Phylogeny Of Bacteria Research Articles

Phylogenomic Analysis Substantiates the gyrB Gene as a Powerful Molecular Marker to Efficiently Differentiate the Most Closely Related Genera Myxococcus, Corallococcus, and Pyxidicoccus.

Rapid and accurate strain identification of the most closely related genera Myxococcus, Corallococcus, and Pyxidicoccus can enhance the efficiency of the mining of novel secondary metabolites through dereplication. However, the commonly used 16S rRNA gene sequencing cannot accurately differentiate members of the three genera above, and the whole-genome sequencing is unable to rapidly and inexpensively provide species assignation toward a large number of isolates. To overcome the limitations, the gyrB gene was investigated as a candidate genetic marker for exploring the phylogenetic relationships of bacteria within the three genera and for developing the gyrB-based typing method. Here, the bacterial phylogeny and species affiliations of the three genera were determined based on the phylogenomic reconstruction and the analysis of digital DNA–DNA hybridization values among 90 genomes, further confirming nine novel taxa and assigning over one-third of genomes to defined species. The phylogenetic relationships of these strains based on the gyrB gene sequences were congruent with those based on their genome sequences, allowing the use of the gyrB gene as a molecular marker. The gyrB gene-specific primers for the PCR-amplification and sequencing of bacteria within the three genera were designed and validated for 31 isolates from our group collection. The gyrB-based taxonomic tool proved to be able to differentiate closely related isolates at the species level. Based on the newly proposed 98.6% identity threshold for the 966-bp gyrB gene and the phylogenetic inference, these isolates were assigned into two known species and eight additional putative new species. In summary, this report demonstrated that the gyrB gene is a powerful phylogenetic marker for taxonomy and phylogeny of bacteria within the closely related genera Myxococcus, Corallococcus, and Pyxidicoccus, particularly in the case of hundreds or thousands of isolates in environmental studies.

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

Fecal microbiota transplantation (FMT) from healthy donor to patient is a treatment for microbiome-associated diseases. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing engraftment in humans are unknown. Here we use an ongoing clinical experiment, the treatment of recurrent Clostridium difficile infection, to uncover the rules of engraftment in humans. We built a statistical model that predicts which bacterial species will engraft in a given host, and developed Strain Finder, a method to infer strain genotypes and track them over time. We find that engraftment can be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. Furthermore, donor strains within a species engraft in an all-or-nothing manner and previously undetected strains frequently colonize patients receiving FMT. We validated these findings for metabolic syndrome, suggesting that the same principles of engraftment extend to other indications.

Phylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species.

A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.

Phylogeny of Bacteria from Steelmaking Wastes and Their Acidic Enrichment Cultures

Currently, millions of tons of steel are produced worldwide. This has become a serious economic and environmental challenge because the ores used for steel production are nonrenewable resources and the production generates huge amount of waste. In this study, we identified and investigated the ability of bacteria from steelmaking waste with low and high zinc concentration to promote leaching of zinc, when enriched by acidic (pH 2) culture conditions. The bioleaching assays indicated removal of Zn, as in chemical leaching. Bacterial communities from crude and enrichment culture wastes were characterized by the 16S rRNA gene. Phylogenetic analysis of the generated clone libraries revealed predominance of Proteobacteria and Firmicutes. The Actino- bacteria, Bacteroidetes, Cyanobacteria, and Deinococcus-Thermus phyla were also encountered. The clones were most closely related to cultivable heterotrophic bacteria. Different genera were identified including iron redox cycling and leaching bacteria such as Chromobacterium, Aeromonas, Escherichia, Bacillus, and Ochrobactrum. These data add significant new information on bacteria which survive in extremely acidic conditions. They are distantly related to typical acidophiles responsible for the leaching process, which makes them good candidates for future studies on metal bioleaching.

Arriving at a correlation between the flagellar arrangement and multicellularity

Cilia and flagella are organelles of motility that enable cells to swim or move liquid over its surface. An exhaustive literature survey for the presence of the organelle in organisms across phyla showed that most animal cells harbor cilia in contrast to very few fungal cells. While this was not unexpected, it was the position and arrangement of this organelle in each cell that intrigued our attention. Natural selection might have favored motility over chemotaxis; and it would have done so to evolve a stable structure that could have undergone an optimization process requiring a precise geometry in the shape of cells and the structure that would help cells to move. The positioning of such a structure would play a pre-dominant role in optimal motility. It is now known that the flagellar position of a cell is a genetically distinct trait, occasionally used in phylogeny of bacteria, distributed in distinguishing patterns over cellular surface, but basically are of two types, either polar (one flagellum arising from one pole per cell) or peritrichous (lateral flagella distributed over the entire cell surface). Irrespective of the cellular habitat, flagella origin, ultrastructure and proteome, the present investigation surveyed 26 sub-types of flagellar arrangements from as many species as possible. A peculiar pattern ensued-Prokaryotes harbored predominantly polar and peritrichous types; eukaryotes showed a mere change of the peritrichous one. These numbers when used to create a Similarity tree depicted a similarity distance of 14 between the Eubacteria and Archaebacteria forming the first neighborhood; Protozoans, Algae, Fungi, Plantae and Animalia formed a second neighborhood. We offer a working hypothesis for this pattern and the gradual shift in the flagellar arrangement from polar, peritrichous, sub-apical, and apical to lateral throughout evolution.

