Phylogenetic basis for a taxonomic dissection of the genus Clostridium

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.     

The conceptual basis for a new classification of the coccidia

At the joint meeting of the 8th International Coccidiosis Conference and the Annual Scientific Meeting of the Australian Society for Parasitology in Palm Cove, Australia, in July 2001, a Controversial Roundtable was held on 'New classification of coccidia'. The aim of this Roundtable was to stimulate and encourage discussion and debate on current classification schemes for the group of parasitic protozoa known as the eimeriid coccidia. In the past, such classifications have been based only on phenotypic characters such as morphology, ultrastructure, life cycles, and host specificity. However, over the past 10-15 years, molecular phylogenetic studies on taxa of the eimeriid coccidia have revealed that several of the families, subfamilies, and genera that have been erected based on non-molecular characters are paraphyletic. Therefore, this Roundtable was an important forum for initial discussions on how a new and more comprehensive classification of the eimeriid coccidia, which takes into consideration both phenotypic and molecular characters, can be devised. The stimulus came from invited speakers who gave introductions into selected areas of taxonomy and classification. Following these introductions, a more general discussion with the audience addressed potential steps that may be taken in future work. This review is the immediate outcome of the Roundtable. It describes advantages and disadvantages of the use of phenotypic or molecular characters as the base for taxonomic schemes for eimeriid coccidia. It gives specific examples for drawbacks of current classifications based only on phenotypic characters as well as potential pitfalls associated with the use of only molecular phylogenies. It addresses current controversies as well as rules of taxonomy and nomenclature relevant for the eimeriid coccidia. Finally, it recommends the establishment of an international group of scientists to meet on a regular basis, stimulate further discussions, and give direction on how the final goal, i.e. a proposal for a revised, and widely accepted, classification of the eimeriid coccidia, may be achieved.     

微孢子虫系统进化研究的变迁与展望

微孢子虫(Microsporidia)是一类专性细胞内寄生的单细胞真核生物,在科研、医疗、农业、商业等领域具有重要影响。由于其不具有某些典型的真核生物细胞结构,如线粒体、过氧化物酶体、高尔基体、鞭毛,曾将其归属于古真核生物谱系,认为其进化历程先于这些细胞器的起源,该假说也得到了一些生物化学和分子生物学研究证据的支持。然而,在最近十年里,通过更深入的研究,尤其是基于分子序列的系统进化分析,表明微孢子虫和真菌具有一定亲缘关系,并认为其结构的简约性恰好体现了微孢子虫营寄生生活的高度退化现象。目前对微孢子虫的系统进化仍存在各种不同意见,对其进化研究历史进行探讨有着重要意义。本文将按照时间顺序回顾微孢子虫进化分类研究过程中的各种研究成果,并讨论为什么微孢子虫独特的细胞和基因组特性会导致众多的学者在其进化分类问题上争执这么久。     

Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions

Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.     

Molecular phylogeny and taxonomic reconsideration of the subfamily Zapodinae (Rodentia: Dipodidae), with an emphasis on Chinese species

Although the subfamily Zapodinae (Rodentia, Dipodidae) contains only five species, the phylogeny and taxonomy of these species are still being disputed. First, whether Eozapus and Napaeozapus should be treated as independent genera or subgenera of Zapus has been argued for a long period. Second, the subspecific genetic differentiation of Chinese jumping mouse (Eozapus setchuanus) has not been studied in detail, neither from morphological nor molecular aspects. In this study, the phylogenetic relationship among all the five species of Zapodinae was reconstructed using DNA sequence data from the mitochondrial cytochrome b gene and the nuclear interphotoreceptor retinoid binding protein gene. Bayesian inference, maximum parsimony and maximum likelihood analyses were conducted. The results showed that two major clades could be recognized within Zapodinae. Eozapus setchuanus, is the species endemic to China, strongly formed a monophyletic clade. In the other clade, genus Zapus received significant support in all analyses to be the sister group of the genus Napaeozapus. By comparing genetic distances among these three genera, we conclude that both Eozapus and Napaeozapus should be considered as valid genera rather than subgenera of Zapus. Furthermore, we observed that the two subspecies of E. setchuanus did not form reciprocally monophyletic groups, thus the traditional taxonomy which divided E. setchuanus into two subspecies based on only one morphological character was questionable.     

