Integrating microplastic research in sustainable agriculture: Challenges and future directions for food production by Marcelo Illanes, María-Trinidad Toro, Mauricio Schoebitz, Nelson Zapata, Diego A. Moreno, María Dolores López-Belchí

“…Currently, the application of omics technologies, including genomics, transcriptomics, and metabolomics, offers novel insights into molecular mechanisms that enable the identification of specific biomarkers associated with MP exposure. …”
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Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem by Paige E. Payne, Loren N. Knobbe, Patricia Chanton, Julian Zaugg, Behzad Mortazavi, Olivia U. Mason

“…Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an ‘omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. …”
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Flavones enrich rhizosphere Pseudomonas to enhance nitrogen utilization and secondary root growth in Populus by Jiadong Wu, Sijia Liu, Haoyu Zhang, Sisi Chen, Jingna Si, Lin Liu, Yue Wang, Shuxian Tan, Yuxin Du, Zhelun Jin, Jianbo Xie, Deqiang Zhang

“…Here, we collect roots and rhizosphere soils from nine Populus species belonging to four sections (Leuce, Aigeiros, Tacamahaca, and Turanga), generate metabolite and transcription data for roots and microbiota data for rhizospheres, and conduct comprehensive multi-omics analyses. We demonstrate that the roots of vigorous Leuce poplar enrich more Pseudomonas, compared with the poorly performing poplar. …”
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Cold-induced metabolic adaptations in the large yellow croaker Larimichthys crocea by Yang Gao, Huirong Lv, Chengzhang Huang, Xiaoyu Qu, Zhangjie Chu, Weiye Li, Xiaolong Yin, Jungyeol Park, Dejun Feng, Junwook Hur

“…Flow rate had a more significant impact on tail beat frequency than temperature, whereas respiratory rate was more affected by temperature than flow rate. Omics data revealed that the ABC transporter, glycolysis and oxidative phosphorylation pathways were downregulated, whereas the citrate cycle pathway was upregulated, suggesting a metabolic adjustment to optimize ATP production and cellular transport mechanisms for efficient energy utilization and metabolic homeostasis. …”
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Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes by Arthur Monjot, Jérémy Rousseau, Lucie Bittner, Cécile Lepère

“…However, the vast amount of data produced by -omics approaches require data-driven methodologies to make predictions about these microorganisms’ role within ecosystems. …”
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Multiomics approach identifies dysregulated lipidomic and proteomic networks in Parkinson’s disease patients mutated in TMEM175 by Federica Carrillo, Marco Ghirimoldi, Giorgio Fortunato, Nicole Piera Palomba, Laura Ianiro, Veronica De Giorgis, Shahzaib Khoso, Tiziana Giloni, Sara Pietracupa, Nicola Modugno, Elettra Barberis, Marcello Manfredi, Teresa Esposito

“…Here, we adopted an untargeted omics approach to disclose lipidomic, metabolomic and proteomic alterations in plasma and in dermal fibroblasts of PD patients carrying mutations in TMEM175 gene. …”
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Exploring the taste presentation and receptor perception mechanism of salty peptides from Stropharia rugosoannulata based on molecular dynamics and thermodynamics simulation by Wen Li, Shuai Sun, Wanchao Chen, Haile Ma, Tingzhao Li, Zhong Zhang, Di Wu, Mengqiu Yan, Yan Yang

“…The taste presentation and receptor perception mechanism of the salty peptide of Stropharia rugosoannulata were predicted and verified using peptide omics and molecular interaction techniques. The combination of aspartic acid (D) and glutamic acid (E), or peptide fragments composed of arginine (R), constitute the characteristic taste structural basis of salty peptides of S. rugosoannulata. …”
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IUPHAR review: Targeted therapies of signaling pathways based on the gut microbiome in autism spectrum disorders: Mechanistic and therapeutic applications by Abdullah Al Mamun, Peiwu Geng, Shuanghu Wang, Chuxiao Shao, Jian Xiao

“…The discussion shows the potential of customized microbiome-based therapeutics and the integration of multi-omics methods to understand the underlying mechanisms. …”
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Virulence factor discovery identifies associations between the Fic gene family and Fap2+ fusobacteria in colorectal cancer microbiomes by Geicho Nakatsu, Duhyun Ko, Monia Michaud, Eric A. Franzosa, Xochitl C. Morgan, Curtis Huttenhower, Wendy S. Garrett

“…Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. …”
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Interleukin-6 as a Pan-Cancer Prognostic Inflammatory Biomarker: A Population-Based Study and Comprehensive Bioinformatics Analysis by Xie H, Wei L, Ruan G, Zhang H, Shi H

