Subspecies Classification Research Articles

Classification of Latilactobacillus sakei subspecies based on MALDI-TOF MS protein profiles using machine learning models.

Latilactobacillus sakei plays a significant role in the realm of food bacteria. One particular subspecies of L. sakei is employed as a protective agent during food fermentation, whereas another strain is responsible for food spoilage. Hence, it is crucial to precisely differentiate between the two subspecies of L. sakei. In this study, machine learning models based on protein mass peaks were developed for the first time to distinguish L. sakei subspecies. Furthermore, the efficacy of three commonly used machine learning algorithms for microbial classification was evaluated. Our results provide the foundation for future research on developing machine learning models for the classification of microbial species or subspecies. In addition, the developed model can be used in the food industry to monitor L. sakei subspecies in fermented foods in a time- and cost-effective method for food quality and safety.

Molecular epidemiology and genetic evolution of avian influenza H5N1 subtype in Nigeria, 2006 to 2021.

Nigeria recorded one of the earliest outbreaks of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1 in 2006, which spread to other African countries. In 2023, 18 countries reported outbreaks of H5N1 in poultry, with human cases documented in Egypt, Nigeria, and Djibouti. There is limited information on the molecular epidemiology of HPAI H5N1 in Nigeria. We determined the molecular epidemiology and genetic evolution of the virus from 2006 to 2021. We investigated the trend and geographical distribution across Nigeria. The evolutionary history of 61 full-length genomes was performed from 13 countries worldwide, and compared with sequences obtained from the early outbreaks in Nigeria up to 2021. MEGA 11 was used to determine the phylogenetic relationships of H5N1 strains, which revealed close ancestry between sequences in Nigeria and those from other African countries. Clade classification was performed using the subspecies classification tool for Bacterial and Viral Bioinformatics Research Center (BV-BRC) version 3.35.5. H5N1 Clade 2.2 was observed in 2006, with 2.3.2, 2.3.2.1f clades observed afterwards and 2.3.4.4b in 2021. Our findings underscore the need for genomics surveillance to track antigenic variation and clades switching to monitor the epidemiological of the virus and safeguard human and animal health.Impacts Specific variations in the hemagglutinin (HA) and neuraminidase (NA) genes of Avian influenza virus are consistent in different geographical regions. H5N1 Clade 2.2 was reported in 2006, with 2.3.2, 2.3.2.1f afterwards and 2.3.4.4b in 2021. Nigeria is an epicentre for avian influenza with three major migratory routes for wild birds transversing the country. It is plausible that the Avian influenza in Northern Nigeria may be linked to wild bird sanctuaries in the region.

Insights into subspecies classification and conservation priorities of Central Asian lynx populations revealed by morphometric and genetic analyses

The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.

Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing.

The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable.IMPORTANCEIn order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.

中国野生报春花属物种多样性与地理分布数据集

Catalogue of Life serves as the background baseline information for the biota of a given natural geographic region or administrative unit. The timely updating of its dynamics is an important basis for the research, management and monitoring of biodiversity conservation. The integration and sharing of biodiversity data can provide a scientific basis for the development of related studies. Primula L. is a typical genus characterized by a broad distribution and a high degree of endemism, with diverse habitats and a complex taxon structure. An in-depth analysis of its geographical distribution pattern and characteristics can provide a foundational basis for the conservation and use of germplasm resources. With the aim of offering a reference for germplasm resource surveys and application research on seed introduction, and based on a large amount of basic data and literature, this paper adopts the taxonomic system used by Flora of China to update the list of wild species of the genus Primula L. distributed in the terrestrial area of China. In the paper, we counted their species diversity, composition and other information, and established a dataset of the diversity and geographical distributions of wild Primula L. in China. This genus predominantly thrives in the temperate and subtropical zones of the Northern Hemisphere. Its diversity center and modern distribution center are also widely distributed in the eastern Himalayas and Hengduan Mountains in broad sense, Tianshan Mountain Area, Qinba Mountain area, Wuling Mountains Area, Qinghai Tibet Plateau, Yunnan Guizhou Plateau and other high-altitude areas. Additionally, it extends to middle and lower altitude areas with prominent karst and Danxia landscapes. As of October 2022, a total of 397 species (28 varieties and 26 subspecies) of the genus Primula L. have been recorded in China, including 296 endemic species (including subspecies classification units, the same below) in China. In addition to the five administrative regions of Jiangsu, Hainan, Shanghai, Hong Kong and Macao, the distribution of wild primroses has been recorded in various provincial administrative regions in China, with Sichuan Province boasting the highest species richness and endemism at the provincial scale (177 species), followed by Yunnan Province (176 species) and the Tibet Autonomous Region (171 species). At the county scale, Shangri-La City ranks first in species richness with 62 species.

Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data.

Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.

Mitochondrial genome-based synthesis and timeline of Eurasian otter (Lutra lutra) phylogeography

ABSTRACT Eurasian otters (Lutra lutra) have a broad distribution across Eurasia, but biogeographic data outside of western Europe is limited to disconnected pockets. Based on current subspecies designations, Asia appears to harbour a large proportion of the species’ diversity, with 10 of 12 Eurasian otter subspecies found in Asia. Here we provide a range-wide synthesis of mitochondrial data, inferring a timeline and pattern of phylogeographic signals. Whole mitochondrial genomes of 27 Eurasian otters across 4 subspecies are presented from newly generated data (n = 6; 4 from Korea, 1 from Hong Kong and 2 from UK), assembled from the Sequence Read Archive (n = 4), and sourced from GenBank (n = 17). We then combined whole mitochondrial genome results with cytochrome b data to increase the sample size and contextualise our results with prior studies. We identified five distinct lineages that were discordant with current subspecies classification. Phylogenetic dating revealed that the earliest diverging lineage was the Japanese lineage, with remaining lineages diverging ≥0.08 million years ago. Mitochondrial diversity calculated by sample locations seemed mainly driven by the presence of multiple lineages. When grouping samples by lineage, genetic diversity was highest in Lineage 1 (primarily found in China and Laos), followed by Lineage 2 (primarily found in Korea), and lowest diversity identified in Lineage 3 (primarily found in Europe). Our findings highlight previously undetected lineage diversity within Eurasian otters, but also the need for further taxonomic and genomic evaluation of the species in Asia. The identified unique, distinct lineages of Eurasian otters also warrant urgent conservation attention.

Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China.

Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation. In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China. Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H d = 0.894, H T = 0.910), strong genetic differentiation (F ST = 0.835), and significant phylogeographical structure (G ST/N ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable. Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.

The Sexome ‐ A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse

The detection and recovery of male DNA post-assault is important in sexual assault investigations, particularly where an offender is unknown to the victim. The collection of DNA evidence often occurs when the female victim undergoes a forensic medical assessment. Analysis regularly results in mixed autosomal DNA profiles with both victim and perpetrator DNA, often making it difficult to interpret a male profile suitable for DNA database searching. While short tandem repeat (STR) profiling of the male Y-chromosome is often used to overcome this challenge, successful identification of an individual can be hindered by the paternal inheritance pattern of Y-STRs and small Y-STR databases. Human microbiome research has suggested that a person’s microbial diversity is unique. Therefore microbiome analysis using Massively Parallel Sequencing (MPS) could serve as a useful adjunct method of perpetrator identification. This study aimed to identify bacteria taxa that were unique to each participant and compare the bacterial communities found on their genitals both pre- and post-coitus. Samples were collected from six male-female sexual partner pairs. Volunteers were asked to self-collect low vaginal (females) and penis shaft and glans (males) samples before and after intercourse. Samples were extracted using the PureLink™ Microbiome DNA Purification Kit. Extracted DNA underwent library preparation using primers targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene (∼450 bp). Libraries were sequenced on the Illumina MiSeq® platform. From the sequence data derived, statistical analysis was performed to investigate if bacteria sequences could be used to infer contact between each male-female pairing. Unique bacterial signatures were detected in low frequencies (<1%) in male and female participants pre-coitus. The data indicated a significant disruption to microbial diversity post-coitus in all samples. A transfer of the female microbiome during intercourse was most significant. As expected, one couple who did not use a barrier contraceptive yielded the most microbial transfer and disruption to diversity demonstrating a proof-of-concept in the utility of microbiome interrogation for sexual assault cases. Further genomic analysis is needed to confirm species and subspecies classification of bacteria that may produce a unique microbial profile that could then be used to identify a specific individual.

