An Assessment of Cumulative Classification

We present a method for building systematics when new knowledge is continuously accumulated. The resulting classification is self-correcting and improves itself by sorting new items as they are added to the material and studied. The formulation is based on Bayesian predictive probability distributions. A new item that has not yet been classified is assigned to the class that has maximal posterior probability or is made to form a group of its own. Such a cumulative classification depends on the order in which the items are classified. The introduction of an already classified training set considerably improves the repeatability of the method. As a case study we applied the method to a large data set for the Enterobacteriaceae. The resulting classifications corresponded well to the general structure of the prevailing taxonomy of Enterobacteriaceae.     

Taxonomy and systematics of pathogenic microorganisms

The modern state of the problem of the systematics of microorganisms is analyzed and the data on the taxonomy of bacteria belonging to the family Enterobacteriaceae are presented. The importance of studies on the taxonomy of microorganisms is emphasized. These studies play a vital role in the development of diagnostic preparations and techniques for the identification of infective agents, as well as in the realization of epidemiological surveillance. Much attention is given to the works of Soviet microbiologists, discussing such problems as the unification of the classification scheme of dysentery bacteria, the intraspecific taxonomy of Francisella tularensis, the systematic position of Allomonas and the antigenic scheme of Hafnia, included into Bergey's Determinative Bacteriology, edition IX (1984).     

New methods for the analysis of binarized BIOLOG GN data of Vibrio species: minimization of stochastic complexity and cumulative classification

We apply minimization of stochastic complexity and the closely related method of cumulative classification to analyse the extensively studied BIOLOG GN data of Vibrio spp. Minimization of stochastic complexity provides an objective tool of bacterial taxonomy as it produces classifications that are optimal from the point of view of information theory. We compare the outcome of our results with previously published classifications of the same data set. Our results both confirm earlier detected relationships between species and discover new ones.     

A new genomic taxonomy system for the Synechococcus collective

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.     

丛枝菌根真菌系统分类及群落研究技术进展

丛枝菌根真菌（AMF）是自然生态系统重要的组成部分,能与植物根系形成互惠共生体.传统的AMF分类主要依赖于对土壤无性孢子的形态鉴定,具有一定的局限性.近年来基于核酸分析的分子鉴定技术使AMF的分类更具科学性和准确性,补充和完善了基于孢子形态鉴定所建立的分类系统.AMF群落研究依赖于AMF的分类鉴定,主要包括孢子形态鉴定和分子生物学分析两类研究法.本文综述了AMF的分类系统和群落研究方法,着重介绍了近年来应用较多的AMF群落研究的分子生物学技术.作者认为,采取形态与分子相结合的办法将有助于推动AMF群落研究和AMF自然分类系统的建立和完善.     

Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria

In this paper, we compare the performance of two iterative clustering methods when applied to an extensive data set describing strains of the bacterial family Enterobacteriaceae. In both methods, the classification (i.e. the number of classes and the partitioning) is determined by minimizing stochastic complexity. The first method performs the minimization by repeated application of the generalized Lloyd algorithm (GLA). The second method uses an optimization technique known as local search (LS). The method modifies the current solution by making global changes to the class structure and it, then, performs local fine-tuning to find a local optimum. It is observed that if we fix the number of classes, the LS finds a classification with a lower stochastic complexity value than GLA. In addition, the variance of the solutions is much smaller for the LS due to its more systematic method of searching. Overall, the two algorithms produce similar classifications but they merge certain natural classes with microbiological relevance in different ways.     

Taxonomy of phytopathogenic viruses identified in the Russian far east

The work is devoted to a problem of study of the taxonomy phytopathogenic viruses of Far East. The performance to genera, species and strain of viruses identified in Far East region is briefly given. A genus Potyvirus in more detail is described, as the greatest number identified on Far East phytoviruses is included into structure of this genus. In the given article the classification phythopathogenic of Russian Far East is represented, for which basis the classification of viruses of the message of International Committee on the taxonomy of viruses (1995) is taken.     

Use of paper indicator discs for determining the minimal inhibitory concentration of antibiotics]

Sensitivity of clinical strains of Staphylococcus and some Enterobacteriaceae to a number of widely used antibiotics was compared simultaneously with the use of two methods, i. e. the agar diffusion method and the method of serial dilutions. Regularities in distribution of the staphylococcal strains according to their sensitivity to antibiotics, such as erythromycin, benzylpenicillin, levomycetin and others were also studied with respect to every year using indicator paper discs. Interrelation observed during the comparison of the microbial sensitivity with the use of the two assay methods provided elaboration of the criteria for classification of the strains as "resistant" or "sensitive". The differentiation boarder for these two groups was determined according to the principle of the assay error minimization. A necessity of using standard dry media for specification of individual characteristics of various drugs in estimation of the microbial sensitivity to them by the agar diffusion method is emphasized.     

近代鸟类分类与系统发育研究进展

简要综述了宏观和微观领域的鸟类分类学研究进展.宏观领域介绍了传统形态分类学、数值分类学和支序分类学,结合鸣声分析强调支序分类学的应用.微观领域介绍了Sibley分类系统和近年来出现的主要基于mtDNA的鸟类系统学研究.通过对大量研究工作的分析提出该领域今后应进行综合性研究.     

