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Teng T, Yang Y, Li H, Song J, Ren J, Liu F. Mechanisms of intestinal injury in polychaete Perinereis aibuhitensis caused by low-concentration fluorene pollution: Microbiome and metabonomic analyses. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134925. [PMID: 38889458 DOI: 10.1016/j.jhazmat.2024.134925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
The polychaete Perinereis aibuhitensis is used for bioremediation; however, its ability to remove fluorene, a common environmental pollutant, from sediments remains unclear, especially at low concentrations of fluorene (10 mg/kg). In this study, we explored the mechanism of intestinal injury induced by low concentrations of fluorene and the reason intestinal injury is alleviated in high fluorene concentration groups (100 and 1000 mg/kg) using histology, ecological biomarkers, gut microbiome, and metabolic response analyses. The results show that P. aibuhitensis showed high tolerance to fluorene in sediments, with clearance rates ranging 25-50 %. However, the remediation effect at low fluorene concentrations (10 mg/kg) was poor. This is attributed to promoting the growth of harmful microorganisms such as Microvirga, which can cause metabolic disorders, intestinal flora imbalances, and the generation of harmful substances such as 2-hydroxyfluorene. These can result in severe intestinal injury in P. aibuhitensis, reducing its fluorene clearance rate. However, high fluorene concentrations (100 and 1000 mg/kg) may promote the growth of beneficial microorganisms such as Faecalibacterium, which can replace the dominant harmful microorganisms and improve metabolism to reverse the intestinal injury caused by low fluorene concentrations, ultimately restoring the fluorene-removal ability of P. aibuhitensis. This study demonstrates an effective method for evaluating the potential ecological risks of fluorene pollution in marine sediments and provides guidance for using P. aibuhitensis for remediation.
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Affiliation(s)
- Teng Teng
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China
| | - Yuting Yang
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China
| | - Huihong Li
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China
| | - Jie Song
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China
| | - Junning Ren
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China
| | - Feng Liu
- Ocean College, Yantai Institute of China Agricultural University, Yantai 264670, Shandong, China.
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Zhou X, Xu L, Zhang Q, Chen W, Xie H. The impact of long-term (≥5 years) cholecystectomy on gut microbiota changes and its influence on colorectal cancer risk: based on 16S rDNA sequencing analysis. Eur J Gastroenterol Hepatol 2024:00042737-990000000-00389. [PMID: 39012652 DOI: 10.1097/meg.0000000000002827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) continues to be a major global health concern. Recent advances in molecular biology have highlighted the gut microbiota's role in CRC. This study investigates long-term (≥5 years) gut microbiota changes in patients postcholecystectomy, comparing them with CRC patients and healthy controls to assess their impact on CRC development. METHODS Sixty participants were divided into three groups: 20 healthy controls, 20 postcholecystectomy (PCE) patients, and 20 CRC patients. Demographic data and stool samples were collected. Gut microbiota composition, abundance, and diversity were analyzed using high-throughput 16S rDNA sequencing. RESULTS Significant differences in microbial community, α-diversity (P < 0.05) and β-diversity (P = 0.006), were observed among the three groups. At the phylum level, Firmicutes abundance was significantly reduced in PCE and CRC groups compared with the control group (P = 0.002), while changes in other phyla were not significant (P>0.05). At the genus level, Bacteroides, Dialister, and Parabacteroides increased progressively from control to PCE to CRC groups (P = 0.004, 0.001, and 0.002). Prevotella decreased across these groups (P = 0.041). Faecalibacterium and Roseburia abundances were reduced in PCE and CRC groups compared with controls (P = 0.001 and 0.003). The Random Forest algorithm identified Parabacteroides, Bacteroides, Roseburia, and Dialister as key distinguishing genera. CONCLUSION The gut microbiota of long-term (≥5 years) PCE patients significantly differs from that of controls and resembles that of CRC patients, suggesting a potential link between cholecystectomy and CRC development through key microbial changes.
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Affiliation(s)
- Xiecheng Zhou
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Liang Xu
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Qixing Zhang
- Department of Pediatrics, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Wenqi Chen
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Hongwei Xie
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
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Li S, Chen J, Zheng Y, Zhang Y. Weissella paramesenteroides NRIC1542 inhibits dextran sodium sulfate-induced colitis in mice through regulating gut microbiota and SIRT1/NF-κB signaling pathway. FASEB J 2024; 38:e23791. [PMID: 38963340 DOI: 10.1096/fj.202401213r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Inflammatory bowel disease (IBD) is a kind of recurrent inflammatory disorder of the intestinal tract. The purpose of this study was to investigate the effects of Weissella paramesenteroides NRIC1542 on colitis in mice. A colitis model was induced by adding 1.5% DSS to sterile distilled water for seven consecutive days. During this process, mice were administered different concentrations of W. paramesenteroides NRIC1542. Colitis was assessed by DAI, colon length and hematoxylin-eosin staining of colon sections. The expressions of NF-κB signaling proteins and the tight junction proteins ZO-1 and occludin were detected by western blotting, and the gut microbiota was analyzed by 16S rDNA. The results showed that W. paramesenteroides NRIC1542 significantly reduced the degree of pathological tissue damage and the levels of TNF-α and IL-1β in colonic tissue, inhibiting the NF-κB signaling pathway and increasing the expression of SIRT1, ZO-1 and occludin. In addition, W. paramesenteroides NRIC1542 can modulate the structure of the gut microbiota, characterized by increased relative abundance of Muribaculaceae_unclassified, Paraprevotella, Prevotellaceae_UCG_001 and Roseburia, and decrease the relative abundance of Akkermansia and Alloprevotella induced by DSS. The above results suggested that W. paramesenteroides NRIC1542 can protect against DSS-induced colitis in mice through anti-inflammatory, intestinal barrier maintenance and flora modulation.
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Affiliation(s)
- Shuang Li
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junyang Chen
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yang Zheng
- Department of Gynecology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yun Zhang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
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Ji J, Yi X, Gao X, Wang B, Zhang X, Shen X, Xia G. Synergistic effects of tilapia head protein hydrolysate and walnut protein hydrolysate on the amelioration of cognitive impairment in mice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5419-5434. [PMID: 38334319 DOI: 10.1002/jsfa.13369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Cognitive impairment (CI) is a significant public health concern, and bioactive peptides have shown potential as therapeutic agents. However, information about their synergistic effects on cognitive function is still limited. Here, we investigated the synergistic effects of tilapia head protein hydrolysate (THPH) and walnut protein hydrolysate (WPH) in mitigating CI induced by scopolamine in mice. RESULTS The results showed that the combined supplementation of THPH and WPH (mass ratio, 1:1) was superior to either individual supplement in enhancing spatial memory and object recognition abilities in CI mice, and significantly lessened brain injury in CI mice by alleviating neuronal damage, reducing oxidative stress and stabilizing the cholinergic system. In addition, the combined supplementation was found to be more conducive to remodeling the gut microbiota structure in CI mice by not only remarkably reducing the ratio of Firmicutes to Bacteroidota, but also specifically enriching the genus Roseburia. On the other hand, the combined supplementation regulated the disorders of sphingolipid and amino acid metabolism in CI mice, particularly upregulating glutathione and histidine metabolism, and displayed a stronger ability to increase the expression of genes and proteins related to the brain-derived neurotrophic factor (BDNF)/TrkB/CrEB signaling pathway in the brain. CONCLUSION These findings demonstrate that tilapia head and walnut-derived protein hydrolysates exerted synergistic effects in ameliorating CI, which was achieved through modulation of gut microbiota, serum metabolic pathways and BDNF signaling pathways. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jun Ji
- College of Food Science and Technology, Hainan Tropical Ocean University, Sanya, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
- Univ. Lyon, University Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - Xiangzhou Yi
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
| | - Xia Gao
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
| | - Bohui Wang
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
| | - Xueying Zhang
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
| | - Xuanri Shen
- College of Food Science and Technology, Hainan Tropical Ocean University, Sanya, China
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
| | - Guanghua Xia
- Hainan Provincial Engineering Research Center of Aquatic Resources Efficient Utilization in the South China Sea, College of Food Science and Technology, Hainan University, Haikou, China
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Rivera-Chacon R, Pacífico C, Ricci S, Petri RM, Reisinger N, Zebeli Q, Castillo-Lopez E. Prolonged feeding of high-concentrate diet remodels the hindgut microbiome and modulates nutrient degradation in the rumen and the total gastrointestinal tract of cows. J Dairy Sci 2024:S0022-0302(24)00971-8. [PMID: 38945264 DOI: 10.3168/jds.2024-24919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet (Forage) for 1 week, followed by stepwise adaptation during one week to a high-concentrate diet (HC; 65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch) as well as the apparent total-tract nutrient digestibility were evaluated in the Forage feeding and in wk 4 on HC. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction of the grain and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of crude protein, fat, starch, NDF, ADF and NFC increased with HC compared with Forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with HC; however, α diversity (number of ASVs) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 on HC onwards. Two microbial enterotypes were identified: one for the Forage diet with abundance of Akkermansia and Anaerosporobacter, and another enterotype for the HC diet with enrichment in Bifidobacterium and Butyrivibrio. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on HC. However, the hindgut microbial diversity of cows adapted after 3 weeks of consuming the starch-rich ration. Thus, feeding HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible non-forage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility.
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Affiliation(s)
- Raul Rivera-Chacon
- Centre for Animal Nutrition and Welfare, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Cátia Pacífico
- Centre for Animal Nutrition and Welfare, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Veterinaerplatz 1, 1210 Vienna, Austria; Current address: Biome Diagnostics GmbH, Vienna, Austria
| | - Sara Ricci
- Centre for Animal Nutrition and Welfare, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Renee M Petri
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - N Reisinger
- dsm-firmenich, AHN R&D Center, 3430 Tulln, Austria
| | - Q Zebeli
- Centre for Animal Nutrition and Welfare, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Ezequias Castillo-Lopez
- Centre for Animal Nutrition and Welfare, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria; Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Veterinaerplatz 1, 1210 Vienna, Austria.
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Cai K, Zhang W, Su S, Yan H, Liu H, Zhu Y, Shang E, Guo S, Liu F, Duan JA. Salvia miltiorrhiza stem-leaf of total phenolic acid conversion products alleviate myocardial ischemia by regulating metabolic profiles, intestinal microbiota and metabolites. Biomed Pharmacother 2024; 177:117055. [PMID: 38941891 DOI: 10.1016/j.biopha.2024.117055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/16/2024] [Accepted: 06/26/2024] [Indexed: 06/30/2024] Open
Abstract
Myocardial ischemia (MI) is a significant contributor to ischemic heart diseases like angina pectoris and myocardial infarction. Reactive oxygen species produced during MI can trigger lipid peroxidation, damaging cell structure and function. Salvia miltiorrhiza (SM) has been widely used clinically in the treatment of cardiovascular diseases. However, in the process of rooting, the aboveground parts of this plant are usually discarded by tons. To make better use of these plant resources, the phenolic acids extracted and purified from the aerial part of SM were studied and chemically transformed, and the potential protective effect and possible mechanism of salvianolic acids containing a higher content of salvianolic acid A on MI were obtained. The transformed products of SM stem-leaves total phenolic acids with 8.16 % salvianolic acid A showed a better protective effect on the isoproterenol (ISO)-induced acute MI injury rat model. It can improve ST segment changes and has good antioxidant, anti-inflammatory and anticoagulant effects. In addition, the dysbiosis of gut microbiota and the related metabolic levels of short chain fatty acids (SCFAs), phenylalanine and glycerophospholipids were improved. This was achieved by reducing the abundance of Bacteroides, Faecalibaculum, and L-phenylalanine levels. In addition, the abundance of probiotics in Butyricoccus, Roseburia, and norank_f_Eubacterium_coprostanoligenes_group, as well as the contents of propionic acid and isobutyric acid, LPCs and PCs were increased. In conclusion, total phenolic acids of SM stem-leaves showed protective effects against ISO-induced rats, especially the strongest effect after conversion, which is a new option for the prevention and treatment of MI.
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Affiliation(s)
- Ke Cai
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wen Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shulan Su
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Hui Yan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Haifeng Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yue Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Erxin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Sheng Guo
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Feng Liu
- Shaanxi Institute of International Trade and Commerce, Xianyang 710061, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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Kallapura G, Prakash AS, Sankaran K, Manjappa P, Chaudhary P, Ambhore S, Dhar D. Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study. PeerJ 2024; 12:e17583. [PMID: 38948211 PMCID: PMC11214429 DOI: 10.7717/peerj.17583] [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: 01/19/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Background Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. Methods A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study. Results The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74-8.85]) to 6.67 (95% CI [6.2-7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.
