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At least 19 recordsLinked to original sources
PubMed2025

Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.

In metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets. However, public molecular databases (i.e., SILVA, EUKARYOME, BOLD) for most microbial metazoan phyla (nematodes, tardigrades, kinorhynchs, etc.) are sparsely populated, negatively impacting our ability to assign ecologically meaningful taxonomy to these understudied groups. Additionally, the choice of bioinformatics parameters and computational algorithms can further impact the accuracy of eDNA taxonomy assignments. Here, we use two in-silico datasets to show that taxonomy assignments using the 18S rRNA gene can be dramatically improved by curating Linnaean taxonomy strings associated with each reference sequence and closing phylogenetic gaps by improving taxon sampling. Using free-living nematodes as a case study, we applied two commonly used taxonomy assignment algorithms (BLAST+ and the QIIME2 Naïve Bayes classifier) across six iterations of the SILVA 138 reference database to evaluate the precision and accuracy of taxonomy assignments. The BLAST+ top hit with a 90% sequence similarity cutoff often returned the highest percentage of correctly assigned taxonomy at the genus level, and the QIIME2 Naïve Bayes classifier performed similarly well when paired with a reference database containing corrected taxonomy strings. Our results highlight the urgent need for phylogenetically-informed expansions of public reference databases (encompassing both genomes and common gene markers), focused on poorly sampled lineages which are now robustly recovered via eDNA metabarcoding approaches. Additional taxonomy curation efforts should be applied to popular reference databases such as SILVA, and taxon sampling could be rapidly improved by more frequent incorporation of newly published GenBank sequences linked to genus and/or species level identifications.

18S rRNA metabarcoding↗
PubMed2001

Two-step high resolution sequence-based HLA-DRB typing of exon 2 DNA with taxonomy-based sequence analysis allele assignment.

A two-step high resolution sequence-based DRB typing method was developed. The system needs only one polymerase chain reaction (PCR) to type all functional DRB alleles of a given individual. It uses a pair of generic PCR primers to amplify exon 2 DNA of all functional DRB genes and a first-step taxonomy-based sequence analysis (FSTBSA) method to assign allele groups after sequencing the PCR products with a generic primer. In the second step, group-specific primers are used to sequence the same PCR products and a taxonomy-based sequence analysis (TBSA) is used to assign alleles. Thus, both low and high resolution DRB typing can be done with PCR amplified exon 2 DNA from a single PCR reaction. Correct allele group assignment by FSTBSA was confirmed by sequencing the PCR products with group-specific primers and correctly assigned all 158 DNA samples including 34 samples pre-typed by PCR-sequence-specific primer or PCR-sequence-specific oligonucleotide probe. FSTBSA correctly assigned 116 heterozygous combinations of 81 DRB1-DRB3/4/5 haplotypes. Sixty-seven DRB1, 6 DRB3, 1 DRB4, and 3 DRB5 alleles were identified in this study. TBSA successfully resolved all heterozygous allele combinations including 31 heterozygous combinations of 33 alleles of DRB1*03, 08, 11, 12, 13, and 14 allele groups, and six heterozygous combinations of six DRB3 alleles.

Alleles↗
PubMed1999

High-resolution sequence typing of HLA-DQA1 and -DQB1 exon 2 DNA with taxonomy-based sequence analysis (TBSA) allele assignment.

High-resolution DNA sequencing of exon 2 of DQA1 and DQB1 genes that uses a taxonomy-based sequence analysis (TBSA) method to assign alleles was developed. The system uses fewer primers for polymerase chain reaction (PCR) amplification and sequencing than other methods and yields accurate DQA1 and DQB1 typing when either homozygous or heterozygous DNA samples are tested. The approach was initially corroborated by the correct typing of 10 blinded samples that had been previously typed by PCR using sequence-specific oligonucleotide probes (PCR-SSOP) or serology, and subsequently confirmed by sequencing of cloned PCR products. DNA from peripheral blood cell samples of 130 individuals enrolled in a case-control analysis of HLA determinants of abdominal aortic aneurysm were subsequently evaluated. Overall, 8 different DQA1 and 19 DQB1 alleles were identified. All 21 DQA1 heterozygous combinations and 45 of 49 DQB1 heterozygous combinations were successfully resolved with TBSA. The two pairs of heterozygous DQB1 combinations that were not unambiguously typed required sequence specific PCR amplification for correct allele identification. We conclude that the method provides precise analysis for HLA-DQ typing.

DNA↗
PubMed2001

The Comprehensive Microbial Resource.

