Taxonomic Classification Research Articles

Re-thinking Eating Disorders as Cultural Pathologies in Contemporary Irish Poetry: A Case Study

Eating disorders—a generic term that includes anorexia nervosa, bulimia, binge eating and many other subtypes of problematic relationships with food and eating—are situated at the interface of disciplines as varied as medicine, biology, history, cultural studies, gender studies and the social sciences. Although the reasons behind the development and experience of an eating disorder are individual as well as cultural, these pathologies tend to be analysed from either an exclusively biomedical perspective—which often excludes the cultural factor—or oversimplified as being the result of the stereotypes of beauty imposed on the female body in western cultural traditions. This essay, in contrast, looks at eating disorders as multi-layered metaphors of cultural dissidence within the social order and literary traditions of contemporary Ireland. It is divided into distinct, though interrelated, sections: a brief introduction to eating disorders; a consideration of the problems posed in the representation of emaciated corporealities; a taxonomical classification of the primary sources found in the course of my research; and the analysis of Mary O’Donnell’s poem “Reading the Sunflowers in September” as a case study to illustrate the literal and metaphorical employment of anorexia in contemporary Irish poetry. Although the análisis is philological, the perspective adopted is that of the Medical Humanities, in that I will make use of literary, cultural and biomedical literature in order to provide a view that is complementary to the scientific discourse around anorexia nervosa. O’Donnell’s poem will be considered in relation to European visual arts, particularly photography, in order to enhance the transnational dimension of eating disorders. At the same time, the close reading of the poem under analysis will be complemented by a comparative analysis with other Irish poems of the late 20th and early 21st centuries to underline the relevance of the national context in interpreting the representation of this disease. Ultimately, this essay aims to proffer new perspectives on the pathology and to contribute to the social understanding of those who experience it.

Diagnostics of Fusarium wilt in banana: Current status and challenges

AbstractGlobal banana production is under threat from the rapidly spreading pathogen Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 (TR4), which is pathogenic to Cavendish and many other varieties. Due to the absence of effective control methods and the lack of other market‐acceptable resistant cultivars, early diagnostics, containment and quarantine measures are important to limit further spread and impact of this pathogen. Early detection and identification of the pathogen require reliable diagnostic assays. The reliability of a molecular diagnostic assay is directly linked to the rigour applied at validating the assay according to predetermined standards. For specific detection of a target pathogen using molecular diagnostics, a well‐resolved taxonomy of the target and related species based on their evolutionary relationships is also required. The advent of sequence‐based phylogenetic analysis has given rise to new insights regarding the taxonomic classification of Foc and provided proof for the polyphyletic origin of Foc races, complicating early and reliable detection of the pathogen. Although numerous diagnostic methods for Foc have been developed, choosing a rigorously validated and fit‐for‐purpose method for adoption is currently challenging as advantages and drawbacks for each assay are not always obvious or put into context with prior methodologies. This review compiles and critically dissects published methods that are reported to detect Foc to date and highlights their benefits and constraints to provide a valuable reference for diagnosticians, researchers and policy makers worldwide.

Skull Base Repair following Resection of Vestibular Schwannoma: A Systematic Review (Part 1: The Retrosigmoid Approach)

Abstract Objective Despite advances in skull-base reconstruction techniques, cerebrospinal fluid (CSF) leaks remain a common complication following retrosigmoid (RS) vestibular schwannoma (VS) surgery. We aimed to review and classify the available strategies used to prevent CSF leaks following RS VS surgery. Methods A systematic review, including studies of adults undergoing RS VS surgery since 2000, was conducted. Repair protocols were synthesized into a narrative summary, and a taxonomic classification of techniques and materials was produced. Additionally, the advantages, disadvantages, and associated CSF leak rates of different repair protocols were described. Results All 42 studies were case series, of which 34 were retrospective, and eight were prospective. Repair strategies included heterogeneous combinations of autografts, xenografts, and synthetic materials. A repair taxonomy was produced considering seven distinct stages to CSF leak prevention, including intraoperative approaches to the dura, internal auditory canal (IAC), air cells, RS bony defect, extracranial soft tissue, postoperative dressings, and CSF diversion. Notably, there was significant heterogeneity among institutions, particularly in the dural and IAC stages. The median postoperative incidence of CSF leaks was 6.3% (IQR: 1.3–8.44%). Conclusions The intraoperative strategies used to prevent CSF leaks during RS VS surgery vary between and within institutions. As a result of this heterogeneity and inconsistent reporting of CSF leak predictive factors, a meaningful comparative analysis of repair protocols was not feasible. Instead, we propose the development of a prospective multicenter observational evaluation designed to accurately capture a comprehensive dataset of potential CSF risk factors, including all stages of the operative repair protocol.