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Yan Z, Hao T, Yan Y, Zhao Y, Wu Y, Tan Y, Bi Y, Cui Y, Yang R, Zhao Y. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR. Appl Microbiol Biotechnol 2024; 108:396. [PMID: 38922447 PMCID: PMC11208268 DOI: 10.1007/s00253-024-13204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.
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Affiliation(s)
- Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongyu Hao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
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Umeda L, Torres A, Kunihiro BP, Rubas NC, Wells RK, Phankitnirundorn K, Peres R, Juarez R, Maunakea AK. Immuno-Microbial Signature of Vaccine-Induced Immunity against SARS-CoV-2. Vaccines (Basel) 2024; 12:637. [PMID: 38932366 PMCID: PMC11209251 DOI: 10.3390/vaccines12060637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Although vaccines address critical public health needs, inter-individual differences in responses are not always considered in their development. Understanding the underlying basis for these differences is needed to optimize vaccine effectiveness and ultimately improve disease control. In this pilot study, pre- and post-antiviral immunological and gut microbiota features were characterized to examine inter-individual differences in SARS-CoV-2 mRNA vaccine response. Blood and stool samples were collected before administration of the vaccine and at 2-to-4-week intervals after the first dose. A cohort of 14 adults was separated post hoc into two groups based on neutralizing antibody levels (high [HN] or low [LN]) at 10 weeks following vaccination. Bivariate correlation analysis was performed to examine associations between gut microbiota, inflammation, and neutralization capacity at that timepoint. These analyses revealed significant differences in gut microbiome composition and inflammation states pre-vaccination, which predicted later viral neutralization capacity, with certain bacterial taxa, such as those in the genus Prevotella, found at higher abundance in the LN vs HN group that were also negatively correlated with a panel of inflammatory factors such as IL-17, yet positively correlated with plasma levels of the high mobility group box 1 (HMGB-1) protein at pre-vaccination. In particular, we observed a significant inverse relationship (Pearson = -0.54, p = 0.03) between HMGB-1 pre-vaccination and neutralization capacity at 10 weeks post-vaccination. Consistent with known roles as mediators of inflammation, our results altogether implicate HMGB-1 and related gut microbial signatures as potential biomarkers in predicting SARS-CoV-2 mRNA vaccine effectiveness measured by the production of viral neutralization antibodies.
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Affiliation(s)
- Lesley Umeda
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA; (L.U.); (B.P.K.); (N.C.R.); (R.K.W.)
| | - Amada Torres
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96822, USA; (A.T.); (K.P.); (R.P.)
| | - Braden P. Kunihiro
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA; (L.U.); (B.P.K.); (N.C.R.); (R.K.W.)
| | - Noelle C. Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA; (L.U.); (B.P.K.); (N.C.R.); (R.K.W.)
| | - Riley K. Wells
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA; (L.U.); (B.P.K.); (N.C.R.); (R.K.W.)
| | - Krit Phankitnirundorn
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96822, USA; (A.T.); (K.P.); (R.P.)
| | - Rafael Peres
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96822, USA; (A.T.); (K.P.); (R.P.)
| | - Ruben Juarez
- Department of Economics and UHERO, University of Hawaii, Honolulu, HI 96822, USA;
- Hawaii Integrated Analytics, LLC, Honolulu, HI 96822, USA
| | - Alika K. Maunakea
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96822, USA; (A.T.); (K.P.); (R.P.)
- Hawaii Integrated Analytics, LLC, Honolulu, HI 96822, USA
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10
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Wester RJ, Baillie LL, McCarthy GC, Keever CC, Jeffery LE, Adams PJ. Dysbiosis not observed in Canadian horse with free fecal liquid (FFL) using 16S rRNA sequencing. Sci Rep 2024; 14:12903. [PMID: 38839848 PMCID: PMC11153561 DOI: 10.1038/s41598-024-63868-1] [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: 12/07/2023] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Free Fecal Liquid (FFL), also termed Fecal Water Syndrome (FWS), is an ailment in horses characterized by variable solid and liquid (water) phases at defecation. The liquid phase can be excreted before, during, or after the solid defecation phase. While the underlying causes of FFL are unknown, hindgut dysbiosis is suggested to be associated with FFL. Three European studies investigated dysbiosis in horses with FFL using 16S rRNA sequencing and reported results that conflicted between each other. In the present study, we also used 16S rRNA sequencing to study the fecal microbial composition in 14 Canadian horses with FFL, and 11 healthy stable mate controls. We found no significant difference in fecal microbial composition between FFL and healthy horses, which further supports that dysbiosis is not associated with FFL.
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Affiliation(s)
- Robert J Wester
- Applied Genomics Centre, Kwantlen Polytechnic University, Surrey, BC, Canada
| | - Lyndsey L Baillie
- Applied Genomics Centre, Kwantlen Polytechnic University, Surrey, BC, Canada
| | - Garrett C McCarthy
- Applied Genomics Centre, Kwantlen Polytechnic University, Surrey, BC, Canada
| | - Carson C Keever
- Faculty of Science, Kwantlen Polytechnic University, Surrey, BC, Canada
| | | | - Paul J Adams
- Applied Genomics Centre, Kwantlen Polytechnic University, Surrey, BC, Canada.
- Faculty of Science, Kwantlen Polytechnic University, Surrey, BC, Canada.
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11
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Tarazi-Riess H, Shani-Levi C, Lesmes U. Heat-moisture and acid treatments can increase levels of resistant starch in arrowroot starch without adversely affecting its prebiotic activity in human colon microbiota. Food Funct 2024; 15:5813-5824. [PMID: 38747641 DOI: 10.1039/d4fo00711e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Carbohydrates are an important macronutrient whose processing and digestive fate can have numerous beneficial or adverse effects on consumer health. This study investigated the impact of heat-moisture treatments (HMT) and citric acid treatments (CAT) on arrowroot starch (ARS) with a focus on its physicochemical properties, digestibility, and influence on gut microbiota. The results revealed that HMT and CAT did not alter the colloidal characteristics of ARS but significantly affected the balance between amorphous and crystalline regions. Changes in thermal properties, morphology, and particle size were also observed. These can influence ARS shelf life and functional properties in various food applications. Furthermore, certain treatments in both processing methods increased the resistant starch (RS) content of ARS, with HMT for 16 hours at 80 °C and CAT with 0.6 M citric acid, resulting in the most pronounced effects. These changes coincided with reductions in rapidly digestible starch (RDS) levels and improvements in the ratio of slowly digestible starch (SDS) to RDS, which could potentially improve glycemic control. This study also examined the impact of processed ARS on colonic microbiota composition. It found that ARS-derived RS formed under HMT and CAT did not negatively affect the prebiotic potential of the RS fraction. Both treatments were associated with lowering the Firmicutes to Bacteroidetes ratio (F/B), a marker of gut health, and decreasing the relative abundance of Proteobacteria, microbes associated with adverse health effects. Additionally, CAT-derived RS showed a significant increase in the relative abundance of Roseburia, a beneficial gut bacterium. In conclusion, processing ARS through HMT and CAT techniques has the potential for enhancing its RS content, improving its glycemic impact, and positively influencing the gut microbiota composition, potentially contributing to gut health and metabolic well-being.
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Affiliation(s)
- Hila Tarazi-Riess
- Laboratory of Chemistry of Foods and Bioactives, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Carmit Shani-Levi
- Laboratory of Chemistry of Foods and Bioactives, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Uri Lesmes
- Laboratory of Chemistry of Foods and Bioactives, Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
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12
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Huang Y, Wang YF, Miao J, Zheng RF, Li JY. Short-chain fatty acids: Important components of the gut-brain axis against AD. Biomed Pharmacother 2024; 175:116601. [PMID: 38749177 DOI: 10.1016/j.biopha.2024.116601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 06/03/2024] Open
Abstract
Alzheimer's disease (AD) comprises a group of neurodegenerative disorders with some changes in the brain, which could lead to the deposition of certain proteins and result in the degeneration and death of brain cells. Patients with AD manifest primarily as cognitive decline, psychiatric symptoms, and behavioural disorders. Short-chain fatty acids (SCFAs) are a class of saturated fatty acids (SFAs) produced by gut microorganisms through the fermentation of dietary fibre ingested. SCFAs, as a significant mediator of signalling, can have diverse physiological and pathological roles in the brain through the gut-brain axis, and play a positive effect on AD via multiple pathways. Firstly, differences in SCFAs and microbial changes have been stated in AD cases of humans and mice in this paper. And then, mechanisms of three main SCFAs in treating with AD have been summarized, as well as differences of gut bacteria. Finally, functions of SCFAs played in regulating intestinal flora homeostasis, modulating the immune system, and the metabolic system, which were considered to be beneficial for the treatment of AD, have been elucidated, and the key roles of gut bacteria and SCFAs were pointed out. All in all, this paper provides an overview of SCFAs and gut bacteria in AD, and can help people to understand the importance of gut-brain axis in AD.
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Affiliation(s)
- Yan Huang
- College of Life Science and Technology, Xinjiang University, Urumqi 830000, China
| | - Yi Feng Wang
- College of Life Science and Technology, Xinjiang University, Urumqi 830000, China
| | - Jing Miao
- School of Pharmaceutical Sciences and Institute of Materia Medica, Xinjiang University, Urumqi 830017, China; Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Xinjiang University, Urumqi 830004, China.
| | - Rui Fang Zheng
- Xinjiang Key Laboratory of Uygur Medical Research, Xinjiang Institute of Materia Medica, Urumqi 830004, China.
| | - Jin Yao Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830000, China; Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Xinjiang University, Urumqi 830004, China.
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13
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Ha M, Yang Y, Wu M, Gong T, Chen Z, Yu L. Astaxanthin could regulate the gut-kidney axis to mitigate kidney injury in high-fat diet/streptozotocin-induced diabetic mice. INT J VITAM NUTR RES 2024; 94:187-197. [PMID: 37434308 DOI: 10.1024/0300-9831/a000786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Accumulating evidences have shown the beneficial effects of astaxanthin (AST) supplementation on metabolic diseases prevention and treatment. The goal of present study was to reveal the favorable interactions among AST supplementation, gut microbiota, and kidneys in vivo, so as to attenuate kidney impairment in diabetic mice. Twenty C57BL/6J mice were assigned to a normal control group and a diabetic model group induced by a high-fat diet plus low-dose streptozotocin, and then the diabetic mice were fed with a high-fat diet without or with AST [0.01% (AST_a) or 0.02% (AST_b)] for 12 weeks. When compared to the diabetes kidney disease (DKD) group, AST supplementation delayed the renal pathological progression, reduced fasting blood glucose (AST_b: 1.53-fold, p<0.05), repressed levels of lipopolysaccharide (LPS; AST_a: 1.24-fold, p=0.008; AST_b: 1.43-fold, p<0.001) and TMAO (AST_a: 1.51-fold, p=0.001; AST_b: 1.40-fold, p=0.003), inhibited IL-6 (AST_a: 1.40-fold, p=0.004; AST_b: 1.57-fold, p=0.001) and reactive oxygen species (ROS; AST_a: 1.30-fold, p=0.004; AST_b: 1.53-fold, p<0.001), as well as regulated the Sirt1/PGC-1α/NFκB p65 signaling pathway. Moreover, the results of 16S rRNA gene-based Illumina deep sequencing in each group revealed that dietary AST supplementation also favorably modulated the gut microbiota compared with the DKD group, as evidenced by the inhibition of the harmful bacteria Clostridium_sensu_stricto_1, Romboutsia, and Coriobacteriaceae_UCG-002, and the enhancement of the probiotics such as Lachnospiraceae_NK4A136_group, Roseburia, and Ruminococcaceae. Taken together, dietary AST supplementation could protect kidneys against inflammation and oxidative stress by adjusting the gut-kidney axis in diabetic mice.
