Omics Tools Research Articles

Plasma metabolomics for diagnostic biomarkers on ectopic pregnancy

Metabolomics is a relatively novel omics tool to provide potential biomarkers for early diagnosis of the diseases and to insight the pathophysiology not having discussed ever before. In the present study, an ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was employed to the plasma samples of Group T1: Patients with ectopic pregnancy diagnosed using ultrasound, and followed-up with beta-hCG level (n = 40), Group T2: Patients with ectopic pregnancy diagnosed using ultrasound, underwent surgical treatment and confirmed using histopathology (n = 40), Group P: Healthy pregnant women (n = 40) in the first prenatal visit of pregnancy, Group C: Healthy volunteers (n = 40) scheduling a routine gynecological examination. Metabolite extraction was performed using 3 kDa pores - Amicon® Ultra 0.5 mL Centrifugal Filters. A gradient elution program (mobile phase composition was water and acetonitrile consisting of 0.1% formic acid) was applied using a C18 column (Agilent Zorbax 1.8 μM, 100 x 2.1 mm). Total analysis time was 25 min when the flow rate was 0.2 mL/min. The raw data was processed through XCMS – R program language edition where the optimum parameters detected using Isotopologue Parameter Optimization (IPO). The potential metabolites were identified using MetaboAnalyst 5.0 and finally 27 metabolites were evaluated to be proposed as potential biomarkers to be used for the diagnosis of ectopic pregnancy.

Cow's Milk: A Benefit for Human Health? Omics Tools and Precision Nutrition for Lactose Intolerance Management.

Cow's milk (CM) is a healthy food consumed worldwide by individuals of all ages. Unfortunately, "lactase-deficient" individuals cannot digest milk's main carbohydrate, lactose, depriving themselves of highly beneficial milk proteins like casein, lactoalbumin, and lactoglobulin due to lactose intolerance (LI), while other individuals develop allergies specifically against these proteins (CMPA). The management of these conditions differs, and an inappropriate diagnosis or treatment may have significant implications for the patients, especially if they are infants or very young children, resulting in unnecessary dietary restrictions or avoidable adverse reactions. Omics technologies play a pivotal role in elucidating the intricate interactions between nutrients and the human body, spanning from genetic factors to the microbiota profile and metabolites. This comprehensive approach enables the precise delineation and identification of distinct cohorts of individuals with specific dietary requirements, so that tailored nutrition strategies can be developed. This is what is called personalized nutrition or precision nutrition (PN), the area of nutrition that focuses on the effects of nutrients on the genome, proteome, and metabolome, promoting well-being and health, preventing diseases, reducing chronic disease incidence, and increasing life expectancy. Here, we report the opinion of the scientific community proposing to replace the "one size fits all" approach with tailor-made nutrition programs, designed by integrating nutrigenomic data together with clinical parameters and microbiota profiles, taking into account the individual lactose tolerance threshold and needs in terms of specific nutrients intake. This customized approach could help LI patients to improve their quality of life, overcoming depression or anxiety often resulting from the individual perception of this condition as different from a normal state.

Regulation, Biosynthesis, and Extraction of Bacillus-Derived Lipopeptides and Its Implications in Biological Control of Phytopathogens

In recent years, the adoption of sustainable pest management strategies has increased interest in the utilization of biopesticides, with a focus on harnessing beneficial microorganisms. Among these, lipopeptides, such as surfactins, iturins, and fengycins produced by the genus Bacillus, have gained significant attention due to their multifaceted biocontrol mechanisms and wide-ranging inhibitory effects. This review aims to address the regulation, biosynthesis, and production of three main lipopeptide families secreted by the genus Bacillus, as well as the identification and quantification analysis used to date, through the omic tools approach. The three families have been identified as key contributors to the biocontrol abilities of these bacteria, with their broad-spectrum activity making them valuable tools in integrated pest management approaches that aim to reduce reliance on chemical pesticides use while maintaining crop health and productivity.

