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Yu Q, Zhang Y, Zeng W, Sun Y, Zhang X, Guo L, Zhang Y, Yu B, Guo M, Wang Y, Li H, Suo Y, Jiang X, Song L. Buyang Huanwu Decoction Alleviates Atherosclerosis by Regulating gut Microbiome and Metabolites in Apolipoprotein E-deficient Mice fed with High-fat Diet. JOURNAL OF PHYSIOLOGICAL INVESTIGATION 2024; 67:88-102. [PMID: 38780293 DOI: 10.4103/ejpi.ejpi-d-23-00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/25/2024] [Indexed: 05/25/2024]
Abstract
ABSTRACT The traditional Chinese herbal prescription Buyang Huanwu decoction (BHD), effectively treats atherosclerosis. However, the mechanism of BHD in atherosclerosis remains unclear. We aimed to determine whether BHD could alleviate atherosclerosis by altering the microbiome-associated metabolic changes in atherosclerotic mice. An atherosclerotic model was established in apolipoprotein E-deficient mice fed high-fat diet, and BHD was administered through gavage for 12 weeks at 8.4 g/kg/d and 16.8 g/kg/d. The atherosclerotic plaque size, composition, serum lipid profile, and inflammatory cytokines, were assessed. Mechanistically, metabolomic and microbiota profiles were analyzed by liquid chromatography-mass spectrometry and 16S rRNA gene sequencing, respectively. Furthermore, intestinal microbiota and atherosclerosis-related metabolic parameters were correlated using Spearman analysis. Atherosclerotic mice treated with BHD exhibited reduced plaque area, aortic lumen occlusion, and lipid accumulation in the aortic root. Nine perturbed serum metabolites were significantly restored along with the relative abundance of microbiota at the family and genus levels but not at the phylum level. Gut microbiome improvement was strongly negatively correlated with improved metabolite levels. BHD treatment effectively slows the progression of atherosclerosis by regulating altered intestinal microbiota and perturbed metabolites.
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Affiliation(s)
- Qun Yu
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Yilin Zhang
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Wenyun Zeng
- Oncology, Ganzhou People's Hospital, Ganzhou, China
| | - Yingxin Sun
- School of Faculty of Health and Exercise Science, Tianjin University of Sport, Tianjin, China
| | - Xiaolu Zhang
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Lin Guo
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Yue Zhang
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Bin Yu
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Maojuan Guo
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Yu Wang
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Huhu Li
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Yanrong Suo
- Oncology, Ganzhou People's Hospital, Ganzhou, China
| | - Xijuan Jiang
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
| | - Lili Song
- School of Integrated Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Jinghai, Tianjin, China
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Ma C, Zhang Y, Jiang S, Teng F, Huang S, Zhang J. Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. mSystems 2023; 8:e0082823. [PMID: 37905808 PMCID: PMC10734426 DOI: 10.1128/msystems.00828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.
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Affiliation(s)
- Chenchen Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yufeng Zhang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Fei Teng
- Qingdao Stomatological Hospital Affiliated to Qingdao University, Qingdao, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, Hainan, China
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Liang Y, Dou S, Zhao G, Shen J, Fu G, Fu L, Li S, Cong B, Dong C. Prediction of BMI traits in the Chinese population based on the gut metagenome. Microb Cell Fact 2023; 22:250. [PMID: 38066544 PMCID: PMC10704812 DOI: 10.1186/s12934-023-02255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and could serve as potential markers for forensic characterization. Previous research has established that predicting body type based on the relative abundance of the gut microbiome is relatively accurate. However, the long-term stability and high individual specificity of the gut microbiome are closely linked to changes at the genome level of the microbiome. No studies have been conducted to deduce body shape from genetic traits. Therefore, in this study, the vital role of gut bacterial community characteristics and genetic traits in predicting body mass index (BMI) was investigated using gut metagenomic data from a healthy Chinese population. RESULTS Regarding the gut microbial community, the underweight group displayed increased α-diversity in comparison to the other BMI groups. There were significant differences in the relative abundances of 19 species among these three BMI groups. The BMI prediction model, based on the 31 most significant species, showed a goodness of fit (R2) of 0.56 and a mean absolute error (MAE) of 2.09 kg/m2. The overweight group exhibited significantly higher α-diversity than the other BMI groups at the level of gut microbial genes. Furthermore, there were significant variations observed in the single-nucleotide polymorphism (SNP) density of 732 contigs between these three BMI groups. The BMI prediction model, reliant on the 62 most contributing contigs, exhibited a model R2 of 0.72 and an MAE of 1.56 kg/m2. The model predicting body type from 44 contigs correctly identified the body type of 93.55% of the study participants. CONCLUSION Based on metagenomic data from a healthy Chinese population, we demonstrated the potential of genetic traits of gut bacteria to predict an individual's BMI. The findings of this study suggest the effectiveness of a novel method for determining the body type of suspects in forensic applications using the genetic traits of the gut microbiome and holds great promise for forensic individual identification.
