Taxonomic Methods Research Articles

Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.

Metagenomic long-read sequencing is gaining popularity for various applications, including pathogen detection and microbiome studies. To analyze the large data created in those studies, software tools need to taxonomically classify the sequenced molecules and estimate the relative abundances of organisms in the sequenced sample. Because of the exponential growth of reference genome databases, the current taxonomic classification methods have large computational requirements. This issue motivated us to develop a new data structure for fast and memory-efficient querying of long reads. Here, we present Taxor as a new tool for long-read metagenomic classification using a hierarchical interleaved XOR filter data structure for indexing and querying large reference genome sets. Taxor implements several k-mer-based approaches, such as syncmers, for pseudoalignment to classify reads and an expectation-maximization algorithm for metagenomic profiling. Our results show that Taxor outperforms state-of-the-art tools regarding precision while having a similar recall for long-read taxonomic classification. Most notably, Taxor reduces the memory requirements and index size by >50% and is among the fastest tools regarding query times. This enables real-time metagenomics analysis with large reference databases on a small laptop in the field.

Trends and Implementation of Electric Vehicle Ecosystem in Indonesia: A Literature Study

This research discusses the implementation of the electric vehicle ecosystem in Indonesia as one of the steps to support the goals stated in the Paris Agreement, namely achieving net zero emissions (NZE) by 2060. Indonesia is one of the countries that implements electric vehicles to achieve NZE. However, Indonesia's technology is not yet established for producing electric vehicles and distributing them to the global market. Therefore, this research was motivated to look at 20 sources of literature that have discussed cooperative relations in the Indonesian automotive industry sector with electric vehicle-producing countries. This research maps this literature using a taxonomy method in three main topics, namely (1) the development of the transportation and automotive sector in Indonesia, (2) China, South Korea, and Japan as cooperation partners in the electric vehicle industry, (3) the readiness of electric vehicle ecosystem implementation in Indonesia. This research also includes the explanation of national interest theory to see the perspective of international relations in the purpose of the Indonesia government in achieving electric vehicle ecosystem.

Financial Inclusion Index and its Determinants among Asian Countries

The study assesses financial inclusion level and its determinants across 30 Asian countries from 2010 to 2020 using the Wroclaw taxonomy method (WTM). A comparative analysis of financial inclusion indexes was conducted, and a panel fixed-effect model was employed to explore influencing factors. Findings revealed high financial inclusion levels in China, Israel, Japan, Singapore, and South Korea, contrasting with low levels in Azerbaijan, Bangladesh, Kyrgyz, Pakistan, Tajikistan, and Timor-Leste. Fourteen countries ranked in the high-middle category, with six in the low category, and only four achieved high financial inclusion in 2020. GDP and bank credit positively impact financial inclusion, while broad money, population, and density contribute positively but insignificantly. Conversely, literacy rate, inflation rate, employment, female ratio, rural ratio, and internet access showed negative effects on financial inclusion

Mapping sustainability: A comparative analysis proposal across EU countries and regions

This paper addresses the need to understand the structure of sustainability change in the face of the unpredictability of modern civilization. The aim of the paper is to examine the structure of sustainability change in relation to smaller spatial units such as the regions of the European Union and to compare these results with those achieved at the country level. For this purpose, the sustainable development indicators available in the Eurostat database were analyzed. Studies published to date have tended to focus on the performance of national economies or selected regions. In this article, the available data on regions are also analyzed. The study aims to compare the level of sustainable development achieved at the level of EU countries and regions located within them. Methodologically, the study uses advanced methods of comparative analysis, and the synthesis of the data enables the construction of a synthetic measure using taxonomic methods, facilitating the classification of EU countries and regions into clusters. The results highlight significant divergences in sustainability achievements between EU countries and regions. The study reveals the importance of studying sustainable development in smaller geographical cross-sections. The results highlight the need to expand access to data at the regional level (sustainability indicators) to facilitate more comprehensive analyses and inform targeted policy interventions. Looking to the future, the study recommends further research into the inter-linkages between sustainability and other critical areas in EU regions, such as innovation and competitiveness.

