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metabolome 2

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Gut microbiota 1

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Microbiome subsets determine 1

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Discovery of the mechanisms of acupuncture in the treatment of migraine based on functional magnetic resonance imaging and omics

Frontiers of Medicine   Pages 993-1005 doi: 10.1007/s11684-023-0989-7

Abstract: Migraine is one of the most prevalent and disabling neurological disease, but the current pharmacotherapies show limited efficacy and often accompanied by adverse effects. Acupuncture is a promising complementary therapy, but further clinical evidence is needed. The influence of acupuncture on migraine is not an immediate effect, and its mechanism remains unclear. This study aims to provide further clinical evidence for the anti-migraine effects of acupuncture and explore the mechanism involved. A randomized controlled trial was performed among 10 normal controls and 38 migraineurs. The migraineurs were divided into blank control, sham acupuncture, and acupuncture groups. Patients were subjected to two courses of treatment, and each treatment lasted for 5 days, with an interval of 1 day between the two courses. The effectiveness of treatment was evaluated using pain questionnaire. The functional magnetic resonance imaging (fMRI) data were analyzed for investigating brain changes induced by treatments. Blood plasma was collected for metabolomics and proteomics studies. Correlation and mediation analyses were performed to investigate the interaction between clinical, fMRI and omics changes. Results showed that acupuncture effectively relieved migraine symptoms in a way different from sham acupuncture in terms of curative effect, affected brain regions, and signaling pathways. The anti-migraine mechanism involves a complex network related to the regulation of the response to hypoxic stress, reversal of brain energy imbalance, and regulation of inflammation. The brain regions of migraineurs affected by acupuncture include the lingual gyrus, default mode network, and cerebellum. The effect of acupuncture on patients’ metabolites/proteins may precede that of the brain.

Keywords： acupuncture     migraine     fMRI     metabolome     proteome    

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characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome

Frontiers of Medicine doi: 10.1007/s11684-023-1029-3

Abstract: characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome

Keywords： tumor prognosis molecular     Microbiome subsets determine     center analysis microbiome     transcriptome data    

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Calorie restriction and its impact on gut microbial composition and global metabolism

Xiaojiao Zheng, Shouli Wang, Wei Jia

Frontiers of Medicine 2018, Volume 12, Issue 6,   Pages 634-644 doi: 10.1007/s11684-018-0670-8

Abstract: The observed phenotypes and the further verification of the direct link between gut microbiota and metabolomeThus, improved gut microbiota composition and metabolome are potential biomarkers for determining the

Keywords： caloric restriction     gut microbiota     metabolome    

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Extending the “Paracentral Dogma” of Biology with the Metabolome: Implications for Understanding Genomic–Glycomic–Metabolic–Epigenomic

Albert Stuart Reece

Engineering 2023, Volume 26, Issue 7,   Pages 16-16 doi: 10.1016/j.eng.2022.07.011

Abstract: Hence, the metabolic state locks in and reinforces the epigenomic state, and the metabolome and epigenomelsquo;paracentral dogma” of biology may be usefully and meaningfully extended by including the metabolome
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Reconstruction and Dynamics of the Human Intestinal Microbiome Observed In Situ Article

Xiaolin Liu, Min Dai, Yue Ma, Na Zhao, Ziyu Wang, Ying Yu, Yakun Xu, Huijie Zhang, Liyuan Xiang, He Tian, Guanghou Shui, Faming Zhang, Jun Wang

Engineering 2022, Volume 15, Issue 8,   Pages 89-101 doi: 10.1016/j.eng.2021.03.015

Abstract:

The human gut microbiome has primarily been studied through the use of fecal samples, a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities. However, this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract (in situ), and the infrequent availability of fecal samples prevents analysis at finer temporal scales (e.g., hours). In our study, we utilized colonic transendoscopic enteral tubing, a technology originally developed for fecal microbiota transplantation, to sample the ileocecal microbiome twice daily; metagenomic and metatranscriptomic analyses were then conducted on these samples. A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers. The ileocecal and fecal microbiomes, as profiled in the five volunteers, were found to be similar in metagenomic profiling, yet their active genes (metatranscriptome) were found to be highly distinct. Both microbiomes were perturbed after laxative exposure; over time, they exhibited reduced dissimilarity to their pre-treatment state, thereby demonstrating resilience as an innate property of the gut microbiome, although they did not fully recover within our observation time window. Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways, particularly those related to short-chain fatty acid production, such as Propionibacterium acnes and coenzyme A biosynthesis II. Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations. Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome, indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health. This study provides novel insights into the human gut microbiome and its inner resilience and diurnal rhythms, as well as the potential consequences of these to the host.

