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Wu H, Liu Z, Li Y. Intestinal microbiota and respiratory system diseases: Relationships with three common respiratory virus infections. Microb Pathog 2025; 203:107500. [PMID: 40139334 DOI: 10.1016/j.micpath.2025.107500] [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: 12/05/2024] [Revised: 03/19/2025] [Accepted: 03/21/2025] [Indexed: 03/29/2025]
Abstract
In recent years, the role of the intestinal microbiota in regulating host health and immune balance has attracted widespread attention. This study provides an in-depth analysis of the close relationship between the intestinal microbiota and respiratory system diseases, with a focus on three common respiratory virus infections, including respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and influenza virus. The research indicates that during RSV infection, there is a significant decrease in intestinal microbial diversity, suggesting the impact of the virus on the intestinal ecosystem. In SARS-CoV-2 infection, there are evident alterations in the intestinal microbiota, which are positively correlated with the severity of the disease. Similarly, influenza virus infection is associated with dysbiosis of the intestinal microbiota, and studies have shown that the application of specific probiotics exhibits beneficial effects against influenza virus infection. Further research indicates that the intestinal microbiota exerts a wide and profound impact on the occurrence and development of respiratory system diseases through various mechanisms, including modulation of the immune system and production of short-chain fatty acids (SCFAs). This article comprehensively analyzes these research advances, providing new perspectives and potential strategies for the prevention and treatment of future respiratory system diseases. This study not only deepens our understanding of the relationship between the intestinal microbiota and respiratory system diseases but also offers valuable insights for further exploring the role of host-microbiota interactions in the development of diseases.
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Affiliation(s)
- Haonan Wu
- Department of Respiratory, Children's Medical Center, The First Hospital of Jilin University, Changchun, China; Clinical Research Center for Child Health, The First Hospital of Jilin University, Changchun, China
| | - Ziyu Liu
- The First Hospital of Jilin University, Changchun, China.
| | - Yanan Li
- Department of Respiratory, Children's Medical Center, The First Hospital of Jilin University, Changchun, China; Clinical Research Center for Child Health, The First Hospital of Jilin University, Changchun, China.
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Ng HM, Maggo J, Wall CL, Bayer SB, Mullaney JA, Cabrera D, Fraser K, Cooney JM, Günther CS, McNabb WC, Foster M, Frampton C, Gearry RB, Roy NC. Effects of defatted rice bran-fortified bread on gut microbiome, cardiovascular risk, gut discomfort, wellbeing and gut physiology in healthy adults with low dietary fibre intake. Clin Nutr ESPEN 2025; 67:362-376. [PMID: 40127766 DOI: 10.1016/j.clnesp.2025.03.045] [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: 01/09/2025] [Accepted: 03/18/2025] [Indexed: 03/26/2025]
Abstract
BACKGROUND & AIMS Inadequate dietary fibre (DF) intake is associated with suboptimal gut function and increased risk of several human diseases. Bread is commonly consumed and is ideal to incorporate cereal bran to increase DF content. No human studies have investigated the effects of defatted rice bran (DRB) in bread, which has triple the DF of white bread, purported hypo-allergenicity and a unique nutrient profile, as a dietary intervention in healthy adults. This study aims to assess the relative abundances of a composite of key faecal microbial genera and species involved in DF fermentation and metabolism following the habitual intake of DRB-fortified bread and its influence on other biological markers of host and microbial interactions, cardiovascular risk profile, patient-reported outcomes, total DF intake, and gut physiology in healthy adults with low baseline DF intake. METHODS Fifty-six healthy adults with low baseline DF intake (<18 g/day (females), <22 g/day (males)) completed a two-arm, placebo-controlled, double-blind, randomised, crossover study. Participants consumed three (females) or four (males) slices of DRB-fortified bread or control bread daily as part of their usual diet for four weeks, with the intervention periods separated by a two-week washout. Outcomes included faecal microbiota composite (primary outcome); relative abundances (taxa and gene); faecal moisture content and bile acid concentrations; plasma and faecal organic acid concentrations; cardiovascular risk profile; gut comfort, psychological wellbeing parameters; total DF intake; whole gut transit time, and were measured at baseline and