Investigating the domestication and early management of reindeer (Rangifer tarandus) in the Sámi archaeological context from teeth geometric morphometrics

For centuries, reindeer herding has been an integral part of the subsistence, lifeways, economy and cosmology of the Sámi of northern Fennoscandia. Despite its importance, the timing and details of early reindeer domestication are still highly debated. Identifying domesticated individuals in the archaeological record remains complicated due to the presence of two interbreeding subspecies in Fennoscandia and a mixed socio-economic organisation by Sámi populations, which was mainly a combination of wild reindeer hunting and small-scale reindeer herding. This study proposes methodological improvement for identifying domestic individuals using 2D landmark and sliding semi-landmark based geometric morphometrics on the isolated lower molars of 389 modern specimens, and 90 teeth from four archaeological sites in Finnish Lapland. Our results indicate that despite the significant impact of wear on overall tooth morphology, our protocol is very useful for identifying subspecies (classification accuracy of the two species is between 78 and 91% depending on the wear class) and understanding the morphological changes induced by the domestication process. We suggest that the morphological variation observable among modern populations has been impacted by recent changes in herding strategies in northern Fennoscandia, and that the archaeological domesticated reindeer populations were relatively different, probably due to selection by the Sámi. This study also highlights the importance of using other direct evidence or contextual archaeological data to better trace the early evidence of a domesticated reindeer economy in northern Fennoscandia, and aid in reconstructing the socio-economic changes in Sámi populations over time.

Preliminary study on genetic differences between two species of finless porpoises, genus Neophocaena, with lack of genetic divergence between two subspecies of the narrow-ridged finless porpoise, N. asiaeorientalis: cytochrome b sequence analyses

Using samples from bycaught finless porpoises, cytochrome b sequences were analysed and phylogenetic trees were constructed. The aims were to: (1) determine genetic divergences within the genus Neophocaena; (2) examine interspecific divergences between N. asiaeorientalis and N. phocaenoides; and (3) examine intraspecific divergence between N.a. asiaeorientalis and N.a. sunameri. For this purpose, complete cytochrome b sequences for 12 N.a. sunameri specimens, collected from fishery markets at Pohang in southeastern Korea, were obtained, and these sequences were compared to the corresponding partial (402bp) and complete (1,140bp) sequences of Neophocaena, obtained from GenBank. From a maximum likelihood tree with the partial sequences of the two Neophocaena species, two clades were detected, corresponding to the two species, with average genetic distance of 1.64%, four fixed site differences (1.00%), and a Gst value of 0.64, although we did not examine the specimens from Southeast Asia and contiguous South China Sea. Furthermore, from the complete sequences, we recognised a lack of genetic divergence between the two subspecies of N. asiaeorientalis, with a Gst value of 0.06 and two pairs of identical sequences between them, indicating that our results do not support current subspecies classification. Thus, we newly found that our cytochrome b sequencing results are useful for the examination of interspecific and intraspecific divergences in Neohpocaena, although further genetic analyses with additional specimens of Neophocaena across its distributional range are necessary to confirm the findings in this study.