The Analyze About Brief Training of Basic Introductory Speech with Affective Taxonomy Method for English Public Speaking at SMK Giki Surabaya

The Analyze About Brief Training of Basic Introductory Speech with Affective Taxonomy Method for English Public Speaking at SMK Giki Surabaya

Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection

Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification.Key points• Forty million sequences are a cost-efficient solution for microbiota profiling• Fifty million sequences allow low-abundance species detection• Twenty million sequences are recommended for ARG identificationGraphical

Streptococcus hohhotensis sp. nov., isolated from the breast milk of a healthy woman.

Human breast milk contains lactic acid bacteria (LAB), which have an important influence on the composition of the intestinal microbia of infants. In this study, one strain of an α-hemolytic species of the genus Streptococcus, IMAU99199T, isolated from the breast milk of a healthy nursing mother in Hohhot city PR China, was studied to characterise its taxonomic status using phenotypic and molecular taxonomic methods. The results indicated that it represented a member of the mitis-suis clade, pneumoniae subclade of the genus Streptococcus. It is a Gram-stain-positive, catalase-negative and oxidase-negative bacterium, and the cells are globular, paired or arranged in short chains. The results of a phylogenetic analysis of its 16S rRNA gene and two housekeeping genes (gyrB and rpoB) placed it in the genus Streptococcus. A phylogenetic tree based on 135 single-copy genes sequences indicated that IMAU99199T formed a closely related branch well separated from 'Streptococcus humanilactis' IMAU99125, 'Streptococcus bouchesdurhonensis' Marseille Q6994, Streptococcus mitis NCTC 12261T, 'Streptococcus vulneris' DM3B3, Streptococcus toyakuensis TP1632T, Streptococcus pseudopneumoniae ATCC BAA-960T and Streptococcus pneumoniae NCTC 7465T. IMAU99199T and 'S. humanilactis' IMAU99125 had the highest average nucleotide identity (93.7 %) and digital DNA-DNA hybridisation (55.3 %) values, which were below the accepted thresholds for novel species. The DNA G+C content of the draft genome of IMAU99199T was 39.8 %. The main cellular fatty acids components of IMAU99199T were C16 : 0 and C16 : 1ω7. It grew at a temperature range of 25-45 °C (the optimum growth temperature was 37 °C) and a pH range of 5.0-8.0 (the optimum growth pH was 7.0). These data indicate that strain IMAU99199T represents a novel species in the genus Streptococcus, for which the name Streptococcus hohhotensis sp. nov. is proposed. The type strain is IMAU99199T (=GDMCC 1.1874T=KCTC 21155T).

Endoparasitic helminth fauna and diet of Geophagus sveni (Pisces) in Upper Paraná River basin.

In freshwater ecosystems, parasite infection patterns are influenced by factors including spatial-temporal variations, host diet, and habitat. Fish often change diets, affecting their parasite communities. This study focused on non-native host fish Geophagus sveni, aiming to characterize diet and endoparasitic helminth fauna patterns in the invaded area, investigating spatial and seasonal possible differences of endoparasite infections and correlating with host diet, in São José dos Dourados River and Tietê River areas. The host fish were collected in these areas during the dry and rainy season using gillnets. The endoparasites were collected and preserved in alcohol and identified using taxonomic methods, and stomach contents were examined for diet analysis. Parasitism descriptors were calculated and evaluated spatially and seasonally by ANOVA and the Kruskal-Wallis tests. PERMANOVA assessed G. sveni diet differences, and RDA correlated the endohelminth abundance with the host diet. Two endoparasites were recorded: metacercariae of Austrodiplostomum compactum (Trematoda) and larvae and adults of Raphidascaris (Sprentascaris) lanfrediae (Nematoda). Spatial differences were observed for the mean abundance and prevalence of R. (S.) lanfrediae and A. compactum prevalence. Seasonal variations of parasitic descriptors occurred for the nematode in the Tietê River area. The detritus and aquatic insects were the most consumed items by G. sveni. Detritus consumption positively correlates with nematode abundance. The findings indicate that factors such as artificial channels and rainfall, which can influence resource availability, may affect the fish's diet and potentially influence the structure of its endoparasite community. The study emphasizes the importance of understanding trophic chain-transmitted parasites and calls for further research in Neotropical environments.

