Plasmids are so closely associated with pathogens and antibiotic resistance that their potential for conferring other traits is often overlooked. Few studies consider how the full suite of traits encoded by plasmids is related to a host\'s environmental adaptation, particularly for Gram-positive bacteria. To investigate the role that plasmid traits might play in microbial communities from natural ecosystems, we identified plasmids carried by isolates of Curtobacterium (phylum Actinomycetota) from a variety of soil environments. We found that plasmids were common, but not ubiquitous, in the genus and varied greatly in their size and genetic diversity. There was little evidence of phylogenetic conservation among Curtobacterium plasmids even for closely related bacterial strains within the same ecotype, indicating that horizontal transmission of plasmids is common. The plasmids carried a wide diversity of traits that were not a random subset of the host chromosome. Furthermore, the composition of these plasmid traits was associated with the environmental context of the host bacterium. Together, the results indicate that plasmids contribute substantially to the microdiversity of a soil bacterium and that this diversity may play a role in niche differentiation and a bacterium\'s adaptation to its local environment.

Staphylococcus haemolyticus, a key species of the Staphylococcus genus, holds significant importance in healthcare-associated infections, due to its notable resistance to antimicrobials, like methicillin, and proficient biofilms-forming capabilities. This coagulase-negative bacterium poses a substantial challenge in the battle against nosocomial infections. Recent research has shed light on Staph. haemolyticus genomic plasticity, unveiling genetic elements responsible for antibiotic resistance and their widespread dissemination within the genus. This review presents an updated and comprehensive overview of the clinical significance and prevalence of Staph. haemolyticus, underscores its zoonotic potential and relevance in the one health framework, explores crucial virulence factors, and examines genetics features contributing to its success in causing emergent and challenging infections. Additionally, we scrutinize ongoing studies aimed at controlling spread and alternative approaches for combating it.

The aim of this study was to assess the environmental and breed risk factors associated with the prevalence of subclinical mastitis (SCM) in cows in the dual-purpose livestock system of Arauca, Colombian Orinoquia. Milk samples were taken from 1924 mammary quarters, corresponding to 481 cows on 28 different farms, and the California Mastitis Test (CMT) was applied. Risk factors associated with SCM were determined using multiple logistic regression analysis. The response variable was the presence (1) or absence (0) of SCM. Breed was included as a genetic risk factor, and daily milk production, number of cows in production, lactation month, calving number, cow age, climatic period, and body condition were included as environmental risk factors. The analysis of the odds ratio (OR) of significant effects indicated that the factors significantly associated with the presence of SCM were the number of cows (OR = 2.29; p = 0.005), milk production (OR = 0.88; p = 0.045), and the Taurus-Indicus breeds (OR = 1.79; p = 0.009) and composite breed (OR = 3.95; p = 0.005). In this study, the occurrence of SCM was determined by the following risk factors: number of cows, milk production, and breed. Likewise, the highest prevalence seemed to occur on farms with less technological development and sanitary management of producers from the lowest socioeconomic stratum.

Prokaryote-virus interactions play key roles in driving biogeochemical cycles. However, little is known about the drivers shaping their interaction network structures, especially from the host features. Here, we compiled 7656 species-level genomes in 39 prokaryotic phyla across environments globally and explored how their interaction specialization is constrained by host life history traits, such as growth rate.
We first reported that host growth rate indicated by the reverse of minimal doubling time was negatively related to interaction specialization for host in host-provirus network across various ecosystems and taxonomy groups. Such a negative linear growth rate-specialization relationship (GrSR) was dependent on host optimal growth temperature (OGT), and stronger toward the two gradient ends of OGT. For instance, prokaryotic species with an OGT ≥ 40 °C showed a stronger GrSR (Pearson\'s r = -0.525, P < 0.001). Significant GrSRs were observed with the presences of host genes in promoting the infection cycle at stages of adsorption, establishment, and viral release, but nonsignificant with the presence of immune systems, such as restriction-modification systems and CRISPR-Cas systems. Moreover, GrSR strength was increased with the presence of temperature-dependent lytic switches, which was also confirmed by mathematical modeling.
Together, our results advance our understanding of the interactions between prokaryotes and proviruses and highlight the importance of host growth rate in interaction specialization during lysogenization. Video Abstract.

