in a broadly sequential relation. Later writings would extend the concept to complementary ways of working and make clearer the concurrence of multiple ways of working and knowing in particular times and domains - there was no teleology here, nor were the ways of knowing/working mutually exclusive.From a Pickstonian standpoint, bacteriology is exemplary in two respects. First, there, the categories of natural philosophy, natural history, analysis, and rationalized synthetic craft are almost always conflated though in changing ways. Second, any working-knowing divide dissolves. There is an enormous emphasis on the pragmatic and operational: theories may underwrite practice, but practice is more important.Bacteriology may fit Pickstone, but does Pickstonizing bring anything to it? Some years ago as a reviewer, I suggested that Ways of knowing had a Kuhn-like potential to inform our understanding of science (and technology and medicine). I thought it might link Kuhn to the emerging literature on technoscientific practice and enrich our characterization of large scale units of activity (i.e., paradigms). That enrichment in turn, might help to clarify their dynamics. Kuhn had seen the overturning of paradigms primarily in epistemic terms. Accumulated anomalies brought revolution. He had not gone far into distinguishing multiple ways of knowing and doing, or to exploring factors that might give a technoscientific enterprise extended and trans-epistemic viability. Pickstone's analytic, by contrast, is applicable not only to diachronic changes within a technoscientific enterprise, but also to synchronic differences within and among the enterprises in a particular time and place: it offers, in short, a complement not only to Kuhn, but to J. ? Merz, whose classic History of European thought in the nineteenth century was equally about ways of knowing. By offering a richer set of categories for appreciating what sorts of work 'working knowledges' might do, Pickstone's approach eased burdens of epistemic accountability without sacrificing the benefits of a systematic comparative framework.REPRESENTATIONS OF BACTERIOLOGYBy the 1930s, a third generation of bacteriologists practised a discipline distinct - in terms of institutional organization, textbook traditions, modes of training, and career possibilities - from botany and zoology; equally from the other main biomedical laboratory science, pathology; and from the applied, and significantly colonial, enterprises of genetics, parasitology and veterinary medicine. They had, as we shall see, subverted an incipient biochemistry, which challenged the sanctity of the bacterial species concept. They had spawned as a parallel endeavour, immunology, and its chief practical arm, serology: the relation of immunology to bacteriology would be ambiguous and often contested - serological specificity was a means of defining bacterial specificity, and yet many serologists leaned dangerously toward general physiology and physical chemistry. Any picture of a community of happy equals, with each bacteriologist investigating the wee beasties of his (or rarely her) chosen domain is misleading. …

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.

A Re-Evaluation of M. prototuberculosis

It has been suggested that a group of smooth tubercle bacilli, isolated from patients with tuberculosis and associated with Djibouti, East Africa, along with the seven species and subspecies that are traditional members of the Mycobacterium tuberculosis complex, should be considered a single species. This suggestion is based on the sequence similarity of the16S rRNA and segments of six housekeeping genes. The very concept of bacterial species is now subject to debate, and I follow the lead of Maynard Smith, who, in a review of the bacterial species concept, suggested that using genetic distance to define bacterial species was “arbitrary and of little merit”. If defining a species by sequence diversity alone is controversial, then it is important to carefully examine the recent claim that strains of M. tuberculosis are descendants and members of a much more ancient and large bacterial species called Mycobacterium prototuberculosis. Furthermore, given the importance of M. tuberculosis as a human pathogen and the implications for research, it is important to verify the claim that our remote hominid ancestors may have suffered from tuberculosis and that the tubercle bacilli originated in Africa.

A molecular phylogeny of enteric bacteria and implications for a bacterial species concept

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.

Differentiation between Haemophilus paraphrophilus, H. aphrophilus, H. influenzae, Actinobacillus actinomycetemcomitans, Pasteurella multocida, P. haemolytica, and P. ureae by high resolution two‐dimensional protein electrophoresis

AbstractThe cellular proteins of Haemophilus paraphrophilus (ATCC 29242, ATCC 29241T, ATCC 29240, HK 477, HK 319, HK 159), H. aphrophilus (ATCC 33389T), H. influenzae (ATCC 31441), Actinobacillus actinomycetemcomitans (ATCC 33384T), Pasteurella multocida (NCTC 10322T), P. haemolytica (9380T), and P. ureae (NCTC 10219T) were analyzed by high resolution two‐dimensional protein electrophoresis and silver staining. The electrophoretic protein patterns of Haemophilus, Actinobacillus and Pasteurella were quite distinct. Also the patterns of P. multocida, P. haemolytica and P. ureae differed markedly. Except for H. paraphrophilus ATCC 29242, it was difficult to distinguish H. paraphrophilus from H. aphrophilus strains. Excluding ATCC 29242, H. paraphrophilus strains were quite similar. A. actinomycetemcomitans could easily be distinguished from all species tested, including the related H. aphrophilus, H. paraphrophilus, P. haemolytica, and P. ureae. High resolution two‐dimensional protein electrophoresis is likely to contribute to a more unifying concept of bacterial species. Among the organisms examined only H. aphrophilus and H. paraphrophilus seem to requires revision of their current taxonomic positions.