Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies.Among nematodes, the free-living model organism Strongyloides: omics to worm-free populations’.This article is part of the Theo Murphy meeting issue ‘ In addition, omics also incorporates advanced functional genomics tools, such as RNAi, transgenesis and CRISPR, which can enable a more focused analysis of the function of one, or a few, specific genes of interest. Indeed, for many higher organisms, multi-omics approaches that incorporate multiple omics technologies, tools and data types have become integrated into well-developed platforms that enhance our capability to unravel complex biological questions.Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data that, in tandem with a robust functional omics toolkit, has become one of the most valuable and widely exploited research platforms in biological and biomedical research [C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, including parasite systems, the sole use of C. elegans as a surrogate system for the study of parasitism and infection biology should be approached cautiously. For example, several parasite-specific gene families are absent or functionally divergent in C. elegans [C. elegans-derived functional data to parasites. Despite this, the C. elegans platform should provide a blueprint for the translation of omics tools and technologies to other nematodes that will pave the way for expansions in omics resources and technologies in therapeutically relevant and experimentally tractable parasitic nematodes [Among nematodes, the free-living model organism research . While C elegans  hinderinematodes .https://parasite.wormbase.org/index.html) and a range of transcriptome resources, consistently updating and improving assemblies and annotations where possible [The availability of high-quality species and life cycle stage-specific omics datasets forms the foundation of robust omics platforms. The accessibility and quality of parasitic nematode omics data are continually improving, providing large-scale, rich datasets ripe for exploitation. Indeed, WormBase ParaSite now provides a centralized repository for 177 nematode genomes  that is currently unrivalled by any other nematode parasite  and rapidly progress understanding of parasite biology by connecting genotype and phenotype data in a therapeutically relevant parasitic nematode.The translation and application of omics approaches to parasitic species continue to be challenged by the nature of the parasitic lifestyles where the inaccessibility of parasite material and difficulty in maintaining life cycle stages arasites ,6. AmongStrongyloides and other nematodes causing Neglected Tropical Diseases will revolutionise the ability to perform comparative omics, evolution, drug resistance and molecular interaction studies that will drive the discovery of new targets for therapeutic intervention, vaccine development and improved diagnostics. Here, we provide an overview of the omics technologies and datasets currently available for Strongyloides species, and discuss approaches to data acquisition, data analysis, challenges and future directions.Sustained investment in the development of parasite omics platforms and multi-omics analyses for . 2Strongyloides species—two parasites of rats, S. ratti (44 Mb) and S. venezulensis (44 Mb), the livestock parasite S. papillosus (61 Mb) and the human parasite S. stercoralis (43 Mb). There are also genome assemblies available for two closely related species—a parasite of possums, Parastrongyloides trichosuri (43 Mb), and a free-living species, Rhabditiophanes ditinus (45 Mb) [S. ratti, S. stercoralis, S. venezulensis and R. ditinus, have since been improved using Oxford Nanopore Technologies (ONT) long-read sequencing [S. ratti, S. venezulensis and R. ditinus genome assemblies also incorporated Hi-C maps that map long-range interactions between regions of the genome in 3D space, which can be used to further improve the assemblies as chromosomes tend to have more contacts with parts of the genome that are physically close in the genome [S. venezulensis and R. ditinus both have chromosome-length scaffolds, and S. ratti has two autosomal scaffolds and the X chromosome is in two scaffolds. The assembly of S. stercoralis has two autosomes at chromosome-level scaffolds and the X chromosome is in six scaffolds [S. papillosus and P. trichosuri are more fragmented due to only being based on short-read Illumina sequencing, and contain 4703 and 1810 scaffolds, respectively, which, in contrast to the other species, lack assignment to chromosomes  . While oquencing  (NCBI GCe genome . Contigucaffolds  (NCBI GComosomes . A custoAUGUSTUS  and MAKEAUGUSTUS  training (a)Caenorhabditis elegans was the first multicellular organism to have its genome assembled. This was achieved using a genetic map built during the 1980s and Sanger capillary sequencing with targeting of regions without a known sequence, resulting in an essentially complete assembly, with only a few known gaps, that has been used for most subsequent research [C. elegans genomes, having missed only 1.8 Mb of repetitive regions [Strongyloides spp., the C. elegans genome is 100.29 Mb, more than double the 43.9 Mb S. ratti genome, and is comprised of six chromosomes, compared to the three chromosomes for S. ratti and S. stercoralis and two chromosomes for S. papillosus and S. venezuelensis. The C. elegans genome also has a higher number of annotated genes—19 981 (WormBase Release 289)—compared to S. ratti's 12 474. The N50 size is also larger (17.5 Mb for C. elegans versus 12.1 Mb for S. ratti); however, this is likely due to the larger size of the C. elegans genome, which has longer chromosomes (size range 12–20 Mb versus 12–18 Mb for S. ratti) (research . Compara regions . Compare. ratti) . (b)S. ratti has had one of the most contiguous genome assemblies among parasitic nematodes since the assembly became available in 2016 [A. suum [Haemonchus contortus [Bursaphelenchus xylophilus [B. malayi [Heterodera glycines [. Like the most recent 2023 Strongyloides genome assemblies, these assemblies have taken advantage of long-read sequencing (e.g. ONT or PacBio HiFi) and Hi-C contact data S. papillosus and P. trichosuri using long-read sequencing and Hi-C contact maps to scaffold is a priority. This will generate assemblies with chromosome length contigs that would open opportunities for comparative genomic analysis such as evaluating the role of gene organization in infection. (ii) Genome sequencing of more Strongyloides species, particularly those that are medically important such as the human parasite S. fuelleborni, to improve genome-level understanding of therapeutically relevant parasitic nematode species. (iii) Current genome assemblies are limited to laboratory-based cultures. S. ratti and S. stercoralis have been maintained in the laboratory since 1960  and 1984 [Strongyloides in real-world infections. Combining these data with clinical information or information about infectivity is also important to determine the genetic basis of Strongyloides parasitism and addressing questions around the zoonotic characteristics of S. stercoralis.(i) Improvement of existing reference genome assemblies of and 1984 , respect. 3Strongyloides samples within a population (population genetics) and between species (phylogenetics). Phylogenomics and population genomics, i.e. where information from genome sequences are used instead of information for a single or a small selection of genes or sequences, is fast becoming a popular method to better study understand relatedness and differentiation within and between populations and species. Here, we summarize the research on Strongyloides using both genetic and genomic-based approaches. Most phylogenetics datasets for Strongyloides focus on the epidemiology of S. stercoralis or S. fuelleborni in two key areas: (i) infection surveillance to track transmission in areas where Strongyloides is endemic and (ii) zoonotic transmission, to identify shared haplotypes of parasites infecting both humans and other animals  gene [Strongyloides species.Although not strictly an omics application, phylogenetics and population genetics are useful tools for exploring evolutionary histories and relatedness across  1) gene . The hyp 1) gene  have speStrongyloides species evolve, and identify differences in genomic variation within and between populations and species. Population genomics has not been explored deeply in Strongyloides spp. Two studies have performed whole genome shotgun sequencing and examined genetic diversity in S. stercoralis isolates from infected patients [S. ratti from wild rat faeces collected in England and Wales found that a few long-lived lines infect many rats across the three distinct sampling sites studies and there was little variation between the sites [Strongyloides parasitism in S. ratti  [Strongyloides species.More recently, there has been an increase in the use of phylogenomics and population genomics, using shotgun genome sequencing and evaluation of SNPs to try to resolve more detailed phylogenies and thereby improve understanding of how patients ,46. Bothhe sites . There iterases) . For all (a)C. elegans population genomics has been used to (i) discover novel genotypes and unravel the genetic underpinnings of phenotypes [C. elegans laboratory strains to, for example, investigate experimental evolution [Strongyloides research in this area is solely concerned with transmission or species specificity; therefore, these C. elegans applications are much more diverse in comparison. There is scope to expand the types of questions and analyses carried out in Strongyloides studies, for example by focusing on other features of their life history or ecology and evolution.Recently, enotypes ; (ii) inenotypes ; (iii) aenotypes ; and (ivenotypes . There hvolution  and studvolution . Most St (b)Strongyloides, addressing a wide range of topics including identifying a genetic locus associated with anthelminthic drug resistance in multiple distinct populations of H. contortus [Trichuris trichiura [Phylogenetics studies have long been carried out on parasitic nematodes using marker genes, and more recently this has extended to phylogenomics and population genomics studies from whole genome sequencing data . These sontortus , and undrichiura . (c)Strongyloides species and over a wider geographical distribution of sampling sites. This would provide information about which regions of the genome are under more evolutionary pressure and how the populations in endemic areas are linked or associations of genetic signatures with anthelminthic drug resistance. This knowledge could be useful when selecting vaccine or drug targets [Strongyloides infection genotypes, and matching this with information on infection phenotypes, e.g. severity of infection or symptoms associated with infection, should be a key focus for this research area. This information could facilitate the prediction of important information associated with infection including transmission dynamics, disease severity and treatment susceptibility. These insights would provide both epidemiological and clinical benefits, resulting in improved modelling of transmission and development of genomic tests to identify more appropriate treatments. We also need to diversify the range of Strongyloides species studied as the majority of published studies focus on human-infecting species. Generating data from a broader range of Strongyloides species, such as S. papillosus, would aid the creation of similar models for livestock treatment. In species such as S. ratti, whole genome population data would additionally facilitate complementary laboratory-based experiments e.g. to test hypothesizes about genotype–phenotype associations.A priority is to perform population genomics studies for a wider range of  targets , as well targets . Improvi. 