This study aims to explore the intra-species distribution of genetic characteristics that favor the persistence in the gastrointestinal tract (GIT) and host interaction of bacteria belonging to species of the Lacticaseibacillus genus. These bacterial species comprise commercial probiotics with the widest use among consumers and strains naturally occurring in GIT and in fermented food. Since little is known about the distribution of genetic traits for adhesion capacity, polysaccharide production, biofilm formation, and utilization of substrates critically important for survival in GIT, which influence probiotic characteristics, a list of genetic determinants possibly involved in such functions was created by a search for specific genes involved in the above aspects in the genome of the extensively characterized probiotic L. rhamnosus GG. Eighty-two gene loci were retrieved and their presence and variability in other Lacticaseibacillus spp. genomes were assessed by alignment with the publicly available fully annotated genome sequences of L. casei, L. paracasei, L. rhamnosus, and L. zeae. Forty-nine of these genes were found to be absent in some strains or species. The remaining genes were conserved and covered almost all the functions considered, indicating that all strains of the genus may exert some probiotic effects. Among the variable loci, a taurine utilization operon and a α-L-fucosidase were examined for the presence/absence in 26 strains isolated from infant feces by PCR-based tests. Results were variable among the isolates, though their common origin indicated the capacity to survive in the intestinal niche. This study indicated that the capacity to exert probiotic actions of Lacticaseibacillus spp. depends on a conserved set of genes but variable genetic factors, whose role is only in part elucidated, are more numerous and can explain the enhanced probiotic characteristics for some strains. The selection of the most promising probiotic candidates to be used in food is feasible by analyzing the presence/absence of a set of variable traits.

Cervical cancer is the fourth leading cause of cancer-related deaths in women worldwide. Although many sequencing studies have been carried out, the genetic characteristics of cervical cancer remain to be fully elucidated, especially in the Asian population. Herein, we investigated the genetic landscape of Chinese cervical cancer patients using a validated multigene next generation sequencing (NGS) panel. We analyzed 64 samples, consisting of 32 tumors and 32 blood samples from 32 Chinese cervical cancer patients by performing multigene NGS with a panel targeting 571 cancer-related genes. A total of 810 somatic variants, 2730 germline mutations and 701 copy number variations (CNVs) were identified. FAT1, HLA-B, PIK3CA, MTOR, KMT2D and ZFHX3 were the most mutated genes. Further, PIK3CA, BRCA1, BRCA2, ATM and TP53 gene loci had a higher frequency of CNVs. Moreover, the role of PIK3CA in cervical cancer was further highlighted by comparing with the ONCOKB database, especially for E545K and E542K, which were reported to confer radioresistance to cervical cancer. Notably, analysis of potential therapeutic targets suggested that cervical cancer patients could benefit from PARP inhibitors. This multigene NGS analysis revealed several novel genetic alterations in Chinese patients with cervical cancer and highlighted the role of PIK3CA in cervical cancer. Overall, this study showed that genetic variations not only affect the genetic susceptibility of cervical cancer, but also influence the resistance of cervical cancer to radiotherapy, but further studies involving a larger patient population should be undertaken to validate these findings.

The changes of coastal topography might have genetically altered the extant species diversity in Chilika Lake. The genetic assessment of stomatopods has never been attempted from this ecosystem. The study generate the first genetic information (mtCOI) of Cloridopsis immaculata. DNA sequences of C. immaculata shows 12.9% genetic divergence with Harpiosquilla harpax and clade as sister species in NJ tree. Alima, Harpiosquilla, and Oratosquilla shows high congeneric/conspecific genetic divergence (20.9%, 15.7%, and 7.2%) and cladded separately in the phylogeny; correlate to their diverse populations. We recommend more extensive survey of stomatopods and generation of molecular data to resolve the taxonomic uncertainty.