Diversity and phylogeny of bacteria on Zimbabwe tobacco leaves estimated by 16S rRNA sequence analysis

Microorganisms play important roles in the tobacco aging process. However, microbial communities on flue-cured tobacco leaves (FCTL) remain largely unknown. In this study, the total microbial genomic DNA of unaged and aging FCTL from Zimbabwe were isolated using a culture-independent method, and the bacterial communities were investigated through analyzing two 16S rRNA gene libraries. Eighty-four and 65 operational taxonomic units were obtained from the libraries of the unaged and aging FCTL, respectively. The following genera were represented more than 4% in both libraries (aging and unaged library): Sphingomonas (4.84%, 4.18%), Stenotrophomonas (4.84%, 5.23%), Erwinia (5.81%, 4.88%), Pantoea (19.35%, 18.47%), and Pseudomonas (21.29%, 24.04%). The dominant species varied between the two libraries. Specifically, several dominant species in unaged FCTL including Pseudomonas fulva, Pseudomonas sp. (AM909658), Klebsiella sp. (HM584796), and Pantoea sp. (AY501386) were not identified in aging FCTL, while several dominant species in aging FCTL such as Pantoea sp. (GU566350), Pseudomonas sp. (EF157292), and Buttiauxella izardii were not found in unaged FCTL. The phylogenetic analysis showed that bacteria from unaged and aging FCTL were divided into two clades, and two unique subclades were identified in aging FCTL. Our results revealed for the first time the bacterial diversities on Zimbabwe tobacco, and provided a basis for clarifying the roles of bacteria in aging process of FCTL.

Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample

Compared with culture-independent approaches, traditionally used culture-dependent methods have a limited capacity to characterize water microbiota. Nevertheless, for almost a century the latter have been optimized to detect and quantify relevant bacteria. A pertinent question is if culture-independent diversity surveys give merely an extended perspective of the bacterial diversity or if, even with a higher coverage, focus on a different set of organisms. We compared the diversity and phylogeny of bacteria in a freshwater sample recovered by currently used culture-dependent and culture-independent methods (DGGE and 454 pyrosequencing). The culture-dependent diversity survey presented lower coverage than the other methods. However, it allowed bacterial identifications to the species level, in contrast with the other procedures that rarely produced identifications below the order. Although the predominant bacterial phyla detected by both approaches were the same (Proteobacteria, Actinobacteria, Bacteroidetes), sequence similarity analysis showed that, in general, different operational taxonomical units were targeted by each method. The observation that culture-dependent and independent approaches target different organisms has implications for the use of the latter for studies in which taxonomic identification has a predictive value. In comparison to DGGE, 454 pyrosequencing method had a higher capacity to explore the bacterial richness and to detect cultured organisms, being also less laborious.

Evolution and Taxonomy of Bacteria, Then (1999/2000) and Now (2009)

One decade is hardly a ripple in respect to biological evolutionary time, but can be significant in regard to the evolution of concepts based on new experimental discoveries. Despite the popularity of the simple idea that a single macromolecule, namely 16S rRNA, is a repository of the evolutionary history of bacteria and can serve as a “Rosetta Stone” for classification, I and several others considered this notion to be an egregious oversimplification. Moreover, changing the names of well-characterized bacterial species on the basis of 16S RNA sequence differences struck me as a particularly objectionable practice. These considerations led me to publish two satires (Gest, 1999/2000) which in the fullness of time can be seen to have struck the bull's eyes of their targets. An editorial sidebar in the year 2000 satire noted: “The following satire is based on Howard Gest's view that the evolutionary history of bacteria was more complex than commonly supposed and cannot be traced with accuracy using 16SrRNA sequences as the sole criterion. Indeed, during recent years, a number of reports summarizing new research findings, including evidence suggesting the widespread occurrence of lateral gene transfer, cast doubt on the validity of bacterial evolutionary phylogeny based on rRNA trees. Gest emphasizes that rRNA sequences will probably prove to be useful eventually for identifying certain kinds of taxonomic relationships, but will not serve to provide an unambiguous evolutionary phylogeny of bacteria. Accordingly, he argues that changing the names of numerous well-known genera and species on the basis of rRNA sequences is premature and counterproductive to formulation of a logical, scientific scheme of bacterial relationships and classification.” “Gest's Postulates” (1999) relate to actual free-living bacteria, and refer to “virtual bacteria” reported to exist in natural sources as indicated by detection of 16S rRNA sequences (“virtuals” are sometimes referred to by the cognoscenti as “computer bacteroids”). The “Postulates” prescribe some penalties for investigators who publish only 16s rRNA sequences and fail to isolate corresponding live organisms within a reasonable length of time.

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

BackgroundDespite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.ResultsTo get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.ConclusionMethods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.

Lonepinella koalarum gen. nov., sp. nov., a New Tannin-Protein Complex Degrading Bacterium

The phylogeny of bacteria that degrade a tannin-protein complex (T-PC) isolated from the fecal biota of koala was investigated. All T-PC degrading bacteria were facultatively anaerobic Gram-negative rods, producing tannase, but negative for catalase and oxidase activities. The 16S rDNA sequence analyses of eight T-PC degrading strains representing biovars a, b, c, and d, revealed that the strains formed a phylogeneric cluster within the family Pasteurellaceae . Furthermore seven strains of biovar a, b, and c formed a 16S rDNA sub-cluster with similarity values in the range 97.6 to 99.8%. As the strains also exhibit a combination of chemotaxonomic and physiological properties not found in other members of the family Pasteurellaceae , it was concluded that the T-PC degrading isolates of biovar a, b, and c represent a new genus and species, for which the name Lonepinella koalarum gen. nov., sp. nov. is proposed.