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Affiliation(s)
- Mei Ha
- School of Nursing, Army Medical University, Chongqing, PR China
| | - Yuhui Yang
- School of Nursing, Army Medical University, Chongqing, PR China
| | - Mingzhu Wu
- Key Lab of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, PR China
| | - Ting Gong
- Chongqing Medical and Pharmaceutical College, PR China
| | - Zongyue Chen
- School of Nursing, Army Medical University, Chongqing, PR China
| | - Luo Yu
- School of Nursing, Army Medical University, Chongqing, PR China
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14
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Lozada‐Martinez ID, Lozada‐Martinez LM, Anaya J. Gut microbiota in centenarians: A potential metabolic and aging regulator in the study of extreme longevity. Aging Med (Milton) 2024; 7:406-413. [PMID: 38975304 PMCID: PMC11222757 DOI: 10.1002/agm2.12336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/30/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Centenarians, those aged 100 years or older, are considered the most successful biological aging model in humans. This population is commonly characterized by a low prevalence of chronic diseases, with favorable maintenance of functionality and independence, thus determining a health phenotype of successful aging. There are many factors usually associated with extreme longevity: genetics, lifestyles, diet, among others. However, it is most likely a multifactorial condition where protective factors contribute individually to some extent. The gut microbiota (GM) has emerged as a potential factor associated with the establishment of a favorable health phenotype that allows for extreme longevity, as seen in centenarians. To understand the possible impact generated by the GM, its changes, and the probable causes for successful aging, the aim of this review was to synthesize evidence on the role of the GM as a potential protective factor for achieving extreme longevity, using its relationship with centenarians.
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Affiliation(s)
- Ivan David Lozada‐Martinez
- Health Research and Innovation Center at Coosalud EPSCartagenaColombia
- Universidad de la CostaBarranquillaColombia
| | | | - Juan‐Manuel Anaya
- Health Research and Innovation Center at Coosalud EPSCartagenaColombia
- Universidad de la CostaBarranquillaColombia
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15
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Wu H, Lou T, Pan M, Wei Z, Yang X, Liu L, Feng M, Shi L, Qu B, Cong S, Chen K, Yang H, Liu J, Li Y, Jia Z, Xiao H. Chaihu Guizhi Ganjiang Decoction attenuates nonalcoholic steatohepatitis by enhancing intestinal barrier integrity and ameliorating PPARα mediated lipotoxicity. JOURNAL OF ETHNOPHARMACOLOGY 2024; 326:117841. [PMID: 38310988 DOI: 10.1016/j.jep.2024.117841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/11/2024] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
BACKGROUND Nonalcoholic steatohepatitis (NASH) is a prominent cause of liver-related death that poses a threat to global health and is characterized by severe hepatic steatosis, lobular inflammation, and ballooning degeneration. To date, no Food and Drug Administration-approved medicine is commercially available. The Chaihu Guizhi Ganjiang Decoction (CGGD) shows potential curative effects on regulation of blood lipids and blood glucose, mitigation of organism inflammation, and amelioration of hepatic function. However, the overall regulatory mechanisms underlying its effects on NASH remain unclear. PURPOSE This study aimed to investigate the efficiency of CGGD on methionine- and choline-deficient (MCD)-induced NASH and unravel its underlying mechanisms. METHODS A NASH model of SD rats was established using an MCD diet for 8 weeks, and the efficacy of CGGD was evaluated based on hepatic lipid accumulation, inflammatory response, and fibrosis. The effects of CGGD on the intestinal barrier, metabolic profile, and differentially expressed genes (DEGs) profile were analyzed by integrating gut microbiota, metabolomics, and transcriptome sequencing to elucidate its mechanisms of action. RESULTS In MCD-induced NASH rats, pathological staining demonstrated that CGGD alleviated lipid accumulation, inflammatory cell infiltration, and fibrosis in the hepatic tissue. After CGGD administration, liver index, liver weight, serum alanine aminotransferase (ALT), and aspartate aminotransferase (AST) contents, liver triglycerides (TG), and free fatty acids (FFAs) were decreased, meanwhile, it down-regulated the level of proinflammatory mediators (TNF-α, IL-6, IL-1β, MCP-1), and up-regulated the level of anti-inflammatory factors (IL-4, IL-10), and the expression of liver fibrosis markers TGFβ, Acta2, Col1a1 and Col1a2 were weakened. Mechanistically, CGGD treatment altered the diversity of intestinal flora, as evidenced by the depletion of Allobaculum, Blautia, norank_f_Erysipelotrichaceae, and enrichment of the probiotic genera Roseburia, Lactobacillus, Lachnoclostridium, etc. The colonic histopathological results indicated that the gut barrier damage recovered in the CGGD treatment group, and the expression levels of colonic short-chain fatty acids (SCFAs)-specific receptors FFAR2, FFAR3, and tight junction (TJs) proteins ZO-1, Occludin, Claudin-1 were increased compared with those in the model group. Further metabolomic and transcriptomic analyses suggested that CGGD mitigated the lipotoxicity caused by glycerophospholipid and eicosanoid metabolism disorders by decreasing the levels of PLA2G4A, LPCAT1, COX2, and LOX5. In addition, CGGD could activate the inhibitory lipotoxic transcription factor PPARα, regulate the proteins of FABP1, APOC2, APOA2, and LPL to promote fatty acid catabolism, and suppress the TLR4/MyD88/NFκB pathway to attenuate NASH. CONCLUSION Our study demonstrated that CGGD improved steatosis, inflammation, and fibrosis on NASH through enhancing intestinal barrier integrity and alleviating PPARα mediated lipotoxicity, which makes it an attractive candidate for potential new strategies for NASH prevention and treatment.
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Affiliation(s)
- Hao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Tianyu Lou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mingxia Pan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zuying Wei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaoqin Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lirong Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Menghan Feng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lixia Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Biqiong Qu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Shiyu Cong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Kui Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Haolan Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jie Liu
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yueting Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhixin Jia
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hongbin Xiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China; Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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16
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Jain S, Safo SE. DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification. Brief Bioinform 2024; 25:bbae339. [PMID: 39007595 DOI: 10.1093/bib/bbae339] [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: 12/08/2023] [Revised: 02/29/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Biomedical research now commonly integrates diverse data types or views from the same individuals to better understand the pathobiology of complex diseases, but the challenge lies in meaningfully integrating these diverse views. Existing methods often require the same type of data from all views (cross-sectional data only or longitudinal data only) or do not consider any class outcome in the integration method, which presents limitations. To overcome these limitations, we have developed a pipeline that harnesses the power of statistical and deep learning methods to integrate cross-sectional and longitudinal data from multiple sources. In addition, it identifies key variables that contribute to the association between views and the separation between classes, providing deeper biological insights. This pipeline includes variable selection/ranking using linear and nonlinear methods, feature extraction using functional principal component analysis and Euler characteristics, and joint integration and classification using dense feed-forward networks for cross-sectional data and recurrent neural networks for longitudinal data. We applied this pipeline to cross-sectional and longitudinal multiomics data (metagenomics, transcriptomics and metabolomics) from an inflammatory bowel disease (IBD) study and identified microbial pathways, metabolites and genes that discriminate by IBD status, providing information on the etiology of IBD. We conducted simulations to compare the two feature extraction methods.
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Affiliation(s)
- Sarthak Jain
- Department of Electrical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Sandra E Safo
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, MN 55455, United States
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17
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Chui ESH, Chan AKY, Ng ACK, Teh MYM, Ho HC, Chan YC. Mechanism and clinical implication of gut dysbiosis in degenerative abdominal aortic aneurysm: A systematic review. Asian J Surg 2024:S1015-9584(24)00947-3. [PMID: 38772822 DOI: 10.1016/j.asjsur.2024.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/27/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
The gut microbiome is the entirety of microorganisms and their genomes residing in the gut, characterised by diversity, stability, and resilience. Disrupted gut microbiome has been implicated in multiple disease entities. The aim of this paper is to summarise the rapidly evolving contemporary evidence of gut dysbiosis on the development and progression of abdominal aortic aneurysm (AAA), discuss possible mechanisms, and explore potential microbiota-targeted interventions and prognostic markers for AAA. A systematic literature search was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement, using PubMed, ScienceDirect, Web of Science, Ovid, Embase. Search terms of "microbiome" OR "dysbiosis" OR "microorganism"; AND "aneurysm" OR "dilatation" OR "aorta" were used. Study endpoints included effects of microbiota on AAA formation, effects of specific type of bacteria and its metabolite on AAA formation, and pre- or post-treatment by novel small-molecules/inhibitors. From May to August 2023, a total of twelve animal studies and eight human studies were included. Akkermansia muciniphila, Lactobacillus acidophilus and species from the Bacteroidetes phylum were associated with lower AAA incidence in both animal and human studies, while Proteobacteria phylum, Campylobacter, Fusobacterium and Faecalibacterium prausnitzii were found to be in abundance in the AAA group and were associated with larger aneurysms. The diversity of gut microbiota was inversely correlated with AAA diameter. Three important mechanisms were identified: including trimethylamine N-oxide pathway, butyric acid pathway, and aberrant tryptophan metabolism. With our expanding knowledge of the downstream pathogenic mechanisms of gut dysbiosis, novel therapeutics such as short-chain fatty acids and spermidine, as well as prognostic biomarkers such as TMAO have yielded promising preclinical results. In conclusion, there is strong evidence corroborating the role of gut dysbiosis in the pathogenesis of AAA, wherein its therapeutic and prognostic potential deserves further exploration.
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Affiliation(s)
- Ernest S H Chui
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region
| | - Aidan K Y Chan
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region
| | - Anson C K Ng
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region
| | - Margaret Y M Teh
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region
| | - Haris C Ho
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region
| | - Yiu Che Chan
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, South Wing, 14th Floor K Block, Queen Mary Hospital, Hong Kong Special Administrative Region.
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18
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Yuzefpolskaya M, Bohn B, Ladanyi A, Pinsino A, Braghieri L, Carey MR, Clerkin K, Sayer GT, Latif F, Koji T, Uriel N, Nandakumar R, Uhlemann AC, Colombo PC, Demmer RT. Alterations in the sarcopenia index are associated with inflammation, gut, and oral microbiota among heart failure, left ventricular assist device, and heart transplant patients. J Heart Lung Transplant 2024:S1053-2498(24)01660-7. [PMID: 38744352 DOI: 10.1016/j.healun.2024.04.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/28/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Sarcopenia, characterized by loss of muscle mass and function, is prevalent in heart failure (HF) and predicts poor outcomes. We investigated alterations in sarcopenia index (SI), a surrogate for skeletal muscle mass, in HF, left ventricular assist device (LVAD), and heart transplant (HT), and assessed its relationship with inflammation and digestive tract (gut and oral) microbiota. METHODS We enrolled 460 HF, LVAD, and HT patients. Repeated measures pre/post-procedures were obtained prospectively in a subset of LVAD and HT patients. SI (serum creatinine/cystatin C) and inflammatory biomarkers (C-reactive protein, interleukin-6, tumor necrosis factor-alpha) were measured in 271 and 622 blood samples, respectively. Gut and saliva microbiota were assessed via 16S ribosomal ribonucleic acid sequencing among 335 stool and 341 saliva samples. Multivariable regression assessed the relationship between SI and (1) New York Heart Association class; (2) pre- versus post-LVAD or HT; and (3) biomarkers of inflammation and microbial diversity. RESULTS Median (interquartile range) natural logarithm (ln)-SI was -0.13 (-0.32, 0.05). Ln-SI decreased across worsening HF class, further declined at 1 month after LVAD and HT, and rebounded over time. Ln-SI was correlated with inflammation (r = -0.28, p < 0.01), gut (r = 0.28, p < 0.01), and oral microbial diversity (r = 0.24, p < 0.01). These associations remained significant after multivariable adjustment in the combined cohort but not for all individual cohorts. The presence of the gut taxa Roseburia inulinivorans was associated with increased SI. CONCLUSIONS SI levels decreased in symptomatic HF and remained decreased long-term after LVAD and HT. In the combined cohort, SI levels covaried with inflammation in a similar fashion and were significantly related to overall microbial (gut and oral) diversity, including specific taxa compositional changes.
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Affiliation(s)
- Melana Yuzefpolskaya
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York.
| | - Bruno Bohn
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Annamaria Ladanyi
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Alberto Pinsino
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Lorenzo Braghieri
- Division of Cardiovascular Medicine, Department of Cardiology, Cleveland Clinic, Cleveland, Ohio
| | - Matthew R Carey
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Kevin Clerkin
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Gabriel T Sayer
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Farhana Latif
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Takeda Koji
- Division of Cardiothoracic Surgery, Department of Surgery, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Nir Uriel
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Renu Nandakumar
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases and Microbiome and Pathogen Genomics Core, Department of Medicine, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Paolo C Colombo
- Division of Cardiovascular Medicine, Department of Cardiology, New York Presbyterian Hospital, Columbia University, New York, New York
| | - Ryan T Demmer
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Division of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York
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19
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Odriozola A, González A, Odriozola I, Álvarez-Herms J, Corbi F. Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics. ADVANCES IN GENETICS 2024; 111:237-310. [PMID: 38908901 DOI: 10.1016/bs.adgen.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.