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Affiliation(s)
- Yu Liang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujie Dou
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangzhong Zhao
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Jie Shen
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Chunnan Dong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
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Calva-Cruz ODJ, Ovando-Vázquez C, De León-Rodríguez A, Veana F, Espitia-Rangel E, Treviño S, Barba-de la Rosa AP. Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial. Foods 2023; 12:2760. [PMID: 37509852 PMCID: PMC10379428 DOI: 10.3390/foods12142760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Amaranth has been recognized as a nutraceutical food because it contains high-quality proteins due to its adequate amino acid composition that covers the recommended requirements for children and adults. Since pre-Hispanic times, amaranth has been consumed as popped grain; the popping process improves its nutritive quality and improves its digestibility. Popped amaranth consumption has been associated with the recovery of malnourished children. However, there is no information on the impact that popped amaranth consumption has on gut microbiota composition. A non-randomized pilot trial was conducted to evaluate the changes in composition, structure, and function of the gut microbiota of stunted children who received four grams of popped amaranth daily for three months. Stool and serum were collected at the beginning and at the end of the trial. Short-chain fatty acids (SCFA) were quantified, and gut bacterial composition was analyzed by 16S rRNA gene sequencing. Biometry and hematology results showed that children had no pathology other than low height-for-age. A decrease in the relative abundance of Alistipes putredinis, Bacteroides coprocola, and Bacteroides stercoris bacteria related to inflammation and colitis, and an increase in the relative abundance of Akkermansia muciniphila and Streptococcus thermophiles bacteria associated with health and longevity, was observed. The results demonstrate that popped amaranth is a nutritious food that helps to combat childhood malnutrition through gut microbiota modulation.
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Affiliation(s)
- Oscar de Jesús Calva-Cruz
- Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí 78216, Mexico
| | - Cesaré Ovando-Vázquez
- CONACYT-Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí 78216, Mexico
| | - Antonio De León-Rodríguez
- Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí 78216, Mexico
| | - Fabiola Veana
- Tecnológico Nacional de México, Instituto Tecnológico de Ciudad Valles, Ciudad Valles 79010, Mexico
| | - Eduardo Espitia-Rangel
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Texcoco 56250, Mexico
| | - Samuel Treviño
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, Ciudad Universitaria, Puebla 72000, Mexico
| | - Ana Paulina Barba-de la Rosa
- Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí 78216, Mexico
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Zhang M, Zheng Y, Sun Z, Cao C, Zhao W, Liu Y, Zhang W, Zhang H. Change in the Gut Microbiome and Immunity by Lacticaseibacillus rhamnosus Probio-M9. Microbiol Spectr 2023; 11:e0360922. [PMID: 36912650 PMCID: PMC10100958 DOI: 10.1128/spectrum.03609-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
With the exploding growth of the global market for probiotics and the rapid awakening of public awareness to manage health by probiotic intervention, there is still an active debate about whether the consumption of probiotics is beneficial for nonpatients, which is due to the lack of systematic analysis based on time series multiomics data sets. In this study, we recruited 100 adults from a college in China and performed a random case-control study by using a probiotic (Lacticaseibacillus rhamnosus Probio-M9) as an intervention for 6 weeks, aiming to achieve a comprehensive evaluation and understanding of the beneficial effect of Probio-M9 consumption. By testing advanced blood immunity indicators, sequencing the gut microbiome, and profiling the gut metabolome at baseline and the end of the study, we found that although the probiotic intervention has a limited impact on the human immunity and the gut microbiome and metabolome, the associations between the immunity indicators and multiomics data were strengthened, and further analysis of the gut microbiome's genetic variations revealed inhibited generation of single nucleotide variants (SNVs) by probiotic consumption. Taken together, our findings indicated an underestimated influence of the probiotic, not on altering the microbial composition but on strengthening the association between human immunity and commensal microbes and stabilizing the genetic variations of the gut microbiome. IMPORTANCE Although the global market for probiotics is growing explosively, there is still an active debate about whether the consumption of probiotics is beneficial for nonpatients. In this study, we recruited 100 adults from a college in China and performed 6 weeks of intervention for half of the volunteers. By analyzing the time series multiomics data in this study, we found that the probiotic intervention (i) has a limited effect on human immunity or the global structure of the gut microbiome and metabolome, (ii) can largely influence the correlation of the development between multiomics data and immunity, which was not able to be discovered by conventional differential abundance analysis, and (iii) can inhibit the generation of SNVs in the gut microbiome instead of promoting it.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Yan Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Zheng Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Chenxia Cao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Wei Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Yangshuo Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Synbiotic Intervention Ameliorates Oxidative Stress and Gut Permeability in an In Vitro and In Vivo Model of Ethanol-Induced Intestinal Dysbiosis. Biomedicines 2022; 10:biomedicines10123285. [PMID: 36552041 PMCID: PMC9816946 DOI: 10.3390/biomedicines10123285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial components to enter the portal vein and induce oxidative stress-induced inflammation in the liver. Only corticosteroids and liver transplants are treatment options for severe alcoholic hepatitis. ALD's pathophysiology is unknown. However, acetaldehyde's toxic effects cause oxidative stress and intestinal permeability. This study investigates the influence of a synbiotic (a combination of aged garlic extract (AGE) and Lactobacillus rhamnosus MTCC1423) on colonic oxidative stress and inflammation in ALD male Wistar rats and Caco2 cells. MDA measurement by HPLC in CaCo2 cells, blood serum, and colon tissue demonstrated that synbiotic treatment in the ALD model reduces oxidative stress. Further, fecal high-throughput 16S rRNA gene sequencing revealed the microbiome's shift towards Firmicutes in the synbiotic group compared to ethanol. In addition, DCFDA labeling and H/E staining demonstrate that the synbiotic is beneficial in inhibiting the development of ALD. In the colon, the synbiotic reduces the activation of CYP2E1 and the inflammatory markers TNF-a and IL-6 while elevating the mRNA expression of ZO-1, occludin, and IL-10. Synbiotics colonize Lactobacillus to restore barrier function and microbiota and reduce colon oxidative stress. Thus, a synbiotic combination can be used in ALD treatment.