4S. venezuelensis were sequenced [a). Genes coding for nicotinamide phosphoribosyltransferase, tuberin and ferrochelatase were identified as putative parasitism-related genes. Strongyloides spp. exhibit a unique life cycle in which genetically identical parasitic adult female (pF) and free-living adult female (flF) generations exist. These life cycle stages can be directly compared to investigate the genes underpinning parasitism; for example, genes significantly upregulated in the pFs versus flFs can identify genes putatively involved in parasitism or other features associated with the parasitic life stage [S. stercoralis, S. ratti, S. papillosus and S. venezuelensis [a). In total, 10–18% of expressed genes were identified as differentially expressed between flFs and pFs in the four Strongyloides species. Across Strongyloides spp., genes from 29 families are upregulated in pFs and are thought to have a putative role in parasitism; including genes that encode acetylcholinesterase, astacin-like metalloendopeptidase and CAP-domain containing proteins  [The transcriptome represents a portion of the genome transcribed into RNA molecules (expressed) in a given tissue, life cycle or organism  and by cequenced . The majfe stage . RNAseq uelensis ,67–69 (fCP/TAPs) ,69.FiguS. stercoralis and 909 in S. ratti which were specifically upregulated in pFs compared with flFs, 18–19% code for astacin-like metalloproteases or CAP-domain containing proteins [cf. flF) of S. stercoralis, S. ratti, S. papillosus and S. venezuelensis differs between species. Specifically, 25–305 gene families were uniquely upregulated in pFs of one species but not the pFs of the other three Strongyloides species. S. venezuelensis is the most divergent and 305 gene families containing 327 genes upregulated in the pF (compared to the flF) are unique to this species [Strongyloides spp. coinciding with the evolution of parasitism within the Strongyloides clade. Also, genes upregulated in the S. ratti pF, compared with the flF or iL3 stage, are physically clustered together on regions of chromosome II, which could be important for the co-regulation of transcription of parasitism-associated genes [Of the 1188 genes in proteins . The typ species , suggested genes .Strongyloides parasitism. The iL3 has both a free-living stage where it is seeking a host, and a parasitic stage where it penetrates and migrates through host tissue en route to the small intestine. iL3s have been recovered from host lungs and the lung is believed to be a common route of infection for iL3s migrating to the small intestine. After the intestine, the lungs are the most common organ to find Strongyloides iL3s located during a disseminated infection [S. venezuelensis has been associated with an upregulation of six astacin-like metalloproteases and two glycoprotein coding genes, predicted to code for proteins in excretory/secretory products [S. venezuelensis and S. stercoralis and based on their transcriptome, larval stages appear to be separated by life cycle stage rather than species, despite S. venezuelensis and S. stercoralis infecting different hosts  [The transcriptome of the iL3 life cycle stage has provided further insight into the genetic basis of nfection . The iL3products . In genectively) .S. stercoralis [Strongyloides and C. elegans, to investigate similarities of molecular regulation of developmental arrest between the C. elegans' dauer larvae and parasitic iL3s [C. elegans) were upregulated in Strongyloides iL3s, compared to other larval stages. In addition, gene homologues of C. elegans dauer arrest and activation insulin-like signalling, and TGFβ signalling, are also upregulated in S. stercoralis iL3s, suggesting a role in iL3 development. In S. papillosus, transcript expression analysis of 10 RNAseq datasets across six life cycle stages indicates a high degree of conservation in developmental regulation across Strongyloides species [S. papillosus genes are developmentally regulated with 73% of genes differentially expressed across life cycle stages; 10% of S. papillosus genes were differentially expressed between pFs and flFs, 21% were differentially expressed between free-living males (flM) and flFs and 42–45% were differentially expressed between flF/pF and iL3s. In a comparative transcriptomic analysis, 55% of orthologues from S. venezuelensis and S. stercoralis were assigned to different developmental stages including eggs, larvae and adult stages [RNAseq transcriptomics of seven life cycle stages of rcoralis  was usedtic iL3s ,72. Gene species . The majt stages .Strongyloides spp. are exposed to different host conditions contributes to our understanding of Strongyloides survival and adaptation to their host [S. ratti, genes involved in collagen regulation, muscle function and repair, are upregulated in immunized versus naive mice, indicating that the S. ratti transcriptome can be altered to facilitate protection against damage and expulsion from the host [S. ratti and this must be taking into consideration when interpreting these results. A comparison of gene expression in S. ratti pF derived from the natural rat host compared with pFs derived from a permissive gerbil host, demonstrated an increase in astacin-like metalloproteases and acetylcholinesterase genes in the gerbil-derived parasites further highlighting a putative link between astacin-like metalloprotease expression and parasitism. Even though fewer iL3s successfully establish infection in gerbils, gerbil-derived S. ratti parasitic adults produce more male larvae and survive/reproduce for longer, thus highlighting differences in S. ratti survival and reproduction when exposed to different hosts [Investigation of genes that are differentially expressed when eir host ,73–75. Int hosts .Strongyloides spp. respond at the transcriptome level to drug treatments. When comparing human patients' faecal samples cultured on nutrient agar plates that are either untreated or treated with the corticosteroid dexamethasone (DXM), free-living adult stages of S. stercoralis display differential expression of 199 and 263 genes upregulated in flFs and flMs, respectively, that are involved in developmental processes, multicellular organismal processes and embryonic morphogenesis [Strongyloides transcriptome data, data repositories and software such as the Strongyloides RNA-seq Browser [Strongyloides species and will facilitate easier comparative gene expression and enrichment analyses.There is a lack of information about how ogenesis . This ra Browser  will be  (a)C. elegans transcriptome (PRJNA13758) contains 31 989 transcript variants for 19 981 protein-coding genes with further 28 138 transcripts for other RNA sequences such as pseudogenes and non-coding RNAs. In Strongyloides spp. the total number of transcripts annotated is similar to the total number of genes (b) (WormBase ParaSite Version WBPS18) [Strongyloides genes are not well annotated. Furthermore, while most transcripts have an average read length of 1202–1237 bp across all four Strongyloides species sequenced, similar to C. elegans, there are an increased number of shorter length transcripts in Strongyloides spp. especially in S. papillosus and S. venezuelensis (c). This may represent genuinely shorter transcripts in Strongyloides spp. but is likely to be indicative of annotations that require improvement. Information on the UTR regions of transcripts is also lacking for Strongyloides spp. C elegans remains at the forefront of nematode transcriptome data availability and annotation quality and is continuously improving through sustained contributions from a large scientific community. Current C. elegans annotations contain 27 371 5′UTR and 47 676 3′UTRs (n.b. some transcript variants have multiple UTR annotations). In C. elegans, long-read cDNA and direct RNA sequencing has further improved transcriptome annotations. Using ONT long-read sequencing 23 865 isoforms have been confirmed from 14 611 genes, out of which 3452 were previously undiscovered, with 16 342 isoforms in the 3′UTR region and polyA identification and annotation in all the major life cycle stages, excluding embryos and the arrested dauer stage [C. elegans to further improve the transcript annotations, identify trans-splicing of mRNAs and confirm splice leaders 1 and 2  [The of genes b (WormBa WBPS18)  because uelensis c. This mer stage . ONT seqL1, SL2) . (b)Brugia malayi (PRJNA10729), Heligmosomoides polygyrus (PRJEB15396) and Trichuris muris (PRJEB126) have transcript variant data available, and 27–64% of transcripts contain UTR annotations (WormBase ParaSite Version WBPS18). In A. suum, over 60 000 transcripts have been annotated and validated from RNAseq data, defining alternatively spliced and trans-spliced transcripts and allowing for an extended annotation of UTR regions of previously annotated transcripts [H. contrortus [H. contrortus 67.8% of transcripts were annotated with UTR regions following long-read sequencing and manual curation, many of which were previously misannotated as coding exons [With the improved availability and affordability of RNAseq, transcriptome data is available for many parasitic nematodes, especially those from the nematode clades III–V –82. The nscripts . Using Prus PRJEB396 and Trus PRJEB396 and Tng exons , further (c)Strongyloides spp. and other parasitic nematodes. In addition, time point comparisons within life cycle stages have demonstrated differential expression [S. papillosus, S. venezuelensis and S. stercoralis (b) and partially from S. ratti for which we have 5′UTR and 3′UTR annotation for only 11% and 17% of the transcriptome (b). Improved UTR data will enable us to bioinformatically more accurately predict target sites for small RNAs (sRNAs) and to improve transcript comparisons between life cycle stages, e.g. are different transcript variants of the same gene used in different life cycle stages? Long-read sequencing technologies such as ONT and PacBio are important tools for improving these annotations in the future. Long-read sequencing enables us to sequence full-length transcripts, accurately characterizing the transcripts from 5′UTR to 3′UTR region, including alternatively splicing of exons. Long-read sequences also reduce the GC and amplification bias of RNAseq, improving the quantification of transcripts [Strongyloides species or for most other parasitic nematodes, but would offer further insights into genes that are important for parasitism and development. The increased availability of sequencing data for more Strongyloides species and strains, along with further research into their life cycle stages—including time points within these stages and data on gene expression for wild isolates—will aid our understanding of Strongyloides species’ adaptation to their environment and their gene regulation response to environmental change.There is limited egg and early stage host-migrating larvae transcript information available for pression  but thespression . While Upression . Additiorcoralis b and parcriptome b. Improvnscripts . Sequenc. 