Deciphering whole genome sequence of a Newcastle disease virus genotype VII.2 isolate from a commercial poultry farm in India

Here we report the isolation and complete genome sequence of virulent Newcastle disease virus (NDV) during the outbreak in 2023. NDV is isolated from the infected egg-laying vaccinated chickens of poultry farms located in Raipur district in Chhattisgarh, India. Next-generation sequencing (NGS) revealed the present NDV isolate has a genome length of 15,118 nucleotides (GenBank: OR185447). The phylogenetic tree illustrates the evolutionary relationship among NDV species and populations indicating the present NDV strain (NDV/Chicken/RPR/01/23) classified as genotype VII in class 2. NDV isolate exhibited 99.19 % and 97.53 % similarities in the nucleotide sequence in comparison with other strains of NDV/Owl/Guwahati/01/20 (GenBank: MZ546197.1) from India and chicken/Banjarmasin/010/10 (GenBank: HQ697254.1) from Indonesia. The present NDV genome is closely aligned with the NDV/Owl/Guwahati/01/20 strain and was clustered in genotype VII in class 2 suggesting possible spillover among the viral strains. The amino acid sequence at the protein Fusion protein (F) cleavage sequence 112RRQKR*F117 which is distinctive with other lentogenic vaccine NDV strain of La Sota and postulated as a major determinant of NDV virulence. Since there is limited information available on the exact cause of the abrupt death of poultry chickens located in Raipur district in Chhattisgarh, India, the present study aims to examine molecular sequencing of circulating NDV strains causing high mortality in this region. The neutralization epitopes of virulent NDV strains will expedite in development next next-generation vaccines to control circulating viral strains across the globe. The derived scientific information on genetic diversity, current taxonomic classification, and antigenic variations that exist within the genome of NDV will help in developing strain-specific vaccines and implementing strict measures.

Human Papillomavirus Infections and the Role Played by Cervical and Cervico-Vaginal Microbiota-Evidence from Next-Generation Sequencing Studies.

This comprehensive review encompasses studies examining changes in the cervical and cervico-vaginal microbiota (CM and CVM) in relation to human papillomavirus (HPV) using next-generation sequencing (NGS) technology. HPV infection remains a prominent global health concern, with a spectrum of manifestations, from benign lesions to life-threatening cervical cancers. The CM and CVM, a unique collection of microorganisms inhabiting the cervix/vagina, has emerged as a critical player in cervical health. Recent research has indicated that disruptions in the CM and CVM, characterized by a decrease in Lactobacillus and the overgrowth of other bacteria, might increase the risk of HPV persistence and the progression of cervical abnormalities. This alteration in the CM or CVM has been linked to a higher likelihood of HPV infection and cervical dysplasia. NGS technology has revolutionized the study of the cervical microbiome, providing insights into microbial diversity, dynamics, and taxonomic classifications. Bacterial 16S rRNA gene sequencing, has proven invaluable in characterizing the cervical microbiome, shedding light on its role in HPV infections and paving the way for more tailored strategies to combat cervical diseases. NGS-based studies offer personalized insights into an individual's cervical microbiome. This knowledge holds promise for the development of novel diagnostic tools, targeted therapies, and preventive interventions for cervix-related conditions, including cervical cancer.

Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines

Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.

Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome.

Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.

Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family.

Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.

Soil taxonomical classification and organic carbon sequestration potential of coastal acid sulfate soils: Kari and Kayal ecosystems of Kerala, India

Soil taxonomical classification and organic carbon sequestration potential of coastal acid sulfate soils: Kari and Kayal ecosystems of Kerala, India

Leveraging machine learning for taxonomic classification of emerging astroviruses.

Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method's pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.

Deciphering the Plastomic Code of Chinese Hog-Peanut (Amphicarpaea edgeworthii Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe.

The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Amphicarpaea edgeworthii Benth., a critical species within this subtribe. Through meticulous genomic sequencing, we identified a plastome size of 148,650 bp, composed of 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Comparative genomic analysis across seven Glycininae species illuminated a universally conserved circular and quadripartite structure, with nine genes exhibiting notable nucleotide diversity, signifying a remarkable genomic variability. Phylogenetic reconstruction of 35 Phaseoleae species underscores the affinity of Amphicarpaea with Glycine, placing Apios as a sister lineage to all other Phaseoleae species, excluding Clitorinae and Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, and Spatholobus, traditionally clumped together in the Erythrininae subtribe, display paraphyletic divergence, thereby contesting their taxonomic coherence. The pronounced structural differences in the quadripartite boundary genes among taxa with unresolved subtribal affiliations demand a reevaluation of Erythrininae's taxonomic classification, potentially refining the phylogenetic contours of the tribe.