Keywords： Diurnal rhythm     Reconstruction     Metagenome     Metatranscriptome     Metabolome     Transendoscopic enteral tubing    

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Multi-Omics Analysis Provides Insight into the Possible Molecular Mechanism of Hay Fever Based on Gut Microbiota Article

Pei Han, Li-Sha Li, Zi-Xi Wang, Lin Xi, Hang Yu, Lin Cong, Zheng-Wei Zhang, Jie Fu, Ran Peng, Li-Bin Pan, Shu-Rong Ma, Xue-Yan Wang, Hong-Tian Wang, Xiang-Dong Wang, Yan Wang, Jin-Lyu Sun, Jian-Dong Jiang

Engineering 2022, Volume 15, Issue 8,   Pages 115-125 doi: 10.1016/j.eng.2021.03.013

Abstract:

Due to the worldwide epidemic of allergic disease and a cure nowhere in sight, there is a crucial need to explore its pathophysiological mechanisms. As allergic disease has been associated with gut dysbiosis, we searched for a possible mechanism from the perspective of the molecular interface between host and microbiota with concurrent metabolomics and microbiome composition analysis. Sprague-Dawley rats were injected with Artemisia pollen extract to stimulate a hyper reaction to pollen. This hyper reaction decreased the circulation of valine, isoleucine, aspartate, glutamate, glutamine, indole-propionate (IPA), and myo-inositol, and reduced short-chain fatty acids (SCFAs) in feces. Several beneficial genera belonging to Ruminococcaceae, Lachnospiraceae, and Clostridiales declined in the model group, whereas Helicobacter and Akkermansia were only expressed in the model group. Furthermore, the expression of intestinal claudin-3 and liver fatty acid binding protein was downregulated in the model group and associated with metabolic changes and bacteria. Our results suggest that alterations in amino acids as well as their derivatives (especially valine, and IPA which is the reductive product of tryptophan) , SCFAs, and the gut microbiome (specifically Akkermansia and Helicobacter) may disrupt the intestinal barrier function by inhibiting the expression of claudin proteins and affecting the mucus layer, which further results in hay fever.

Keywords： Metabolome     Gut microbiota     Hay fever     Allergic diseases     Intestinal barrier dysfunction    

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Title Author Date Type Operation

Discovery of the mechanisms of acupuncture in the treatment of migraine based on functional magnetic resonance imaging and omics

Journal Article

characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome

Journal Article

Calorie restriction and its impact on gut microbial composition and global metabolism

Xiaojiao Zheng, Shouli Wang, Wei Jia

Journal Article

Extending the “Paracentral Dogma” of Biology with the Metabolome: Implications for Understanding Genomic–Glycomic–Metabolic–Epigenomic

Albert Stuart Reece

Journal Article

Reconstruction and Dynamics of the Human Intestinal Microbiome Observed In Situ

Xiaolin Liu, Min Dai, Yue Ma, Na Zhao, Ziyu Wang, Ying Yu, Yakun Xu, Huijie Zhang, Liyuan Xiang, He Tian, Guanghou Shui, Faming Zhang, Jun Wang

Journal Article

Multi-Omics Analysis Provides Insight into the Possible Molecular Mechanism of Hay Fever Based on Gut Microbiota

Pei Han, Li-Sha Li, Zi-Xi Wang, Lin Xi, Hang Yu, Lin Cong, Zheng-Wei Zhang, Jie Fu, Ran Peng, Li-Bin Pan, Shu-Rong Ma, Xue-Yan Wang, Hong-Tian Wang, Xiang-Dong Wang, Yan Wang, Jin-Lyu Sun, Jian-Dong Jiang

Journal Article