5Proteomics is an important tool for understanding the molecular basis of parasitism, where the application of proteomics tools has the potential to characterize protein fingerprints associated with parasite infection, development and parasite–host–microbe interactions. With the advent of tandem liquid-chromatography–mass spectrometry (LC–MS/MS) and improvements in nematode genomic and transcriptomic resources, research into nematode proteomics has expanded in recent years. Most of the current nematode proteomics research can be divided into three main categories based on the source material: (i) somatic (whole-worm) lysate, (ii) excretory–secretory products (ESPs) and (iii) extracellular vesicles (EVs).Strongyloides spp. has focused on the iL3 stage to better understand strategies used to establish infection [Strongyloides spp. was conducted with S. stercoralis, followed by studies in S. ratti [S. venezuelensis [S. stercoralis proteomics study used iL3s obtained from infected patients and identified 26 proteins including myosin, actin, elongation factors, ATP synthases, galectin and stress response proteins [S. stercoralis draft genome in 2016 [S. stercoralis iL3 proteome to identify 430 proteins (3.3% of the predicted protein dataset) in S. stercoralis iL3 whole-worm lysates [S. ratti [S. venezuelensis [S. stercoralis host tissue penetration, parasite development and host immune evasion [Strongyloides spp. transcriptomic, genomic and proteomic analyses by confirming the presence of proteins that were predicted to be associated with Strongyloides spp. parasitism. Collectively the data derived from the above Strongyloides spp. studies highlight the benefits of a multi-omics approach whereby the combination of in silico approaches (genomic and transcriptomic) with experimental proteomics (LC–MS/MS) has the potential to identify proteins associated with parasitism and reveal complex host–parasite interactions, reviewed here and also elsewhere in this issue [Nematode somatic proteomes are typically derived from whole-worm lysates whereby nematode tissue has been mechanically disrupted, resuspended in a lysis buffer and subjected to protein extraction. Most of the somatic proteomics research in nfection ,87–89 , with CAP domain-containing proteins, galectins and enolases among the most abundant proteins detected [S. ratti and S. venezuelensis iL3 ESP and are upregulated (at both the gene and protein levels) in S. ratti pFs [Ancylostoma caninum iL3 ESP, where they are associated with the free-living to parasitic lifestyle transition, host invasion and host immune system cross-talk [Strongyloides spp. iL3 ESP proteomes will shed light on the importance of these proteins in iL3 biology. Further life stage-specific ESP comparisons identified both conserved and species-specific proteins in S. venezuelensis and S. ratti [S. ratti, 196, 79 and 35 proteins were unique to iL3s, pFs and fLFs, respectively [S. venezuelensis, 350 proteins were specific to iL3s and 94 proteins specific to pFs [Strongyloides and Parastronyloides spp. to aid the characterization of proteins that may be key to parasitism or parasite development.Excretory–secretory products (ESPs), released by helminths into the host environment, are considered an important facet of host–parasite–microbe interactions . As suchectively    that areipelines –111 prov (a)et al. [C. elegans tissue [et al. [C. elegans [C. elegans biology, including reproduction and development [C. elegans ESP, including transthyretin-like proteins, C-type lectins, proteases and fatty acid binding proteins [C. elegans ESP but present in parasitic nematode ESP, suggesting a common functional role in parasitism [Strongyloides spp. pFs appear to secrete unique trypsin-inhibitor like (TIL) domain-containing proteins [Stongyloides spp. parasitism [C. elegans EV cargo is lagging behind the somatic and ESP proteome analysis; however, 224 proteins have been identified in C. elegans EVs and demonstrated that C. elegans EV protein composition differs considerably from whole-worm lysate [By exploiting LC–MS/MS and shotgun proteomics, Merrihew et al.  identifis tissue . Followi [et al.  detected elegans . Since telopment , ageing elopment ,116 and elopment –119. Oneproteins . Interesproteins . A numberasitism ,121. Of proteins ,120,122 rasitism . Like pam lysate . (b)Trichinella spiralis, H. contortus, H. polygyrus and Nippostrongylus brasiliensis that enable species and life stage comparative analyses [Strongyloides spp., there appear to be a core set of proteins  that are conserved between parasite life stages, indicating that the majority of proteins detected appear to be life stage-specific [Strongyloides spp., there are ESP proteomic profiles for 20 parasitic nematode species including A. caninum, Necator americanus, H. contortus and H. polygyrus [Strongyloides spp., numerous studies have characterized EV protein cargo in other parasitic nematode spp. [T. muris EV proteomes yielded different data [Over the past 10–15 years significant progress has been made in proteomics platforms for identification of nematode somatic proteins that hold potential as biomarkers or therapeutic targets . Life stanalyses –130. Indspecific ,131. Parolygyrus –136. Comolygyrus ,137–139 olygyrus . While pode spp. ,140–142.ode spp. ,140,142;ent data  and thisent data ,124. (c)Strongyloides spp. biology. Indeed, more generally, the standardization of proteomics methods is also critical to the delivery of experimentally robust datasets that will inform nematode biology. Primarily, the priority for Strongyloides spp. should be the generation of equivalent proteomics data for somatic, ESP and EVs across Strongyloides spp. and life stages to facilitate robust comparative analyses and drive the discovery of new biomarkers and control targets for strongyloidiasis. These data would also enable interrogation of the Strongyloides host–parasite interface and the influence of abiotic/biotic environmental factors on the Strongyloides ESP and EV proteomes.Expansion and improvement of genome and predicted protein datasets will facilitate the growth and enhancement of nematode proteomic data derived from somatic (whole-worm) lysate, ESP and EV sources . The con. 6Strongyloides spp.Peptidomics is classed as a subset of proteomics and is defined as the peptides (approx. less than 10 kDa) produced in a cell, tissue or organism at a specific timepoint . Relativ (a)Drosophila melanogaster for application in C. elegans. This has resulted in the identification of a raft of C. elegans neuropeptides [C. elegans peptidomics highlights the need for expanded LC–MS/MS studies in parasitic nematodes that exploit in silico analyses [C. elegans peptidomics data parallel advances in LC–MS/MS technology, it will become possible to map specific cell/neuron peptide expression and dynamics to provide novel insights into nematode peptide biology that will also aid our understanding of parasite systems.The Schoofs laboratory has developed a high-throughput LC–MS/MS peptidomics approach adapted from peptides –149 thatpeptides ,151. Advanalyses ,153 and  (b)A. suum [H. contortus has been studied in addition to A. suum, and the focus has primarily been the identification of neuropeptide and antimicrobial peptide profiles in somatic extracts [in silico genomics and transcriptomics with LC–MS/MS has further advanced proteomic and peptidomics research [Much of the initial parasitic nematode peptidomics research was focused on the pig parasite A. suum –157. Sinextracts ,151,158.research , and theresearch . (c)Strongyloides spp. peptidomics studies will rely on the continued expansion, improvement and integration of in silico datasets, peptidomics tools, LC–MS/MS technologies and optimized analysis pipelines. Specifically, future research in this area should prioritize the translation of the peptidomics pipelines used for H. contortus [C. elegans [Strongyloides spp., life cycle stage, somatic, ESP and EV peptidomes. These analyses will facilitate downstream functional analyses to inform aspects of Strongyloides peptide biology, including host–parasite–microbiome interactions.The advancement of ontortus ,151 and  elegans  to probe. 7sRNAs are non-coding RNA molecules of typically 18–30 nt in length that regulate genes at the post transcriptional level. The regulation of genes by sRNAs is an important mechanism required for the survival and reproduction of parasitic nematodes in the host and environment . The rolS. ratti, S. papillosus, S. stercoralis and the close relative P. trichosuri [. The first study characterizing sRNA expression in Strongyloides was carried out in S. ratti iL3s and free-living adults [S. ratti miRNA sequences were annotated, of which 18 were identified in mixed life cycle stages, eight in iL3s and 80 in both stages. Two miRNAs (mir-34 and mir-71) were highlighted as potentially important in regulating stress and ageing. Further analysis on the miRNA seed sequence (the 2–8 nt region associated with regulating gene expression) revealed that 37 of the 106 miRNAs contain conserved miRNA seed families shared with C. elegans and Pristionchus pacificus, among 24 miRNA seed families conserved between the three species investigated [S. ratti, S. papillosus and P. trichosuri iL3s and free-living adults (mixed sex) was further compared using two different library preparations to capture sRNAs that have either a 5′ monophosphate or 5′ polyphosphate modification [S. ratti miRNAs identified 33 new miRNAs in addition to the 106 previously reported, bringing the total number of characterized miRNAs in S. ratti to 139 [S. papillosus and P. trichosuri, respectively, and miRNA sequences are largely conserved across Strongyloides spp. and P. trichosuri. miRNAs 22–23nt in length represent 79%, 55% and 80% of all genome-mapped sRNA reads in the 5′ monophosphate-enriched library for S. ratti, S. papillosus and P. trichosuri, respectively, and have a propensity for a 5′ uracil (U) in all three species [S. ratti, S. papillosus and P. trichosuri), 65, 73 and 99 miRNAs, respectively, exhibited a differential level of expression between iL3s and free-living adult life cycle stages. Strongyloides stercoralis miRNA expression has been investigated in L1 and iL3s isolated from human stool [S. stercoralis, substantially more than the number of miRNAs identified in other Strongyloides spp. Upon comparison, 169 novel miRNAs showed no sequence similarity with miRNAs from S. ratti, S. papillosus or C. elegans, suggesting that there are many species-specific miRNAs in S. stercoralis or that miRNAs associated with the L1 stage in other Strongyloides spp. are yet to be discovered. Interestingly, the miRNAs expressed in iL3s were more transcriptionally active than those derived from L1s and were predicted to target and regulate the expression of parasitism-associated genes including astacin-like metalloproteases [sRNA sequencing has confirmed that sRNAs are expressed in ichosuri –166. Theg adults . Using ag adults , 106 