Cluster methods in function better selection

Cluster analysis methods, also known as taxonomic methods, are intended for grouping objects and subjects according to certain characteristics, attributes and properties. Cluster analysis looks at relevant objects and attributes, classifying them into two or more independent groups. Cluster analysis supplemented with discriminant analysis is used in confirmatory and fundamental research. In numerous statistical-methodological procedures, these methods are applied when setting up and testing various hypotheses. Grouping methods are particularly useful in the process of different selections with the aim of forming coherent groups, which may or may not necessarily be statistically different. There are several models of clustering (grouping), always with one goal, which is greater proximity (similarity) of an entity belonging to a group compared to an entity belonging to another group. Two basic grouping models are recognizable, Hierarchical and Non-Hierarchical. Both models have the same goal, which is the formation of several independent homogeneous groups from one common group of entities. The hierarchical approach does not define the number of clusters in advance (a priori), in contrast to the Non-Hierarchical Model which defines in advance number of clusters. The grouping model is chosen depending on the specific problem and the set goal of grouping. In the process, several different models are often applied, and then one is chosen as in this research. It is important to point out that the theoretical number of clusters (groups) is often not realistically applicable in practice. Using the example of this research, it was proven that the first grouping was not a good solution. Through the subsequent, second and third iteration, as well as the application of additional discriminative methods, three optimal clusters were determined in the population of girls and boys. Satisfactory optimal grouping was obtained on the basis of gender criteria and achieved results on psycho-motor tests.

Comparison of the density and composition of bacteria and fungi in the air of anoxic and aeration tanks in the wastewater treatment plant

The bioaerosols from the wastewater treatment plant can be propagated into the air, affecting the health of residents, animals, and plants around the area. This study was conducted to evaluate the density and composition of bioaerosols (bacteria and fungi) in anoxic and aeration tanks of a domestic wastewater treatment plant. Bioaerosol samples were taken by the active method with SKC Biostage. The agar dishes were placed at a height of 1.5 m above the ground. After sample collection, the dishes were incubated at 37 ±1 °C for 24h-48h for bacteria and at 25 ±1 °C for 72h-120h for fungi. Then, these microorganisms were identified by 16S rRNA (16S Metabarcoding) method for bacteria and taxonomy method for fungi. The results showed that the density of bacteria and mold in the anoxic tank ranged from 233.2 ±7.8 to 339.2 ±13.9 CFU/m3 and 91.8 ±3.2 to 197.9 ±10.1 CFU/m3, respectively. Meanwhile, bacterial and mold densities of aeration tank ranged from 275.6 ±10.4 to 424.0 ±17.3 CFU/m3 and 176.7 ±5.8 to 254.4 ±12.1 CFU/m3, respectively. The density of bacteria and mold in the aeration tank is higher than in the anoxic tank. On the other hand, the 16S Metabarcoding analysis for the microbial diversity detects more than 100 species in two tanks, the predominant bacterial species are: Bacillus megaterium (B. megaterium), Bacillus cereus (B. cereus), Staphylococcus sciuri (S. sciuri) and two common fungi Aspergillus tamarii (A. tamarii), and Penicillium rubers (P. rubers). This preliminary survey in Viet Nam reveals the existence and diversity of bioaerosols in the air from the biological treatment tanks of the wastewater treatment plant.

Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.

Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.

Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme called run-block compression. Run-block compression achieves sublinear space complexity and is effective at compressing diverse microbial databases like RefSeq while supporting fast rank queries. Combining this compression method with other strategies for compacting the Ferragina-Manzini (FM) index, Centrifuger reduces the memory footprint by half compared to other FM-index-based approaches. Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.

An integrative taxonomic study on needlefishes (Belonidae) unveils two new species within the genus Ablennes from the Indian Ocean

The needlefish genus Ablennes remains monotypic, characterized by the globally distributed flat needlefish known as Ablennes hians. Their taxonomy has been mired with ambiguities due to the greater-than-average morphological variations observed in samples from different regions. Utilizing integrated taxonomic methods relying on mitochondrial molecular markers, it was revealed that the species initially perceived as a single entity is, in fact, a complex comprising at least three different species. In this context, we introduce two new species: Ablennes joseberchmansis sp. nov. and Ablennes gracalii sp. nov., They are morphologically distinct: in view of the morphometry and meristic characteristics. A. joseberchmansis sp. nov. and A. gracalii sp. nov. display distinct differentiation characteristics from A. hians in terms of dorsal fin, nostril position, dorsal fin origin, vertebrae count, scale counts, head length, eye diameter, interorbital width, maxilla length, dorsal ray height, depth at pelvic origin, lower lobe of the caudal fin, and caudal peduncle depthcaudal peduncle depth. These variations highlight their unique morphological traits and aid in their differentiation within the genus Ablennes. We assessed genetic relationships using a Maximum likelihood (ML) phylogenetic tree, revealing three distinct clades of morphological differences in Ablennes specimens from different morphological groups. The genetic variation, as represented by Kimura 2 parameter (K2P) distances, within the three Ablennes species spans from 6.5% to 9.4%. More specifically, we observed a 7.5% genetic difference between A. hians and A. joseberchmansis sp. nov., and a 6.5% distinction between A. hians and A. gracalii sp. nov. The interspecies divergence between the two newly identified species measured at 9.4%. These findings, which showcase the genetic distinctions among the three morphologically distinct Ablennes specimens, provide strong confirmation for the existence of three separate species within the Ablennes genus of needlefish in the Indian Ocean.

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'.

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.

The Main Directions of State Policy in Ensuring Technological Sovereignty

An analysis of the reforms in the scientific and technological complex and higher education system in Russia shows that the tasks assigned have been successfully achieved. However, in current conditions, the need for a new state-led scientific and technical strategy is evident. The main goals are to achieve technological sovereignty and transition the economy into a full cycle of innovation. The goal of this article is to identify new objectives and priorities for scientific and technological advancement to ensure technological sovereignty. Descriptive, comparative, and taxonomical methods are employed in the analysis. The paper identifies the main areas of government policy aimed at achieving technological sovereignty in Russia, and this constitutes the main finding. Additionally, it is essential to develop new objectives and strategies for scientific and technological growth. In fact, the new scientific and technological policy should include the following issues: organizing scientific research, developing innovative territories, integrating science and education, conducting scientific diplomacy, providing resource and legislative support, and measuring the effectiveness of the scientific-technological complex.

Miara stabilności w wyborze liczby grup w taksonomii zagregowanej z zastosowaniem analizy spektralnej i metody propagacji podobieństwa

Since the 1990s, the aggregate approach and the stability of grouping methods have been concepts frequently discussed in the field of taxonomy. So far, they have been considered separately, but recently, there has been a postulate in the literature to combine these two concepts in the form of the PAC (proportion of ambiguously clustered pairs) stability measure, which can be used in the aggregate approach to taxonomy and which is intended to serve as a criterion for selecting an optimal number of groups. The aim of the research presented in this article is to compare the results of the selection of the optimal number of groups in aggregate taxonomy on the example of the attainment of three Sustainable Development Goals (SDGs) by EU countries. The PAC measure and selected classic indices, namely the Caliński-Harabasz, the Dunn and the Davies-Bouldin indices were applied for this purpose. The affinity propagation method and spectral clustering served as base methods in the aggregate approach. The study used Eurostat data for 2019. The obtained results demonstrate that both the choice of the criterion for determining the number of groups and the choice of the base method in aggregate taxonomy have an influence on the final decision on how to determine the number of groups. Regardless of whether the affinity propagation method or spectral taxonomy with classic indices was used, or whether these methods were used as base ones in the aggregate approach and the number of groups was selected using the PAC measure, the differences between the indicated numbers of groups were very large.