“…The IL-6 co-expression network was analyzed using the LinkedOmics database.Results: Serum IL-6 is an independent prognostic factor for cancer, especially gastrointestinal cancers. …”
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Deep learning in microbiome analysis: a comprehensive review of neural network models by Piotr Przymus, Krzysztof Rykaczewski, Adrián Martín-Segura, Jaak Truu, Enrique Carrillo De Santa Pau, Mikhail Kolev, Mikhail Kolev, Irina Naskinova, Aleksandra Gruca, Alexia Sampri, Alexia Sampri, Marcus Frohme, Alina Nechyporenko, Alina Nechyporenko

“…These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics datasets. Deep learning algorithms have shown remarkable capabilities in pattern recognition, feature extraction, and predictive modeling, enabling researchers to uncover hidden relationships within microbial ecosystems. …”
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Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude by Xiaozhen Liu, He Ding, Xiaoxue Zhang, Na Ta, Jinmei Zhao, Qian Zhang, Huiyun Liu, Mengjiao Sun, Xiaoqing Zhang

“…Results A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. …”
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Mitochondrial KMT9 methylates DLAT to control pyruvate dehydrogenase activity and prostate cancer growth by Yanhan Jia, Sheng Wang, Sylvia Urban, Judith M. Müller, Manuela Sum, Qing Wang, Helena Bauer, Uwe Schulte, Heike Rampelt, Nikolaus Pfanner, Katrin M. Schüle, Axel Imhof, Ignasi Forné, Christopher Berlin, August Sigle, Christian Gratzke, Holger Greschik, Eric Metzger, Roland Schüle

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Effects of maternal Escherichia coli lipopolysaccharide exposure on offspring: insights from lncRNA analysis in laying hens by Lei Liu, Wei Wang, Adeyinka Abiola Adetula, Zhixun Yan, Huagui Liu, Ying Yu, Qin Chu

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A simple and efficient method to extract polar metabolites from guar leaves (Cyamopsis tetragonoloba (L.) Taub.) for GC-MS metabolome analysis by S. B. Teplyakova, A. L. Shavarda, T. V. Shelenga, E. A. Dzyubenko, E. K. Potokina

“…Due to the progress of “omics” technologies and the marker-assisted selection, there is a huge interest in the studies that compare the metabolites of various guar varieties, employing metabolomics as a method of functional genomics. …”
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Genetic context modulates aging and degeneration in the murine retina by Olivia J. Marola, Michael MacLean, Travis L. Cossette, Cory A. Diemler, Amanda A. Hewes, Alaina M. Reagan, Jonathan Nyandu Kanyinda, Daniel A. Skelly, Gareth R. Howell

“…Conclusions Genetic context is a strong determinant of retinal aging, and our multi-omics resource can aid in understanding age-related diseases of the eye and brain. …”
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Multi-ancestry genome-wide association analyses: a comparison of meta- and mega-analyses in the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study by Alan Kuang, Marie-France Hivert, M. Geoffrey Hayes, William L. Lowe, Denise M. Scholtens

“…For the heterogeneous ancestry mega-analysis pipeline, data for all individuals were collectively imputed to the Trans-Omics for Precision Medicine (TOPMed) cosmopolitan reference panel, and GWAS was conducted using a unified mega-analysis. …”
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Dietary secoisolariciresinol diglucoside ameliorates high-fat diet-induced atherosclerosis via regulating immunological inflammation and reshaping gut microbiota in ApoE-/- mice by Yiwei Li, Jing Wang, Jian Liu, Ting Wang, Yuanyuan Liu, Yajuan Liu, Li Guo, Zhixia Bai, Wenke Shen, Ru Yan, Huiyan Ma, Juan Liu, Hao Wang, Xiaoxia Zhang

“…Due to the critical role of gut-vascular axis in AS, multi-omics analysis revealed that the modulation of gut microbiota and metabolism, including reductions in Firmicutes, Intestinimonas, Bilophila, Oscillibacter and Negativibacillus and increases in linoleic acid and 12,13-DHOME, may contribute to the attenuation of SDG on gut dysbiosis. …”
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Identification of TUBB3 as an immunotherapy target in lung cancer by genome wide in vivo CRISPR screening by Dan Zhao, Ravindra Deshpande, Kerui Wu, Abhishek Tyagi, Sambad Sharma, Shih-Ying Wu, Fei Xing, Stacey O'Neill, Jimmy Ruiz, Feng Lyu, Kounosuke Watabe

“…We integrated our results with multi-omics clinical data and performed both in vitro and in vivo assays to evaluate the role of the top candidate in regulating cytotoxic T cell killing. …”
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Unraveling metabolic signatures in SARS-CoV-2 variant infections using multiomics analysis by Sunho Lee, Sunho Lee, Jueun Lee, Kwang-Soo Lyoo, Yourim Shin, Yourim Shin, Dong-Min Shin, Jun-Won Kim, Jeong-Sun Yang, Kyung-Chang Kim, Joo-Yeon Lee, Geum-Sook Hwang, Geum-Sook Hwang

“…DiscussionThe study suggests that multi-omics is a valuable approach for understanding immunometabolic responses to infectious diseases, and providing insights for effective treatment strategies.…”
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