matstigated . sRNA exfication . Annotati to 139 . A total species . Among aan stool . A totalroteases   and intergenic sequences in the genome, hypothesized to be siRNAs [C. elegans. The siRNAs expressed in S. ratti, S. papilllosus and P. trichosuri have a length of 27nt with an equal bias towards a 5′ guanine (G) and adenine (A) (27GAs). The targets of 27GAs based on sequence complementarity were predicted to be TEs in S. ratti pFs, free-living adults and iL3s, S. papillosus and P. trichosuri free-living adults and iL3s [S. ratti pF and flF, the 27GA siRNAs are predicted to target and regulate the expression of TEs predominantly located on the X-chromosome [S. stercoralis has not yet been investigated.Non-miRNA classes of sRNAs including siRNAs and piRNAs have also been investigated in e siRNAs . These pand iL3s . In S. rromosome , but thiromosome . Althougromosome , siRNA eStrongyloides [S. ratti, S. papillosus and P. trichosuri iL3 and free-living adults. However, the pF stage of S. ratti expresses a piRNA-like class of sRNAs with a length of 21–22 nt and propensity towards a 5′ uracil (21–22U) [C. elegans and D. melanogaster, including their length, 5′ uracil, 5′ monophosphate modification, clustering and overlapping of sequences in the genome and an AT rich downstream sequence. However, these piRNA-like sRNAs did not have an upstream Ruby motif, as found for C. elegans piRNAs. The 21–22U piRNA-like sRNAs are specifically highly expressed in the pF compared with flF, indicating that they may be directly related to parasitism or features associated with the parasitic life cycle [The piRNA class of sRNAs has been lost in nematodes outside of clade V nematodes, including gyloides ,161,164 (21–22U) . The piRfe cycle . (a)C. elegans and this species has become an important model organism for the study sRNA biology [C. elegans expresses 253 precursors and 437 mature miRNAs [Strongyloides miRNAs, including a 5′ monophosphate modification, with a length of 21–22 nt and bias towards 5′ U or 5′ A. Comparison of Strongyloides miRNAs to those found in C. elegans has revealed that 31 seed families are shared between S. ratti and C. elegans, while 30 are shared between S. papillosus and C. elegans [let-7, lin-4, mir-34 and mir-37, indicating that the conservation of these miRNAs is essential in nematodes. In comparison to Strongyloides, C. elegans siRNAs and the sRNA pathways they belong to are well characterized, with distinct biological functions depending on their biogenesis. C. elegans expresses primary 26G siRNAs containing a 5′ monophosphate modification, which is important in the regulation of gene expression during spermatogenesis and zygotic development [Strongyloides, it has been suggested that 27GA siRNAs are equivalent to 22Gs in C. elegans [Strongyloides spp.—C. elegans is known to produce and express piRNAs, also known as 21U sRNAs, that are important in regulating the activity of TEs [Strongyloides have evolved an alternative class of piRNA-like sRNAs, the 21–22Us, which are predicted to be important in regulating TEs in the absence of piRNAs [sRNAs were originally identified in  biology ,169. C. e miRNAs . These m elegans . Among telopment . The 26Gelopment . As ther elegans ,166. As y of TEs . Strongy (b)Strongyloides, piRNAs in clades I–IV nematode including A. suum (clade III) [B. pahangi [C. elegans piRNAs [S. ratti [H. polygyrus [H. polygyrus ELVs shared sequence similarity with the host miRNAs. Further analysis of sRNAs using the 5′ phosphate-independent library revealed a prevalence of siRNAs derived from repetitive elements and intergenic regions [Nematodes in clades I–V express conserved miRNAs . Howeverade III)  and B. p pahangi  are losts piRNAs ,174,176 S. ratti . In addiolygyrus . These Eolygyrus . miRNAs  regions . (c)Strongyloides species. To gain a deeper understanding of the role of sRNAs in parasitism, it is crucial to conduct research on a range of life cycle stages, such as the pF and free-living adult stages of S. stercoralis, and species, such as S. fuelleborni and S. venezuelensis. (ii) Secretion of parasite-derived EVs containing sRNAs taken up by host cells. Further research is needed to understand the specific functions of sRNAs in these interactions, including how parasites use sRNAs to manipulate the host environment. This knowledge could not only enhance our understanding of host–parasite relationships, but also provide valuable diagnostic tools. ELV-bound sRNAs have not been investigated in Strongyloides. (iii) sRNAs as biomarkers. sRNAs have potential to be useful biomarkers for disease diagnosis and prognosis in humans and animals. As there is currently no gold standard method for detecting Strongyloides infections in the host, sRNAs present an opportunity to be developed as a diagnostic tool. For instance, the research carried out on sRNAs in S. stercoralis from human infections [Strongyloides in humans. (iv) Validation of sRNAs and their targets. Most sRNA research to date has used sequencing followed by computational analysis, predicting targets through sequence complimentary. This work needs to be validated using high-throughput approaches such as Argonaute cross-linking immunoprecipitation (CLIP) [in vivo sRNA–target interactions, allowing us to better understand the role that sRNAs play in parasitism and host–parasite interactions. Understanding the regulatory networks of sRNAs could provide insight into their roles in the control of gene expression and other biological processes.(i) sRNA expression across a range of fections  providesn (CLIP)  that ide. 8Strongyloides spp. are described above [S. ratti, TE sequences are distributed throughout the genome but TE-associated sRNAs and their predicted TE targets are clustered on the X-chromosome of both S. ratti female adult stages [TEs are mobile genetic elements occupying the genomes of organisms across all branches of life. TEs can be a major driving force behind genetic variation but can also disrupt regular gene activity via different routes of mutagenesis . The pered above ,166. TEsed above . In S. rde novo and homology-based algorithms have been developed to identify and annotate TEs, often a substantial amount of manual curation is still required to acquire a reliable TE consensus sequence library [S. ratti genome has been carried out by four groups employing different methods of annotation: (i) Suleiman et al. [S. ratti genome, they were further annotated by using the LTR specific tools LTRharvest [S. ratti, S. venezuelensis, S. stercoralis and S. papillosus, as well as close relatives P. trichosuri and R. ditinus. To annotate the repeat features, a pipeline including RepeatMasker [et al. [S. ratti, S. venezuelensis, S. papillosus and P. trichosuri. This curation used a homology-based method that based TE sequence searches on a nematode-specific de novo constructed library, rather than the more general Dfam or RepBase libraries [in silico study conducted by the International Helminth Genomes Consortium constructed repeat libraries for the genomes of 56 parasitic and free-living nematodes. For each species, repeat libraries were constructed by combining libraries generated from RepeatModeler [Mutations induced by strong negative selection pressure have left TE sequences deteriorated and repetitive in nature, which makes their annotation notoriously difficult, especially in assemblies produced from short-read sequences. While several bioinformatics tools with  library . TE sequn et al.  construcn et al.  and Repen et al.  to annotn et al. . As LTR Rharvest  and LTRdRharvest ; (ii) WoRharvest  was usedatMasker , DustMasatMasker  and TRF atMasker  was empl [et al.  have assibraries ,192. Aftibraries  and One ibraries , while fibraries  and LTRHibraries . (iv) AntModeler , TranspotModeler . The libtModeler .Strongyloides spp. by Suleiman et al. [S. ratti, S. venezuelensis, S. papillosus and P. trichosuri [S. ratti TE library comprises 657 TE families occupying 11.2% of the genome, while the International Helminth Genomes Consortium library consists of 3 TE families covering 1.8% of the genome. The Suleiman library contains 5526 TE families that comprise 8.45% of the genome, and the WormBase ParaSite library contains 111 TE families that cover 5.64% of the genome. In addition to mapping to variable proportions of the S. ratti genome, the four TE consensus libraries also vary in the annotation and quantification of different TE families C. elegans. Various methods have been used to annotate the repetitive sequences, including TEs, in the C. elegans genome [Meloidogyne spp. genomes, DNA transposons make up the majority of expanded TEs. Furthermore, repetitive sequences of the free-living nematode P. pacificus were recently annotated via a custom ‘sliding window’ method, where 1 kbp sequence ‘windows’ are extracted and analysed for repeats using 11 different de novo and library-based tools illustrating that 24% of the P. pacificus genome consists of TEs [S. ratti, retrotransposons are the most abundant class of TEs in the P. pacificus genome, accounting for 50% of masked repeats.Despite being the first animal to have its genome sequenced and assembled to a complete level, little is known about TE dynamics in the model organism s genome –200 and s of TEs . Similar (b)Meloidogyne enterolobii was recently sequenced and assembled using PacBio and Illumina reads [M. enterolobii genome is composed of repetitive elements. However, only 8.7% of the repeats were annotated as TEs, where DNA elements seem to have expanded at a greater rate (5.83%) than retrotransposons (2.87%). A consensus TE library was deduced for the closely related species M. incognita using the same workflow described by Koutsovoulos et al. [Meloidogyne spp. have a lower proportion of TEs in their genomes compared to Strongyloides spp. despite them leading similar parasitic lifestyles. Furthermore, DNA transposons have experienced a much larger expansion in the genomes of Meloidogyne spp. in comparison to S. ratti, whose genome seems to include a large number of LTRs. The repeatome of the pig parasite A. suum was also identified using a combination of homology and de novo-based tools [Ascaris genome was assembled using long PacBio reads, revealing that approximately 41% of the genome comprises repetitive sequences. However, the specific classification of these repeats and the familial identities of Ascaris TEs have not been reported [The International Helminth Genomes Consortium TE annotation of 56 helminth genomes was analysed via a multiple regression model to reveal that variations in genome size within the nematode phylum were primarily influenced by variations in genome repeat content, ranging from 3.8% to 54.5%. Notably, the significant contributors to this variation were LTRs, DNA transposons and simple repeats . The afona reads . A TE cona reads  for TE pna reads , where ana reads . It was s et al. . The reps et al. . Meloidoed tools . The Ascreported . (c)Strongyloides spp., researchers have the opportunity to explore potential variations in transposition and TE repression patterns between free-living and parasitic stages. This exploration may elucidate the molecular mechanisms responsible for variances in gene regulation and epigenetic patterns resulting from TE activity, particularly within germline cells [Strongyloides TEs, a library consisting of consensus sequences corresponding to the different TE families present in the genomes of Strongyloides species must be curated. Utilizing long and short sequencing in a de novo pipeline as described by Koutsovoulos et al. [Strongyloides spp. to construct consensus libraries. However, as some previously uncharacterized TE families could be Strongyloides-specific, some manual curation will be required to compile an accurate consensus library, as described by Goubert et al. [Strongyloides genome will allow for a deeper investigation into the role of TEs in genome architecture and their expression patterns. On a broader scale, accurately annotated TE libraries can facilitate comparative studies on TE load across different species and populations. These results can shed light on whether factors such as environment, lifestyle and stress influence the abundance and diversity of an organism's TE dynamics, and to help elucidate what regulatory roles differences in composition, load and activity may play. Furthermore, investigating the TE content of diverse Strongyloides species and strains inhabiting different environments can shed light on the impact of the environment on genome organization, as shown previously in the parasitic flatworms Schistosoma mansoni and S. japonicum [TEs contribute to gene regulation by acting as regulatory elements that manipulate transcription and epigenetic states . By studne cells  and how s et al.  could bet et al. . The estaponicum .. 