Range-wide population genomics of the spongy moth, Lymantria dispar (Erebidae): Implications for biosurveillance, subspecies classification and phylogeography of a destructive moth.

The spongy moth, Lymantria dispar, is an irruptive forest pest native to Eurasia where its range extends from coast to coast and overspills into northern Africa. Accidentally introduced from Europe in Massachusetts in 1868-1869, it is now established in North America where it is considered a highly destructive invasive pest. A fine-scale characterization of its population genetic structure would facilitate identification of source populations for specimens intercepted during ship inspections in North America and would enable mapping of introduction pathways to help prevent future incursions into novel environments. In addition, detailed knowledge of L.dispar's global population structure would provide new insight into the adequacy of its current subspecies classification system and its phylogeographic history. To address these issues, we generated >2000 genotyping-by-sequencing-derived SNPs from 1445 contemporary specimens sampled at 65 locations in 25 countries/3 continents. Using multiple analytical approaches, we identified eight subpopulations that could be further partitioned into 28 groups, achieving unprecedented resolution for this species' population structure. Although reconciliation between these groupings and the three currently recognized subspecies proved to be challenging, our genetic data confirmed circumscription of the japonica subspecies to Japan. However, the genetic cline observed across continental Eurasia, from L.dispar asiatica in East Asia to L.d.dispar in Western Europe, points to the absence of a sharp geographical boundary (e.g., the Ural Mountains) between these two subspecies, as suggested earlier. Importantly, moths from North America and the Caucasus/Middle East displayed high enough genetic distances from other populations to warrant their consideration as separate subspecies of L.dispar. Finally, in contrast with earlier mtDNA-based investigations that identified the Caucasus as L.dispar's place of origin, our analyses suggest continental East Asia as its evolutionary cradle, from where it spread to Central Asia and Europe, and to Japan through Korea.

Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones

The present research aimed to evaluate the diversity of all monkeypox virus strains with a special focus on recently isolated ones by a comprehensive phylogenetic analysis of all available sequences, based on the concatenate of four viral genes. Almost all current strains from 2022 showed a high level of similarity to each other on the analyzed stretches: 218 strains shared identical sequence. Among all analyzed strains, the highest number of differences was counted compared to a RefSeq strain (Zaire-96-I-16) on the whole concatenate. Our analysis supported the distinction between Clade I (formerly Congo Basin clade), IIa and IIb (together formerly West African clade) strains and classified all 2022 strains in the last one. The high number of differences and long branch observable concerning strain Zaire-96-I-16 is most probably caused by a sequencing error. As this strain represents one of the two available reference sequences in GenBank, it is recommendable to confirm or exclude the concerning mutation. The developed method, based on four gene sequences, reflected the established whole-genome-based intraspecies classification. Although this method provides significantly less information about the strains compared to whole genome analyses, since its resolution is much lower, it still enables the rapid subspecies classification of the strains into the established clades. The genes in the analyzed concatenate are so conserved that further differentiation of contemporary strains is impossible; these strains are identical in the analyzed sections. On the other hand, since whole genome analyses are compute-intensive, the described method offers a simpler and more accessible alternative for monitoring and preliminary typing of newly sequenced monkeypox virus strains.

Cucullanus pinnai pinnai and C. pinnai pterodorasi (Nematoda Cucullanidae): what does the integrative taxonomy tell us about these species and subspecies classification?