Omics technologies for understanding the plant–fungal endophyte interactions: crop improvement for future security

Fungi are a unique group of microbes that exist in all of the world’s niches having different habitats and environments. They are known to interact with various species present on the earth, including plants. Fungi interact with different niches of plants such as roots (rhizosphere), tissue, and internal spaces (endophytic) and surfaces (epiphytic). The fungi that inhabit the plants are specifically known as endophytic fungi. These plant–fungal interactions play a significant role for the host, such as protecting the plants from biotic and abiotic factors known as major growth constraints. Fungal endophytes also supply several nutrients and plant growth hormones, which help in plant growth enhancement. Additionally, nitrogen fixation, solubilization of minerals, production of phytohormones, antibiotics, secondary metabolites, hydrogen cyanide proteolytic enzymes, and activation of plant responses to stresses are the various mechanisms of endophytic fungi. Endophytic fungi have been known for various biotechnological applications that were unraveled through exploring biodiversity and understanding the interaction of plant–fungal endophyte. There are many unexplored species and interaction studies that need to be explored, and for the study, omics tools are recognized as the finest approach. In the present review, different omics tools that could be used for a deeper understanding of plant–fungal endophyte interactions and endophytic fungi biodiversity have been detailed.

Transcriptomic Analysis During the Induction of Somatic Embryogenesis in Coffea canephora.

Omic tools have changed the way of doing research in experimental biology. The somatic embryogenesis (SE) study has not been immune to this benefit. The transcriptomic tools have been used to compare the genes expressed during the induction of SE with the genes expressed in zygotic embryogenesis or to compare the development of the different stages embryos go through. It has also been used to compare the expression of genes during the development of calli from which SE is induced, as well as many other applications. The protocol described here is employed in our laboratory to extract RNA and generate several transcriptomes for the study of SE on Coffea canephora.

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

AbstractThe adverse effects of mounting environmental challenges, including extreme temperatures, threaten the global food supply due to their impact on plant growth and productivity. Temperature extremes disrupt plant genetics, leading to significant growth issues and eventually damaging phenotypes. Plants have developed complex signaling networks to respond and tolerate temperature stimuli, including genetic, physiological, biochemical, and molecular adaptations. In recent decades, omics tools and other molecular strategies have rapidly advanced, offering crucial insights and a wealth of information about how plants respond and adapt to stress. This review explores the potential of an integrated omics‐driven approach to understanding how plants adapt and tolerate extreme temperatures. By leveraging cutting‐edge omics methods, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics, phenomics, and ionomics, alongside the power of machine learning and speed breeding data, we can revolutionize plant breeding practices. These advanced techniques offer a promising pathway to developing climate‐proof plant varieties that can withstand temperature fluctuations, addressing the increasing global demand for high‐quality food in the face of a changing climate.

In silico-based Safety Assessment of the EPSPS CP4 single event expressed in genetically modified crops

In silico-based Safety Assessment of the EPSPS CP4 single event expressed in genetically modified crops

Extrathymic AIRE-Expressing Cells: A Historical Perspective.

Since its discovery, Aire has been the topic of numerous studies in its role as a transcriptional regulator in the thymus where it promotes the "promiscuous" expression of a large repertoire of tissue-restricted antigens (TRAs) that are normally expressed only in the immune periphery. This process occurs in specialized medullary thymic epithelial cells (mTECs) and mediates the elimination of self-reactive T cells or promotestheir conversion to the Foxp3+ regulatory T cell lineage, both of which are required for the prevention of autoimmunity. In recent years, there has been increasing interest in the role of extrathymic Aire expression in peripheral organs. The focus has primarily been on the identification of the cellular source(s) and mechanism(s) by which extrathymic AIRE affects tolerance-related or other physiological processes. A cadre of OMICs tools including single cell RNA sequencingand novel transgenic models to trace Aire expression to perform lineage tracing experiments haveshed light on a phenomenon that is more complex than previously thought. In this chapter, we provide a deeper analysis of how extrathymic Aire research hasdeveloped and progressed, how cellular sources were identified, and how the function of AIRE was determined. Current data suggests that extrathymic AIRE fulfills a function that differs from what has been observed in the thymus and strongly argues that its main purpose is to regulate transcriptional programs in a cell content-dependent manner. Surprisingly, there is data that also suggests a non-transcriptional role of extrathymic AIRE in the cytoplasm. We have arrived at a potential turning point that will take the field from the classical understanding of AIRE as a transcription factor in control of TRA expression to its role in immunological and non-immunological processes in the periphery.

Chemical and microbial diversity of a tropical intertidal ascidian holobiont

The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.

Serum proteomics reveals a tolerant immune phenotype across multiple pathogen taxa in wild vampire bats.