9Strongyloides spp. and C. elegans. Moving forward, the priority in Strongyloides omics includes (i) investigating more species, including those important to human and livestock health; (ii) investigating samples from wild and clinically important settings as well as laboratory-based populations to understand variation and diversity; and (iii) the application of the latest technologies e.g. long-read sequencing, to improve genome and transcriptome assemblies. There are also areas of omics that have received little or no attention, such as peptidomics, metabolomics, long non-coding RNA, chromatin organization and histone modifications. Numerous projects are now underway within the Strongyloides scientific community to address these areas, which will further close the gap between C. elegans and Strongyloides spp. and improve our understating of the omics biology underpinning parasitism. Advances in omics technologies and data availability will aid identification and development of new ways to detect and control Strongyloides infections and treat the disease that they cause.Recent advances in technologies and omics analysis pipelines will continue to reduce the gap between omics data availability for


The oral cavity microbiome comprises benign and pathogenic bacteria, with more than 700 species identified. However, the current literature regarding resident bacterial flora in the oropharyngeal cavities in cleft lip/palate (CLP) patients still needs to be completed. This review aims to evaluate the role of the oral microbiome of cleft patients as an indicator in systemic diseases for which cleft patients might be at higher risk in the short or long term.A literature review was performed in July 2020 using Biomedical Reference Collection Comprehensive, Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, Dentistry & Oral Sciences Source via Elton B. Stephens Company/Online Database (EBSCO), Turning Research into Practice (TRIP), and PubMed. The keywords used were "oral, bacteria, microbiome, biota, flora, cleft, palate." The resulting 466 articles were deduplicated using Endnote. The total amount of articles' abstracts without duplicates was filtered using a set criterion. The title and abstract filter criteria included 1) cleft lip (CL) and/or cleft palate (CP) patients, 2) changes in the oral microbiome in CL and/or CP patients, 3) male and female patients 0-21 years old, and 4) English language. The full-text filter criteria included 1) CL and/or CP patients vs. non-cleft control patients, 2) oral bacteria, 3) nonprocedural measurements of microorganisms, and 4) case-control studies. A Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) flow chart was created using the EndNote data results.Streptococcus mitis and Streptococcus salivarius; 2) lower levels of Streptococcus gordonii, Bordetella dentium, Fusobacterium nucleatum, Veillonella parvula, Bacillus and Lautropia when compared to the control group; 3) higher levels of Staphylococcus epidermidis and Methicillin-sensitive Staphylococcus aureus compared to the control group; 4) presence of Enterobacter cloacae 36.6%, Klebsiella pneumoni 53.3%, and Klebsiella oxytoca 76.6% vs. absence in the control non-cleft group.The final five articles of the systematic search indicated that the oral cavity of cleft lip and/or palate patients resulted in 1) contradicting levels of S. mitis, S. salivarius, S. gordini, and F. nucleatum in the oral cavity of cleft patients could be linked as a possible cause of the higher incidence of tooth decay, gingivitis and periodontal disease as high levels of these bacteria are associated with oral disease. Further, the higher incidence of sinusitis in cleft patients might be linked to low levels of S. salivarius in the oral profile of these patients. Likewise, E. cloacae, K. oxycota, and K. pneumoni have been linked with pneumonia and bronchiolitis, both of which are increased in cleft patients. The oral bacterial dysbiosis of cleft patients observed in this review may play a vital function in the oral microbiome's diversity, which could play a role in disease progression and disease markers. The pattern seen in cleft patients potentially demonstrates how structural abnormalities can lead to the onset of severe infection.Patients with CL and/or CP are at higher risk for caries, periodontal diseases, and upper and lower respiratory infections. The results from this review indicate that relative levels of certain bacteria may be associated with these issues. The lower levels of  Worldwide, oral clefts occur in about one in every 700 live births . In the Cleft children are at risk for bacterial infections that may cause severe complications. Post-surgical health care needs for cleft patients include but are not limited to breathing, hearing, and speech therapy . FamilieThe oral cavity of CL and/or CP patients is one of the primary culprits for many benign and pathogenic bacteria, as there are more than 700 bacteria species in this anatomical region . The curMethodsA literature review was performed in July 2020 using Biomedical Reference Collection Comprehensive, Collection Comprehensive, Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, Dentistry & Oral Sciences Source via Elton B. Stephens Company/Online Database (EBSCO), Turning Research into Practice (TRIP), and PubMed. The keywords used were “oral, bacteria, microbiome, biota, flora, cleft, palate.” The resulting 466 articles were deduplicated using EndNote. The total amount of articles’ abstracts without duplicates was filtered using a set criterion. The title and abstract filter criteria included 1) CL and/or CP patients, 2) changes in the oral microbiome in CL and/or CP patients, 3) male and female patients 0-21 years old, and 4) English language. If the articles’ abstracts focus on 1) other congenital anatomical abnormalities than CL and/or CP, 2) changes in the gut microbiome, 3) male and female patients older than 21 years old, 4) other languages than English, 5) non-human oral microbiome changes, the articles were excluded. The full-text filter criteria included 1) CL and/or CP patients vs. non-cleft control patients, 2) oral bacteria, 3) nonprocedural measurements of microorganisms, and 4) case-control studies. Articles were excluded if they were 1) case series/reports, review articles, clinical trials, retrospective, or other studies; 2) yeast, virus, fungi, or other microorganisms than bacteria measurements; 3) procedural measurements of bacteria, caries, surgeries, procedures; 4) no statistical analyses; 5) antibiotic, experimental, other treatments influence oral bacteria; 6) articles before 2000. A Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) flow chart was created using the EndNote data results  and three of 27 children in the control group (11.11%) tested positive for P. nigrescensin. Costa et al. found no significant level changes in P. nigrescens between control and cleft patients  and Lautropia (cleft 40% vs. non-cleft 90%) between the cleft vs non-cleft control group , S. salivarius (cleft 100% vs. non-cleft 84%), and S. epidermidis (cleft 83.30% vs. non-cleft 28%), MSSA (cleft 93.30% vs. non-cleft 20%), E. cloacae (cleft 36.6% vs. non-cleft 0%), K. pneumoni (cleft 53.3% vs. non-cleft 0%), and K. oxytoca (cleft 76.6% vs. non-cleft) , S. gordonii (cleft 61% vs. non-cleft 82%), S. salivarius (cleft 35% vs. 57% non-cleft), B dentium (cleft 6% vs. 18% non-cleft), F. nucleatum (cleft 55% vs. 75% non-cleft), and V. parvula (cleft 6% vs. 18%) when compared to their non-cleft control  glycoproteins that bind salivary mucin [S. mutans [S. salivarius at higher oral levels. This research also found low levels of a late colonizer F. nucleatum [S. gordinii in biofilm formation of healthy and diseased teeth and gingiva [F. nucleatum and S. gordinii and their role in biofilm formation involves a second outer membrane protein, CmpA. CmpA acts as a dual-species biofilm formation with S. gordinii V288 to further form and maintain the biofilm matrix [Per the Centers for Disease and Control Prevention, periodontal diseases are conditions that involve infections, attachment loss, and inflammation of the gingiva, along with other structures that surround the tooth . Oral St gingiva . These b gingiva . The bio gingiva . The lacormation . S. gordry mucin . It is i. mutans , which sucleatum , which i gingiva . Lima etm matrix . This syChildren and adolescents with CL and/or CP have an increased prevalence of caries, gingivitis, and mild periodontitis . PassinaUpper Respiratory Diseases: Sinusitis S. salivarius. Strains of this bacterium have an anti-Streptococcus pyogenes activity role and have increasingly been used as preventative measures for sinusitis and upper respiratory tract infections such as tonsillitis and pharyngitis [S. salivarius TOV-R strain's inhibitory activity towards Streptococcus pyogenes and Streptococcus pneumoniae has been directly linked to its bacteriocin production [S. salivarius affects immunity by inhibiting inflammatory pathways activated by these bacteria via inhibition of IL-8 secretion and innate immune response pathways in alveolar, bronchial and pharyngeal epithelial cells [ S. salivarius might be an opportunity to provide probiotics to boost the immune protective role of S. salivarius against both upper and lower respiratory infections and decrease the higher incidence of sinusitis in CL and/or CP patients. Sinusitis has been associated with cleft lip and palate -41. Wei ryngitis -45. S. soduction . Additioal cells . The dimLower Respiratory Diseases: Bronchiolitis and PneumoniaK. pneumoni is an etiology of community-acquired pneumonia and hospital-acquired pneumonia [K. pneumoni has historically been identified as a pathogen in hospital-acquired infections [K. pneumoni were found in this research