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At least 19 recordsLinked to original sources
PubMed2026

Benchmarking Assembly-Free K-mer Methods for Species Identification in Complex Plant Groups: A Case Study in Populus.

Species identification in taxonomically complex plant groups is frequently limited by the inadequacy of organellar markers, whose phylogenetic signal is disrupted by cytonuclear discordance and chloroplast capture. Using the taxonomically complex genus Populus as a model, we evaluated an assembly-free k-mer workflow against a curated SNP reference benchmark. Whole-genome resequencing data from 235 Populus individuals were curated to a 202-individual, 34-species reference dataset in which all retained species are strictly monophyletic in a genome-wide SNP analysis. Independent maximum likelihood analyses further confirmed that the 31 non-hybrid backbone species each maintained high-support monophyly, while taxa of documented reticulate origin showed placement patterns consistent with their reticulate histories. ABBA-BABA D-statistics detected widespread residual allele sharing within the backbone, though the strongest signals did not correspond to the species pairs responsible for the few k-mer identification failures. Against this benchmark, complete plastomes showed limited resolution, recovering only 3.0% species monophyly and 71.1% nearest-neighbor assignment. The optimized k-mer workflow, operating directly on raw reads without assembly or alignment, recovered 91.2% species monophyly, 99.0% nearest-neighbor assignment, and 98.0% group-average assignment. K-mer length was the primary accuracy-controlling parameter, with k = 31 falling within a stable accuracy plateau. Distance-based metrics reached near-saturation at 0.2× sequencing depth, indicating that low-coverage genome skimming can support scalable nuclear genome-based identification with standard computational resources. K-mer distance heatmaps also flagged unusual genomic affinities in hybrid-origin and outlier samples, providing a rapid screen for subsequent population genomic analyses. These results support assembly-free k-mer distances as an efficient tool for reference-based species identification and sample screening in complex plant groups, with residual limitations concentrated near recently diverged species boundaries. Model-based phylogenomic, coalescent, and network analyses remain necessary for resolving deeper species relationships and detailed introgression histories.

Populus↗
PubMed1979

Fish species identification by thin layer isoelectric focusing.

Conventional electrophoretic techniques generally lack the resolution and reproducibility needed for the reliable identification of fish species. Variations in stabilizing media composition, sample application technique, separation time, applied voltage or current, and the analyst's skill all affect the protein pattern. Thin layer polyacrylamide gel isoelectric focusing (TLIEF), a high resolution protein separation technique, has been applied to the identification of fish species. Sarcoplasmic proteins are separated according to their isoelectric points in a stable, reproducible pH gradient. Protein patterns for 12 species of fish are compared in 4.0% polyacrylamide gels with pH 4.0--6.0 and pH 3.5--10 gradients. Similar patterns are shown in commercially prepared 5.0% polyacrylamide gels with pH 4.0--6.5 and pH 3.5--9.5 gradients (LKB PAG plates). The protein patterns are reproducible in each pH gradient and also correlate well between user-prepared and commercially prepared gels. The inherent high resolution and excellent reproducibility of TLIEF should allow the positive identification of fish species without the costly procedure of using known species as standards.

Animals↗
PubMed2026

Species identification, discovery, and biomonitoring: Strategic priorities for DNA barcoding in Europe, set in a global context.

The International Barcode of Life (iBOL) initiative is building a globally accessible DNA-based system for species identification and discovery. This paper outlines the mission and strategic priorities for the iBOL community in Europe (iBOL Europe), set in a global context. The mission of iBOL Europe is to produce, curate, and provide access to a complete DNA barcode reference library of European eukaryotic biodiversity, catalyzing species discovery and enabling comprehensive, harmonized species identification and biomonitoring, and supporting the global iBOL program. Immediate objectives include completing reference libraries for priority taxa, democratizing access to sequencing technologies, and strengthening a distributed community of practice. Key actions identified span five thematic areas: community building, sample collection and taxonomic verification, sequencing infrastructure, data management, and mainstreaming DNA-based approaches to meet societal needs. The strategy emphasizes integration with European research infrastructures to ensure long-term sustainability and resilience for biodiversity genomics in Europe.