Morphometrics and Truss-networking distances among three species of croaker (Johnius borneensis, Johnius argentatus and Johnius belangerii) from Bangladesh coast of the Bay of Bengal

Morphometric features are efficiently used for the differentiation of species and long-term management of fish populations. Truss analysis is a frequently used taxonomic method as well as a stock identification tool to dissimilitude the morphologically similar species. Using landmark-based truss networking techniques following 18 morphometric lengths, 10 meristic counts, and 23 truss-network distance, the morphological variation of three croaker species viz. Johnius borneensis, Johnius argentatus, and Johnius belangerii were examined from Bangladesh coast. Data were analyzed and visualized through univariate ANOVA, canonical discriminate function analysis (DFA), and principal component analysis (PCA). Results found that the first DFA was responsible for 80.6% & 81.1%, whereas the second DFA was responsible for 19.4% & 18.9% variations among three species for the morphometric and truss-distances, respectively. In addition, 14 out of 18 morphometric and 12 out of 23 truss-network measurements were significantly different (p < 0.05) among means of three species. 1st PCA found 70.76% & 64.49% explained variations and 2nd PCA displayed 12.8% & 11.5% explained variations respectively for morphometric and truss distances. The findings of the study demonstrates that J. borneensis and J. belangerii are highly morphologically similar and J. argentatus is completely distinct which might be due to their physiological and genetic variations. The present study might be helpful in differentiating species and managing existing stocks of marine fish. Further studies regarding the molecular characterization of the Cytochrome c oxidase subunit I (COI) gene could confirm the genetic variations among these species. Bangladesh J. Zool. 51(3): 233-251, 2023

Mapping the Literature on the Relationship between Indonesia and Chile as Non-Traditional Partners

Indonesia and Chile formed a comprehensive trade cooperation called the Indonesia-Chile Comprehensive Economic Partnership Agreement (IC-CEPA). Empirically, the relationship between Indonesia and Chile is not strong, so it is interesting to see how are the dynamics of the relationship between the two countries which are non-traditional partners but established comprehensive trade cooperation. Therefore, this literature review found 25 literatures that have discussed the dynamics of the relationship between Indonesia and Chile. This literature review maps the literature using the taxonomy method into three main topics, namely (1) the historical relationship between Indonesia and Chile, (2) the political relationship between Indonesia and Chile, (3) the economic relationship between Indonesia and Chile. This literature review found that the relationship between Indonesia and Chile in various fields shows a fluctuating trend because they still focus on traditional partners, the relationship between the two countries is pragmatic, lack of political will, and lack of information about each other's characteristics.

Quantitative integrative taxonomy informs species delimitation in Teloschistaceae (lichenized Ascomycota): the genus Wetmoreana as a case study

The genus Wetmoreana was studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus Fulgogasparrea is synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthii comb. nov., W. bahiensis sp. nov., W. brachyloba comb. nov., W. brouardii, W. chapadensis comb. nov., W. circumlobata sp. nov., W. decipioides, W. intensa comb. nov., W. ochraceofulva comb. nov., W. rubra sp. nov., W. sliwae sp. nov., W. sliwae ssp. subparviloba subsp. nov., W. subnitida comb. nov., W. texana, and W. variegata sp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthii and W. intensa, are transferred to Wetmoreana without additional analysis but based on previous studies. The W. brouardii and W. ochraceofulva species complexes are discussed in detail. Additionally, Caloplaca muelleri and C. rubina var. evolutior are transferred to Squamulea, and the latter is elevated to the species rank.

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy.

Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.