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Affiliation(s)
- Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñaki Odriozola
- Health Department of Basque Government, Donostia-San Sebastián, Spain
| | - Jesús Álvarez-Herms
- Phymo® Lab, Physiology, and Molecular Laboratory, Collado Hermoso, Segovia, Spain
| | - Francesc Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), Centre de Lleida, Universitat de Lleida (UdL), Lleida, Spain
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20
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Schwenger KJP, Sharma D, Ghorbani Y, Xu W, Lou W, Comelli EM, Fischer SE, Jackson TD, Okrainec A, Allard JP. Links between gut microbiome, metabolome, clinical variables and non-alcoholic fatty liver disease severity in bariatric patients. Liver Int 2024; 44:1176-1188. [PMID: 38353022 DOI: 10.1111/liv.15864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/25/2024] [Accepted: 01/28/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND AND AIMS Bacterial species and microbial pathways along with metabolites and clinical parameters may interact to contribute to non-alcoholic fatty liver disease (NAFLD) and disease severity. We used integrated machine learning models and a cross-validation approach to assess this interaction in bariatric patients. METHODS 113 patients undergoing bariatric surgery had clinical and biochemical parameters, blood and stool metabolite measurements as well as faecal shotgun metagenome sequencing to profile the intestinal microbiome. Liver histology was classified as normal liver obese (NLO; n = 30), simple steatosis (SS; n = 41) or non-alcoholic steatohepatitis (NASH; n = 42); fibrosis was graded F0 to F4. RESULTS We found that those with NASH versus NLO had an increase in potentially harmful E. coli, a reduction of potentially beneficial Alistipes putredinis and an increase in ALT and AST. There was higher serum glucose, faecal 3-(3-hydroxyphenyl)-3-hydroxypropionic acid and faecal cholic acid and lower serum glycerophospholipids. In NAFLD, those with severe fibrosis (F3-F4) versus F0 had lower abundance of anti-inflammatory species (Eubacterium ventriosum, Alistipes finegoldii and Bacteroides dorei) and higher AST, serum glucose, faecal acylcarnitines, serum isoleucine and homocysteine as well as lower serum glycerophospholipids. Pathways involved with amino acid biosynthesis and degradation were significantly more represented in those with NASH compared to NLO, with severe fibrosis having an overall stronger significant association with Superpathway of menaquinol-10 biosynthesis and Peptidoglycan biosynthesis IV. CONCLUSIONS In bariatric patients, NASH and severe fibrosis were associated with specific bacterial species, metabolic pathways and metabolites that may contribute to NAFLD pathogenesis and disease severity.
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Affiliation(s)
| | - Divya Sharma
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yasaman Ghorbani
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Wendy Lou
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Elena M Comelli
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy D Jackson
- Division of General Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of General Surgery, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Allan Okrainec
- Division of General Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of General Surgery, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Johane P Allard
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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21
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Giridhar P, Pradhan S, Dokania S, Venkatesulu B, Sarode R, Welsh JS. Microbiome and Abdominopelvic Radiotherapy Related Chronic Enteritis: A Microbiome-based Mechanistic Role of Probiotics and Antibiotics. Am J Clin Oncol 2024; 47:246-252. [PMID: 38193365 DOI: 10.1097/coc.0000000000001082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Chronic diarrhea and abdominal pain after radiotherapy continue to be a problem in cancer survivors. Gut microbiomes are essential for preventing intestinal inflammation, maintaining intestinal integrity, maintaining enterohepatic circulation, regulating bile acid metabolism, and absorption of nutrients, including fat-soluble vitamins. Gut microbiome dysbiosis is expected to cause inflammation, bile acid malabsorption, malnutrition, and associated symptoms. Postradiotherapy, Firmicutes and Bacteroidetes phylum are significantly decreased while Fusobacteria and other unclassified bacteria are increased. Available evidence suggests harmful bacteria Veillonella, Erysipelotrichaceae, and Ruminococcus are sensitive to Metronidazole or Ciprofloxacin. Beneficial bacteria lactobacillus and Bifidobacterium are relatively resistant to metronidazole. We hypothesize and provide an evidence-based review that short-course targeted antibiotics followed by specific probiotics may lead to alleviation of radiation enteritis.
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Affiliation(s)
| | | | | | - Bhanuprasad Venkatesulu
- Department of Radiation Oncology, Loyola University Chicago, Stritch School of Medicine, Cardinal Bernardin Cancer Center, Maywood
- Department of Radiation Oncology, MPMMCC/HBCH Varanasi Edward Hines Veteran Affairs Hospital, Chicago, IL
| | - Rahul Sarode
- Department of Microbiology, Mahamana Pandit Madanmohan Malaviya Cancer Centre/Homi Bhabha Cancer hospital, Tata Memorial Centre, Varanasi, India
| | - James S Welsh
- Department of Radiation Oncology, Loyola University Chicago, Stritch School of Medicine, Cardinal Bernardin Cancer Center, Maywood
- Department of Radiation Oncology, MPMMCC/HBCH Varanasi Edward Hines Veteran Affairs Hospital, Chicago, IL
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22
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Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, Dowd JB, Jones HE, Davis S, Segata N, Huttenhower C, Waldron L. BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nat Biotechnol 2024; 42:790-802. [PMID: 37697152 PMCID: PMC11098749 DOI: 10.1038/s41587-023-01872-y] [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: 10/24/2022] [Accepted: 06/20/2023] [Indexed: 09/13/2023]
Abstract
The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures. These data allow assessment of microbiome differential abundance within and across experimental conditions, environments or body sites. Database-wide analysis reveals experimental conditions with the highest level of consistency in signatures reported by independent studies and identifies commonalities among disease-associated signatures, including frequent introgression of oral pathobionts into the gut.
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Affiliation(s)
- Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Chloe Mirzayi
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Fatima Zohra
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Rimsha Azhar
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Shaimaa Elsafoury
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Clare Grieve
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Jennifer Wokaty
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Samuel David Gamboa-Tuz
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | | | - Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Rafael S Gonçalves
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA, USA
| | - Eric Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Vincent Carey
- Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, MA, USA
| | - Jennifer B Dowd
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK
| | - Heidi E Jones
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA
| | - Sean Davis
- Departments of Biomedical Informatics and Medicine, University of Colorado Anschutz School of Medicine, Denver, CO, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- Istituto Europeo di Oncologia (IEO) IRCSS, Milan, Italy
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Levi Waldron
- Institute for Implementation Science in Population Health, City University of New York School of Public Health, New York, NY, USA.
- Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, USA.
- Department CIBIO, University of Trento, Trento, Italy.
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23
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Tang Y, Lin TC, Yang H, Zhou Y, Sibeko L, Liu Z. High-fat diet during early life reshapes the gut microbiome and is associated with the disrupted mammary microenvironment in later life in mice. Nutr Res 2024; 127:1-12. [PMID: 38763113 DOI: 10.1016/j.nutres.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/21/2024]
Abstract
The influence of gut microbiota on gut health is well-documented, but it remains obscure for extraintestinal diseases such as breast cancer. Moreover, it is entirely unknown how gut dysbiosis during early life contributes to breast tumorigenesis later in life. In this study, we hypothesized that a high-fat diet during early life leads to alterations in the gut microbiome and is associated with disruptions in the mammary microenvironment. Female C57BL/6 mice were fed a low-fat diet (10% kcal fat) or a high-fat diet (HF, 60% kcal fat) for 8 weeks from the age of 4 to 12 weeks, which is equivalent to human childhood and adolescence. Twelve mice were sacrificed immediately after the 8-week feeding, the remainder were euthanized after switching to a normal lifecycle-supporting diet for an additional 12 weeks; the gut microbiome was then sequenced. The 8-week HF diet feeding altered the beta-diversity (Bray & Jaccard P < .01), and the difference remained significant after switching the diet (Bray & Jaccard P < .05). Immediately after HF feeding, a greater number of microbial taxa (>50) were altered, and about half of the taxa (25) remained significantly changed after switching the diet. The abundance of Alistipes, Bilophila, and Rikenellaceae stood out as significantly associated with multiple metabolic and inflammatory biomarkers in mammary tissue, including aromatase, Ccl2, and Cox2. In conclusion, an 8-week early-life HF feeding reshaped the gut microbiome, which connected with disrupted mammary microenvironments.
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Affiliation(s)
- Ying Tang
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA; Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Ting-Chun Lin
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Hong Yang
- Department of Oncology and Pathology, Hunan Provincial People's Hospital, Changsha, China
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, USA; Hunan, China
| | - Lindiwe Sibeko
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Zhenhua Liu
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA; UMass Cancer Center, University of Massachusetts Chan Medical Chan Medical School, Worcester, MA, USA.
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24
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Tian H, Huang D, Wang J, Li H, Gao J, Zhong Y, Xia L, Zhang A, Lin Z, Ke X. The role of the "gut microbiota-mitochondria" crosstalk in the pathogenesis of multiple sclerosis. Front Microbiol 2024; 15:1404995. [PMID: 38741740 PMCID: PMC11089144 DOI: 10.3389/fmicb.2024.1404995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
Multiple Sclerosis (MS) is a neurologic autoimmune disease whose exact pathophysiologic mechanisms remain to be elucidated. Recent studies have shown that the onset and progression of MS are associated with dysbiosis of the gut microbiota. Similarly, a large body of evidence suggests that mitochondrial dysfunction may also have a significant impact on the development of MS. Endosymbiotic theory has found that human mitochondria are microbial in origin and share similar biological characteristics with the gut microbiota. Therefore, gut microbiota and mitochondrial function crosstalk are relevant in the development of MS. However, the relationship between gut microbiota and mitochondrial function in the development of MS is not fully understood. Therefore, by synthesizing previous relevant literature, this paper focuses on the changes in gut microbiota and metabolite composition in the development of MS and the possible mechanisms of the crosstalk between gut microbiota and mitochondrial function in the progression of MS, to provide new therapeutic approaches for the prevention or reduction of MS based on this crosstalk.
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Affiliation(s)
- Huan Tian
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dunbing Huang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiaqi Wang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huaqiang Li
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiaxin Gao
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Zhong
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Libin Xia
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Anren Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhonghua Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- Rehabilitation Medicine Center, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincia Hospital, Fuzhou, China
| | - Xiaohua Ke
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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25
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Sun X, Zhou C, Ju M, Feng W, Guo Z, Qi C, Yang K, Xiao R. Roseburia intestinalis Supplementation Could Reverse the Learning and Memory Impairment and m6A Methylation Modification Decrease Caused by 27-Hydroxycholesterol in Mice. Nutrients 2024; 16:1288. [PMID: 38732535 PMCID: PMC11085097 DOI: 10.3390/nu16091288] [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: 03/04/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/13/2024] Open
Abstract
The abnormality in N6-methyladenosine (m6A) methylation is involved in the course of Alzheimer's disease (AD), while the intervention of 27-Hydroxycholesterol (27-OHC) can affect the m6A methylation modification in the brain cortex. Disordered gut microbiota is a key link in 27-OHC leading to cognitive impairment, and further studies have found that the abundance of Roseburia intestinalis in the gut is significantly reduced under the intervention of 27-OHC. This study aims to investigate the association of 27-OHC, Roseburia intestinalis in the gut, and brain m6A modification in the learning and memory ability injury. In this study, 9-month-old male C57BL/6J mice were treated with antibiotic cocktails for 6 weeks to sweep the intestinal flora, followed by 27-OHC or normal saline subcutaneous injection, and then Roseburia intestinalis or normal saline gavage were applied to the mouse. The 27-OHC level in the brain, the gut barrier function, the m6A modification in the brain, and the memory ability were measured. From the results, we observed that 27-OHC impairs the gut barrier function, causing a disturbance in the expression of m6A methylation-related enzymes and reducing the m6A methylation modification level in the brain cortex, and finally leads to learning and memory impairment. However, Roseburia intestinalis supplementation could reverse the negative effects mentioned above. This study suggests that 27-OHC-induced learning and memory impairment might be linked to brain m6A methylation modification disturbance, while Roseburia intestinalis, as a probiotic with great potential, could reverse the damage caused by 27-OHC. This research could help reveal the mechanism of 27-OHC-induced neural damage and provide important scientific evidence for the future use of Roseburia intestinalis in neuroprotection.
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Affiliation(s)
| | | | | | | | | | | | | | - Rong Xiao
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.S.); (C.Z.); (M.J.); (W.F.); (Z.G.); (C.Q.); (K.Y.)