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

Bacteria↗
PubMedDate not supplied

[The esterase activity of a pigmented bacterial group belonging to the Pseudomonas genus].

Bacteria belonging to the Pseudomonas genus and isolated from zonal soils in different geographical zones of the USSR as well as from the rhizosphere of cultivated and wild plants were tested for their esterase activity. The studied collection of cultures included 205 strains of different pigmented Pseudomonas species which, according to the conventional taxonomy, were assigned to the so-called "Pseudomonas fluorescens complex". As was shown in this study, many Pseudomonas species are potential producers of nonspecific esterases. P. maltophilia and P. geniculata synthesizing pyomelanin have the highest activity of esterase. The activity of esterase correlates with the formation of a melanin-like pigment in Pseudomonas cultures. It also correlates with the species to which a culture belongs, which makes it possible to use this property as an additional criterion for the identification of Pseudomonas species.

Esterases↗
PubMed2026

A novel transformer model of protein domains for viral taxonomy classification.

MOTIVATION: Viruses with carefully curated taxonomic assignments (such as those in the ICTV taxonomy) still represent only a small fraction of viruses identified through sequencing data from virome or microbiome projects. It is therefore critical to develop methods that can assign viruses at multiple taxonomic ranks, so that a virus deemed novel at a given rank may still be placed into a higher-level taxon. Sequence-similarity-based approaches can classify viruses that share substantial genomic similarity with known viruses (e.g. those belonging to the same species or genus); however, their performance drops significantly when applied to more divergent viruses. Recent deep learning models, such as ViTax, which utilize DNA language models, aim to address these limitations, but their performance also degrades when applied to novel viruses lacking genus-level similarity to known references. Proteins are more conserved than genomic sequences, and the multiple proteins encoded by a virus can be leveraged to reveal evolutionary relationships among viruses. RESULTS: We propose a new tool, D2T (Domain-to-Taxonomy), that leverages recent advances in protein language models to improve viral taxonomic assignment. D2T represents a virus as a sequence of protein domain tokens and learns a transformer-based model for taxonomic classification. Experiments on multiple closed-set and open-set datasets show that D2T excels at assigning higher-level taxonomic labels (family and above). Furthermore, by combining D2T with Kraken2, which performs well at the genus level, the hybrid method (K+D2T) achieves accurate viral taxonomic classification across multiple taxonomic ranks. AVAILABILITY AND IMPLEMENTATION: D2T is available as a GitHub repository at https://github.com/mgtools/D2T.

Viruses↗
PubMed2025

Comparison of whole-genome sequencing-based analysis methods for taxonomic classification of isolates unclassified by MALDI-TOF MS.

Taxonomic identification of clinical isolates is routinely achieved using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). If the species cannot be reliably identified, whole-genome sequencing can be applied. The aim of this study was to compare the results of approaches for taxonomic assignment for classification of isolates that are difficult to identify. Fifty-seven isolates were included in the study. The isolates were whole-genome sequenced and de novo assembled. Assembly-based classification was performed with the Genome Taxonomy Database Toolkit (GTDB-Tk), BLAST against 16S rRNA gene databases, the Type (Strain) Genome Server (TYGS), and ribosomal MLST (rMLST). Read-based classification was performed with MetaPhlAn4 and Kraken2. Thirty-two isolates were assigned to the same species with all four assembly-based classifiers, while the remaining 25 showed diverging assignments. When evaluating the results for the latter isolates, GTDB-Tk performed better than the other classifiers regarding which assignments were most likely correct. Of the read-based classifiers, MetaPhlAn4 performed better than Kraken2. Our evaluation identified GTDB-Tk to be the strongest tool for taxonomic assignment of isolates that are difficult to identify. Disagreements between classifiers are likely due to database limitations, wrongly assigned taxonomy, or unreliable 16S rRNA gene-based assignments.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗
PubMed1998

Taxonomic problems, seasonality and histopathology of Henneguya creplini (Myxosporea) infection of the pikeperch Stizostedion lucioperca in Lake Balaton.

Plasmodia of a Henneguya species measuring 70-900 microns and exhibiting season-dependent stages of development were detected throughout a three-year study on gill myxosporosis of Lake Balaton pikeperch (Stizostedion lucioperca (L.)). Sixty-five out of 160 fish (41%) examined in the period of study were infected by the parasite. Infection was the most prevalent (48%) among pikeperch specimens exceeding 40 cm in length. The highest prevalence of infection (58%) was recorded in 1995-1996 while the lowest (30%) in 1996-1997. The youngest plasmodia appeared in April, and started to develop within the capillaries of the secondary lamellae of the gill filaments. The round or ellipsoidal plasmodia which continued their gradual growth in the subsequent months of the year achieved a size of 800-900 microns by the late autumn months, but remained in intralamellar location throughout the developmental cycle. Mature spores developed in the plasmodia by the end of winter. On the basis of their shape and size, the spores were identified as Henneguya creplini (Gurley, 1894). However, because of the uncertain taxonomy of species assigned to the genus Henneguya the taxonomic position of the parasite requires further study. The host reaction consisting of epithelial proliferation and granulation tissue formation starts around the infected secondary lamella only after the maturation of spores and the disruption of plasmodia.