as part of the baseline oral profile in CP and/or CL patients, linking the higher incidence of pneumonia in this patient population.Lower respiratory tract infections (LRTI) are prevalent in children with CL and/or CP. Sato et al. found that children under one year of age with CL and CP have a higher incidence of pneumonia and bronchiolitis than those in the non-cleft control group . K. pneuneumonia . The polneumonia . K. pneufections . Higher E. cloacae levels were found in CLP compared to the complete absence of the bacteria in the non-cleft controls. E. cloacae has been reported as an opportunistic and multi-resistant bacterial pathogen for humans in hospital wards for the last 30 years [Enterobacter is a versatile bacterium that responds promptly to antibiotic treatment in the colonized patient when treated timely [K. oxytoca has recently emerged as a bacterial isolate causing hospital-acquired infection in adults with multiple drug resistance to commonly used antibiotics [K. oxytoca has been isolated from different clinical samples, mainly from the blood and respiratory secretions, and is gaining clinical significance in immunocompromised and debilitated patients admitted to Intensive Critical Care Units (ICUs) [E. cloacae and K. oxycota found in CLP patients and their high antibiotic resistance features could be related to the higher LRTI experienced by cleft patients [Furthermore, higher levels of 30 years . Enterobd timely . Mainly d timely . This bad timely . Furtheribiotics . K. oxyts (ICUs) . The higpatients . This knThe oral cavity of CL and/or CP patients is polymicrobial. Oral bacteria dysbiosis plays a vital function in the oral microbiome's diversity, which could play a role in disease progression and disease markers. Cleft patients have some significant differences when contrasted with non-cleft patients. These differences in the oral microbiome of CL and/or CP might be associated with a higher incidence of caries, periodontal disease, and upper and lower respiratory infections.The pattern seen in cleft patients potentially demonstrates how structural abnormalities can lead to the onset of severe infection. CL and/or CP patients and the corresponding oral dysbiosis that comes with the anatomical changes might increase the risk for caries, periodontal diseases, sinusitis, bronchiolitis, and pneumonia. Thus, it is vital to maintain a healthy balance between the commensal and pathogenic bacteria in the oral cavity of cleft patients to diminish their risk for these diseases.S. salivarius against upper and lower respiratory infections in CL and/or CP patients; (2) To analyze the protective commensal bacteria S. salivarious and S. gordini's protective role in caries development in CL and/or CP patients; (3) To examine if on-time targeting of the resistant E. cloacae and K. oxycota decreases the higher incidence of LRTI in CL and/or CP patients.Furthermore, this review highlighted three scenarios further research should focus on to reduce the short and long-term burden caries, periodontal, and upper and lower respiratory infections have on CL and/or CP patients: (1) To investigate the immune protective role of


Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length of 169,341 bp, comprising a large single-copy region of 102,323 bp, a small single-copy region of 7744 bp, and a pair of inverted repeats (IRa/IRb) of 29,637 bp each. Out of a total 120 genes, 76 were protein-coding genes, 36 were transfer RNA genes, and eight were ribosomal RNA genes. The genomic characteristics of C. carpatica are similar to those of other Campanula species in terms of repetitive sequences, sequence divergence, and contraction/expansion events in the inverted repeat regions. A phylogenetic analysis of 63 shared genes in 16 plant species revealed that Campanula zangezura is the closest relative of C. carpatica. Phylogenetic analysis indicated that C. carpatica was within the Campanula clade, and C. pallida occupied the outermost position of that clade. C. carpatica) belongs to the family Campanulaceae and is one of the more than 300 species in the Campanula genus. C. carpatica is a herbaceous plant native to Eastern Europe and has bell-shaped purple flowers [C. carpatica have been carried out [Campanula species are important horticultural crops that show remarkable morphological and habitat diversity [The Carpathian bellflower  is widely used for the genetic identification and phylogenetic analysis of plant species . The plaC. carpatica using de novo next-generation sequencing (NGS) and reference-guided assembly. We described the basic characteristics of the genome, such as gene content, genome structure, and repeat sequences, and analyzed phylogenetic relationships among the Campanula species.In this study, we assembled and annotated the complete chloroplast genome of C. carpatica was collected from the National Institute of Agricultural Sciences in Wanju, Korea. Genomic DNA was isolated from fresh leaves, and its integrity, DNA purity, and concentration were analyzed using 1% agarose gel electrophoresis and a NanoDrop spectrophotometer . Libraries were prepared by constructing Illumina paired-end (PE) and Oxford Nanopore Technologies (ONT) libraries according to the manufacturer’s instructions. The Illumina PE library was sequenced on an Illumina HiSeq X platform . The ONT library was prepared on a Nanopore GridION platform .C. carpatica were mapped to the reference genome of C. punctata (NCBI accession number NC_033337). Self-correction was performed on the mapped reads, and de novo assembly was performed using Canu [https://github.com/nanoporetech/medaka/, accessed on 15 September 2022). The Pilon program was used to calibrate the draft genome with Illumina short reads, and the Medaka program was used to calibrate the draft genome with ONT reads. Polishing was performed in various ways, including gap filling, indels of bases in the genome, block substitution, and single-base differences. The chloroplast genome sequence was annotated using the GeSeq tool [C. carpatica chloroplast genome was visualized using the OGDRAW program [Raw reads obtained for ing Canu . ONT anding Canu  and MedaSeq tool  with NCB program .C. carpatica chloroplast genome. First, SSRs were identified using the MISA-Web software  with the following parameters: at least ten repeat units for mononucleotides, six repeat units for di-nucleotides, five repeat units for tri-nucleotides, and four repeat units for tetra-, penta-, and hexa-nucleotide repeats. Compound SSRs were defined as repeats that were interrupted by a non-repeat sequence of a maximum of 100 nucleotides. Tandem repeats were detected using the Tandem Repeats Finder software . Tandem repeats observed in at least one copy were considered significant. The parameters were set as follows: alignment parameters of matches = 2, mismatches = 2, indels = 7, minimum alignment score = 50, maximum period size = 500, and maximum tandem repeat array size = 2. Finally, dispersed repeats were identified using the Vmatch tool with two types  on the 30 bp minimal repeat size .Simple sequence repeats (SSRs), long tandem repeats , and dispersed repeats were searched in the Campanula genus in NCBI GenBank (accessed on 20 January 2023): C. pallida (NC_063742), C. punctata (NC_033337), C. takesimana (NC_026203), and C. zangezura (NC_057269). Comparative analyses of pseudogene content, percentage identity, and gene content were undertaken to determine the similarities between C. carpatica and the four Campanula species. The mVISTA program [Campanula species. Multiple genome alignments were performed using the Mauve program [C. carpatica and the four reported Campanula species.Four chloroplast genome sequences were available for the  program  displaye program  with defmana NC_0203, and C. carpatica, we used complete chloroplast genome sequences of 15 Campanulaceae species and Helianthus annuus of the Asteraceae family as an outgroup. The following 16 complete chloroplast genome sequences were downloaded from the NCBI GenBank database (accessed on 6 April 2023): Adenophora triphylla (MT649408), C. carpatica (OP677559), Campanula pallida (NC_063742), Campanula punctata (NC_033337), Campanula takesimana (NC_026203), Campanula zange-zura (NC_057269), Centropogon nigricans (NC_035761), Codonopsis lanceolate (MH251613), Dialypetalum floribundum (NC_035357), Grammatotheca bergiana (NC_036095), Hanabusaya asiatica (NC_024732), Lobelia muscoides (NC_035379), Platycodon grandiflorus (NC_035624), Siphocampylus krauseanus (NC_035760), Trachelium caeruleum (NC_010442), and H. annuus (NC_007977). These sequences were concatenated using only shared protein-coding sequences among the 16 species. Multiple genome alignments among the 16 species were performed using the MAFFT program [C. carpatica within the Campanulaceae family, we generated a maximum likelihood (ML) phylogenetic tree with 1000 bootstrap replicates using the MEGA11 software [To infer the phylogeny of  program  to reconsoftware .C. carpatica chloroplast genome . The C. carpatica chloroplast genome is 169,341 bp long and has a typical circular structure with an LSC region of 102,323 bp, an SSC region of 7744 bp, and a pair of 29,637 bp inverted repeats (IRa/IRb). The length of C. carpatica was within the range reported for higher plant species, that is, 120–180 kb [atpF, rpl2, rpl16, petD, petB, ycf3, rpoC1, ndhA (×2), and ndhB) and one trans-spliced gene (rps12) were identified in the C. carpatica chloroplast genome. The ycf3 gene contained two introns, whereas the remaining nine cis-spliced genes contained only one intron , C. punctata (NC_033337), C. takesimana (NC_026203), and C. zangezura (NC_057269). DNA sequence divergence among the species is a function of neutral, deleterious, and advantageous mutation rates [Campanula species, multi-alignment results indicated that the genome structure, gene order, and gene content have highly conserved sequences among the five Campanula species. A comparison of the LSC, IR, and SSC regions revealed that the LSC region contained more divergent genes  in the IR region. These breakpoints were formed because the chloroplast genomes had positional differences in each genome location. Although the comparison revealed small structural rearrangements in the chloroplast genomes of the five Campanula species, they occurred in the IR region  ,39. To cy blocks . Mauve aR region .Campanula species were compared  region in all the chloroplast genomes, whereas its corresponding pseudogene ndhE fragment (158–164 bp) copy was found at SSC/IRb (JSB) except for C. pallida. The trnH sequences were observed in the LSC regions of all chloroplast genomes, and this gene was located 117–120 bp away from the IRa/LSC border region. Two copies of the rrn16 genes were observed in C. pallida, C. punctata, C. takesimana, and C. zangezura. The rrn16 genes were located in the IRa and IRb regions near the LSC/IR borders; however, two copies of rrn16 genes in C. carpatica were not observed in the near LSC/IR and SSC/IR borders. Additionally, the ycf2 gene was mainly located in the LSC region of other Campanula species, whereas C. carpatica did not contain the ycf2 gene.The expansion and contraction of the border regions in IRs are important factors for variation in the chloroplast genome ,41. The compared . The ycfC. carpatica, an ML tree was constructed using 63 shared protein-coding genes from the chloroplast genomes of 15 species of the Campanulaceae family, including one outgroup species from the family Asteraceae.To resolve the phylogenetic relationships of H. annuus, had the most distinct characteristics (C. carpatica was the closest relative to C. zangezura. Although phylogenetic relationships among the species of the Campanulaceae family are well supported, they do not clearly show the evolutionary relationship because of the low number of chloroplasts in the Campanula species. Nevertheless, our phylogenetic analysis is the first to clarify the phylogenetic position of C. carpatica within the family Campanulaceae.Chloroplast genomes have been widely used to explore phylogenies because of their low rate of nucleotide evolution, absence of recombination, and uniparental inheritance ,43. The eristics . Most CaC. carpatica chloroplast genome was sequenced and assembled for the first time. This demonstrates that the combination of Illumina and ONT sequence libraries is sufficient for a high-quality chloroplast genome assembly. Detailed characteristics of the C. carpatica chloroplast genome were determined based on analyses of chloroplast features, repeat sequences, sequence divergence, and boundaries between plastome regions. The genome has a typical circular structure, is 169 kb long, and contains 120 functional genes. Genome size, gene content, genomic composition, and phylogenetic relationships were similar to those of other Campanula species. Overall, we revealed the complete chloroplast genome sequence of C. carpatica and identified 157 repetitive sequences as potential molecular markers for the Campanulaceae family. These findings enrich our knowledge of gene composition, genome evolution, and genetic diversity of the Campanulaceae species. In addition, these genetic resources provide a reference for further genomic studies on the Campanulaceae species.The


Apicystis bombi was isolated almost exclusively from bumble bees (Bombus spp.) where it disrupts adipose tissue, increasing hosts’ mortality rates. Records in solitary bees are scarce worldwide. To check for its presence in carpenter bees (genus Xylocopa), campaigns were performed in Argentina capturing 154 individuals of five species . The presence of A. bombi was detected by molecular means in X. augusti, X. atamisquensis, and X. nigrocincta in four of the nine provinces screened. The pathogenesis and eventual impact that A. bombi may cause in individuals or populations of Xylocopa species remain unknown. The presence of A. bombi in northern Argentina would be contradictory to the hypothesis that its occurrence is the exclusive result of its introduction to South America through invasive, infected exotic bumble bees.Historically, the neogregarine   •Xylocopa individuals were scrutinized for the neogregarine Apicystis bombi.•Apicystis bombi was found in X. augusti, X. atamisquensis and X. nigrocincta.•Xylocopa – A. bombi were found in four Argentine provinces.The new associations  The neous spp.) . Lipa anpicystis . Since tty rates . During ty rates , althougty rates .Xylocopa spp.; Apidae: Xylocopini) are solitary,Passiflora edulis Sims [Passion fruit], Vaccinium corymbosum L. [Blueberry], Solanum melongena L. [Eggplant] , X. splendidula (n = 31), X. atamisquensis (n = 21), X. frontalis (n = 6), and X. nigrocincta (n = 5)] were captured in natural (protected areas), rural roadsides and agricultural lands from 29 localities (nine provinces) of Argentina throughout Spring-Summer seasons between 2009 and 2019  and amplified by qPCR using two pair of primers: ApBF1 and ApBR1 - which targets tica DNA  , Buenos Aires (Arana and Mar del Plata), and Corrientes (Colonia Pellegrini), three X. atamisquensis [two from Formosa province (Ibarreta and Las Lomitas) and one from Río Negro ], and one X. nigrocincta captured in Formosa  (A. bombi. Two of the isolates were double-sequenced and deposited in Genbank as follows: NCBI accession number MT547746 corresponds to Villa Regina (Río Negro) sampled from X. augusti, and MT547735 to Palo Santo (Formosa) sampled from X. nigrocincta.Presence of o Santo) . Sequence.g., sluggishness, disorientation, inability/difficulty for flying , a solitary bee, seem to be seriously affected by A. bombi, a similar virulence in Xylocopa species might be possible, yet remains to be determined  and pear (Pyrus communis L.) (A. mellifera) play a leading role as pollinating agents and occupy an ecological niche in the region similar to that of Bombus  . Presencunis L.) . It is lf Bombus . Therefoera apis , variousera apis , AmFV  and Formosa  (Bombus ruderatus and B. terrestris) were introduced in Chile for pollination purposes in 1982 and 1998, respectively, becoming established and expanding in both Chilean and Argentine Patagonia region  b turns oa region . It has cies see . Since bong axis b, arrow]ong axis , the arrColombia  and BrazColombia  would su America .A. bombi in Río Negro valley (northern Patagonia), where many beekeepers bring transhumant hives from the Pampas region (Xylocopa (A. bombi in the Pampas.Finally, the Pampas region is located in the center-east of Argentina and contains more than one million honey bee hives that generate almost half of the total production in the country . Detectis region , could rXylocopa , and retNone.


Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups . A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.Commensal  Escherichia coli is a very versatile bacterium that is known to survive in different niches including in warm blooded mammals and the environment due to its genomic plasticity. It comprises pathogenic and non-pathogenic strains which sometimes co-exist in specific niches such as the gut. To survive in the gut, they must be able to withstand the conditions therein, including the assault by the host gut immune system and other chemicals that reach the gut, such as antimicrobial agents. Those that are susceptible to the host immune system and antibacterial agents will be eliminated. The gut commensal bacteria must therefore possess minimal protective attributes such as virulence traits and antimicrobial resistance to the antimicrobials they are frequently exposed to. These traits enable the bacteria to survive the assault and competition with other microbes within those systems [ systems .E. coli are generally known to belong to A, B1, B2, C, D, E, and F phylogenetic groups. The phylogroup classification is based on the presence or absence of four genes  [E. coli (IPEC) and extra-intestinal pathogenic E. coli (ExPEC). There are several pathotypes based on the disease and/or pathogenesis, including uropathogenic E. coli (UPEC), neonatal meningitis E. coli , avian pathogenic E. coli (APEC), enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC); enterohemorrhagic E. coli (EHEC); enterotoxigenic E. coli (ETEC); enteroinvasive E. coli (EIEC); and enteroaggregative E. coli (EAEC), diffuse adhering E. coli (DAEC), adherent-invasive E. coli (AIEC), sepsis-associated E. coli (SEPEC) and unspecified ExPEC, as previously described [nd arpA) . The patE. coli produce “Shiga toxins”, encoded by the stx1 and/or stx2 gene common to all EHEC bacteria, and are also pathogenic for animals and humans [E. coli and others has been challenged because of the frequent genomic alterations and genetic exchanges within and between strains, where non-pathogenic strains acquire virulent genes gradually gaining specific traits for specific pathotypes [Several of these pathotypes, such as APEC, EPEC, EHEC, and ETEC, cause disease in animals with similar virulence factors as in humans. The EHEC strains of d humans . The difthotypes .E. coli has been found to be the largest contributor to the global burden of antimicrobial resistance causing death in humans [E. coli strains that have acquired resistance to multiple antibiotics and a diverse array of virulence factors that have been successfully disseminated globally. Strains that produce extended-spectrum β-lactamases (ESBL), in particular, often result in longer hospitalization, higher morbidity, and increased health-care costs [E. coli have a broad habitat, including the gastrointestinal tract of most warm-blooded animals as commensals, soil, water, and sewage, where they are frequently exposed to antibiotics and other chemicals that have made them develop survival mechanisms. They are, therefore, frequently used as resistance indicators [E. coli that cause intestinal and extraintestinal infections have been reported both in animals and humans.n humans . For a lre costs ,9. E. codicators . A few oE. coli, commensal bacterial are known to harbor and exchange resistance and virulence loci and can provide a reservoir of resistance genes, which may be transferred between bacterial species, including pathogens [E. coli strains within the ecological environment where they survive. The sharing of genetic information among E. coli strains is a threat to public health, animal health, and environmental health from one health perspective [ampC, which under normal conditions are not expressed but high-level expression is often induced by mutation or induction by specific β-lactams that lead to clinical resistance [A lot of interest has been focused on the burden of multi-drug resistant (MDR) strains in humans  and theiathogens . The resspective . Severalspective . The presistance .E. coli strains pathogenic to human [E. coli isolates from livestock in Uganda.Human studies have more frequently reported highly successful globally disseminated pandemic high-risk clones, such as ST-131, ST-648, ST-10, and others , which ato human . This stA total of 729 samples were collected from: cattle (n = 225), swine (n = 245), and poultry (n = 257) from September 2020 to April 2021, using a series of cross-sectional studies at swine slaughter places, cattle abattoirs, and live poultry markets in Kampala and Wakiso districts. For cattle and swine, fecal samples were collected, while for poultry, fecal droppings were collected in 275 mL of peptone water.E. coli with API-20E kits . Isolates were subjected to antibiotic susceptibility testing by standard disk diffusion test according to CLSI [Samples were suspended in peptone water, incubated overnight, and inoculated directly onto Xylose/Lysine/Deoxycholate (XLD) selective agar and incubated at 37 °C overnight. Yellow colonies that were catalase positive and oxidase negative were confirmed as  to CLSI . Multi-dA total of 63 multidrug resistant isolates were selected and grown on MacConkey agar for 48 h at 37 °C. The isolates were collected in 1.5 mL tubes and extraction of DNA was completed with DNeasy UltraClean microbial kit . DNA libraries were prepared using Kapa HyperPlus kit . Libraries’ concentrations were evaluated in a CFX96 real-time iCycler machine  using KAPA™ Library Quantification Kits (Roche Diagnostics). Paired-end sequencing was performed at MRSN on the Illumina NextSeq machine .https://itol.embl.de/, accessed on 1 March 2023) for viewing and annotation. The in silico ClermonTyping was used to group the isolates into different phylogroups [E. coli isolates based on the MLST scheme [Removal of sequence adapters from raw reads was performed using Btrims . Denovo