Cucullanus pinnai has been divided in two subspecies (C. pinnai pinnai and C. pinnai pterodorasi) based on the morphology of oesophastome. While C. pinnai pinnai apparently shows low host specificity and broad geographic occurrence, with certain morphological variations, C. pinnai pterodorasi was reported once, parasitizing Pterodoras granulosus. We used an integrative taxonomic approach to evaluate whether or not populations of C. pinnai pinnai from Trychomycterus spegazzinii (Escoipe River, Argentina) and Pimelodus fur (Miranda River, Brazil), and of C. pinnai pterodorasi from Pterodoras granulosus (Miranda River, Brazil) are conspecific. Parasites were observed using light microscopy and genetically characterized based on partial sequences of the 18S and 28S rDNA, ITS1-5.8S-ITS2, and COI mtDNA. Phylogenies were reconstructed and the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (bPTP), and Automatic Barcode Gap Discovery (ABGD) were used for species delimitation purposes. The present samples formed well-supported monophyletic assemblages, corroborating in part the results of morphological analyses; however, they grouped according to geographic origin. Species delimitation suggested conspecificity of C. pinnai pinnai with C. pinnai pterodorasi from Brazil; consequently, the morphology of oesophastome may be an intraspecific variation. Results also indicated that C. pinnai may represent a species complex as samples from Argentina were suggestive of an independent specific entity. However, definitive affirmations are premature, since there is no autapomorphy for separating C. pinnai from Brazil and Argentina and sampling was limited to three host species from two river basins. The phylogenetic reconstructions also confirmed the artificiality of some genera within Cucullanidae.

A box on the river: The phylogenetics and phylogeography of Eucalyptus baueriana (Eucalyptus sect. Adnataria ser. Heterophloiae).

We present a phylogeographic study of the tree species Eucalyptus baueriana Schauer, which occurs in disjunct areas on the near coastal plains and ranges of the south-east Australian mainland. DArTseq data are used to build a phylogeny including E. baueriana and closely related taxa to test its monophyly, test the genetic distinctness of the three subspecies of E. baueriana, and investigate relationships between its disjunct populations. Additionally, we use population structure analysis to investigate the genetic distinctness of populations, and MaxEnt to investigate the environmental factors potentially influencing the species' distribution. We show E. baueriana is monophyletic and most closely related to three other Blue Box eucalypt species: E. conica H.Deane &amp; Maiden, E. dalveenica T.L.Collins, R.L.Andrew &amp; J.J.Bruhl and E. magnificata L.A.S.Johnson &amp; K.D.Hill, with some evidence for genetic introgression between these taxa. Within E. baueriana, the deepest genetic breaks do not correspond with the subspecies classification as the two geographically restricted subspecies, together with samples of the more widespread E. baueriana subsp. baueriana from west of the Gippsland lowlands, form a south-western clade with that is sister to other populations of subsp. baueriana. The oldest genetic break in the species occurs in far eastern Gippsland (Victoria), corresponding to one of the shortest geographic disjunctions in the species' distribution. Genetic breaks in other species have been observed in this region which is broadly referred to as the southern transition zone. Both total annual rainfall and the seasonality of this rainfall are hypothesised to affect the species' distribution; gaps in its distribution are in areas of higher rainfall that support closed forest and in regions with more winter dominated rainfall.

ESG and Sustainability of Industrial Enterprise Development: Integrated Assessment Methodology

The article provides the assessment of the sustainability of an industrial enterprise based on the concept of the global economic trend of ESG development. The authors propose classification of subspecies of enterprise sustainability and evaluate the indicator of the level of interaction with the institutions of state power. The article considers the influence of GR activity on the sustainable development of an industrial enterprise in contemporary reality. The authors conclude about the main characteristics of the activity of the GR structure in the management of an industrial enterprise and the place of GR management in the system of organizational and managerial activity of the enterprise.

Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach.