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Chen YC, Lin HY, Chien Y, Tung YH, Ni YH, Gau SSF. Altered gut microbiota correlates with behavioral problems but not gastrointestinal symptoms in individuals with autism. Brain Behav Immun 2022; 106:161-178. [PMID: 36058421 DOI: 10.1016/j.bbi.2022.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/09/2022] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite inconsistent results across studies, emerging evidence suggests that the microbial micro-environment may be associated with autism spectrum disorder (ASD). Geographical and cultural factors highly impact microbial profiles, and there is a shortage of data from East Asian populations. This study aimed to comprehensively characterize microbial profiles in an East Asian sample and explore whether gut microbiota contributes to clinical symptoms, emotional/behavioral problems, and GI symptoms in ASD. METHODS We assessed 82 boys and young men with ASD and 31 typically developing controls (TDC), aged 6-25 years. We analyzed the stool sample of all participants with 16S V3-V4 rRNA sequencing and correlated its profile with GI symptoms, autistic symptoms, and emotional/behavioral problems. RESULTS Autistic individuals, compared to TDC, had worse GI symptoms. There were no group differences in alpha diversity of species richness estimates (Shannon-wiener and Simpson diversity indices). Participants with ASD had an increased relative abundance of Fusobacterium, Ruminococcus torques group (at the genus level), and Bacteroides plebeius DSM 17135 (at the species level), while a decreased relative abundance of Ruminococcaceae UCG 013, Ervsipelotrichaceae UCG 003, Parasutterella, Clostridium sensu stricto 1, Turicibacter (at the genus level), and Clostridium spiroforme DSM 1552 and Intestinimonas butyriciproducens (at the species level). Altered taxonomic diversity in ASD significantly correlated with autistic symptoms, thought problems, delinquent behaviors, self dysregulation, and somatic complaints. We did not find an association between gut symptoms and gut microbial dysbiosis. CONCLUSIONS Our findings suggest that altered microbiota are associated with behavioral phenotypes but not GI symptoms in ASD. The function of the identified microbial profiles mainly involves the immune pathway, supporting the hypothesis of a complex relationship between altered microbiome, immune dysregulation, and ASD that may advance the discovery of molecular biomarkers for ASD.
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Affiliation(s)
- Yu-Chieh Chen
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Yuan Lin
- Azrieli Adult Neurodevelopmental Centre, Centre for Addiction and Mental Health, Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yiling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yu-Hung Tung
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Hsuan Ni
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Susan Shur-Fen Gau
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
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Liu Y, Hu X, Zheng W, Zhang L, Gui L, Liang G, Zhang Y, Hu L, Li X, Zhong Y, Su T, Liu X, Cheng J, Gong M. Action mechanism of hypoglycemic principle 9-(R)-HODE isolated from cortex lycii based on a metabolomics approach. Front Pharmacol 2022; 13:1011608. [PMID: 36339561 PMCID: PMC9633664 DOI: 10.3389/fphar.2022.1011608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 11/23/2022] Open
Abstract
The 9-(R)-HODE is an active compound isolated from cortex lycii that showed significant hypoglycemic effects in our previous in vitro study. In this study, 9-(R)-HODE’s in vivo hypoglycemic activity and effect on alleviating diabetic complications, together with its molecular mechanism, was investigated using a metabolomics approach. The monitored regulation on dynamic fasting blood glucose, postprandial glucose, body weight, biochemical parameters and histopathological analysis confirmed the hypoglycemic activity and attenuation effect, i.e., renal lesions, of 9-(R)-HODE. Subsequent metabolomic studies indicated that 9-(R)-HODE induced metabolomic alterations primarily by affecting the levels of amino acids, organic acids, alcohols and amines related to amino acid metabolism, glucose metabolism and energy metabolism. By mediating the related metabolism or single molecules related to insulin resistance, e.g., kynurenine, myo-inositol and the branched chain amino acids leucine, isoleucine and valine, 9-(R)-HODE achieved its therapeutic effect. Moreover, the mediation of kynurenine displayed a systematic effect on the liver, kidney, muscle, plasma and faeces. Lipidomic studies revealed that 9-(R)-HODE could reverse the lipid metabolism disorder in diabetic mice mainly by regulating phosphatidylinositols, lysophosphatidylcholines, lysophosphatidylcholines, phosphatidylserine, phosphatidylglycerols, lysophosphatidylglycerols and triglycerides in both tissues and plasma. Treatment with 9-(R)-HODE significantly modified the structure and composition of the gut microbiota. The SCFA-producing bacteria, including Rikenellaceae and Lactobacillaceae at the family level and Ruminiclostridium 6, Ruminococcaceae UCG 014, Mucispirillum, Lactobacillus, Alistipes and Roseburia at the genus level, were increased by 9-(R)-HODE treatment. These results were consistent with the increased SCFA levels in both the colon content and plasma of diabetic mice treated with 9-(R)-HODE. The tissue DESI‒MSI analysis strongly confirmed the validity of the metabolomics approach in illustrating the hypoglycemic and diabetic complications-alleviation effect of 9-(R)-HODE. The significant upregulation of liver glycogen in diabetic mice by 9-(R)-HODE treatment validated the interpretation of the metabolic pathways related to glycogen synthesis in the integrated pathway network. Altogether, 9-(R)-HODE has the potential to be further developed as a promising candidate for the treatment of diabetes.