A protein taxonomy based on secondary structure.

Does a protein's secondary structure determine its three-dimensional fold? This question is tested directly by analyzing proteins of known structure and constructing a taxonomy based solely on secondary structure. The taxonomy is generated automatically, and it takes the form of a tree in which proteins with similar secondary structure occupy neighboring leaves. Our tree is largely in agreement with results from the structural classification of proteins (SCOP), a multidimensional classification based on homologous sequences, full three-dimensional structure, information about chemistry and evolution, and human judgment. Our findings suggest a simple mechanism of protein evolution.     

放线菌的分子分类

在放线菌分类学研究中,最初是根据形态特征、生理生化特征等表观分类学特征进行研究。随着分子生物学的飞速发展,放线菌的分类鉴定亦从传统的表型分类进入到各种基因型分类水平。分子分类在放线菌分类研究中起到越来越重要的作用,目前放线菌的分子分类研究主要包括:G Cmol%测定、DNA杂交、核酸结构分析以及DNA指纹图谱分析等方面。     

Enterobacter radicincitans sp. nov., a plant growth promoting species of the family Enterobacteriaceae

A plant growth promoting bacterial isolate (D5/23T) from the phyllosphere of winter wheat, able to fix atmospheric nitrogen and to produce auxines and cytokinins was investigated in a polyphasic taxonomy approach. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly indicated that the strain belonged to the family Enterobacteriaceae, most closely related to Enterobacter cloacae with 99.0% and Enterobacter dissolvens with 98.5% sequence similarity. Phylogenetic analysis derived from the sequence of the rpoB gene showed the highest sequence similarities to Enterobacter cowanii (93.0%) but supported the distinct position of strain D5/23T. The isolate produced a fatty acid pattern typical for members of the family Enterobacteriaceae. On the basis of the phylogenetic analyses, DNA-DNA hybridizations, and the unique physiological and biochemical characteristics, we propose that strain D5/23T represents a new species of the genus Enterobacter for which we propose the name Enterobacter radicincitans sp. nov.     

Numerical taxonomy: criticisms and critiques: Presidential address to the Systematics Association, November 1970

Some recent criticisms and critiques of numerical taxonomy are reviewed, together with some of its present shortcomings. It is pointed out that most of the problems are equally severe for orthodox taxonomy, and many of them can only be investigated by numerical techniques. The reasons for the general success of numerical methods in bacterial classification are discussed. Besides bringing deeper insights into taxonomy as a whole, numerical taxonomy is entering a new and heuristic phase, which includes potential applications to the study of evolution.     

Bayesian predictive identification and cumulative classification of bacteria

In this paper we give a mathematically precise formulation of an old idea in bacterial taxonomy, namely cumulative classification, where the taxonomy is continuously updated and possibly augmented as new strains are identified. Our formulation is based on Bayesian predictive probability distributions. The criterion for founding a new taxon is given a firm theoretical foundation based on prediction and it is given a clear-cut interpretation. We formulate an algorithm for cumulative classification and apply it to a large database of bacteria belonging to the family Enterobacteriaceae. The resulting taxonomy makes microbiological sense.     

Classification of weevils as a data-driven science: leaving opinion behind

Data and explicit taxonomic ranking criteria, which minimize taxonomic change, provide a scientific approach to modern taxonomy and classification. However, traditional practices of opinion-based taxonomy (i.e., mid-20^th century evolutionary systematics), which lack explicit ranking and naming criteria, are still in practice despite phylogenetic evidence. This paper discusses a recent proposed reclassification of weevils that elevates bark and ambrosia beetles (Scolytinae and Platypodinae) to the ranks of Family. We demonstrate that the proposed reclassification 1) is not supported by an evolutionary systematic justification because the apparently unique morphology of bark and ambrosia beetles is shared with other unrelated wood-boring weevil taxa; 2) introduces obvious paraphyly in weevil classification and hence violates good practices on maintaining an economy of taxonomic change; 3) is not supported by other taxonomic naming criteria, such as time banding. We recommend the abandonment of traditional practices of an opinion-based taxonomy, especially in light of available data and resulting phylogenies.     

醋酸菌多相分类研究进展

醋酸菌是一大群革兰氏染色阴性、绝对好氧的细菌的总称, 能将乙醇或糖类不完全氧化为有机酸。醋酸菌的分类在近30年经历了很大变化, 早期的分类系统主要以表型和生化特征为基础。如今, 大多采用结合表型、化学分类法和基因型数据的多相分类法对醋酸菌进行分类。本文综述了醋酸菌的多相分类研究进展, 主要介绍了醋酸菌的现行分类情况及表型分类、化学分类和基因分型等方法在醋酸菌分类中的应用。     

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.     

丛枝菌根真菌分类最新进展

近10a来,随着分子生物学技术在丛枝菌根(arbuscularmycorrhiza,AM)研究中的应用,AM真菌分类学得到迅速发展。重点介绍AM真菌的最新分类系统,并对其发展简史作一简单回顾。     

VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment

Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.     

Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.