Animals↗
PubMed2005

Analyzing aphasia data in a multidimensional symptom space.

The utility of single-case vs. group studies has been debated in neuropsychology for many years. The purpose of the present study is to illustrate an alternative approach to group studies of aphasia, in which the same symptom dimensions that are commonly used to assign patients to classical taxonomies (fluency, naming, repetition, and comprehension) are used as independent and continuous predictors in a multivariate design, without assigning patients to syndromes. One hundred twenty-six Italian-speaking patients with aphasia were first classified into seven classic aphasia categories, based on fluency, naming, auditory comprehension, and repetition scales. There were two goals: (1) compare group analyses based on aphasia types with multivariate analyses that sidestep classification and treat aphasic symptoms as continuous variables; (2) present correlation-based outlier analyses that can be used to identify individuals who occupy unusual positions in the multivariate "symptom space." In the service of the first goal, group performance on an external validation measure (the Token Test) was assessed in three steps: analyses of variance based on aphasia type, regressions using the same cut-offs for fluency, naming, comprehension and repetition as independent but dichotomous predictors, and regressions using the same subscales as continuous predictors (with no cut-offs). More variance in Token Test performance was accounted for when symptoms were treated as continuous predictors than with the other two methods, though use of independent but dichotomous predictors accounted for more variance than aphasia taxonomies. Thus, if we by-pass classical taxonomies and treat patients as points in a multidimensional symptom space, better predictions are obtained. Outlier analyses show that group results depend on heterogeneity among patients, which can be used as a search tool to identify potentially interesting dissociations. Hence this multivariate group approach is complementary to and compatible with single-case methods.

Aphasia↗
PubMed2002

Lactic acid bacteria and proteomics: current knowledge and perspectives.

Lactic acid bacteria (LAB) are widely used in the agro-food industry. Some of the LAB also participate in the natural flora in humans and animals. We review here proteomic studies concerning LAB. Two methods of research can be distinguished. In the first one, a systematic mapping of proteins is attempted, which will be useful for taxonomy and to function assignment of proteins. The second one focuses particularly on proteins whose synthesis is induced by various environmental situations or stresses. However, both approaches are complementary and will give new insights for the use of bacteria in industry, in human health and in the struggle against bacterial pathogens. Interest in LAB is growing, showing thus an increasing concern of their rational use and one can foresee in the near future an increasing use of proteomics as well as genomics.

Bacterial Proteins↗
PubMed1985

Assignment of Actinomyces viscosus and Actinomyces naeslundii strains to numerical taxonomy clusters by immunofluorescence based on antifibril antisera.

A previous observation, using a few representative laboratory strains, that rabbit antisera raised against isolated surface fibrils might be useful in identifying Actinomyces viscosus and Actinomyces naeslundii isolates to their correct numerical taxonomy clusters was reexamined with a large culture collection, including clinical isolates from three different laboratories. Strains were first identified by a slower standard procedure, including agglutination with anti-whole-cell antisera, catalase test, and gas and paper chromatography as needed. Indirect immunofluorescence tests indicated that antisera raised against fibrils of strains representing the three principal taxonomic clusters could separate most strains into their correct clusters. The antisera were particularly successful in separating two taxonomically distinct groups of A. naeslundii, clusters 3 and 5, but could not separate A. viscosus belonging to the principal cluster (no. 1) and minor clusters (no. 2, 4, 6).

Actinomyces↗
PubMed2002

Aerobic and facultatively anaerobic cellulolytic bacteria from the gut of the termite Zootermopsis angusticollis.