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26
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Liu C, Liu F, Nie D, Xiao Y, Wu W, Jia Y, Jin L, Qiao N, Cai K, Ru S, Liu X, Song Y, Xu J, Cao L, Gui S. Gut microbiota composition and metabolic characteristics in patients with Craniopharyngioma. BMC Cancer 2024; 24:521. [PMID: 38658858 PMCID: PMC11044453 DOI: 10.1186/s12885-024-12283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Emerging evidence suggests that the gut microbiota is associated with various intracranial neoplastic diseases. It has been observed that alterations in the gut microbiota are present in gliomas, meningiomas, and pituitary neuroendocrine tumors (Pit-NETs). However, the correlation between gut microbiota and craniopharyngioma (CP), a rare embryonic malformation tumor in the sellar region, has not been previously mentioned. Consequently, this study aimed to investigate the gut microbiota composition and metabolic patterns in CP patients, with the goal of identifying potential therapeutic approaches. METHODS We enrolled 15 medication-free and non-operated patients with CP and 15 healthy controls (HCs), conducting sequential metagenomic and metabolomic analyses on fecal samples to investigate changes in the gut microbiota of CP patients. RESULTS The composition of gut microbiota in patients with CP compared to HCs show significant discrepancies at both the genus and species levels. The CP group exhibits greater species diversity. And the metabolic patterns between the two groups vary markedly. CONCLUSIONS The gut microbiota composition and metabolic patterns in patients with CP differ significantly from the healthy population, presenting potential new therapeutic opportunities.
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Affiliation(s)
- Chunhui Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Fangzheng Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Ding Nie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100071, China
| | - Youchao Xiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Wentao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Yanfei Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Lu Jin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Ning Qiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Kefan Cai
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Siming Ru
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Xin Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Yifan Song
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Jintian Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Lei Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100071, China.
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Cadena-Ullauri S, Guevara-Ramírez P, Ruiz-Pozo VA, Tamayo-Trujillo R, Paz-Cruz E, Zambrano-Villacres R, Simancas-Racines D, Zambrano AK. The effect of intermittent fasting on microbiota as a therapeutic approach in obesity. Front Nutr 2024; 11:1393292. [PMID: 38725575 PMCID: PMC11079193 DOI: 10.3389/fnut.2024.1393292] [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: 02/28/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Obesity, a public health challenge, arises from a complex interplay of factors such as dietary habits and genetic predisposition. Alterations in gut microbiota, characterized by an imbalance between Firmicutes and Bacteroidetes, further exacerbate metabolic dysregulation, promoting inflammation and metabolic disturbances. Intermittent fasting (IF) emerges as a promising dietary strategy showing efficacy in weight management and favoring fat utilization. Studies have used mice as animal models to demonstrate the impact of IF on gut microbiota composition, highlighting enhanced metabolism and reduced inflammation. In humans, preliminary evidence suggests that IF promotes a healthy microbiota profile, with increased richness and abundance of beneficial bacterial strains like Lactobacillus and Akkermansia. However, further clinical trials are necessary to validate these findings and elucidate the long-term effects of IF on microbiota and obesity. Future research should focus on specific tissues and cells, the use of advanced -omics techniques, and exploring the interaction of IF with other dietary patterns, to analyze microbiota composition, gene expression, and potential synergistic effects for enhanced metabolic health. While preliminary evidence supports the potential benefits of IF in obesity management and microbiota regulation, further research with diverse populations and robust methodologies is necessary to understand its implications and optimize personalized dietary interventions. This review explores the potential impact of IF on gut microbiota and its intricate relationship with obesity. Specifically, we will focus on elucidating the underlying mechanisms through which IF affects microbiota composition, as well as its subsequent effects on obesity.
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Affiliation(s)
- Santiago Cadena-Ullauri
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Viviana A. Ruiz-Pozo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Elius Paz-Cruz
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Daniel Simancas-Racines
- Centro de Investigación de Salud Pública y Epidemiología Clínica (CISPEC), Universidad UTE, Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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Zhang Z, Zhao H, Chen X, Tian G, Liu G, Cai J, Jia G. Enhancing pig growth and gut health with fermented Jatropha curcas cake: Impacts on microbiota, metabolites, and neurotransmitters. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 38648292 DOI: 10.1111/jpn.13960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/23/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
Given the escalating global crisis in feed protein availability, Jatropha curcas L. cake has attracted significant interest as a viable alternative protein source in animal feed. This experiment was conducted to investigate the effects of fermented Jatropha curcas L. cake (FJCC) as a protein feed in the diet of pigs. A total of 96 growing pigs with an average weight of 27.60 ± 1.59 kg were divided into three dietary groups with varying FJCC inclusion levels (0, 2.5, and 5%) for a 28 d trial. Results showed that the diet with 5% FJCC (FJCC5) demonstrated significant improvements in average daily gain (p = 0.009), feed-to-gain ratio (p = 0.036), nutrient digestibility, and intestinal morphology. Furthermore, the FJCC5 diet resulted in a decrease in pH values in different gut sections (jejunum p = 0.045, cecum p = 0.001, colon p = 0.012), and favorably altered the profile of short-chain fatty acids (SCFAs) with increased butyric acid content (p = 0.005) and total SCFAs (p = 0.019). Additionally, this diet notably decreased IL-6 levels in the jejunum (p = 0.008) and colon (=0.047), significantly reduced IL-1 levels in the hypothalamus (p < 0.001), and lowered IL-1, IL-6, and IL-10 levels in plasma (p < 0.05). Microbiota and metabolite profile analysis revealed an elevated abundance of beneficial microbes (p < 0.05) and key metabolites such as 4-aminobutyric acid (GABA) (p = 0.003) and serotonin (5-HT) (p = 0.022), linked to neuroactive ligand-receptor interaction. Moreover, FJCC5 significantly boosted circulating neurotransmitter levels of 5-HT (p = 0.006) and GABA (p = 0.002) in plasma and hypothalamus, with corresponding increases in precursor amino acids (p < 0.05). These findings suggest that FJCC, particularly at a 5% inclusion rate, can be an effective substitute for traditional protein sources like soybean meal, offering benefits beyond growth enhancement to gut health and potentially impacting the gut-brain axis. This research underscores FJCC's potential as a valuable component in sustainable animal nutrition strategies.
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Affiliation(s)
- Zhenyu Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
- Institute of Animal Husbandry and Veterinary Medicine, Meishan Vocational Technical College, Meishan, China
- Agricultural and Rural Bureau of Dongpo District, Meishan, China
| | - Hua Zhao
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Chen
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangmang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jingyi Cai
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Jia
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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Filidou E, Kandilogiannakis L, Shrewsbury A, Kolios G, Kotzampassi K. Probiotics: Shaping the gut immunological responses. World J Gastroenterol 2024; 30:2096-2108. [PMID: 38681982 PMCID: PMC11045475 DOI: 10.3748/wjg.v30.i15.2096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/28/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Probiotics are live microorganisms exerting beneficial effects on the host's health when administered in adequate amounts. Among the most popular and adequately studied probiotics are bacteria from the families Lactobacillaceae, Bifidobacteriaceae and yeasts. Most of them have been shown, both in vitro and in vivo studies of intestinal inflammation models, to provide favorable results by means of improving the gut microbiota composition, promoting the wound healing process and shaping the immunological responses. Chronic intestinal conditions, such as inflammatory bowel diseases (IBD), are characterized by an imbalance in microbiota composition, with decreased diversity, and by relapsing and persisting inflammation, which may lead to mucosal damage. Although the results of the clinical studies investigating the effect of probiotics on patients with IBD are still controversial, it is without doubt that these microorganisms and their metabolites, now named postbiotics, have a positive influence on both the host's microbiota and the immune system, and ultimately alter the topical tissue microenvironment. This influence is achieved through three axes: (1) By displacement of potential pathogens via competitive exclusion; (2) by offering protection to the host through the secretion of various defensive mediators; and (3) by supplying the host with essential nutrients. We will analyze and discuss almost all the in vitro and in vivo studies of the past 2 years dealing with the possible favorable effects of certain probiotic genus on gut immunological responses, highlighting which species are the most beneficial against intestinal inflammation.
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Affiliation(s)
- Eirini Filidou
- Faculty of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Leonidas Kandilogiannakis
- Faculty of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Anne Shrewsbury
- Department of Surgery, Aristotle University of Thessaloniki, Thessaloniki 54636, Greece
| | - George Kolios
- Faculty of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Katerina Kotzampassi
- Department of Surgery, Aristotle University of Thessaloniki, Thessaloniki 54636, Greece
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Qu K, Li MX, Gan L, Cui ZT, Li JJ, Yang R, Dong M. To analyze the relationship between gut microbiota, metabolites and migraine: a two-sample Mendelian randomization study. Front Microbiol 2024; 15:1325047. [PMID: 38690367 PMCID: PMC11058981 DOI: 10.3389/fmicb.2024.1325047] [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: 10/20/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Background It has been suggested in several observational studies that migraines are associated with the gut microbiota. It remains unclear, however, how the gut microbiota and migraines are causally related. Methods We performed a bidirectional two-sample mendelian randomization study. Genome-wide association study (GWAS) summary statistics for the gut microbiota were obtained from the MiBioGen consortium (n = 18,340) and the Dutch Microbiota Project (n = 7,738). Pooled GWAS data for plasma metabolites were obtained from four different human metabolomics studies. GWAS summary data for migraine (cases = 48,975; controls = 450,381) were sourced from the International Headache Genetics Consortium. We used inverse-variance weighting as the primary analysis. Multiple sensitivity analyses were performed to ensure the robustness of the estimated results. We also conducted reverse mendelian randomization when a causal relationship between exposure and migraine was found. Results LachnospiraceaeUCG001 (OR = 1.12, 95% CI: 1.05-1.20) was a risk factor for migraine. Blautia (OR = 0.93, 95% CI: 0.88-0.99), Eubacterium (nodatum group; OR = 0.94, 95% CI: 0.90-0.98), and Bacteroides fragilis (OR = 0.97, 95% CI: 0.94-1.00) may have a suggestive association with a lower migraine risk. Functional pathways of methionine synthesis (OR = 0.89, 95% CI: 0.83-0.95) associated with microbiota abundance and plasma hydrocinnamate (OR = 0.85, 95% CI: 0.73-1.00), which are downstream metabolites of Blautia and Bacteroides fragilis, respectively, may also be associated with lower migraine risk. No causal association between migraine and the gut microbiota or metabolites was found in reverse mendelian randomization analysis. Both significant horizontal pleiotropy and significant heterogeneity were not clearly identified. Conclusion This Mendelian randomization analysis showed that LachnospiraceaeUCG001 was associated with an increased risk of migraine, while some bacteria in the gut microbiota may reduce migraine risk. These findings provide a reference for a deeper comprehension of the role of the gut-brain axis in migraine as well as possible targets for treatment interventions.
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Affiliation(s)
| | | | | | | | | | | | - Ming Dong
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
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Chen See JR, Leister J, Wright JR, Kruse PI, Khedekar MV, Besch CE, Kumamoto CA, Madden GR, Stewart DB, Lamendella R. Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities. Front Microbiol 2024; 15:1398018. [PMID: 38680911 PMCID: PMC11045941 DOI: 10.3389/fmicb.2024.1398018] [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: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.