A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs.

Molecular systematic studies of the anthozoan class Octocorallia have revealed widespread incongruence between phylogenetic relationships and taxonomic classification at all levels of the Linnean hierarchy. Among the soft coral taxa in order Malacalcyonacea, the family Alcyoniidae and its type genus Alcyonium have both been recognised to be highly polyphyletic. A recent family-level revision of Octocorallia established a number of new families for genera formerly considered to belong to Alcyoniidae, but revision of Alcyonium is not yet complete. Previous molecular studies have supported the placement of Alcyoniumverseveldti (Benayahu, 1982) in family Cladiellidae rather than Alcyoniidae, phylogenetically distinct from the other three genera in that family. Here we describe a new genus, Ofwegenumgen. nov. to accommodate O.verseveldticomb. nov. and three new species of that genus, O.coronalucissp. nov., O.kloogisp. nov., and O.collisp. nov., bringing the total number of species in this genus to four. Ofwegenumgen. nov. is a rarely encountered genus so far known from only a few locations spanning the Indian and western Pacific Oceans. We present the morphological characters of each species and use molecular data from both DNA barcoding and target-enrichment of conserved elements to explore species boundaries and phylogenetic relationships within the genus.

The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids.

The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.

Exploring the taxonomic classification of Curvularia genera: Enhancing understanding of phytopathogenic species in Poaceae through morphological and molecular approaches

Exploring the taxonomic classification of Curvularia genera: Enhancing understanding of phytopathogenic species in Poaceae through morphological and molecular approaches

Metagenomic investigation of 16S rRNA marker gene samples to analyze the role of race, ethnicity, and location in preterm birth: A comprehensive vaginal microbiome meta-analysis

The vaginal microbiome is essential to women's reproductive health and numerous studies have demonstrated that any microbial dysbiosis can increase the risk of Preterm Birth (PTB). The present study utilized an integrated computational methodology to conduct a meta-analysis of PTB vaginal microbiome samples from women of different racial, ethnic, and geographical locations, across multiple studies derived from public repositories. Taxonomic classification, functional profiling, and statistical analysis of the PTB samples revealed that Finegoldia, Haemophilus, and Lactobacillus showed the highest variation in their microbial abundances while the Sensory system pathway, Substance dependence pathway, and Circulatory system pathway showed the highest variation in their expression levels based on race, ethnicity, and locations respectively. All of these factors cause subsequent variations in the etiology of PTB across the aforementioned demographic attributes. LEfSE and ANCOM-BC approaches were performed to identify race, ethnicity, and geographic location-specific microbial biomarkers. To the best of our knowledge, our work is one of the first to provide a detailed analysis of the complex delineations between socioeconomic constructs of race and ethnicity at a global scale, considering the eight racial groups and the geographical location of the participants who faced PTB. We believe these findings will have significant implications for the development of more targeted and efficacious strategies for the prevention and treatment of PTB.

Assessing the metabolism, phylogenomic, and taxonomic classification of the halophilic genus Halarchaeum.

In this study, a genomic approach was employed to evaluate the metabolic potentials and taxonomic classification of the halophilic genus Halarchaeum. Genomic analysis revealed that Halarchaeum members exhibit a predilection for amino acids as their primary energy source in high-salinity environments over carbohydrates. Genome analysis unveiled the presence of crucial genes associated with metabolic pathways, including the Embden-Meyerhof pathway, semi-phosphorylative Entner-Doudoroff pathway, and the urea cycle. Furthermore, the genomic analysis indicated that Halarchaeum members employ diverse mechanisms for osmotic regulation (encompassing both salt-in and salt-out strategies). Halarchaeum members also encode genes to alleviate acid and heat stress. The average nucleotide identity value between Halarchaeum solikamskense and Halarchaeum nitratireducens exceeded the established threshold (95%-96%) for defining distinct species. This high similarity suggests a close relationship between these two species, prompting the proposal to reclassify Halarchaeum solikamskense as a heterotypic synonym of Halarchaeum nitratireducens. The results of this study contribute to our knowledge of taxonomic classification and shed light on the adaptive strategies employed by Halarchaeum species in their specific ecological niches.