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Affiliation(s)
- Yueqiu Liu
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu, China
| | - Xinyi Hu
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Zheng
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Zhang
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Luolan Gui
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Ge Liang
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Zhang
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Li
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Liu
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Meng Gong,
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Gupta H, Kim SH, Kim SK, Han SH, Kwon HC, Suk KT. Beneficial Shifts in Gut Microbiota by Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus R0052 in Alcoholic Hepatitis. Microorganisms 2022; 10:microorganisms10071474. [PMID: 35889193 PMCID: PMC9319967 DOI: 10.3390/microorganisms10071474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Gut microbiota performs indispensable functions in the pathophysiology of alcoholic hepatitis (AH). We investigated the effects of Lacticaseibacillus rhamnosus R0011 and Lactobacillus helveticus for gut microbial restoration toward eubiosis in patients with AH. A multicenter, double-blind, and randomized trial was conducted. Probiotics (n = 44) and placebo (n = 45) groups received, during 7 days, L. rhamnosus R0011/L. helveticus R0052 at 120 mg/day and placebo. All patients were hospitalized to ensure abstinence. Liver function, lipopolysaccharide level, and stool analysis were evaluated in patients before and after 7 days of treatment. At baseline, the dominant bacteria were Gram-negative in both groups which decreased after the probiotics treatment and exhibited a significant reduction in lipopolysaccharide level (p < 0.001). The probiotics ameliorated the Child−Pugh scores (p < 0.001). Furthermore, the probiotics group showed a decline in the levels of alanine aminotransferase and gamma-glutamyltranspeptidase (p < 0.05). The probiotics changed the gut microbial composition at various taxonomical levels. The proportion of Bacteroidetes (147%) was increased after 7 days of probiotics supplementation while Proteobacteria (30%) and Fusobacteria (0%) were decreased. Administration of L. rhamnosus R0011 and L. helveticus R0052 conceivably associated with restoration of gut microbiome in AH patients and improved AH by modulating the gut−liver axis.
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Affiliation(s)
- Haripriya Gupta
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (H.G.); (S.K.K.)
| | - Sung Hun Kim
- Korea Institute of Science and Technology, Gangneung 25451, Korea;
| | - Seul Ki Kim
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (H.G.); (S.K.K.)
| | - Sang Hak Han
- Department of Pathology, Hallym University College of Medicine, Chuncheon 24252, Korea;
| | - Hak Cheol Kwon
- Korea Institute of Science and Technology, Gangneung 25451, Korea;
- Correspondence: (H.C.K.); (K.T.S.)
| | - Ki Tae Suk
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea; (H.G.); (S.K.K.)
- Correspondence: (H.C.K.); (K.T.S.)
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10
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Liu P, Hu S, He Z, Feng C, Dong G, An S, Liu R, Xu F, Chen Y, Ying X. Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome. Front Microbiol 2022; 13:828254. [PMID: 35602026 PMCID: PMC9119422 DOI: 10.3389/fmicb.2022.828254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.
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Affiliation(s)
- Pu Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chao Feng
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Fang Xu
- Yongkang First People’s Hospital, Yongkang, China
| | - Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
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11
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Liu Z, Zhang T, Wu K, Li Z, Chen X, Jiang S, Du L, Lu S, Lin C, Wu J, Wang X. Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:260-273. [PMID: 34252627 PMCID: PMC9684085 DOI: 10.1016/j.gpb.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 01/05/2023]
Abstract
Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Keke Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou 325000, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China
| | - Chongxiang Lin
- Department of Stomatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China,Corresponding authors.
| | - Xiaobing Wang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China,Corresponding authors.
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12
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Ma C, Chen K, Wang Y, Cen C, Zhai Q, Zhang J. Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. Gut Microbes 2022; 13:1-6. [PMID: 33430705 PMCID: PMC7808391 DOI: 10.1080/19490976.2020.1869505] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Current metagenomic species-based colorectal cancer (CRC) microbial biomarkers may confuse diagnosis because the genetic content of different microbial strains, even those belonging to the same species, may differ from 5% to 30%. Here, a total of 7549 non-redundant single nucleotide variants (SNVs) were annotated in 25 species from 3 CRC cohorts (n = 249). Then, 22 microbial SNV markers that contributed to distinguishing subjects with CRC from healthy subjects were identified by the random forest algorithm to construct a novel CRC predictive model. Excitingly, the predictive model showed high accuracy both in the training (AUC = 75.35%) and validation cohorts (AUC = 73.08%-88.02%). We further explored the specificity of these SNV markers in a broader background by performing a meta-analysis across 4 metabolic disease cohorts. Among these SNV markers, 3 SNVs that were enriched in CRC patients and located in the genomes of Eubacterium rectale and Faecalibacterium prausnitzii were CRC specific (AUC = 72.51%-94.07%).