logroups . AssigniT scheme . SerotypT scheme  and FimTT scheme . mlplasmT scheme . ContigsT scheme . VirulenT scheme . For allE. coli isolated from chickens, swine, and cattle, whereas resistance to ampicillin antibiotics was particularly high among E. coli isolated from cattle and swine. All E. coli isolated from chicken were found to be resistant to ciprofloxacin. Resistance to ciprofloxacin was equally high among E. coli isolated from swine.The antimicrobial susceptibility test was performed on nine antibiotics. Generally, there were significantly high levels of antibiotic resistance observed with amoxicillin/clavulanate and ampicillin (≥93.65%) antibiotics. Antibiotics with moderate levels of resistance were ceftazidime (47.62%), ciprofloxacin (57.14%), gentamicin (49.21%), and trimethoprim/sulfamethoxazole (53.97%), whereas the majority of isolates were susceptible to chloramphenicol (79.37%), cefotaxime (63.49%), and meropenem (80.95%) antibiotics. Resistance to amoxicillin/clavulanate was significantly high in E. coli sequence types associated with the animals.Phylogroups B1 (57.81%) and A (31.25%) were most commonly associated with the three host species, while phylogroups E, C, and D were marginally detected. Phylogroups’ compositions were largely dependent on the animal species. For example, phylogroup A was principally isolated from swine and chicken, whereas phylogroup B1 was predominantly isolated from cattle. A total of 39 known MLST groups were detected among the 63 isolates . ST10 (9E. coli isolates (10.94%) were from novel STs. The distribution of the different MLST groups were determined by the different phylogroups and animal species. The ST-206 and ST-10 were essentially detected only in phylogroup A  had only one antimicrobial-resistant gene within their genome. The most-frequent antibiotic-resistant gene detected was the blaEC-15, which occurs among (71.88%) of the E. coli isolates. The other beta-lactam genes detected were blaEC (14.06%), blaEC-18 (12.50%), and blaTEM-1 (6.25%). Tetracycline-resistant, tet(A) gene was detected among 20.31% of isolates. Only a limited proportion (4.69%) of isolates were found to carry the tet(B) gene. The quinolone group of antibiotics occurs only within a limited number of E. coli isolates (n = 5). Among the quinolone genes detected were the qnrS1 (4.36%), qnrB19 (1.56%), and qnrS13 (1.56%). The folate pathway antagonist genes detected were dfrA14 (6.25%), sul2 (6.25%), sul3 (4.6%), and sul1 (1.56%). The aph-(3)-Ib and aph-(6)-Id aminoglycoside-resistant genes were both detected at a frequency of 9.38%. Other rare aminoglycoside genes were aadA1 (6.25%), aadA2 (3.13%), and aph(3)-Ia (3.13%). The O9-serogroup isolate was associated with multiple antibiotic-resistant genes including blaEC-15, blaTEM-1, (aph (3)-Ib, aph (6)-Id), sul2, tet(A), catA1, and qnrS1. The blaEC-15 and tet(A) genes were predominantly located within phylogroups (B1 and A), whereas the blaEC gene was restricted among phylogroups (B1 and E). The aminoglycoside genes, aph (3)-Ib and aph (6)-Id, were associated with phylogroup A.A limited occurrence of different antimicrobial-resistant genes within the genomes of the blaEC-15 genes were located within the plasmid. However, the blaEC-15 genes were bordered by the fumarate reductase gene cluster upstream and the lipocalin  and qnrS1 antimicrobial resistant genes.None of the ipocalin . The blad efflux . Only twE. coli isolated from cattle compared to those isolated from swine and chicken. Two classes of exotoxin virulent genes were detected: the colicin-like Usp toxin gene was rare and occurred within E. coli isolated from swine (phylogroup E and serogroup-O178). Meanwhile, cattle (phylogroup B1) were the major source of E. coli carrying Shiga toxin genes. The stx2B (23.44%) and stx2A (21.88%) were the most common Shiga toxin genes carried by most E. coli isolated from cattle . Among the genes that regulate iron uptake, the ireA gene was limited to two isolates of phylogroup B1 (serogroup O22), whereas the iha gene was widely distributed among isolates of phylogroup B1. Another iron uptake gene, chuA, had limited occurrence in isolates of phylogroup E. Other virulence genes found exclusively among phylogroup E were eilA and air gene. The only members of the serine protease autotransporters gene family detected were espP and Tsh genes. The espP gene occurs mainly within cattle, whereas the Tsh gene was from E. coli isolated from chicken. Swine was the major carrier of E. coli isolates with katP gene for plasmid-encoded catalase-peroxidase protein and was encoded within the plasmid. Overall, most of the virulence-associated genes were detected at moderate proportion (20%-29%), whereas others, such as terC, gad, iss, lpfA, traT, and ompT, were very common (>55%) among E. coli from animal sources  and was encoded by plasmid.The virulent gene classes detected were those belonging to exotoxin, adhesins, iron uptake, serine protease autotransporters (SAT), and more. The distribution of the different virulent genes largely depended on the host species, phylogroups, and serogroups . A predom cattle . Additiom cattle . For exa sources . The ompE. coli in view of their resistome and virulome, which may be of relevance to transmission of these pathogenic strains. Many studies have tended to focus on pathogens, with limited focus on non-pathogenic bacteria that are regularly excluded from surveillance programs, yet may serve as reservoirs of AMR in the environment and the food chains, underscoring the need for more comprehensive analyses and monitoring of food environmental and animal reservoirs of AMR [The current study examined the genomic diversity of commensal s of AMR ,31. Withs of AMR ,33,34.E. coli has been reported several times in most parts of the world, including Uganda [E. coli is among the international, globally disseminated high-risk pandemic clones that have been frequently incriminated in several human ExPEC infections. This ST clone has been reported in synanthropic animals carrying several resistance genes to antibiotics frequently used in humans [E. coli, especially the ExPEC but also those of intestinal disease agents. These findings are consistent with other studies [The commensal isolates in this study showed a high genetic diversity with as many sequence types as the isolates themselves. This phenomenon of high genomic plasticity within g Uganda . The plag Uganda . We idenn humans . Similarn humans ,39, cons studies ,40,41 thblaEC genes, with 71.88% carrying the blaEC-15 gene. Similar findings have been reported [Enterobacteriaceae [Enterobacteriaceae [tet(A) and tet(B) genes; quinolone resistance genes qnrS1, qnrB19, and qnrS13; as well as a few isolates with resistance genes for folate pathway antagonist genes and aminoglycoside-resistant genes. Resistance often follows antibiotic use patterns in animal populations [While the isolates in the current study demonstrated carriage of a limited number of antimicrobial resistance genes, they were all AmpC beta-lactamase producers carrying mainly β-lactamase class reported . The claeriaceae . Althougeriaceae . A smallulations . The maiulations ,46,47.E.coli consists of commensals that are not associated with disease but could cause disease under certain circumstances. To survive in the gut, E. coli strains frequently carry and are capable of toxin secretion, aggregative colonization, and multiplying in the gastrointestinal tract, and with the acquisition of additional genes could cause damage to different environments through the adaptation of key genetic elements, resulting in the formation of new pathotypes [A broad repertoire of virulence genes with invasion/adherence, exotoxin, and siderophore factors among the isolates obtained was demonstrated. Enteric thotypes .terC, gad, iss, lpfA, and ompT virulence genes commonly found across the different animal hosts while the Shiga toxin genes  occur mainly among E. coli of cattle origin. All isolates had the terC gene, which is part of the tellurite resistance gene operon (ter) that is known to exist widely and in many bacteria, particularly pathogenic species. The terC is part of the ter operon that is known to confer resistance to the oxyanion form of the rare nonessential trace element tellurium, namely, tellurite oxide (TeO3−2), and is implicated in tellurite resistance, phage inhibition, colicine resistance, and pathogenicity [ter operon is required for fitness to survive in the gut where colicins from other competing bacteria and host antimicrobial peptides limit their survival. In Klebsiella pnemoniae, the terC has been reported to offer tolerance to ofloxacin, polymyxin B, and cetylpyridinium chloride as well [ter operon has also been demonstrated to be associated with stress tolerance factor and enhancing fitness in the gut, particularly against stress induced by the indigenous gut microbiota during colonization [gad gene which encodes the glutamate decarboxylase pathway (GDP), which is a major acid resistance mechanism enabling microorganisms’ survival in low pH environments. The glutamate-dependent acid resistance system is said to be the most potent acid resistance system in commensal and pathogenic Escherichia coli. These gut bacteria need these traits to overcome the acidic environment during transit through the host stomach to successfully colonize the gut.Most of the isolates had the genicity . It has  as well . The ternization . This coE. coli strains (the Shiga toxin-producing Escherichia coli) which causes hemorrhagic colitis and hemolytic uremic syndrome [stx genes by animal E.coli does not necessarily indicate that they cause disease. It has been suggested that ruminants in particular do not have vascular globotriaosylceramide receptors where Shiga toxin binds and are always asymptomatic [E. coli in their feces and are considered reservoirs for Shiga toxin producing E.coli for humans.The Isolates had several other genes directly involved in pathogenicity. The Shiga toxin virulence genes, in particular, mediate the production of Shiga toxin among the enteric pathogenic syndrome . Possessptomatic . HoweverE. coli from animal sources highlights the role of livestock in perpetuating infections in humans, including Shiga toxin-producing E. coli strain as reservoirs. While commensal E. coli commonly reside in human and animal gut without causing disease, they may occasionally cause opportunistic infections when the host immunity is impaired or injured. Their ability to acquire and transmit virulence and AMR genes within the gut both to non-virulent bacteria and pathogenic ones poses a serious threat that needs routine monitoring. They have been particularly found to be efficient in acquiring and transmitting these genes through mobile genetic elements such as transposons and plasmids [The similarity in virulence factors between human ExPEC and plasmids .E. coli isolates in livestock in the country with a limited number of the international high-risk clones of pandemic importance. These clones have the potential to share both virulence and/or resistance genes to pathogenic E. coli or other pathogenic bacteria within the gastroenteric system.Taken together, this study established the convergence of a limited resistome and a wide virulome among commensal AmpC beta-lactamase producing