The Sicilian black pig (SB) (Nero Siciliano), also known as the Nero dei Nebrodi, Nero delle Madonie, or Nero dell\'Etna pig ecotype, is an autochthonous Italian breed. The origins of this breed date back to Greek and Carthaginian dominations. In ancient times, its breeding was fairly common throughout Sicily, registering only a temporary reduction during the Arab domination. This breed is known primarily for its distinctive black coat, although some individuals display wattles and a partially or wholly white face. The SB pig has a birth rate with an average per sow of 7.6 piglets, each of 1.4 kg live body weight, showing an average daily gain (ADG) of 346 g/day during the fattening period. Slaughter generally takes place at an average age of 390 days, with an average live weight of 95 kg. This breed also appears to withstand adverse climatic conditions and resist disease. The purpose of this manuscript is to offer a general overview regarding the Sicilian Black pig and to consider the recent findings related to genome investigation. The recent application of Next Generation Sequencing (NGS) technologies in the study of the genome of autochthonous breeds showed that polymorphisms of some candidate genes for production performance and phenotypic traits represent important information for selection processes. The protection of autochthonous breeds, intended as sources of genomic diversity for the further improvements of pigs for commercial use, constitutes a valuable opportunity to create new sustainable pig chains.

Trophoblast cells play essential roles in the maintenance of normal embryo implantation, growth and development. The study of abnormal gene changes in trophoblastic cells from arrested embryos is helpful to understand the developmental mechanism of embryo developmental cessation or adverse pregnancy outcomes. In this study, we sequenced and analyzed the transcriptomes of the villi from ten women who have undergone abortion with either normal pregnancy or embryo development cessation. We found that there were 436 differentially expressed genes, of which 406 mRNA were significantly up-regulated and 32 mRNA were significantly down-regulated. Gene enrichment analysis showed that these genes were significantly enriched in immune-related functions and intercellular adhesion, such as lymphocyte activation, myeloid cell activation, extracellular matrix and collagen junction. And their potential regulatory pathways were enriched in terms of complement and coagulation cascade, extracellular matrix degradation. In addition, in this study the co-expression analysis of WGCNA was used to obtain the lncRNA with co-expression relationship with the differential genes. According to the different functions of the modules, two network diagrams were drawn, and four key genes were obtained, namely VSIG4, C1QC, CD36 and SPP1. These differential genes obtained in this study can be used as key molecules with potential effects on embryo development cessation. The enriched entries can provide a theoretical basis and new direction for further understanding of the etiology and mechanism of embryo development cessation or adverse pregnancy outcomes.
滋养层细胞对维持正常胚胎植入、生长发育有重要作用。研究停育胚胎的滋养层细胞的基因表达差异有助于了解胚胎发育停止或不良妊娠结局的发生发展机制。本研究通过对26例正常妊娠、胚胎停育妇女的绒毛组织进行全转录组测序和初步生物信息学分析,发现胚胎停育组存在436个差异基因,其中406个mRNA为显著上调基因,32个mRNA为显著下调基因。基因富集分析显示这些基因显著富集于免疫相关功能、细胞间黏附等方面,如淋巴细胞激活、髓系细胞激活、细胞外基质及胶原连接等,其潜在调控通路富集到补体及凝血级联反应和细胞外基质降解等条目。此外,本研究利用WGCNA共表达分析得到和差异基因存在共表达关系的lncRNA。根据模块功能不同,绘制了两个网络图,可得4个关键基因,分别为VSIG4、C1QC、CD36和SPP1。本研究得到的这些差异基因可作为对胚胎停育具有潜在影响的关键分子,所富集到的条目可为深入了解胚胎发育停止或不良妊娠结局的病因及机制提供理论依据及方向。.

Acute intermittent porphyria (AIP) is a dominant inherited disorder with a low penetrance that is caused by mutations in the gene coding for hydroxymethylbilane synthase (HMBS). Information about the epidemiology and molecular genetic features of this rare disorder is crucial to clinical research, and particularly to the evaluation of new treatments. Variations in the prevalence and penetrance of AIP in various studies may due to the different inclusion criteria and methods of assessment. Here, the prevalence and penetrance of AIP are analyzed systematically, and the genetic traits of different populations and findings regarding the genotype-phenotype correlation are summarized. In addition, quite a few studies have indicated that AIP susceptibility was affected by other factors, such as modifying genes. Findings regarding possible modifying genes are documented here, helping to reveal the pathogenesis of and treatments for AIP. The status of research on AIP in China reveals the lack of epidemiological and genetic studies of the Chinese population, a situation that needs to be promptly remedied.