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Affiliation(s)
- Chenchen Ma
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China
| | - Kaining Chen
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Yuanyuan Wang
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China
| | - Chaoping Cen
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, P. R China,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China,Qixiao Zhai State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, P. R China
| | - Jiachao Zhang
- College of Food Science and Engineering, Hainan University, Haikou, Hainan, P. R. China,Key Laboratory of Food Nutrition and Functional Food of HainanProvince, Hainan University, Haikou, Hainan, China,CONTACT Jiachao Zhang College of Food Science and Engineering, Hainan University, Haikou, Hainan570228, P. R. China
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13
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Ma C, Zhang C, Chen D, Jiang S, Shen S, Huo D, Huang S, Zhai Q, Zhang J. Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota. Commun Biol 2021; 4:1198. [PMID: 34663913 PMCID: PMC8523657 DOI: 10.1038/s42003-021-02724-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022] Open
Abstract
The adaptive evolution in indigenous intestinal microbes derived from probiotics is critical to safety and efficacy evaluation of probiotics, yet it is still largely underexplored. Here, through 11 publicly accessible datasets, we demonstrated that probiotic consumption can lead to widespread single-nucleotide variants (SNVs) in the native microbiota. Interestingly, the same probiotic strains introduced far more SNVs in mouse gut than humans. Furthermore, the pattern of probiotics-induced SNVs was highly probiotic-strain specific, and 17 common SNVs in Faecalibacterium prausnitzii genome were identified cross studies, which might lead to changes in bacterial protein structure. Further, nearly 50% of F. prausnitzii SNVs can be inherited for six months in an independent human cohort, whereas the other half only transiently occurred. Collectively, our study substantially extended our understanding of co-evolution of the probiotics and the indigenous gut microbiota, highlighting the importance of assessment of probiotics efficacy and safety in an integrated manner. Chenchen Ma, Chengcheng Zhang, and Denghui Chen et al. examine how probiotic consumption impacts gut microbiota composition in human and mice through a global, cross-cohort metagenomic analysis. Their results suggest that probiotic consumption may result in widespread variation among the native microbiota in both the human and mouse gut.
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Affiliation(s)
- Chenchen Ma
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122, Wuxi, China
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shuaiming Jiang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Siyuan Shen
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Dongxue Huo
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Shi Huang
- Department of Pediatrics and Center for Microbiome Innovation at Jacobs School of Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China.
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14
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Chen Y, Liu P, Liu R, Hu S, He Z, Dong G, Feng C, An S, Ying X. Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. mSystems 2021; 6:e0077521. [PMID: 34342541 PMCID: PMC8407477 DOI: 10.1128/msystems.00775-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/09/2021] [Indexed: 01/11/2023] Open
Abstract
Liver cirrhosis (LC) has been associated with gut microbes. However, the strain diversity of species and its association with LC have received little attention. Here, we constructed a computational framework to study the strain heterogeneity in the gut microbiome of patients with LC. Only Faecalibacterium prausnitzii shows different single-nucleotide polymorphism (SNP) patterns between the LC and healthy control (HC) groups. Strain diversity analysis discovered that although most F. prausnitzii genomes are more deficient in the LC group than in the HC group at the strain level, a subgroup of 19 F. prausnitzii strains showed no sensitivity to LC, which is inconsistent with the species-level result. The functional differences between this subgroup and other strains may involve short-chain fatty acid production and chlorine-related pathways. These findings demonstrate functional differences among F. prausnitzii subgroups, which extend current knowledge about strain heterogeneity and relationships between F. prausnitzii and LC at the strain level. IMPORTANCE Most metagenomic studies focus on microbes at the species level, thus ignoring the different effects of different strains of the same species on the host. In this study, we explored the different microbes at the strain level in the intestines of patients with liver cirrhosis and of healthy people. Previous studies have shown that the species Faecalibacterium prausnitzii has a lower abundance in patients with liver cirrhosis than in healthy people. However, our results found multiple F. prausnitzii strains that do not decrease in abundance in patients with liver cirrhosis. It is more sensitive to select the appropriate strains as indicators to distinguish between the disease and the control samples than to use the entire species as an indicator. We clustered multiple F. prausnitzii strains and discuss the functional differences of different clusters. Our findings suggest that more attention should be paid to metagenomic studies at the strain level.
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Affiliation(s)
- Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Pu Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chao Feng
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
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15
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Liu J, Zhao F, Wang T, Xu Y, Qiu J, Qian Y. Host Metabolic Disorders Induced by Alterations in Intestinal Flora under Dietary Pesticide Exposure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6303-6317. [PMID: 34048223 DOI: 10.1021/acs.jafc.1c00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A dietary pesticide residue causes underestimated influences on body health. In this work, experimental mice were exposed to commonly used pesticides that cause insulin resistance, inflammation, and non-alcoholic fatty liver diseases. Alterations in intestinal flora were detected in the exposure groups. The abundance of the flora causing high endotoxin production was intensively increased and led to body inflammation. High Firmicutes/Bacteroidetes and obesity-related flora characteristics were also found. The metabolisms of intestinal flora and host circulation were investigated through metabolomics. The associations of flora with their metabolites and host circulation were also established. Association analysis can determine the influences of pesticide exposure on such a complex system. The affected metabolic pathways in the liver were also determined to clarify the mechanism underlying the effect of pesticide exposure on host physiology. Interventions with fructooligosaccharides and fecal microbiota transplantation alleviated the metabolic disorders, thus directly confirming that the intestinal flora mediates the effects of pesticide exposure on host circulation. This work elucidated the intestinal-flora-mediated effects of dietary pollutant exposure on body health and provided potential measures for regulating flora and host circulation.