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Affiliation(s)
| | | | - Justin R. Wright
- Juniata College, Huntingdon, PA, United States
- Wright Labs LLC, Huntingdon, PA, United States
| | | | | | | | - Carol A. Kumamoto
- Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
| | - Gregory R. Madden
- University of Virginia School of Medicine, Charlottesville, VA, United States
| | - David B. Stewart
- Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL, United States
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Shen W, Chen Q, Lin R, Hu Z, Luo M, Ren Y, Huang K, Wang L, Chen S, Wang L, Ruan Y, Feng L. Imbalance of gut microbiota in gestational diabetes. BMC Pregnancy Childbirth 2024; 24:226. [PMID: 38561737 PMCID: PMC10983739 DOI: 10.1186/s12884-024-06423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
AIM To investigate the differences in gut microbiota composition among nonpregnant women of reproductive age, healthy pregnant women, and gestational diabetes (GD) patients. METHODS A total of 45 outpatients were enrolled and divided into three groups: nonpregnant women of reproductive age (control group, n = 23), healthy pregnant women (normal group, n = 10), and GD patients (GD group, n = 12). Faecal samples were collected and sequenced using 16S rRNA gene sequencing to analyse the microbial composition. RESULTS (1) Pregnant patients exhibited an increase in the abundance of Streptococcus (Pnormal = 0.01286, PGD = 0.002965) and Blautia (Pnormal = 0.0003924, PGD = 0.000246) but a decrease in the abundance of Roseburia (Pnormal = 0.0361, PGD = 0.007075), Phascolarctobacterium (Pnormal = 0.0003906, PGD = 0.02499) and Lachnoclostridium (Pnormal = 0.0003906, PGD = 0.03866). (2) Compared with healthy pregnant women, GD patients had an excessive increase in Streptococcus abundance and decrease in Roseburia abundance. The increase in Blautia abundance and the decrease in Phascolarctobacterium and Lachnoclostridium abundance in GD patients were less than those in healthy pregnant women. (3) The abundance of Faecalibacterium prausnitzii decreased significantly in GD patients (PGD = 0.02985) but not in healthy pregnant patients (Pnormal = 0.1643). CONCLUSIONS Abnormal increases and decreases in the abundances of gut microbiota components, especially Faecalibacterium prausnitzii, were observed in GD patients. TRIAL REGISTRATION The cross-sectional research was conducted in accordance with the Declaration of Helsinki, and approved by Sir Run Run Shaw Hospital Clinical Trials and Biomedical Ethics Committee. The study has been registered in the Chinese Clinical Trial Registry (ChiCTR1900026164, 24/09/2019, http://www.chictr.org.cn/showproj.aspx?proj=43,455 ).
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Affiliation(s)
- Weiyi Shen
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang Province, China
| | - Qianyi Chen
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Renbin Lin
- Department of Gastroenterology, Hangzhou Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medicine University, Hangzhou, 310005, Zhejiang Province, China
| | - Zhefang Hu
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Man Luo
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Yanwei Ren
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Keren Huang
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Li Wang
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Shujie Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang Province, China
| | - Lan Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
- Prevention and Treatment Research Center of Senescent Disease, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang Province, China
| | - Yu Ruan
- Department of Endocrinology and Metabolism, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China
| | - Lijun Feng
- Department of Nutriology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang Province, China.
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Vega-Abellaneda S, Dopazo C, Yañez F, Soler Z, Xie Z, Canalda-Baltrons A, Pons-Tarín M, Bilbao I, Manichanh C. Microbiome composition recovery after liver transplantation correlates with initial liver disease severity and antibiotics treatment. Am J Transplant 2024:S1600-6135(24)00248-X. [PMID: 38556088 DOI: 10.1016/j.ajt.2024.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/02/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Liver transplantation (LT) is crucial for end-stage liver disease, but it is linked to infection risks. Pathobionts, microorganisms potentially harmful under specific conditions, can cause complications posttransplant. Monitoring such pathogens in fecal samples can be challenging and therefore remains underexplored post-LT. This study aimed to analyze the gut microbiome before and after LT, tracking pathobionts and correlating clinical data. The study involved 17 liver transplant recipients, 17 healthy relatives (spouses), and 13 donors. Gut samples collected pretranplantation and posttransplantation underwent bacterial and fungal profiling through DNA sequencing. Quantitative polymerase chain reaction was used to assess microbial load. Statistical analyses included alpha and beta diversity measures, differential abundance analysis, and correlation tests between microbiome and clinical parameters. Microbiome analysis revealed dynamic changes in diversity posttransplant. Notably, high-severity patients showed persistent and greater dysbiosis during the first months post-LT compared with low-severity patients, partly due to an antibiotic treatment pre-LT. The analysis identified a higher proportion of pathogens such as Escherichia coli/Shigella flexneri in high-severity cases posttransplant. Furthermore, butyrate producers including Roseburia intestinalis, Anaerostipes hadrus, and Eubacterium coprostanoligenes were positively correlated with levels of albumin. This study offers valuable insights into post-LT microbiome changes, shedding light on the need for tailored prophylactic treatment post-LT.
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Affiliation(s)
- Sara Vega-Abellaneda
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Cristina Dopazo
- Department of HPB Surgery and Transplants, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Universitat Autónoma de Barcelona, Barcelona, Spain; CIBER of Hepatic and Digestive Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Francisca Yañez
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Zaida Soler
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Aleix Canalda-Baltrons
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Marc Pons-Tarín
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Itxarone Bilbao
- Department of HPB Surgery and Transplants, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Universitat Autónoma de Barcelona, Barcelona, Spain; CIBER of Hepatic and Digestive Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; CIBER of Hepatic and Digestive Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), Madrid, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Kim GH, Kim BR, Yoon HJ, Jeong JH. Alterations in Gut Microbiota and Their Correlation with Brain Beta-Amyloid Burden Measured by 18F-Florbetaben PET in Mild Cognitive Impairment Due to Alzheimer's Disease. J Clin Med 2024; 13:1944. [PMID: 38610709 PMCID: PMC11012963 DOI: 10.3390/jcm13071944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/16/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
(1) Background: This study investigated changes in the gut microbial composition of individuals with mild cognitive impairment (MCI) due to Alzheimer's disease (AD) and their relationship with positron emission tomography (PET) amyloid accumulation. (2) Methods: In total, 17 cognitively normal individuals without amyloid-beta (Aβ) accumulation (Aβ-NC) and 24 with Aβ-positive mild cognitive impairment (Aβ+MCI) who underwent 18F-florbetaben PET and fecal bacterial 16S ribosomal RNA gene sequencing were enrolled. The taxonomic compositions of the Aβ-NC and Aβ+MCI groups were compared. The abundance of taxa was correlated with the standardized uptake value ratio (SUVR), using generalized linear models. (3) Results: There were significant differences in microbiome richness (ACE, p = 0.034 and Chao1, p = 0.024), alpha diversity (Shannon, p = 0.039), and beta diversity (Bray-Curtis, p = 0.018 and Generalized UniFrac, p = 0.034) between the Aβ-NC and Aβ+MCI groups. The global SUVR was positively correlated with the genus Intestinibacter (q = 0.006) and negatively correlated with the genera Roseburia (q = 0.008) and Agathobaculum (q = 0.029). (4) Conclusions: In this study, we identified significant changes in the gut microbiota composition that occur in individuals with MCI due to AD. In particular, the correlation analysis results between PET amyloid burden and gut microbial abundance showed that amyloid deposition is associated with a reduction in specific taxa involved in butyrate production.
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Affiliation(s)
- Geon Ha Kim
- Department of Neurology, Ewha Womans University College of Medicine, Seoul 07804, Republic of Korea;
| | - Bori R. Kim
- Ewha Medical Research Institute, Ewha Womans University, Seoul 07804, Republic of Korea;
| | - Hai-Jeon Yoon
- Department of Nuclear Medicine, Ewha Womans University College of Medicine, Seoul 07804, Republic of Korea
| | - Jee Hyang Jeong
- Department of Neurology, Ewha Womans University College of Medicine, Seoul 07804, Republic of Korea;
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Dong J, Wang B, Xiao Y, Liu J, Wang Q, Xiao H, Jin Y, Liu Z, Chen Z, Li Y, Fan S, Li Y, Cui M. Roseburia intestinalis sensitizes colorectal cancer to radiotherapy through the butyrate/OR51E1/RALB axis. Cell Rep 2024; 43:113846. [PMID: 38412097 DOI: 10.1016/j.celrep.2024.113846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
The radioresistant signature of colorectal cancer (CRC) hampers the clinical utility of radiotherapy. Here, we find that fecal microbiota transplantation (FMT) potentiates the tumoricidal effects of radiation and degrades the intertwined adverse events in azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced CRC mice. FMT cumulates Roseburia intestinalis (R. intestinalis) in the gastrointestinal tract. Oral gavage of R. intestinalis assembles at the CRC site and synthetizes butyrate, sensitizing CRC to radiation and alleviating intestinal toxicity in primary and CRC hepatic metastasis mouse models. R. intestinalis-derived butyrate activates OR51E1, a G-protein-coupled receptor overexpressing in patients with rectal cancer, facilitating radiogenic autophagy in CRC cells. OR51E1 shows a positive correlation with RALB in clinical rectal cancer tissues and CRC mouse model. Blockage of OR51E1/RALB signaling restrains butyrate-elicited autophagy in irradiated CRC cells. Our findings highlight that the gut commensal bacteria R. intestinalis motivates radiation-induced autophagy to accelerate CRC cell death through the butyrate/OR51E1/RALB axis and provide a promising radiosensitizer for CRC in a pre-clinical setting.
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Affiliation(s)
- Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Bin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yunong Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Jia Liu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qi Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Huiwen Xiao
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuxiao Jin
- Department of Anesthesiology, Changshu No. 2 People's Hospital, Changshu, Jiangsu Province 215501, China
| | - Zhihong Liu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province 215004, China
| | - Zhiyuan Chen
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
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Agbalalah T, Bur D, Nwonu EJ, Rowaiye AB. Gut Microbiota: Potential Therapeutic Target for Sickle Cell Disease Pain and Complications. Anemia 2024; 2024:5431000. [PMID: 38533265 PMCID: PMC10965282 DOI: 10.1155/2024/5431000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
Aim Sickle cell disease has witnessed a 41.4% surge from 2000 to 2021, significantly affecting morbidity and mortality rates, particularly in children from regions with elevated under-5 mortality rates. Gut microbiota dysbiosis is increasingly recognised in SCD, exacerbating complications, particularly chronic pain, marked by significant alterations of proinflammatory bacteria abundance. This review explores the therapeutic potential of Akkermansia muciniphila and Roseburia spp. in alleviating SCD-related complications, emphasising their roles in maintaining gut barrier integrity, reducing inflammation, and modulating immune responses. Method A literature search up to November 2023 using PubMed, MEDLINE, and Google Scholar databases explored SCD pathophysiology, gut microbiota composition, Akkermansia muciniphila and Roseburia spp. abundance, pain and gut dysbiosis in SCD, and butyrate therapy. Result A. muciniphila and Roseburia spp. supplementation shows promise in alleviating chronic pain by addressing gut dysbiosis, offering new avenues for sustainable SCD management. This approach holds the potential for reducing reliance on reactive treatments and improving overall quality of life. This research underscores the pivotal role of the gut microbiome in SCD, advocating for personalised treatment approaches. Conclusion Further exploration and clinical trials are needed to harness the full potential of these gut bacteria for individuals affected by this challenging condition.
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Affiliation(s)
- Tarimoboere Agbalalah
- Department of Anatomy, Faculty of Basic Medical Sciences, Baze University, Abuja, Nigeria
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
| | - Doofan Bur
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
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Ahn S, Datta S. Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values. BMC Bioinformatics 2024; 25:117. [PMID: 38500042 PMCID: PMC10946111 DOI: 10.1186/s12859-024-05689-7] [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: 05/06/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under different biological conditions. However, the existing methods to the DN analysis for microbiome data do not adjust for other clinical differences between subjects. RESULTS We propose a Statistical Approach via Pseudo-value Information and Estimation for Differential Network Analysis (SOHPIE-DNA) that incorporates additional covariates such as continuous age and categorical BMI. SOHPIE-DNA is a regression technique adopting jackknife pseudo-values that can be implemented readily for the analysis. We demonstrate through simulations that SOHPIE-DNA consistently reaches higher recall and F1-score, while maintaining similar precision and accuracy to existing methods (NetCoMi and MDiNE). Lastly, we apply SOHPIE-DNA on two real datasets from the American Gut Project and the Diet Exchange Study to showcase the utility. The analysis of the Diet Exchange Study is to showcase that SOHPIE-DNA can also be used to incorporate the temporal change of connectivity of taxa with the inclusion of additional covariates. As a result, our method has found taxa that are related to the prevention of intestinal inflammation and severity of fatigue in advanced metastatic cancer patients. CONCLUSION SOHPIE-DNA is the first attempt of introducing the regression framework for the DN analysis in microbiome data. This enables the prediction of characteristics of a connectivity of a network with the presence of additional covariate information in the regression. The R package with a vignette of our methodology is available through the CRAN repository ( https://CRAN.R-project.org/package=SOHPIE ), named SOHPIE (pronounced as Sofie). The source code and user manual can be found at https://github.com/sjahnn/SOHPIE-DNA .
