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Frontiers of Medicine Pages 993-1005 doi: 10.1007/s11684-023-0989-7
Keywords: acupuncture migraine fMRI metabolome proteome
Frontiers of Medicine doi: 10.1007/s11684-023-1029-3
Keywords: tumor prognosis molecular Microbiome subsets determine center analysis microbiome transcriptome data
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
Keywords: caloric restriction gut microbiota metabolome
Albert Stuart Reece
Engineering 2023, Volume 26, Issue 7, Pages 16-16 doi: 10.1016/j.eng.2022.07.011
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
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
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
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
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