Bats carry many zoonotic pathogens without showing pronounced pathology, with a few exceptions. The underlying immune tolerance mechanisms in bats remain poorly understood, although information-rich omics tools hold promise for identifying a wide range of immune markers and their relationship with infection. To evaluate the generality of immune responses to infection, we assessed the differences and similarities in serum proteomes of wild vampire bats (Desmodus rotundus) across infection status with five taxonomically distinct pathogens: bacteria (Bartonella spp., hemoplasmas), protozoa (Trypanosoma cruzi), and DNA (herpesviruses) and RNA (alphacoronaviruses) viruses. From 19 bats sampled in 2019 in Belize, we evaluated the up- and downregulated immune responses of infected versus uninfected individuals for each pathogen. Using a high-quality genome annotation for vampire bats, we identified 586 serum proteins but found no evidence for differential abundance nor differences in composition between infected and uninfected bats. However, using receiver operating characteristic curves, we identified four to 48 candidate biomarkers of infection depending on the pathogen, including seven overlapping biomarkers (DSG2, PCBP1, MGAM, APOA4, DPEP1, GOT1, and IGFALS). Enrichment analysis of these proteins revealed that our viral pathogens, but not the bacteria or protozoa studied, were associated with upregulation of extracellular and cytoplasmatic secretory vesicles (indicative of viral replication) and downregulation of complement activation and coagulation cascades. Additionally, herpesvirus infection elicited a downregulation of leukocyte-mediated immunity and defense response but an upregulation of an inflammatory and humoral immune response. In contrast to our two viral infections, we found downregulation of lipid and cholesterol homeostasis and metabolism with Bartonella spp. infection, of platelet-dense and secretory granules with hemoplasma infection, and of blood coagulation pathways with T. cruzi infection. Despite the small sample size, our results suggest that vampire bats have a similar suite of immune mechanisms for viruses distinct from responses to the other pathogen taxa, and we identify potential biomarkers that can expand our understanding of pathogenesis of these infections in bats. By applying a proteomic approach to a multi-pathogen system in wild animals, our study provides a distinct framework that could be expanded across bat species to increase our understanding of how bats tolerate pathogens.

Assembly strategies for rubber-degrading microbial consortia based on omics tools.

Numerous microorganisms, including bacteria and fungus, have been identified as capable of degrading rubber. Rubber biodegradation is still understudied due to its high stability and the lack of well-defined pathways and efficient enzymes involved in microorganism metabolism. However, rubber products manufacture and usage cause substantial environmental issues, and present physical-chemical methods involve dangerous chemical solvents, massive energy, and trash with health hazards. Eco-friendly solutions are required in this context, and biotechnological rubber treatment offers considerable promise. The structural and functional enzymes involved in poly (cis-1,4-isoprene) rubber and their cleavage mechanisms have been extensively studied. Similarly, novel bacterial strains capable of degrading polymers have been investigated. In contrast, relatively few studies have been conducted to establish natural rubber (NR) degrading bacterial consortia based on metagenomics, considering process optimization, cost effective approaches and larger scale experiments seeking practical and realistic applications. In light of the obstacles encountered during the constructing NR-degrading consortia, this study proposes the utilization of multi-omics tools to discern the underlying mechanisms and metabolites of rubber degradation, as well as associated enzymes and effective synthesized microbial consortia. In addition, the utilization of omics tool-based methods is suggested as a primary research direction for the development of synthesized microbial consortia in the future.

Improved cell-type identification and comprehensive mapping of regulatory features with spatial epigenomics 96-channel microfluidic platform.

Gene expression is subject to epigenetic regulation and is dependent upon cellular context. Spatial omics tools can provide insight into cellular context; however, development has centered on spatial transcriptomics and proteomics. Deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) was the first spatial epigenomics platform at the cellular level. Here we present a comparison of spatial epigenomic profiling on both 50-channel and 96-channel platforms. The new 96-channel microfluidics chip design greatly improved precision in cell typing and identification of regulatory elements by spatial-ATAC-seq. Spatial mapping reveals complexity of glial cell and neuronal localization within brain structures as well as cis-regulatory elements controlling cellular function. This technology streamlines spatial analysis of the epigenome and contributes a new layer of spatial omics to uncover the context dependent regulatory mechanisms underpinning development, disease, and normal cellular function.

From microbiome composition to functional engineering, one step at a time.

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data.

The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcriptsand a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.

