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Multi-Omics Approaches for Health and Disease
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Multi-Omics Approaches for Health and Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 4927

Special Issue Editor

Dr. Avinash V. Karpe

E-Mail Website
Guest Editor
Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
Interests: microbiology; metabolomics; proteomics; analytical chemistry; bioprocessing; host-parasite interactions; synbiotics; pre- and pro-biotics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Gut, skin and respiratory environments consist of interaction networks of multiple organisms. Individual organisms and biofilms contribute to these networks through various proteomic activities and metabolic exchanges.

The recent trends have highlighted that one omic platform is no longer sufficient in systems biology. While genomic/transcriptomic studies highlight the expressions of specific genes, these expressions do not completely address the interaction omics. Similarly, numerous metabolism-based analytical chemistry studies have indicated that similar types of metabolites are involved in multiple biochemical reactions, decreasing the utilization of individual metabolites as effective biomarkers. Instead, it has been increasingly observed that a biomarker panel, a mix of certain metabolites and proteins, combined with specific genomic aspects (e.g., certain microbial species or individual gene/gene sets), could be a more reliable biomarker.

Bioinformatic toolboxes analyse integrated proteome/metabolome and genome/metabolome datasets and biochemical interactions. Newer AI-ML-based platforms are employed to analyse these large datasets for biomarker discovery, and host–parasite–microbiome interactions, among others. These applications are applied to address the mechanisms of multi-organ axes, antimicrobial resistance (AMR), and biological passports.

This Special Issue “Multi-Omics Approaches for Health and Disease” aims to explore the applications of integrated multiomics in various diseases, disorders, infections and nutritional aspects to develop the field of precision medicine in clinical and veterinary health. We welcome original scientific research articles, comprehensive reviews, communications, case reports, letters, commentaries and editorials that contribute to this field.

Dr. Avinash V. Karpe
Guest Editor

Manuscript Submission Information

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Keywords

  • metabolomics and metaproteomics
  • genomics, microbiomes, mycobiome and virome
  • omics integration workflows, network modelling, and platforms
  • metabolic pathway analysis toolboxes (R, MATLAB, Python, etc.)
  • systems biology and biomarker discovery
  • multi-organism interactions, e.g., host–parasite–microbiome interaction
  • precision health, environment, agriculture and food

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Published Papers (3 papers)