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Affiliation(s)
- Jingkun Liu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, People's Republic of China
| | - Fangfang Zhao
- Analysis & Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, People's Republic of China
| | - Tianrun Wang
- Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Yanyang Xu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, People's Republic of China
| | - Jing Qiu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, People's Republic of China
| | - Yongzhong Qian
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, People's Republic of China
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16
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Li H, Zhao L, Zhang M. Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children. Front Microbiol 2021; 12:683714. [PMID: 34135881 PMCID: PMC8200495 DOI: 10.3389/fmicb.2021.683714] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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17
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Liu J, Zhao F, Xu Y, Qiu J, Qian Y. Gut Flora-Mediated Metabolic Health, the Risk Produced by Dietary Exposure to Acetamiprid and Tebuconazole. Foods 2021; 10:835. [PMID: 33921314 PMCID: PMC8070257 DOI: 10.3390/foods10040835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/20/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
The low-level and long-term exposure of pesticides was found to induce metabolic syndrome to mice. Metabolic pathways and mechanisms were investigated by detecting gut flora with metabolites, host circulation, and their interrelations. Results showed that the abundances of flora species and their metabolism were altered, consequently leading to metabolic disorders. A correlation analysis between gut flora and their metabolic profiling further explained these changes and associations. The metabolic profiling of host circulation was also performed to characterize metabolic disorders. The associations of host circulation with gut flora were established via their significantly different metabolites. Alterations to the liver metabolism clarified potential pathways and mechanisms for the disorders. Metabolic disorders were evidently released by dietary and micro-ecological intervention, directly proving that gut flora comprise a vital medium in metabolic health risk caused by pesticide exposure. This work supplied theoretical bases and intervention approaches to body metabolic problems caused by pesticide exposure mediated by gut flora.
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Affiliation(s)
- Jingkun Liu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.L.); (Y.X.); (Y.Q.)
| | - Fangfang Zhao
- Analysis & Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Yanyang Xu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.L.); (Y.X.); (Y.Q.)
| | - Jing Qiu
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.L.); (Y.X.); (Y.Q.)
| | - Yongzhong Qian
- Institute of Quality Standards & Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China; (J.L.); (Y.X.); (Y.Q.)
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18
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An J, Lee H, Lee S, Song Y, Kim J, Park IH, Kong H, Kim K. Modulation of Pro-inflammatory and Anti-inflammatory Cytokines in the Fat by an Aloe Gel-based Formula, QDMC, Is Correlated with Altered Gut Microbiota. Immune Netw 2021; 21:e15. [PMID: 33996171 PMCID: PMC8099612 DOI: 10.4110/in.2021.21.e15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/08/2023] Open
Abstract
Abnormal inflammatory responses are closely associated with intestinal microbial dysbiosis. Oral administration of Qmatrix-diabetes-mellitus complex (QDMC), an Aloe gel-based formula, has been reported to improve inflammation in type 2 diabetic mice; however, the role of the gut microbiota in ameliorating efficacy of QDMC remains unclear. We investigated the effect of QDMC on the gut microbiota in a type 2 diabetic aged mouse model that was administered a high-fat diet. Proinflammatory (TNF-α and IL-6) and anti-inflammatory (IL-4 and IL-10) cytokine levels in the fat were normalized via oral administration of QDMC, and relative abundances of Bacteroides, Butyricimonas, Ruminococcus, and Mucispirillum were simultaneously significantly increased. The abundance of these bacteria was correlated to the expression levels of cytokines. Our findings suggest that the immunomodulatory activity of QDMC is partly mediated by the altered gut microbiota composition.
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Affiliation(s)
- Jinho An
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Heetae Lee
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Sungwon Lee
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Youngcheon Song
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Jiyeon Kim
- Climacteric Natural Products Research Institute, Sahmyook University, Seoul 01795, Korea
| | - Il Ho Park
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Hyunseok Kong
- Climacteric Natural Products Research Institute, Sahmyook University, Seoul 01795, Korea.,College of Animal Biotechnology and Resource, Sahmyook University, Seoul 01795, Korea
| | - Kyungjae Kim
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
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19
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Wang P, Wang T, Zheng X, Cui W, Shang J, Zhao Z. Gut microbiota, key to unlocking the door of diabetic kidney disease. Nephrology (Carlton) 2021; 26:641-649. [PMID: 33715272 PMCID: PMC8360003 DOI: 10.1111/nep.13874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
This review discusses the influence of gut microbiota dysbiosis on diabetic kidney disease through metabolite profile changes and immune and inflammatory mechanisms. We also elaborate on the mechanism of dysbiosis in the onset and development of other kidney diseases. This review presents scientific evidence on the pathophysiologic links between gut microbiota and diabetic kidney disease (DKD), highlighting the influence of gut microbiota dysbiosis on DKD through metabolite profile changes and immunologic mechanisms.
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Affiliation(s)
- Peipei Wang
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Ting Wang
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Xuejun Zheng
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Wen Cui
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Jin Shang
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Zhanzheng Zhao
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
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20
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Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome. ENTROPY 2021; 23:e23020187. [PMID: 33540903 PMCID: PMC7913240 DOI: 10.3390/e23020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/26/2022]
Abstract
Quantitative metagenomics is an important field that has delivered successful microbiome biomarkers associated with host phenotypes. The current convention mainly depends on unsupervised assembly of metagenomic contigs with a possibility of leaving interesting genetic material unassembled. Additionally, biomarkers are commonly defined on the differential relative abundance of compositional or functional units. Accumulating evidence supports that microbial genetic variations are as important as the differential abundance content, implying the need for novel methods accounting for the genetic variations in metagenomics studies. We propose an information theoretic metagenome assembly algorithm, discovering genomic fragments with maximal self-information, defined by the empirical distributions of nucleotides across the phenotypes and quantified with the help of statistical tests. Our algorithm infers fragments populating the most informative genetic variants in a single contig, named supervariant fragments. Experiments on simulated metagenomes, as well as on a colorectal cancer and an atherosclerotic cardiovascular disease dataset consistently discovered sequences strongly associated with the disease phenotypes. Moreover, the discriminatory power of these putative biomarkers was mainly attributed to the genetic variations rather than relative abundance. Our results support that a focus on metagenomics methods considering microbiome population genetics might be useful in discovering disease biomarkers with a great potential of translating to molecular diagnostics and biotherapeutics applications.