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Affiliation(s)
- Seungjun Ahn
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Somnath Datta
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
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Kemp KM, Orihuela CA, Morrow CD, Judd SE, Evans RR, Mrug S. Associations between dietary habits, socio-demographics and gut microbial composition in adolescents. Br J Nutr 2024; 131:809-820. [PMID: 37850446 PMCID: PMC10864997 DOI: 10.1017/s0007114523002271] [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: 05/02/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
The relationship between dietary habits and microbiota composition during adolescence has not been well examined. This is a crucial knowledge gap to fill considering that diet-microbiota interactions influence neurodevelopment, immune system maturation and metabolic regulation. This study examined the associations between diet and the gut microbiota in a school-based sample of 136 adolescents (Mage = 12·1 years; age range 11-13 years; 48 % female; 47 % Black, 38 % non-Hispanic White, 15 % Hispanic or other minorities) from urban, suburban and rural areas in the Southeast USA. Adolescents completed the Rapid Eating Assessment for Participants and provided stool samples for 16S ribosomal RNA gene sequencing. Parents reported their child and family socio-demographic characteristics. The associations between diet and socio-demographics with gut microbiota diversity and abundance were analysed using multivariable regression models. Child race and ethnicity, sex, socio-economic status and geographic locale contributed to variation within microbiota composition (β-diversity). Greater consumption of processed meat was associated with a lower microbial α-diversity after adjusting for socio-demographic variables. Multi-adjusted models showed that frequent consumption of nutrient-poor, energy-dense foods (e.g. sugar-sweetened beverages, fried foods, sweets) was negatively associated with abundances of genera in the family Lachnospiraceae (Anaerostipes, Fusicatenibacter and Roseburia), which are thought to play a beneficial role in host health through their production of short-chain fatty acids (SCFAs). These results provide new insights into the complex relationships among socio-demographic factors, diet and gut microbiota during adolescence. Adolescence may represent a critical window of opportunity to promote healthy eating practices that shape a homoeostatic gut microbiota with life-long benefits.
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Affiliation(s)
- Keri M. Kemp
- Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294, USA
| | - Catheryn A. Orihuela
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suzanne E. Judd
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Retta R. Evans
- Department of Human Studies, School of Education, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sylvie Mrug
- Department of Psychology, University of Alabama at Birmingham, Birmingham, AL, USA
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Zhou X, Xu J, Zhang X, Zhao Y, Duan X. Causal relationships between Gut microbiota and primary open-angle Glaucoma: A Mendelian randomization and mediation analysis of Glaucoma endophenotypes. Exp Eye Res 2024; 240:109788. [PMID: 38218362 DOI: 10.1016/j.exer.2024.109788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Primary open-angle glaucoma (POAG) is a widespread condition responsible for irreversible blindness, and its prevalence is expected to increase substantially in the coming decades. Despite its significance, the exact cause of POAG remains elusive, necessitating a comprehensive exploration of its pathogenesis. Emerging research suggests a potential link between alterations in gut microbiota composition and POAG. However, establishing causality in these associations remains a challenge. In this study, we employed Mendelian randomization (MR) analysis to investigate the potential causal relationships between gut microbiota (GM) and POAG. Significant bacteria taxa were further analyzed with POAG endophenotypes. We utilized data from genome-wide association studies (GWAS) for GM and POAG, as well as for glaucoma endophenotypes, including intraocular pressure (IOP), retinal nerve fiber layer (RNFL) thickness, vertical cup-to-disc ratio (VCDR), and central corneal thickness (CCT). Univariable, multivariable MR and mediation effect analysis were conducted. Our analysis revealed that certain taxa, including phylum Euryarchaeota, genus Odoribacter, Rumnicoccaceae UCG009, Ruminiclostridium9, unknown genus id.2071, and Eubacterium rectale group, were associated with an increased risk of POAG. On the other hand, family Victivallaceae, Lacchnospiraceae, genus Lachnoclostridium, Oscillospira, Ruminococcaceae UCG011, Alloprevotella, and Faecalibacterium were found to be associated with a decreased risk of POAG. Furthermore, some of these taxa were found to be connected to glaucoma endophenotypes. Through further multivariable MR analysis, it was determined that IOP, VCDR, and CCT might played mediating roles between GM and POAG. In conclusion, this study utilizes MR analysis to elucidate potential causal associations between GM and POAG, providing insights into specific GM taxa that influence POAG risk and related endophenotypes. These findings emphasize the potential role of the gut microbiota in the pathogenesis of POAG and pave the way for future research and therapeutic interventions.
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Affiliation(s)
- Xiaoyu Zhou
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Jiahao Xu
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Xinyue Zhang
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yang Zhao
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Xuanchu Duan
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China.
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Li T, Chen X, Qi Q, Feng X. Bovine Milk Derived Exosomes Affect Gut Microbiota of DSS-Induced Colitis Mice. Indian J Microbiol 2024; 64:100-109. [PMID: 38468747 PMCID: PMC10924850 DOI: 10.1007/s12088-023-01131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/27/2023] [Indexed: 03/13/2024] Open
Abstract
The objective of this study was to investigate the effect of bovine milk derived exosomes (MDEs) on the gut microbiota of Dextran sodium sulfate (DSS)-induced colitis mice. Total of 42 specific pathogen free (SPF) male BALB/c mice (3 weeks old) were randomly assigned to three groups including control group, DSS group (DSS) and bovine milk derived exosome group (Exo), with 7 replicates/cages per treatment and two mice in one cage. 16S rRNA gene sequencing of cecal digesta samples was conducted. DSS significantly decreased the average daily feed intake of mice in DSS and Exo groups (P = 0.03). Shannon index of the DSS group was significantly lower than the control group (P < 0.05) whereas no difference between the control group and Exo group was observed. Administration of MDEs tended to increase the relative abundance of Campylobaterota. Compared to the control group, the relative abundance of Roseburia was significantly decreased in the DSS group (P < 0.05) whereas no difference between the Exo group and control group was observed. MDEs also tended to increase the relative abundance of Lachnospiraceae_UCG_006. In conclusion, oral administration of 10 µL MDEs (1 mg/mL) positively affected gut microbiota of DSS-induced colitis mice. The results of this study provided valuable reference for MDEs application in the prevention and treatment of colitis.
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Affiliation(s)
- Tonghao Li
- School of Life Science and Engineering, Foshan University, No. 33 Guangyun Road, Nanhai District, Foshan, Guangdong China
| | - Xiaolin Chen
- School of Life Science and Engineering, Foshan University, No. 33 Guangyun Road, Nanhai District, Foshan, Guangdong China
| | - Qien Qi
- School of Life Science and Engineering, Foshan University, No. 33 Guangyun Road, Nanhai District, Foshan, Guangdong China
| | - Xin Feng
- School of Life Science and Engineering, Foshan University, No. 33 Guangyun Road, Nanhai District, Foshan, Guangdong China
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Molina CA, Quiroz-Moreno C, Jarrín-V P, Díaz M, Yugsi E, Pérez-Galarza J, Baldeón-Rojas L. Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador. JOURNAL OF WATER AND HEALTH 2024; 22:536-549. [PMID: 38557569 DOI: 10.2166/wh.2024.290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 04/04/2024]
Abstract
Bacterial communities in drinking water provide a gauge to measure quality and confer insights into public health. In contrast to urban systems, water treatment in rural areas is not adequately monitored and could become a health risk. We performed 16S rRNA amplicon sequencing to analyze the microbiome present in the water treatment plants at two rural communities, one city, and the downstream water for human consumption in schools and reservoirs in the Andean highlands of Ecuador. We tested the effect of water treatment on the diversity and composition of bacterial communities. A set of physicochemical variables in the sampled water was evaluated and correlated with the structure of the observed bacterial communities. Predominant bacteria in the analyzed communities belonged to Proteobacteria and Actinobacteria. The Sphingobium genus, a chlorine resistance group, was particularly abundant. Of health concern in drinking water reservoirs were Fusobacteriaceae, Lachnospiraceae, and Ruminococcaceae; these families are associated with human and poultry fecal contamination. We propose the latter families as relevant biomarkers for establishing local standards for the monitoring of potable water systems in highlands of Ecuador. Our assessment of bacterial community composition in water systems in the Ecuadorian highlands provides a technical background to inform management decisions.
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Affiliation(s)
- C Alfonso Molina
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521 Quito, Ecuador; Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521, Quito, Ecuador E-mail:
| | - Cristian Quiroz-Moreno
- Department of Horticulture and Crop Science, Ohio State University, 2021 Coffey Road, Columbus OH 43210
| | - Pablo Jarrín-V
- Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Gestión de la Innovación, Instituto Nacional de Biodiversidad INABIO, Pje. Rumipamba N341 y Av. de los Shyris, Quito, Ecuador
| | - Magdalena Díaz
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Cdla. Universitaria y Gaspar de Carvajal s/n., 170521, Quito, Ecuador; Facultad de Ingeniería Química, Universidad Central del Ecuador, Ritter s/n y Bolivia, 170521 Quito, Ecuador; Institute of Integrative Systems Biology (I2SysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Carrer del Catedràtic Agustín Escardino Benlloch, 46980 Paterna, Valencia, Spain
| | - Elizabeth Yugsi
- Centro de Biotecnología 'Dr Daniel Alkalay Lowitt', Universidad Técnica Federico Santa María, General Bari 699, 2390136, Valparaíso, Chile
| | - Jorge Pérez-Galarza
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Iquique N14-121 y Sodiro, Quito, Ecuador; Instituto de Investigación en Biomedicina, Universidad Central del Ecuador, Capitán Giovanni Calles y Derby, Quito, Ecuador
| | - Lucy Baldeón-Rojas
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Iquique N14-121 y Sodiro, Quito, Ecuador; Instituto de Investigación en Biomedicina, Universidad Central del Ecuador, Capitán Giovanni Calles y Derby, Quito, Ecuador
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Yuan L, Zhao J, Liu Y, Zhao J, Olnood CG, Xu YJ, Liu Y. Multiomics analysis revealed the mechanism of the anti-diabetic effect of Salecan. Carbohydr Polym 2024; 327:121694. [PMID: 38171651 DOI: 10.1016/j.carbpol.2023.121694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
Salecan, a natural β-glucan compromising nine residues connected by β-(1 → 3)/α-(1 → 3) glycosidic bonds, is one of the newly approved food ingredients. Salecan has multiple health-improving effects, yet its mechanism against Type 2 diabetes mellitus (T2DM) remains poorly understood. In this study, the hypoglycemic effect and underlying mechanism of Salecan intervention on STZ-induced diabetic model mice were investigated. After 8 weeks of gavage, Salecan attenuated insulin resistance and repaired pancreatic β cells in a dose-dependent manner. In addition, Salecan supplement remodel the structure of the gut microbiota and altered the level of intestinal metabolites. Serum metabolites, especially unsaturated fatty acids, were also affected significantly. In addition, tight junction proteins in the colon and autophagy-related proteins in the pancreas were upregulated. Multiomics analysis indicated that Lactobacillus johnsonii, Muribaculaceae, and Lachnoclostridium were highly associated with fatty acid esters of hydroxy fatty acids (FAHFA) levels in the colon, accordingly enhancing arachidonic acid and linoleic acid in serum, and promoting GLP-1 release in the intestine and insulin secretion in the pancreas, thus relieving insulin resistance and exhibiting hypoglycemic effects. These findings provide a novel understanding of the anti-diabetic effect of Salecan in mice from a molecular perspective, paving the way for the wide use of Salecan.
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Affiliation(s)
- Liyang Yuan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Juan Zhao
- Sichuan Synlight Biotech Ltd, 88 Keyuan South Road, Chengdu 610000, Sichuan, China
| | - Yanjun Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jialiang Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Chen Guang Olnood
- Sichuan Synlight Biotech Ltd, 88 Keyuan South Road, Chengdu 610000, Sichuan, China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
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Ng HY, Liao Y, Zhang R, Chan KH, To WP, Hui CH, Seto WK, Leung WK, Hung IFN, Lam TTY, Cheung KS. The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac. Int J Mol Sci 2024; 25:2583. [PMID: 38473829 DOI: 10.3390/ijms25052583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
CoronaVac immunogenicity decreases with time, and we aimed to investigate whether gut microbiota associate with longer-term immunogenicity of CoronaVac. This was a prospective cohort study recruiting two-dose CoronaVac recipients from three centres in Hong Kong. We collected blood samples at baseline and day 180 after the first dose and used chemiluminescence immunoassay to test for neutralizing antibodies (NAbs) against the receptor-binding domain (RBD) of wild-type SARS-CoV-2 virus. We performed shotgun metagenomic sequencing performed on baseline stool samples. The primary outcome was the NAb seroconversion rate (seropositivity defined as NAb ≥ 15AU/mL) at day 180. Linear discriminant analysis [LDA] effect size analysis was used to identify putative bacterial species and metabolic pathways. A univariate logistic regression model was used to derive the odds ratio (OR) of seropositivity with bacterial species. Of 119 CoronaVac recipients (median age: 53.4 years [IQR: 47.8-61.3]; male: 39 [32.8%]), only 8 (6.7%) remained seropositive at 6 months after vaccination. Bacteroides uniformis (log10LDA score = 4.39) and Bacteroides eggerthii (log10LDA score = 3.89) were significantly enriched in seropositive than seronegative participants. Seropositivity was associated with B. eggerthii (OR: 5.73; 95% CI: 1.32-29.55; p = 0.022) and B. uniformis with borderline significance (OR: 3.27; 95% CI: 0.73-14.72; p = 0.110). Additionally, B. uniformis was positively correlated with most enriched metabolic pathways in seropositive vaccinees, including the superpathway of adenosine nucleotide de novo biosynthesis I (log10LDA score = 2.88) and II (log10LDA score = 2.91), as well as pathways related to vitamin B biosynthesis, all of which are known to promote immune functions. In conclusion, certain gut bacterial species (B. eggerthii and B. uniformis) and metabolic pathways were associated with longer-term CoronaVac immunogenicity.
