Multi-omics analysis reveals the metabolic regulators of duodenal low-grade inflammation in a functional dyspepsia model

Ji, Shuai; You, Yanting; Peng, Baizhao; Zhong, Tianyu; Kuang, Yuxiang; Li, Shasha; Chen, Liqian; Sun, Xiaohan; Dai, Jiaojiao; Huang, Suiping; Wu, Yuyao; Liu, Yanyan

doi:10.3389/fimmu.2022.944591

Cited by 4 publications

(2 citation statements)

References 59 publications

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“…Then, the transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using Perl scripts. After the final transcriptome was generated, StringTie ( Ji et al., 2023 ) and Ballgown ( Leek, 2014 ) were used to estimate all transcript expression levels. Simply put, it is used to determine mRNA expression levels by calculating the fragments per kilobase of transcript per million mapped reads (FPKM).…”

Section: Methodsmentioning

confidence: 99%

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China

Jia,

Zhao,

Jia

et al. 2024

Front. Plant Sci.

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Phragmites australis is a prevalent species in the Chongming Dongtan wetland and is capable of thriving in various tidal flat environments, including high salinity habitats. P. australis population displays inconsistent ecological performances, highlighting the need to uncover their survival strategies and mechanisms in tidal flats with diverse soil salinities. Upon comparing functional traits of P. australis at multiple tidal flats (low, middle, and high) and their responses to soil physicochemical properties, this study aimed to clarify the salt-tolerant strategy of P. australis and the corresponding mechanisms. These results showed that leaf characteristics, such as specific leaf area and leaf dry matter content, demonstrated more robust stability to soil salinity than shoot height and dry weight. Furthermore, as salt stress intensified, the activities of superoxide dismutase (SOD), catalase (CAT) and peroxisome (POD) in P. australis leaves at low tidal flat exhibited an increased upward trend compared to those at other tidal flats. The molecular mechanism of salt tolerance in Phragmites australis across various habitats was investigated using transcriptome sequencing. Weighted correlation network analysis (WGCNA) combined with differentially expressed genes (DEGs) screened out 3 modules closely related to high salt tolerance and identified 105 core genes crucial for high salt tolerance. Further research was carried out on the few degraded populations at low tidal flat, and 25 core genes were identified by combining WGCNA and DEGs. A decrease in the activity of ferroptosis marker gonyautoxin-4 and an increase in the content of Fe3+ in the degenerated group were observed, indicating that ferroptosis might participate in degradation. Furthermore, correlation analysis indicated a possible regulatory network between salt tolerance and ferroptosis. In short, this study provided new insights into the salt tolerance mechanism of P. australis population along tidal flats.

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Section: Methodsmentioning

confidence: 99%

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China

Jia,

Zhao,

Jia

et al. 2024

Front. Plant Sci.

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“…The gut microbiota emerges as a pivotal determinant for changes in certain metabolites. Previous studies have reported the impact of alterations in duodenal microbiota on gastric emptying and mild duodenal inflammation in patients with FD [10,11]. Notably, probiotics have been suggested as a promising therapeutic approach for FD [12,13].…”

Section: Introductionmentioning

confidence: 99%

Metabolite and Gut Microbiota Profiles in Patients with Functional Dyspepsia: An Integrative Multi-omics Analysis

Wen,

Liang,

et al. 2024

Preprint

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Background: The pathophysiology of functional dyspepsia (FD) remains insufficiently understood, and the pain and economic constraints associated with endoscopic examinations hinder the precise definition and treatment of this disorder. Exploring the potential of multi-omics biomarkers for FD could yield promising targets for effectively diagnosing and treating this condition. Methods: We recruited 54 FD patients and 29 healthy volunteers and characterized their gut microbiota by shotgun metagenomic sequencing and their serum and urine metabolites by liquid chromatography-mass spectrometry (LC-MS). Results: We identified the changes in circulating metabolites associated with FD and linked to the gut microbial alterations. Among the differential circulating metabolites, we particularly highlighted the strong association of L-glutamate deficiency with the severity of FD symptoms and its strong predictive value for FD. Although no significant changes were noted in the gut microbial community structure of the FD samples, this might be attributed to symptom overlap between epigastric pain syndrome (EPS) and postprandial distress syndrome (PDS). However, significant alterations in the abundance of certain species were observed, including a substantial increase in the abundance of Streptococcus in the digestive tract of patients with FD. Finally, a cross-omics correlation network integrating metabolomic data with microbial community abundance was established, uncovering potential host-microbe-metabolite interactions. Conclusions: This work provides the first comprehensive description of the disrupted state of blood and urine metabolite composition and gut microbiota in patients with FD. These findings potentially offer promising targets for the diagnosis and treatment of this condition through a multi-omics approach, with particular emphasis on serum metabolomics.

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Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids

Wang,

Yao,

Zhu

et al. 2024

Arab Journal of Gastroenterology

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Multi-omics analysis reveals the metabolic regulators of duodenal low-grade inflammation in a functional dyspepsia model

Cited by 4 publications

References 59 publications

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China

Metabolite and Gut Microbiota Profiles in Patients with Functional Dyspepsia: An Integrative Multi-omics Analysis

Combination of Simo Decoction and Golden Bifid alleviates functional dyspepsia through a mechanism involving intestinal microbiota and short-chain fatty acids

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