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21
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Zhu X, Qin J, Tan C, Ning K. The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns. BMC Genomics 2021; 22:83. [PMID: 33509082 PMCID: PMC7842071 DOI: 10.1186/s12864-021-07372-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/07/2021] [Indexed: 12/21/2022] Open
Abstract
Background Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level. Results In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis. Conclusions Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07372-0.
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Affiliation(s)
- Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Jiyue Qin
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Chongyang Tan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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22
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Modulation of Short-Chain Fatty Acids as Potential Therapy Method for Type 2 Diabetes Mellitus. ACTA ACUST UNITED AC 2021; 2021:6632266. [PMID: 33488888 PMCID: PMC7801078 DOI: 10.1155/2021/6632266] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022]
Abstract
In recent years, the relationship between intestinal microbiota (IM) and the pathogenesis of type 2 diabetes mellitus (T2DM) has attracted much attention. The beneficial effects of IM on the metabolic phenotype of the host are often considered to be mediated by short-chain fatty acids (SCFAs), mainly acetate, butyrate, and propionate, the small-molecule metabolites derived from microbial fermentation of indigestible carbohydrates. SCFAs not only have an essential role in intestinal health but might also enter the systemic circulation as signaling molecules affecting the host's metabolism. In this review, we summarize the effects of SCFAs on glucose homeostasis and energy homeostasis and the mechanism through which SCFAs regulate the function of metabolically active organs (brain, liver, adipose tissue, skeletal muscle, and pancreas) and discuss the potential role of modulation of SCFAs as a therapeutic method for T2DM.
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23
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Liu F, Zhang N, Wu Y, Jiang P, Jiang T, Wang Y, Zhang Y, Zhai Q, Zou Y, Feng N. The pelvis urinary microbiome in patients with kidney stones and clinical associations. BMC Microbiol 2020; 20:336. [PMID: 33153435 PMCID: PMC7643416 DOI: 10.1186/s12866-020-01992-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The long-held notion that, without urinary tract or circulatory infection, bladder urine and blood are sterile biofluids has been disproven. There have been no previous reports on the kidney pelvis urinary microbiome after bladder disinfection in kidney stone patients. This study aimed to determine whether a kidney pelvis urinary microbiome is present after eliminating the influence of the bladder urinary microbiome, whether the microbiome composition is different in patients with stone kidney pelvis (SKP) and non-stone kidney pelvis (NSKP), and the correlation between SKP and patient clinical characteristics. RESULTS Comparisons of bacterial diversity and community structure exhibited that urine in bladder was similar to SKP and NSKP. However, the comparisons showed that urine samples were different from blood. The most common operational taxonomic units were shared by all three types of urine samples. Corynebacterium was significantly higher in SKP compared to NSKP. Several bacteria were associated with patient characteristics, including Lactobacillus, which was positively correlated with fasting blood glucose, and Prevotella was negatively correlated with BMI. Lactobacillus was significantly higher in SKP compared to blood but not in NSKP compared to blood. CONCLUSIONS The composition of the kidney pelvis urinary microbiome after disinfection of the bladder and its similarity to the bladder microbiome indicate that bladder urine can be used to replace kidney pelvis urine in microbiome research. Additionally, the comparison of SKP and NSKP and clinical associations suggest that the occurrence of kidney stones is responsible for the SKP urinary microbiome.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China.,Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Nan Zhang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Yunhong Wu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Peng Jiang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | | | - Yang Wang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Yuwei Zhang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
| | - Yeqing Zou
- Basic Medical School, Jiangsu Vocational College of Medicine, Yancheng, 224000, China.
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China.
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24
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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25
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Li X, Guo R, Wu X, Liu X, Ai L, Sheng Y, Song Z, Wu Y. Dynamic digestion of tamarind seed polysaccharide: Indigestibility in gastrointestinal simulations and gut microbiota changes in vitro. Carbohydr Polym 2020; 239:116194. [DOI: 10.1016/j.carbpol.2020.116194] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/07/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
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26
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Li Z, Zhu H, Guo Y, Du X, Qin C. Gut microbiota regulate cognitive deficits and amyloid deposition in a model of Alzheimer's disease. J Neurochem 2020; 155:448-461. [PMID: 32319677 DOI: 10.1111/jnc.15031] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 12/21/2022]
Abstract
Gut microbiota, comprising a vast number of microorganism species with complex metagenome, are known to be associated with Alzheimer's disease (AD) and amyloid deposition. However, studies related to gut microbiota have been mostly restricted to comparisons of amyloid deposits, while investigations on neurobehavioral changes and the pathogenesis of AD are limited. Therefore, we aimed to identify the relationship between changes in the intestinal microbiome and the pathogenesis of AD. APPswe /PS1ΔE9 (PAP) transgenic mice and wild-type (WT) mice of different age groups were used. The composition of intestinal bacterial communities in the mice was determined by 16S ribosomal RNA sequencing (16S rRNA Seq), and the Y maze was used to measure cognitive function. Transcriptome sequencing (RNA Seq) and Gene Expression Omnibus (GEO) database (GSE 36980) were used to filter differentially expressed genes (DEGs) between specific pathogen-free (SPF) and germ-free (GF) mice. Quantitative reverse-transcriptase PCR (qRT-PCR) and western blot (WB) were used to verify the results. We found that the intestinal microbiota was significantly different between 5-month-old PAP and WT mice and the cognition of SPF PAP mice was diminished compared to GF PAP and SPF WT mice. DEGs in 5-month-old SPF and GF mice were enriched in the MAPK signalling pathway, and expression of amyloid precursor protein and amyloid deposition increased in 5-month-old SPF PAP mice. Results from this study showed that changes in intestinal microbiota were correlated with impairment of cognitive function and might promote amyloid deposition by stimulating the MAPK signalling pathway in the brain.