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Background

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck.

Results

To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS – Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets.

Conclusions

RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0503-6) contains supplementary material, which is available to authorized users.     

西藏金丝野牦牛的遗传分类地位初步分析

在西藏羌塘国家级自然保护区发现有种群数量约200头的全身被毛为金色的野牦牛。为探究该种金丝野牦牛与普通野牦牛(Bos grunniens mutus)和家牦牛(Bos grunniens)的遗传差异,本研究通过分析金丝野牦牛线粒体DNA中的细胞色素b(Cyt b)和D-loop区基因序列差异,初步探讨了金丝野牦牛遗传分类地位。结果表明:金丝野牦牛的这两个基因片段的序列结构特征、长度、核苷酸组成与其他牦牛相似;金丝野牦牛与普通野牦牛的遗传距离最小,在系统树中,它们聚集为一支,说明金丝野牦牛与普通野牦牛亲缘关系最近;但金丝野牦牛与普通野牦牛的遗传距离较普通野牦牛个体间平均遗传距离大,加上毛色等形态区别,我们认为金丝野牦牛为野牦牛的一个亚种或者重要保护单元。但由于样本数量有限,仍需进一步深入研究确定。     

Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units

The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.     

Phylogeny and classification of the Asteroidea (Echinodermata)

Post-Palaeozoic asteroids share a large number of derived characters of the ambulacral column and the mouth frame, and constitute the crown group of the monophyletic group Asteroidea. This crown group is here called the Neoasteroidea (new subclass). The stem species of the crown group lived in the Permian or early Triassic and so the evolution of the asteroids parallels that of the echinoids. Character distribution within the Neoasteroidea, especially morphology of the skeleton, digestive system, larvae and tube feet, allows subdivision into four orders (Paxillosida, Notomyotida, Valvatida, Forcipulatida). The latter three orders possess the synapomorphy of suckered tube feet and are united as the Surculifera (new superorder); the Paxillosida are their primitive sister group. Palaeozoic asteroids represent the stem group of the class, and may be divided into plesions according to the order of appearance of synapomorphies with the crown group. Classification of Palaeozoic asteroids requires much further study. The appearance of new characters within the crown group asteroids, such as suckered tube feet, implies that these were absent in the stem group. The range of life-habits possible in Palaeozoic asteroids can thus be partly deduced from evidence provided by living asteroids. Palaeozoic asteroids are deduced to have lacked suckered tube feet and were presumably unable to evert the stomach; hence they were precluded from life on hard substrates and extraoral feeding on epifaunal organisms. It is suggested that they lived on soft substrates by deposit feeding, scavenging and predation on small benthos.     

A re-evaluation of taxonomic status of Montivipera (Squamata: Viperidae) from Iran using a DNA barcoding approach

Mitochondrial COI sequences were used to re-evaluate the taxonomic status of Montivipera from Iran including all of the known Iranian species. Considering the genetic distances among species, the topology of the phylogenetic trees and principles of species definition, the number of species within the genus Montivipera in Iran should be reduced from four to one species, Montivipera raddei, exhibiting several pretty color patterns. It looks as if superficial differences in morphology and particularly color pattern induced herpetologists in describing species such as Montivipera albicornuta, Montivipera latifii and Montivipera kuhrangica.     

The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium

The celC gene codifies for a cellulase that fulfils a very significant role in the infection process of clover by Rhizobium leguminosarum. This gene is located in the celABC operon present in the chromosome of strains representing R. leguminosarum, Rhizobium etli and Rhizobium radiobacter whose genomes have been completely sequenced. Nevertheless, the existence of this gene in other species of the genus Rhizobium had not been investigated to date. In this study, the celC gene was analysed for the first time in several species of this genus isolated from legume nodules and plant tumours, in order to compare the celC phylogeny to those of other chromosomal and plasmidic genes. The results obtained showed that phylogenies of celC and chromosomal genes, such as rrs, recA and atpD, were completely congruent, whereas no relation was found with symbiotic or virulence genes. Therefore, the suitability and usefulness of the celC gene to differentiate species of the genus Rhizobium, especially those with closely related rrs genes, was highlighted. Consequently, the taxonomic status of several strains of the genus Rhizobium with completely sequenced genomes is also discussed.     