DNA barcoding↗
PubMed2026

Plant species identification by genome skimming across the vascular plant tree of life.

Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution. We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL, matK, trnH-psbA and ITS resolved about half of species (49.3%), with six genera showing <&#x2009;25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k-mer analysis, achieving 66.8% species discrimination - an average gain of 17.5% over standard barcodes - while eliminating cases of extreme failure (<&#x2009;25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.

DNA Barcoding, Taxonomic↗
PubMed2026

PCR-based species identification tools for wireworms (Coleoptera: Elateridae) of economic importance in Canada.

BACKGROUND: Coexistence of pest and non-pest wireworms (Coleoptera: Elateridae) in agricultural fields makes species-level identification critical to determine when pest management measures are required. However, morphological identification of wireworms (larval stage of click beetles) is challenging, as larvae are difficult to distinguish based on morphological features and misidentifications are common. Here, we developed species-specific primers for 15 click beetle species to be used in PCR-based species-level identification for agricultural fields across Canada. RESULTS: Partial sequences of the gene regions cytochrome c oxidase I (COXI), 16S, 12S, 28S, 18S, internal transcribed spacer 2 (ITS2), cytochrome-b (CYTB), elongation factor 1 (EF1), ATP6/8, NADH dehydrogenase 1 (ND1), NADH dehydrogenase 2 (ND2), NADH dehydrogenase 3 (ND3), NADH dehydrogenase 4 (ND4), NADH dehydrogenase 5 (ND5) and NADH dehydrogenase 6 (ND6) were generated for elaterid species of interest. Of these gene regions, primers were designed on the mitochondrial gene regions COXI, CYTB and ND1 that had sufficient variation to discriminate among species and tested for species specificity using additional pest and non-pest species from the families Elateridae, Carabidae, Scarabidae and Silphidae. Specificity testing confirmed that all primer sets were species-specific. CONCLUSION: The novel primers designed in this study allow for PCR-based species identification of 15 economically important click beetle pest species in Canada. Further testing is needed to validate the assay for use outside of Canada. Accurate species-level identification will benefit pest management professionals by informing management decisions and reducing the use of insurance insecticide applications due to difficulties with identifications of wireworm pest species. &#xa9; 2026 His Majesty the King in Right of Canada and The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. Reproduced with the permission of the Minister of Agriculture and Agri-Food.

Animals↗
PubMedDate not supplied

The species identification of very old human blood-stains.

The efficiency of 5% ammonia as an extractant of proteins from human bloodstains has been compared with that of water. Ammonia was shown to be a better extractant of protein than water and this allows the species identification of human bloodstains up to four years' old using conventional electrophoretic techniques.

Ammonia↗
PubMed1978

Species identification of coagulase-negative staphylococci from urinary tract isolates.

A new scheme for identification of coagulase-negative staphylococci was applied to 138 consecutive urinary isolates of coagulase-negative staphylococci. The most common species were Staphylococcus epidermidis (53%), S. hominis (12%), and S. haemolyticus (10%). S. saprophyticus comprised only 5%. The disk method for antibiotic susceptibility for all species grouped together disclosed resistance most commonly to penicillin (35%), tetracycline (33%), methicillin (27%), and sulfonamide (24%). This pattern was also seen specifically with S. epidermidis. Further studies are needed to determine the incidence of species-specific antibiotic resistance and species-specific infection by site. This may be of particular interest in those patients with nosocomial infections due to coagulase-negative staphylococci.

Anti-Bacterial Agents↗
PubMed1977

[Experiences with the API 20A system in routine species identification of anaerobes (author's transl)].