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Research

13 pages, 3294 KiB  
Article
Differential Type-I Interferon Response in Buffy Coat Transcriptome of Individuals Infected with SARS-CoV-2 Gamma and Delta Variants
by Guilherme C. da Fonseca, Liliane T. F. Cavalcante, Otávio J. Brustolini, Paula M. Luz, Debora C. Pires, Emilia M. Jalil, Eduardo M. Peixoto, Beatriz Grinsztejn, Valdilea G. Veloso, Sandro Nazer, Carlos A. M. Costa, Daniel A. M. Villela, Guilherme T. Goedert, Cleber V. B. D. Santos, Nadia C. P. Rodrigues, Fernando do Couto Motta, Marilda Mendonça Siqueira, Lara E. Coelho, Claudio J. Struchiner and Ana Tereza R. Vasconcelos
Int. J. Mol. Sci. 2023, 24(17), 13146; https://doi.org/10.3390/ijms241713146 - 24 Aug 2023
Cited by 1 | Viewed by 1342
Abstract
The innate immune system is the first line of defense against pathogens such as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The type I-interferon (IFN) response activation during the initial steps of infection is essential to prevent viral replication and tissue damage. SARS-CoV [...] Read more.
The innate immune system is the first line of defense against pathogens such as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The type I-interferon (IFN) response activation during the initial steps of infection is essential to prevent viral replication and tissue damage. SARS-CoV and SARS-CoV-2 can inhibit this activation, and individuals with a dysregulated IFN-I response are more likely to develop severe disease. Several mutations in different variants of SARS-CoV-2 have shown the potential to interfere with the immune system. Here, we evaluated the buffy coat transcriptome of individuals infected with Gamma or Delta variants of SARS-CoV-2. The Delta transcriptome presents more genes enriched in the innate immune response and Gamma in the adaptive immune response. Interactome and enriched promoter analysis showed that Delta could activate the INF-I response more effectively than Gamma. Two mutations in the N protein and one in the nsp6 protein found exclusively in Gamma have already been described as inhibitors of the interferon response pathway. This indicates that the Gamma variant evolved to evade the IFN-I response. Accordingly, in this work, we showed one of the mechanisms that variants of SARS-CoV-2 can use to avoid or interfere with the host Immune system. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Health and Disease)
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24 pages, 6973 KiB  
Article
Molecular Interplay between Non-Host Resistance, Pathogens and Basal Immunity as a Background for Fatal Yellowing in Oil Palm (Elaeis guineensis Jacq.) Plants
by Cleiton Barroso Bittencourt, Thalliton Luiz Carvalho da Silva, Jorge Cândido Rodrigues Neto, André Pereira Leão, José Antônio de Aquino Ribeiro, Aline de Holanda Nunes Maia, Carlos Antônio Ferreira de Sousa, Betania Ferraz Quirino and Manoel Teixeira Souza Júnior
Int. J. Mol. Sci. 2023, 24(16), 12918; https://doi.org/10.3390/ijms241612918 - 18 Aug 2023
Cited by 1 | Viewed by 1656
Abstract
An oil palm (Elaeis guineensis Jacq.) bud rod disorder of unknown etiology, named Fatal Yellowing (FY) disease, is regarded as one of the top constraints with respect to the growth of the palm oil industry in Brazil. FY etiology has been a [...] Read more.
An oil palm (Elaeis guineensis Jacq.) bud rod disorder of unknown etiology, named Fatal Yellowing (FY) disease, is regarded as one of the top constraints with respect to the growth of the palm oil industry in Brazil. FY etiology has been a challenge embraced by several research groups in plant pathology throughout the last 50 years in Brazil, with no success in completing Koch’s postulates. Most recently, the hypothesis of having an abiotic stressor as the initial cause of FY has gained ground, and oxygen deficiency (hypoxia) damaging the root system has become a candidate for stress. Here, a comprehensive, large-scale, single- and multi-omics integration analysis of the metabolome and transcriptome profiles on the leaves of oil palm plants contrasting in terms of FY symptomatology—asymptomatic and symptomatic—and collected in two distinct seasons—dry and rainy—is reported. The changes observed in the physicochemical attributes of the soil and the chemical attributes and metabolome profiles of the leaves did not allow the discrimination of plants which were asymptomatic or symptomatic for this disease, not even in the rainy season, when the soil became waterlogged. However, the multi-omics integration analysis of enzymes and metabolites differentially expressed in asymptomatic and/or symptomatic plants in the rainy season compared to the dry season allowed the identification of the metabolic pathways most affected by the changes in the environment, opening an opportunity for additional characterization of the role of hypoxia in FY symptom intensification. Finally, the initial analysis of a set of 56 proteins/genes differentially expressed in symptomatic plants compared to the asymptomatic ones, independent of the season, has presented pieces of evidence suggesting that breaks in the non-host resistance to non-adapted pathogens and the basal immunity to adapted pathogens, caused by the anaerobic conditions experienced by the plants, might be linked to the onset of this disease. This set of genes might offer the opportunity to develop biomarkers for selecting oil palm plants resistant to this disease and to help pave the way to employing strategies to keep the safety barriers raised and strong. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Health and Disease)
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14 pages, 4320 KiB  
Article
Enhanced Cell Wall and Cell Membrane Activity Promotes Heat Adaptation of Enterococcus faecium
by Li Wang, Aike Li, Jun Fang, Yongwei Wang, Lixian Chen, Lin Qiao and Weiwei Wang
Int. J. Mol. Sci. 2023, 24(14), 11822; https://doi.org/10.3390/ijms241411822 - 23 Jul 2023
Cited by 2 | Viewed by 1445
Abstract
Enterococcus faecium (E. faecium) is widely used in foods and is known as a probiotic to treat or prevent diarrhea in pets and livestock. However, the poor resistance of E. faecium to high temperature processing procedures limits its use. Strain domestication [...] Read more.
Enterococcus faecium (E. faecium) is widely used in foods and is known as a probiotic to treat or prevent diarrhea in pets and livestock. However, the poor resistance of E. faecium to high temperature processing procedures limits its use. Strain domestication is a low-cost and effective method to obtain high-temperature-resistant strains. In this study, heat treatment was performed from 45 °C to 70 °C and the temperature was gradually increased by 5 °C every 3 days. After domestication, the survival rates of the high temperature adaptation strain RS047-wl under 65 °C water bath for 40 min was 11.5 times higher than WT RS047. Moreover, the saturated fatty acid (SFA) contents in cell membrane and the cell volume significantly increased in the RS047-wl. The combined transcriptomic, metabolomic, and proteomics analysis results showed a significant enhancement of cell wall and membrane synthesis ability in the RS047-wl. In conclusion, one of the main factors contributing to the improved high temperature resistance of RS047-wl was its enhanced ability to synthesize cell wall and membrane, which helped maintain normal cell morphology. Developing a high-temperature-resistant strain and understanding its mechanism enables it to adapt to high temperatures. This lays the groundwork for its future development and application. Full article
(This article belongs to the Special Issue Multi-Omics Approaches for Health and Disease)
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