Differential cell size reduction of two sympatric Epithemia (Bacillariophyta) taxa in Nakaikemi Wetland, Japan

SUMMARYWe observed contrasting temporal changes in cell size between two Epithemia taxa. The life cycle of diatoms is closely linked to their cell size, with a gradual decrease during the vegetative stage and a recovery through sexual reproduction. Sexual reproduction is triggered when cells become smaller than a species‐specific size threshold and receive species‐specific environmental cues. Few studies have documented the life cycles and frequency of sexual reproduction in diatoms, combining field observations and laboratory culture. We collected two Epithemia taxa, Epithemia gibba var. ventricosa and Epithemia sp. from a pond in Nakaikemi Wetland, and measured their valve lengths monthly for almost 3 years. Additionally, we established cultures of both taxa to examine the rates of cell size reduction, which affect the duration of the vegetative stage. In the field, E. gibba var. ventricosa exhibited a wide range of cell sizes and signs of size recovery. Furthermore, the cultures of this taxon showed a clear decrease in cell size through division, suggesting that sexual reproduction is required for size recovery. On the other hand, Epithemia sp. showed no obvious change in cell size both in the field and in the laboratory. This suggests that either sexual reproduction is not necessary for this taxon to maintain its population or their life cycle extends over several years to several decades. Thus, our findings reveal congeneric taxa sharing a common habitat and substratum, yet exhibiting distinct sexual and asexual strategies. Furthermore, we question the validity of taxonomic classifications previously assigned to these diatoms based on the range of morphological characteristics observed in the present study.

Cataloging variation in 16S rRNA gene sequences of female urobiome bacteria

Continued efforts to isolate and sequence bacteria of the urinary tract has increased representation of these species in publicly available databases. This in turn has improved taxonomic classifications of the urinary microbiome (urobiome). Short-read sequencing targeting a variable region(s) of the 16S rRNA gene sequence has been fundamental in characterizing the urobiomes of males and females with and without lower urinary tract symptoms, as well as cancers of the urinary tract. Here, we have compiled a data set of full-length or near-full-length 16S rRNA gene sequences for the urobiome. To generate this data set, we first plated 203 isolates from the bladder on differential media and sequenced their full-length 16S rRNA gene sequence. We combined this data set with publicly available genomes from primarily the female urinary tract. The final data set includes 399 sequences representative of 160 different species from 73 genera. We assessed the ability of publicly available databases to correctly predict these sequences based on the V1-V3, V4, and V4-V6 variable regions. As expected, species designations based upon these variable regions is often not possible or incorrect. We also detected incorrect genus-level classifications. This data set can be used to supplement existing databases, by increasing urobiome species variation, and thus improve future studies characterizing urobiomes.

HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.

Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining the functional roles of microbial communities. A key challenge in analyzing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxa of origin. While still performing worse relative to reference-based short-read tools in species classification, ML algorithms have shown promising results in taxonomic classification at higher ranks. A recent approach exploited to enhance the performance of ML tools, which can be translated to reference-dependent classifiers, has been to integrate the hierarchical structure of taxonomy within the tool's predictive algorithm. Here, we introduce HiTaxon, an end-to-end hierarchical ensemble framework for taxonomic classification. HiTaxon facilitates data collection and processing, reference database construction and optional training of ML models to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. In addition, through exploring hierarchical methods for HiTaxon, we highlight that our custom approach to hierarchical ensembling improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensembles over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally derived reads. HiTaxon is available at: https://github.com/ParkinsonLab/HiTaxon.

Protein homeostasis imprinting across evolution.

Protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how cellular proteostasis machines have evolved to adjust protein biogenesis needs to environmental constraints. Herein, we describe a novel computational approach, based on semantic network analysis, to evaluate proteostasis plasticity during evolution. We show that the molecular components of the proteostasis network (PN) are reliable metrics to deconvolute the life forms into Archaea, Bacteria and Eukarya and to assess the evolution rates among species. Semantic graphs were used as new criteria to evaluate PN complexity in 93 Eukarya, 250 Bacteria and 62 Archaea, thus representing a novel strategy for taxonomic classification, which provided information about species divergence. Kingdom-specific PN components were identified, suggesting that PN complexity may correlate with evolution. We found that the gains that occurred throughout PN evolution revealed a dichotomy within both the PN conserved modules and within kingdom-specific modules. Additionally, many of these components contribute to the evolutionary imprinting of other conserved mechanisms. Finally, the current study suggests a new way to exploit the genomic annotation of biomedical ontologies, deriving new knowledge from the semantic comparison of different biological systems.