AIMS: To demonstrate the occurrence of cellulolytic bacteria in the termite Zootermopsis angusticollis. METHODS AND RESULTS: Applying aerobic cultivation conditions we isolated 119 cellulolytic strains from the gut of Z. angusticollis, which were assigned to 23 groups of aerobic, facultatively anaerobic or microaerophilic cellulolytic bacteria. 16S rDNA restriction fragment pattern and partial 16S rDNA sequence analysis, as well as numerical taxonomy, were used for the assignment of the isolates. The Gram-positive bacteria of the actinomycetes branch could be assigned to the order Actinomycetales including the genera Cellulomonas/Oerskovia, Microbacterium and Kocuria. The Gram-positive bacteria from the order Bacillales belonged to the genera Bacillus, Brevibacillus and Paenibacillus. Isolates related to the genera Afipia, Agrobacterium/Rhizobium, Brucella/Ochrobactrum, Pseudomonas and Sphingomonas/Zymomonas from the alpha-proteobacteria and Spirosoma-like from the "Flexibacteriaceae" represented the Gram-negative bacteria. CONCLUSIONS: A cell titre of up to 10(7) cellulolytic bacteria per ml, determined for some isolates, indicated that they may play a role in cellulose digestion in the termite gut in addition to the cellulolytic flagellates and termite's own cellulases. SIGNIFICANCE AND IMPACT OF THE STUDY: The impact of bacteria on cellulose degradation in the termite gut has always been a matter of debate. In the present survey we investigated the aerobic and facultatively anaerobic cellulolytic bacteria in the termite gut.

Aerobiosis↗
PubMed1988

FR65814, a novel immunosuppressant isolated from a Penicillium strain. Taxonomy, fermentation, isolation, physico-chemical and biological characteristics and structure assignment.

FR65814, a novel immunosuppressant, was isolated from the cultured broth of Penicillium jensenii F-2883. The structure was assigned to be 5,6-dihydroxy-4-(1,2-epoxy-1,5-dimethyl-4-hexenyl)-1-oxaspiro++ +[2,5]octane by spectroscopic analyses. The compound suppressed the immune response at low concentration. In addition, a structually related component fumagillol, a known carcinolytic agent, was also isolated and found to show immunosuppressive activity.

Animals↗
PubMed2001

What are the baselines for protein fold recognition?

MOTIVATION: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein-ranging from the length of the sequence to a knowledge of its secondary structure-to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications? EXPERIMENTS PERFORMED: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure. RESULTS: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP-59% and the optimum secondary structure alignment method-32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system. CONCLUSIONS: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.

Computational Biology↗
PubMed2003

Mortality associated with birth defects: influence of successive disease classification revisions.

INTRODUCTION: The National Vital Statistics System is the fundamental source of mortality statistics in the United States. The cause-of-death classification which is used to assign medical terms to a standard taxonomy is revised periodically, and it is necessary to account for these changes when investigating trends. This paper presents birth defects mortality statistics and preliminary information on the most recent transition between revisions of the classification. METHODS: Descriptive statistics are presented using multiple cause and underlying cause counts, rankings of leading causes of death, infant mortality rates, and age-adjusted death rates. Comparability results are based upon records that have been coded using two separate classifications. RESULTS: Birth defects remain the leading cause of death for infants and among the leading causes for younger age groups. The trend for birth defect mortality shows that the risk of dying from birth defects decreased between 1950 and 2000. The effect of implementing successive revisions of the cause-of-death classification was relatively minor until the implementation of the most recent revision. Fewer records are assigned to birth defects in the latest revision than in the previous revision. DISCUSSION: Researchers investigating mortality trends related to birth defects need to be aware that the cause-of-death classification changes periodically. The effect of the changes between two successive classifications can be measured and explained.

Cause of Death↗
PubMed1999

Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification.

Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.

Amino Acid Sequence↗
PubMed2005

Classification and identification of bacteria using mass spectrometry-based proteomics.

Timely classification and identification of bacteria is of vital importance in many areas of public health. Mass spectrometry-based methods provide an attractive alternative to well-established microbiologic procedures. Mass spectrometry methods can be characterized by the relatively high speed of acquiring taxonomically relevant information. Gel-free mass spectrometry proteomics techniques allow for rapid fingerprinting of bacterial proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or, for high-throughput sequencing of peptides from protease-digested cellular proteins, using mass analysis of fragments from collision-induced dissociation of peptide ions. The latter technique uses database searching of product ion mass spectra. A database contains a comprehensive list of protein sequences translated from protein-encoding open reading frames found in bacterial genomes. The results of such searches allow the assignment of experimental peptide sequences to matching theoretical bacterial proteomes. Phylogenetic profiles of sequenced peptides are then used to create a matrix of sequence-to-bacterium assignments, which are analyzed using numerical taxonomy tools. The results thereof reveal the relatedness between bacteria, and allow the taxonomic position of an investigated strain to be inferred.

Animals↗
PubMed2006

Sequences, sequence clusters and bacterial species.

Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

Bacteria↗