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Affiliation(s)
- Ho-Yu Ng
- School of Clinical Medicine, The University of Hong Kong, Hong Kong
| | - Yunshi Liao
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Ruiqi Zhang
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Kwok-Hung Chan
- Department of Microbiology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Wai-Pan To
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Chun-Him Hui
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Wai-Kay Seto
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Ivan F N Hung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Tommy T Y Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong
- Centre for Immunology & Infection Ltd., 17W Hong Kong Science & Technology Parks, Hong Kong
- Laboratory of Data Discovery for Health Ltd., 19W Hong Kong Science & Technology Parks, Hong Kong
- School of Public Health, The University of Hong Kong, Hong Kong
| | - Ka-Shing Cheung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A, Kosciolek T. Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study. PLoS One 2024; 19:e0297858. [PMID: 38381714 PMCID: PMC10880968 DOI: 10.1371/journal.pone.0297858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024] Open
Abstract
The influence of human gut microbiota on health and disease is now commonly appreciated. Therefore, it is not surprising that microbiome research has found interest in the sports community, hoping to improve health and optimize performance. Comparative studies found new species or pathways that were more enriched in elites than sedentary controls. In addition, sport-specific and performance-level-specific microbiome features have been identified. However, the results remain inconclusive and indicate the need for further assessment. In this case-control study, we tested two athletic populations (i.e. strength athletes, endurance athletes) and a non-athletic, but physically active, control group across two acute exercise bouts, separated by a 2-week period, that measured explosive and high intensity fitness level (repeated 30-s all-out Wingate test (WT)) and cardiorespiratory fitness level (Bruce Treadmill Test). While we did not identify any group differences in alpha and beta diversity or significant differential abundance of microbiome components at baseline, one-third of the species identified were unique to each group. Longitudinal sample (pre- and post-exercise) analysis revealed an abundance of Alistipes communis in the strength group during the WT and 88 species with notable between-group differences during the Bruce Test. SparCC recognized Bifidobacterium longum and Bifidobacterium adolescentis, short-chain fatty acid producers with probiotic properties, species strongly associated with VO2max. Ultimately, we identified several taxa with different baseline abundances and longitudinal changes when comparing individuals based on their VO2max, average power, and maximal power parameters. Our results confirmed that the health status of individuals are consistent with assumptions about microbiome health. Furthermore, our findings indicate that microbiome features are associated with better performance previously identified in elite athletes.
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Affiliation(s)
- Kinga Humińska-Lisowska
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Kinga Zielińska
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
| | - Jan Mieszkowski
- Faculty of Health Sciences, University of Lomza, Lomza, Poland
| | | | - Paweł Cięszczyk
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Paweł P Łabaj
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Frączek
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
- Department of Sports Medicine and Human Nutrition, Institute of Biomedical Sciences, University School of Physical Education, Cracow, Poland
| | - Anna Grzywacz
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | | | - Tomasz Kosciolek
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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Ye W, Fan J, Wu W, Chen Z, Huang Q, Qian L. Effects of fecal microbiota transplantation on metabolic health of DBA mice. Front Microbiol 2024; 15:1352555. [PMID: 38444807 PMCID: PMC10912182 DOI: 10.3389/fmicb.2024.1352555] [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: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Numerous studies have demonstrated that C57BL/6 mice exhibit superior growth rates and overall growth performance compared to DBA mice. To investigate whether this discrepancy in growth performance is linked to the composition of gut microorganisms, we conducted fecal microbiome transplantation (FMT) experiments. Methods Specifically, we transplanted fecal fluids from adult C57BL/6 mice, high-fat C57BL/6 mice, and Wistar rats into weaned DBA mice (0.2mL/d), and subsequently analyzed their gut contents and gene expression through 16S rRNA sequencing and transcriptome sequencing. During the test period, C57BL/6 mice and Wistar rats were provided with a normal diet, and high-fat C57BL/6 mice were provided with a high-fat diet. Results The results of our study revealed that mice receiving FMT from all three donor groups exhibited significantly higher daily weight gain and serum triglyceride (TG) levels compared to mice of CK group. 16S rRNA sequensing unveiled substantial differences in the abundance and function of the gut microbiota between the FMT groups and the CK group. Transcriptome analysis revealed a total of 988 differential genes, consisting of 759 up-regulated genes and 187 down-regulated genes, between the three experimental groups and the CK group. Functional Gene Ontology (GO) annotation suggested that these genes were primarily linked to lipid metabolism, coagulation, and immunity. Pearson correlation analysis was performed on the differential genes and clusters, and it revealed significant correlations, mainly related to processes such as fatty acid metabolism, fat digestion and absorption, and cholesterol metabolism. Discussion In summary, FMT from dominant strains improved the growth performance of DBA mice, including body weight gain, institutional growth, and immune performance. This change may be due to the increase of probiotic content in the intestinal tract by FMT and subsequent alteration of intestinal gene expression. However, the effects of cross-species fecal transplantation on the intestinal flora and gene expression of recipient mice were not significant.
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Affiliation(s)
- Wenxin Ye
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jinghui Fan
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Wenzi Wu
- Hainan Institute of Zhejiang University, Sanya, China
| | - Zhuo Chen
- Hainan Institute of Zhejiang University, Sanya, China
| | - Qixin Huang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lichun Qian
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
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Gao Q, Li D, Wang Y, Zhao C, Li M, Xiao J, Kang Y, Lin H, Wang N. Analysis of intestinal flora and cognitive function in maintenance hemodialysis patients using combined 16S ribosome DNA and shotgun metagenome sequencing. Aging Clin Exp Res 2024; 36:28. [PMID: 38334873 PMCID: PMC10857965 DOI: 10.1007/s40520-023-02645-y] [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: 08/16/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
BACKGROUND Cognitive impairment is widely prevalent in maintenance hemodialysis (MHD) patients, and seriously affects their quality of life. The intestinal flora likely regulates cognitive function, but studies on cognitive impairment and intestinal flora in MHD patients are lacking. METHODS MHD patients (36) and healthy volunteers (18) were evaluated using the Montreal Cognitive Function Scale, basic clinical data, and 16S ribosome DNA (rDNA) sequencing. Twenty MHD patients and ten healthy volunteers were randomly selected for shotgun metagenomic analysis to explore potential metabolic pathways of intestinal flora. Both16S rDNA sequencing and shotgun metagenomic sequencing were conducted on fecal samples. RESULTS Roseburia were significantly reduced in the MHD group based on both 16S rDNA and shotgun metagenomic sequencing analyses. Faecalibacterium, Megamonas, Bifidobacterium, Parabacteroides, Collinsella, Tyzzerella, and Phascolarctobacterium were positively correlated with cognitive function or cognitive domains. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included oxidative phosphorylation, photosynthesis, retrograde endocannabinoid signaling, flagellar assembly, and riboflavin metabolism. CONCLUSION Among the microbiota, Roseburia may be important in MHD patients. We demonstrated a correlation between bacterial genera and cognitive function, and propose possible mechanisms.
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Affiliation(s)
- Qiuyi Gao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dianshi Li
- Centre for Empirical Legal Studies, Faculty of Law, University of Macau, Macau, China
| | - Yue Wang
- Department of Nephrology, Binzhou Medical University Affiliated Shengli Oilfield Central Hospital, Binzhou, China
| | - Chunhui Zhao
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Mingshuai Li
- School of Graduate, Dalian Medical University, Dalian, China
| | - Jingwen Xiao
- School of Graduate, Dalian Medical University, Dalian, China
| | - Yan Kang
- School of Graduate, Dalian Medical University, Dalian, China
| | - Hongli Lin
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Nan Wang
- Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
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Contino KF, Cook KL, Shiozawa Y. Bones and guts - Why the microbiome matters. J Bone Oncol 2024; 44:100523. [PMID: 38274305 PMCID: PMC10808965 DOI: 10.1016/j.jbo.2024.100523] [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: 11/01/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The importance of the gut microbiota in human health has become increasingly apparent in recent years, especially when the relationship between microbiota and host is no longer symbiotic. It has long been appreciated that gut dysbiosis can be detrimental to human health and is associated with numerous disease states. Only within the last decade, however, was the gut microbiota implicated in bone biology. Dubbed osteomicrobiology, this emerging field aims to understand the relationship between the gut microbiome and the bone microenvironment in both health and disease. Importantly, the key to one of the major clinical challenges facing both bone and cancer biologists: bone metastasis, may lie in the field of osteomicrobiology; however the link between gut bacteria and bone metastasis is only beginning to be explored. This review will discuss (i) osteomicrobiology as an emerging field, and (ii) the current understanding of osteomicrobiology in the context of cancer in bone.
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Affiliation(s)
- Kelly F. Contino
- Department of Cancer Biology, Wake Forest University School of Medicine, and Atrium Health Wake Forest Baptist Comprehensive Cancer, Winston-Salem, NC, USA
| | - Katherine L. Cook
- Department of Cancer Biology, Wake Forest University School of Medicine, and Atrium Health Wake Forest Baptist Comprehensive Cancer, Winston-Salem, NC, USA
| | - Yusuke Shiozawa
- Department of Cancer Biology, Wake Forest University School of Medicine, and Atrium Health Wake Forest Baptist Comprehensive Cancer, Winston-Salem, NC, USA
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Paiano L, Mastronardi M, Campisciano G, Rosso N, Casagranda B, Comar M, de Manzini N, Palmisano S. Liver Bacterial Colonization in Patients with Obesity and Gut Dysbiosis. Obes Surg 2024; 34:402-408. [PMID: 38102371 DOI: 10.1007/s11695-023-06989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
PURPOSE Recently, the link between gut microbiota, liver inflammation, and obesity has become an interesting focus of research. The aim of this study is to show the possible relation between gut microbiota dysbiosis in patients with obesity and the presence of bacterial genomes in their liver biopsies. MATERIALS AND METHODS A prospective study on patients undergoing bariatric surgery was carried out. Anthropometric and metabolic data, comorbidities, stool samples, and hepatic biopsies were collected and analyzed at the time of surgery. The V3-16S rRNA region was sequenced using the Ion Torrent new-generation sequencing platform. RESULTS In each of the 23 patients enrolled, the bacterial population was analyzed both in the stools and liver. In eight patients (34.7%), Prevotella (62.5%), Bacteroides (50%), Streptococcus (12.5%), and Dalister (12.5%) were found in both samples, simultaneously; in 15 cases, the liver was free from colonization. The statistically significant difference between groups was a Roseburia intestinalis reduction in fecal samples of patients with liver biopsies colonized by bacteria (1% vs 3%; p = 0.0339). CONCLUSION To the best of our knowledge, this is the first study reporting the presence of bacterial genome in a liver biopsy on bariatric patients, instead of the microbe-associated molecular patterns. Notably, in literature, the presence of Roseburia intestinalis in stool samples has been shown to prevent intestinal inflammation playing its role in the gut barrier integrity. In our population, the Roseburia reduction was associated with the presence of bacterial genome in the liver, probably related to a greater permeability of the gut and vascular barriers.
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Affiliation(s)
- Lucia Paiano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Manuela Mastronardi
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy.
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy.
| | - Giuseppina Campisciano
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Natalia Rosso
- Fondazione Italiana Fegato, Centro Studi Fegato, Area Science Park Basovizza Bldg.Q SS14 Km, 163.5, 34149, Trieste, Italy
| | - Biagio Casagranda
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Manola Comar
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Nicolò de Manzini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Silvia Palmisano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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