Two misconceptions of phylogeny and classification

A recent contribution embodies the assumptions that organisms may be excluded from relationship with others on the basis of autopomorphy, and that its position in a classification is an inherent characteristic of an organism. Both of these assumptions are fallacious.     

Phylogenetic relationships among Southern Balkan Rutilus species inferred from cytochrome b sequence analysis: Micro-geographic resolution and taxonomic implications

The phylogenetic relationships and geographic distribution of Greek roaches (Rutilus spp.) were investigated by analyzing the complete mitochondrial cytochrome b gene sequence of 84 specimens collected from 15 southern Balkan lakes. Phylogenetic analysis revealed the existence of five highly divergent haplotype groups with mean pairwise sequence divergence between them ranging from 4.1 to 9%, namely at the level of values reported for different species. These five groups correspond to four species namely Rutilus rutilus, Rutilus prespensis, Rutilus panosi and Rutilus ylikiensis. On the other hand, the existence of two highly divergent haplotype groups, which are currently attributed to R. rutilus, suggests the re-examination of the current taxonomic status of this species.     

Seasonal variations in macrobenthic taxonomic diversity and the application of taxonomic distinctness indices in Bohai Bay,northern China

Taxonomic diversity indices have a number of desirable properties as indicators in the assessment of environmental quality, and have become an important measure in biodiversity studies. Macrobenthic taxonomic variations were studied in Bohai Bay, northern China, an area under threat from rapid human development. Four seasonal cruise datasets were collected between 2006 and 2007. Environmental conditions exhibited large fluctuations due to human development; nitrogen and phosphorus were the main environmental stressors. A total of 97 macrofauna taxa were identified belonging to 88 genera, 72 families, 36 orders, 14 classes, and nine phyla. Analysis of similarity indicated that there were significant assemblage differences across sampling stations as well as seasons. Four taxonomic indices, taxonomic diversity (Δ), taxonomic distinctness (Δ*), average taxonomic distinctness (Δ⁺), and variation in taxonomic distinctness (Λ⁺) were calculated using abundance data. Among the stations and seasons, there were greater variations in both Δ and Λ⁺ than in Δ* and Δ⁺. The funnel plot of Δ⁺ could identify disturbed stations to some extent, but was not always a strong indicator of disturbance. The Δ⁺ performance was better in autumn than in spring, but could not identify a disturbed station in autumn due to a low number of species. The efficiency of taxonomic distinctness may depend on taxa or the pollution indicators. Taxonomic distinctness indices can be effective at assessing environmental degradation when correctly applied; however, they are unsuitable for directly assessing environmental quality in a new area prior to efficiency testing.     

基于系统发生探讨绿带翠凤蝶和西番翠凤蝶的分类地位(英文)

绿带翠凤蝶和西番翠凤蝶的分类问题存在一定的争议。应用分子系统学方法对这一问题进行了研究。对6个不同地区的24个绿带翠凤蝶、2个地区的16个西番翠凤蝶个体的COI(579bp)和COII(655bp)基因测序,绿带翠凤蝶与西番翠凤蝶的遗传距离为0至0.6%,共获得了15个单倍型。结果显示这些单倍型不能形成各自独立的单系群,因此认为绿带翠凤蝶和西番翠凤蝶为近期分化的两个种。     

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

Background

With the advent of low cost, fast sequencing technologies metagenomic analyses are made possible. The large data volumes gathered by these techniques and the unpredictable diversity captured in them are still, however, a challenge for computational biology.

Results

In this paper we address the problem of rapid taxonomic assignment with small and adaptive data models (< 5 MB) and present the accelerated k-mer explorer (AKE). Acceleration in AKE’s taxonomic assignments is achieved by a special machine learning architecture, which is well suited to model data collections that are intrinsically hierarchical. We report classification accuracy reasonably well for ranks down to order, observed on a study on real world data (Acid Mine Drainage, Cow Rumen).

Conclusion

We show that the execution time of this approach is orders of magnitude shorter than competitive approaches and that accuracy is comparable. The tool is presented to the public as a web application (url: https://ani.cebitec.uni-bielefeld.de/ake/, username: bmc, password: bmcbioinfo).

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0384-0) contains supplementary material, which is available to authorized users.     

Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges

Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.