The API 20A System was tested in three modifications: a) The microtubes were inoculated with the API anaerobe basal medium, filled up completely with sterile mineral oil and incubated aerobically. b) The test strips were inoculated with the basal medium and incubated in an anaerobic chamber. c) The strips were inoculated with a modified Viande-Levure medium containing Tween 80, vitamin K3 and hemin. The microtubes were covered with sterile mineral oil and incubated in an anaerobic chamber. Each procedure was compared with the conventional method (PRAS) of the Virginia Polytechnic Institute. The overall agreement between the three modifications of the API System and the conventional method was 83.2, 91.7, and 98.5% related to the number of tests performed. The advantage of the modified medium was also demonstrated by measuring the growth rate of some anaerobes in thioglycolate broth, API basal medium and VL-medium, modified as mentioned above, nephelometrically. So the micromethod is more accurate and reliable when inoculated with an improved medium.

Anaerobiosis↗
PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗
PubMed2026

Comparative evaluation of molecular technologies for the identification of prevalent non-tuberculous mycobacteria in pulmonary infections: a systematic review and meta-analysis.

BACKGROUND: The increasing prevalence of non-tuberculous mycobacteria pulmonary disease (NTM PD) is a burden to public health. Successful management of NTM PD critically depends on accurate species identification and reliable drug susceptibility testing to guide appropriate antibiotic therapy. Emerging molecular technologies offer rapid diagnostic solutions compared to conventional methods, but their performance varies. This study aims to provide a comprehensive evaluation of current molecular techniques for NTM identification and to present a global antibiotic resistance profile. METHODS: A systematic literature search was conducted in PubMed and Web of Science for studies published between 2005 and 2024. Studies applying molecular methods for NTM identification and resistance detection in humans were included. Data on study characteristics, diagnostic methods, sample types, sample sizes, identification sensitivity, and drug susceptibility results were extracted. Meta-analysis was performed using R with the meta4diag package. The quality of included studies was assessed using the QUADAS-2 tool. RESULTS: The analysis included 49 studies on NTM identification and 33 studies on antibiotic resistance. For species identification, all evaluated molecular technologies (MALDI-TOF MS, PCR-based methods, Sequencing, DNA chip, and DNA strip) demonstrated high pooled sensitivities (>0.92). Subgroup analysis revealed that sample type significantly affected performance for MALDI-TOF MS. Preliminary analysis of antibiotic resistance rates revealed varying patterns. For slowly growing mycobacteria, a significantly high Ethambutol resistance rate was observed in M. avium (69.20%). Among rapidly growing mycobacteria, resistance to Imipenem was notable (54.22%), and Clarithromycin resistance varied significantly within the Mycobacterium abscessus complex. CONCLUSION: Emerging molecular technologies have revolutionized the methodology for NTM identification with excellent performance. However, their performance can be influenced by sample type, particularly for MALDI-TOF MS. The alarming and heterogeneous antibiotic resistance patterns also highlight the critical need for rapid and accurate species identification and drug susceptibility testing to inform effective therapeutic strategies. Key messagesMolecular technologies demonstrate high accuracy for NTM identification.Antibiotic resistance is a serious concern with variations among NTM species and subspecies.Rapid and accurate species identification and drug susceptibility testing are crucial for guiding effective clinical management of NTM PD.

Humans↗
PubMed2026

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.

BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results. METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus. FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%. INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation. FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.

Humans↗
PubMed2026

SSR marker development for analysis of the genetic diversity and identification of species and infraspecific ranks in the genus Phyllostachys.