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Affiliation(s)
- Zhuo Li
- Comparative Medicine Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Hua Zhu
- Comparative Medicine Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Yaxi Guo
- Comparative Medicine Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Xiaopeng Du
- Comparative Medicine Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Chuan Qin
- Comparative Medicine Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS), Beijing, China
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27
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Zhao HJ, Luo X, Shi YC, Li JF, Pan F, Ren RR, Peng LH, Shi XY, Yang G, Wang J, Hu LY, Zou LP, Yang YS. The Efficacy of Fecal Microbiota Transplantation for Children With Tourette Syndrome: A Preliminary Study. Front Psychiatry 2020; 11:554441. [PMID: 33424650 PMCID: PMC7793740 DOI: 10.3389/fpsyt.2020.554441] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Therapies for Tourette syndrome (TS) are insufficient, and novel therapies are needed. Fecal microbiota transplantation (FMT) has been a potential therapy for several neurological diseases. Here, we report a preliminary study to investigate the effects of FMT on patients with TS. Five patients with TS received a single administration of FMT via endoscopy. Tic symptoms were assessed by Yale Global Tic Severity Scale-Total Tic Score (YGTSS-TTS) and adverse effects were recorded at week 8 following FMT. Lipopolysaccharide (LPS) levels and 14 cytokines levels were measured. The microbiota profile in feces were analyzed by shotgun metagenomics. Four patients (4/5) responded positively to FMT (YGTSS-TTS reduction rate >25%) at week 8 with high safety. The levels of LPS and cytokines varied after FMT. FMT shifted the composition of the gut microbiota in patients close to that of the donor and continuously changed the abundance of Bacteroides coprocola, Dialister succinatiphilus and Bacteroides vulgatus. The restoration of B.coprocola was correlated with the improvement in tic symptoms (Spearman R = -0.900, P = 0.037). In conclusion, FMT was indicated a potential effective and safe alternative for patients with TS. However, larger clinical trials are needed to confirm the influence of microbiota in TS. Trial Registration: chictr.org.cn Identifier: ChiCTR-IIR-17011871, URL: http://www.chictr.org.cn/showproj.aspx?proj=19941.
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Affiliation(s)
- Hui-Jun Zhao
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xi Luo
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yi-Chao Shi
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jian-Feng Li
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Fei Pan
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Rong-Rong Ren
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Li-Hua Peng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xiu-Yu Shi
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Guang Yang
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jing Wang
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lin-Yan Hu
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Li-Ping Zou
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yun-Sheng Yang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
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28
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Lee H, Kim J, An J, Lee S, Kong H, Song Y, Choi HR, Lee SJ, Chae KS, Kwon JW, Kim K. Amelioration of hyperglycemia by Rubus occidentalis (black raspberry) and increase in short-chain fatty acids producing bacteria. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.01.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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29
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Wang F, Zhu H, Hu M, Wang J, Xia H, Yang X, Yang L, Sun G. Perilla Oil Supplementation Improves Hypertriglyceridemia and Gut Dysbiosis in Diabetic KKAy Mice. Mol Nutr Food Res 2018; 62:e1800299. [PMID: 30358922 PMCID: PMC6646911 DOI: 10.1002/mnfr.201800299] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/13/2018] [Indexed: 12/18/2022]
Abstract
SCOPE The aim of this study is to examine whether perilla oil supplementation improves glucolipid metabolism and modulates gut microbiota in diabetic KKAy mice. METHODS AND RESULTS The successfully established diabetic KKAy mice are randomized into four groups: diabetic model (DM), low-dose perilla oil (LPO), middle-dose perilla oil (MPO), and high-dose perilla oil (HPO). C57BL/6J mice are fed a chow diet as normal control (NC). At the end of 12 weeks, mice are euthanized and glucolipid indications are analyzed. Gut microbiota analysis is carried out based on the sequencing results on V4 region of 16S rRNA. Although serum glucose, insulin, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, abundance-based coverage estimator, and shannon are unchanged, serum triglyceride significantly decreases in LPO compared with DM. The histopathological changes of hepatocellular macrovesicular steatosis and adipocyte hypertrophy are ameliorated by perilla oil supplementation. Blautia is significantly decreased in LPO, MPO, and HPO, compared with DM. Nonmetric multidimensional scaling analysis shows NC and LPO are relatively coherent. CONCLUSION These findings indicate that dietary supplementation with perilla oil can improve hypertriglyceridemia and gut dysbiosis in diabetic KKAy mice, which can be associated with potential benefits to human health.
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Affiliation(s)
- Feng Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
- Tianjin Institute of Environmental and Operational MedicineTianjinChina
| | - Hangju Zhu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
- Jiangsu Cancer HospitalNanjingChina
| | - Mingyuan Hu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
| | - Jing Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
| | - Hui Xia
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
| | - Xian Yang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
| | - Ligang Yang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
| | - Guiju Sun
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public HealthSoutheast UniversityNanjingChina
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