Lacticaseibacillus paracasei species are widely used for their health-promoting properties in food and agricultural applications. These bacteria have been isolated from various habitats such as the oral cavity, cereals, vegetables, meats, and dairy products conferring them the ability to consume different carbohydrates. Two subspecies are recognized, Lacticaseibacillus paracasei subsp. paracasei and Lacticaseibacillus paracasei subsp. tolerans according to their acid production from carbohydrates. Some strains are currently used as probiotics. In this study, we performed a comparative genomic analysis of 181 genomes of the Lacticaseibacillus paracasei species to reveal genomic differences at the subspecies level and to reveal adaptive and probiotic features, and special emphasis is given to inulin consumption. No clear distinction at the subspecies level for L. paracasei was shown using a phylogenetic tree with orthologous genes from the core-genome set. In general, a good correlation was observed between genomic distance and isolation origin, suggesting that L. paracasei strains are adapted to their natural habitat, giving rise to genetic differences at the genomic level. A low frequency of undesirable characteristics such as plasmids, prophages, antibiotic resistance genes, absence of virulence factors, and frequent bacteriocin production supports these species being good candidates for use as probiotics. Lastly, we found that the inulin gene cluster in L. paracasei strains seems to differ slightly in the presence or absence of some genes but maintains a core defined by at least three fructose-PTS proteins, one hypothetical protein, and extracellular β-fructosidase. Finally, we conclude that further work has to be done for L. paracasei subspecies classification. Improving outgroup selection criteria is a key factor for their correct subspecies assignation.

Rapid methicillin resistance detection and subspecies discrimination in Staphylococcus hominis clinical isolates by MALDI-TOF MS

PurposeStaphylococcus hominis is a coagulase-negative opportunistic pathogen responsible for implanted medical device infections. Rapid identification and virulence factors detection are crucial for appropriate antimicrobial therapy. We aimed to search protein biomarker peaks for rapid classification of antibiotic resistance and subspecies of S. hominis using MALDI-TOF MS. MethodsS. hominis clinical isolates (n = 148) were screened for subspecies differentiation by novobiocin resistance. Biofilm composition and formation were determined by detachment assay and crystal violet staining, respectively. Antibiotic susceptibility was performed by the broth microdilution method. The search for potential biomarkers peaks was enabled by ClinProTools 3.0, flexAnalysis 3.4, and Biotools 3.2 for statistical analysis, peak visualization, and protein/peptide alignment, respectively. ResultsOf 148 isolates, 12.16% were classified as S. hominis subsp. novobiosepticus, 77.77% were biofilm producers, and ˃ 50% were multidrug-resistant. Two potential biomarker peaks, 8975 m/z and 9035 m/z were detected for the discrimination of methicillin resistance with a sensitivity of 96.72%. The following peaks were detected for subspecies differentiation: 2582 m/z, 2823 m/z, and 2619 m/z with 88.89–98.28% of sensitivity. ConclusionsWe found potential biomarker peaks to predict methicillin resistance and discriminate S. hominis subspecies during routine MALDI-TOF MS identification in a clinical setting to enable better antibiotic treatment.

Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways.

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.

Climatic comparison of the gray wolf (Canis lupus) subspecies in North America using niche-based distribution models and its implications for conservation programs

Abstract The gray wolf, Canis lupus, once inhabited much of the northern hemisphere worldwide; however, persecution drove its populations almost to extinction. In North America, diverse conservation programs have been implemented in the last decades to recover its populations in the wild, many of them guided by the historical distribution of the gray wolf subspecies. Over time, several authors have proposed different subspecies classifications. Nevertheless, most of them are mutually inconsistent regarding the number and distribution of subspecies, creating controversy when implementing conservation programs. This study used niche-based distribution models and cluster analysis to explore the bioclimatic profiles of C. lupus across North America and compare them with different subspecies classifications to identify environmental correlatives that support the proposed designations. Our cluster analysis results indicate that the optimal number of climatic groups was five, designated as Northern, Eastern, Western, Coastal, and Southern groups, with transitional overlap boundaries located at their peripheries, indicating climatic gradients between them and supporting the idea of intergrading zones. The geographic ranges of these groups mismatched to a different extent with all subspecies delimitations. In general, the boundaries of putative subspecies did not match the climatic patterns of North America. Our results may contribute to the recovery programs underway for this carnivore by identifying suitable areas for the release of individuals from specific lineages. New approaches to characterizing the intraspecific variation of the gray wolf should include all evidence available, including genetic, morphological, and ecological information.