Bamboo plants possess important ecological, economic, and cultural values. However, it is difficult to accurately identify them on the basis of their morphological traits alone. Here, based on the whole-genome data of moso bamboo (Phyllostachys edulis) and its 20 forms, we conducted preliminary identification and comparative analyses of simple sequence repeats (SSRs) to develop molecular markers. In total, 3,835,632 SSR loci were identified from 31,537.81&#xa0;Mb of genomic sequences, among which dinucleotide SSRs were the most abundant. Most SSRs were located in intergenic regions, whereas relatively fewer were in genic regions. In addition, we found that SSR-containing genes involved in plant hormone signal transduction may be associated with the morphogenesis of moso bamboo, which was speculated to be related to differential gene expression patterns among different forms. Furthermore, 206 SSR primer pairs with polymorphisms were obtained to analyse the genetic diversity of moso bamboo and its forms, which exhibited moderate polymorphism. The proportion of genetic variation among species within the genus Phyllostachys was 58%, while that within species was 42%. Moso bamboo and its 20 forms had relatively close genetic relationships and low genetic differentiation, while 20 species of the genus Phyllostachys were clustered into three groups with distinct levels of genetic diversity. Finally, DNA fingerprints and molecular identity cards were constructed for 20 moso bamboo forms and 20 species of the genus Phyllostachys using core SSR markers. These results provide novel SSR markers for bamboo identification, germplasm conservation, and molecular marker-assisted breeding.

Microsatellite Repeats↗
PubMed2026

SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.

Identification of unique and shared genomic regions between organisms has substantial translational potential for the development of marker-based diagnostic assays and sequence homology-driven taxonomic classification. An automated pipeline capable of performing genome comparisons at both the intra- and inter-species levels with minimal computational requirements can significantly advance genome-driven translational research. Species-specific genomic regions are particularly valuable for sequence-based species identification and for developing DNA amplification- or hybridization-based diagnostic assays. Here, we present SURE-Pipe, an automated and flexible pipeline for genome comparison and extraction of unique and shared genomic regions (https://github.com/BPaul-bioinfoLAB/SURE-Pipe). Benchmarking of this pipeline using simulated datasets demonstrated high accuracy for shared and unique region identification. Using the pairwise genome comparison module, six genome pairs from diverse microorganisms were analysed, and identified the unique and shared regions. In addition, the multigenome comparison module was applied to 96 genomes representing 24 Bacillus species and identified species-specific genomic regions. These regions were highly conserved among four strains of a species (>98% sequence identity) and exhibit little to no similarity with other species. Species-specific primers designed for all 24 Bacillus species showed no off-target amplification in in-silico polymerase chain reaction analysis, indicating their specificity. Overall, SURE-Pipe provides a robust and multipurpose framework for comparative genomics, and the outcomes can be used for species identification and the development of genome-based diagnostic approaches.

Genome, Bacterial↗
PubMed1979

Identification of species of Candida, Cryptococcus, and Torulopsis by gas-liquid chromatography.

Gas-liquid chromatography was used to identify species of Candida, Cryptococcus, and Torulopsis by fatty-acid analysis of the whole-cell hydrolysate. Candida albicans characteristically revealed 2-OH C14:0 and C19:0 (chain length:number of double bonds); these were absent in other organisms. Candida curvata was characterized by a ratio of C16:1 to C16:0 of greater than 1.0. Candida guilliermondii contained C10:0, and Candida tropicalis had no C12:0, these features were used for their identification. Cryptococcus was characterized by the absence of C16:1. Torulopsis was characterized by a C16:1 to C16:0 ratio of greater than 10 accompanied by the presence of one unidentified fatty acid. These data suggested that certain Candida, Cryptococcus, and Torulopsis (the clinically important yeast-like organisms) may be identified by gas-liquid chromatography.

Candida↗
PubMed1979

Identification of species in cooked crabmeat by thin layer isoelectric focusing.

Thin layer polyacrylamide gel isoelectric focusing (TLIEF) is described for characterizing the species-specific, heat-denatured proteins of 8 species of crab: red (Geryon quinquedens), rock (Cancer irroratus), Jonah (Cancer borealis), blue (Callinectes sapidus), king (Paralithodes camtschatica), snow (Chionoectes spp.), European edible (Cancer pagurus), and dungeness (Cancer magister). Protein pattern differences are shown not only among species, but also between 2 modes of heat processing of the crabmeat. Individual variation within the species as to sex, size and maturity, length of frozen storage, and body parts chosen for sampling do not alter the species banding pattern. The reproducible species-specific fingerprint obviates the need to analyze authenticated samples simultaneously with the unknown crabmeat.

Animals↗