Isolation of soil bacteria able to degrade the anthelminthic compound albendazole

Anthelmintic (AHs) veterinary drugs constitute major environmental contaminants. The use of AH-contaminated fecal material as manures in agricultural settings constitutes their main route of environmental dispersal. Once in soils, these compounds induce toxic effects to soil fauna and soil microbiota, both having a pivotal role in soil ecosystem functioning. Therefore, it is necessary to identify mitigation strategies to restrict the environmental dispersal of AHs. Bioaugmentation of AH-contaminated manures or soils with specialized microbial inocula constitutes a promising remediation strategy. In the present study, we aimed to isolate microorganisms able to actively transform the most widely used benzimidazole anthelminthic albendazole (ABZ). Enrichment cultures in minimal growth media inoculated with a soil known to exhibit rapid degradation of ABZ led to the isolation of two bacterial cultures able to actively degrade ABZ. Two oxidative products of ABZ, ABZSO and ABZSO2, were detected at low amounts along its degradation. This suggested that the oxidation of ABZ is not a major transformation process in the isolated bacteria which most probably use other biotic pathways to degrade ABZ leading to the formation of products not monitored in this study. Full length sequencing of their 16S rRNA gene and phylogenetic analysis assigned both strains to the genus Acinetobacter. The sequences were submitted in GeneBank NCBI, database with the accession numbers OP604271 to OP604273. Further studies will employ omic tools to identify the full transformation pathway and the associated genetic network of Acinetobacter isolates, information that will unlock the potential use of these isolates in the bioaugmentation of contaminated manures.

Biomarker screening in fetal growth restriction based on multiple RNA-seq studies

ObjectiveFetal growth restriction (FGR) is a severe pathological complication associated with compromised fetal development. The early diagnosis and prediction for FGR are still unclear. Sequencing technologies present a huge opportunity to identify novel biomarkers. However, limitation of individual studies (e.g., long lists of dysregulated genes, small sample size and conflicting results) hinders the selection of the best-matched ones. Study designA multi-step bioinformatics analysis was performed. We separately reanalyzed data from four public RNA-seq studies, followed by a combined analysis of individual results. The differentially expressed genes (DEGs) were identified based on DESeq2. Then, function enrichment analyses and protein-protein interaction network (PPI) were conducted to screen for hub genes. The results were further verified by using external microarray data. ResultsA total of 65 dysregulated genes (50 down and 15 upregulated) were identified in FGR compared to controls. Function enrichment and PPI analysis revealed ten hub genes closely related to FGR. Validation analysis found four downregulated candidate biomarkers (CEACAM6, SCUBE2, DEFA4, and MPO) for FGR. ConclusionsThe use of omics tools to explore mechanism of pregnancies disorders contributes to improvements in obstetric clinical practice.

Effective omics tools are still lacking for improvement of stress tolerance in polyploid crops.

Effective omics tools are still lacking for improvement of stress tolerance in polyploid crops.

Genomics for monitoring and understanding species responses to global climate change.

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau.

The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied. Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively. A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics. Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.

Goat mammary gland metabolism: An integrated Omics analysis to unravel seasonal weight loss tolerance

Seasonal weight loss (SWL), is a major limitation to animal production. In the Canary Islands, there are two dairy goat breeds with different levels of tolerance to SWL: Majorera (tolerant) and Palmera (susceptible). Our team has studied the response of these breeds to SWL using different Omics tools. The objective of this study was to integrate such results in a data driven approach and using dedicated tools, namely the DIABLO method. The outputs of our analysis mainly separate unrestricted from restricted goats. Metabolites behave as “hub” molecules, grouping interactions with several genes and proteins. Unrestricted goats upregulated protein synthesis, along with arginine catabolism and adipogenesis pathways, which are related with higher anabolic rates and a larger proportion of secretory tissue, in agreement with their higher milk production. Contrarily, restricted goats seemingly increased the synthesis of acetyl-CoA through serine and acetate conversion into pyruvate. This may have occurred to increase fatty acid synthesis and/or to use them as an energy source in detriment to glucose, which was more available in the diet of unrestricted goats. Lastly, restricted Palmera upregulated the expression of PEBP4 and GPD1 genes compared to all other groups, which might support their use as putative biomarkers for SWL susceptibility. SignificanceSeasonal weight loss (SWL) is a major issue influencing animal production in the tropics and Mediterranean. By studying its impact on the mammary gland of tolerant and susceptible dairy goat breeds, using Omics, we aim at surveying the tissue for possible biomarkers that reflect these traits. In this study, data integration of three Omics (transcriptomics, proteomics and metabolomics) was performed using bioinformatic tools, to relate putative biomarkers and evaluate all three levels of information; in a novel approach. This information can enhance selection programs, lowering the impact of SWL on food production systems.