following each intervention phase. Additionally, in a sub-study, 15 participants ingested gas-sensing capsules to assess whole and regional gut transit times, and total and regional colonic hydrogen and carbon dioxide concentrations at the same timepoints. RESULTS DRB-fortified bread consumption significantly increased total DF intake from 20.7 g/day to 43.4 g/day (p < 0.001). No significant differences were observed in the primary outcome, microbial taxa composite within and between groups (False Discovery Rate (FDR) correction, p > 0.10). As compared to control, the DRB group had increased relative abundances of Faecalibacterium prausnitzii (unadjusted p = 0.04), Bifidobacterium longum (unadjusted p = 0.12), and Bacteroides ovatus (unadjusted p = 0.10); lower relative abundances in Coprococcus genus (unadjusted p = 0.09), Roseburia faecis (unadjusted p = 0.02) and Prevotella copri species (unadjusted p = 0.05). However, no significant differences were observed in the relative abundances of these taxa within and between groups (FDR correction p > 0.10) and for most of the other outcomes between groups (p > 0.05). Only mean serum high-density lipoprotein (HDL) concentrations significantly increased (p = 0.006), and mean total cholesterol (TC) to HDL concentration ratio significantly lowered (p = 0.02) in the DRB group compared to the control group. CONCLUSION This is the first human study to show that a high-DF DRB-fortified bread improved DF intake, HDL cholesterol profiles, and may affect the gut microbiota composition in healthy adults with low DF intake. These findings support the substitution of white bread with DRB-fortified bread as an effective method to improve DF intake, which may have subsequent benefits on gut physiology and metabolic health.
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Affiliation(s)
- Hwei Min Ng
- Department of Medicine, University of Otago, Christchurch, New Zealand; High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Jasjot Maggo
- Department of Medicine, University of Otago, Christchurch, New Zealand; High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Catherine L Wall
- Department of Medicine, University of Otago, Christchurch, New Zealand; High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Simone B Bayer
- Department of Medicine, University of Otago, Christchurch, New Zealand; High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Jane A Mullaney
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; AgResearch Grasslands, Palmerston North, New Zealand.
| | - Diana Cabrera
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; AgResearch Grasslands, Palmerston North, New Zealand; Plant and Food Research, Palmerston North, New Zealand.
| | - Karl Fraser
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; AgResearch Grasslands, Palmerston North, New Zealand.
| | - Janine M Cooney
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Plant and Food Research, Ruakura Research Centre, Hamilton, New Zealand.
| | - Catrin S Günther
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Plant and Food Research, Ruakura Research Centre, Hamilton, New Zealand.
| | - Warren C McNabb
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand.
| | - Meika Foster
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; Edible Research Limited, Ohoka, New Zealand.
| | - Chris Frampton
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand.
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand; High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Nicole C Roy
- High-Value Nutrition National Science Challenge, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; Department of Human Nutrition, University of Otago, Dunedin, New Zealand.
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Budin M, Sandiford NA, Gehrke T, Citak M. Body mass index matters: morbid obese patients have different microorganism profiles in the setting of periprosthetic hip joint infections. INTERNATIONAL ORTHOPAEDICS 2025; 49:1309-1317. [PMID: 40183945 DOI: 10.1007/s00264-025-06513-4] [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: 02/10/2025] [Accepted: 03/20/2025] [Indexed: 04/05/2025]
Abstract
PURPOSE This study investigated the relationship between BMI and microorganism profiles, with a particular focus on gut microorganisms in patients with PJI following total hip arthroplasty (THA). It also explored comorbidities, that may contribute to these variations. METHODS This study included all patients treated at our institution for a PJI of a THA between 1996 and 2021. Patients were categorized into four distinct BMI groups: <30; 30-34.9; 35-39.9; ≥ 40. Bivariate and logistic regression analysis were conducted, with presentation of odds ratio (OR) and 95% confidence interval (CI). RESULTS A total of 3645 hip PJI cases were recruited for the final analysis. Patients with a BMI ≥ 40 had approximately a ten fold higher risk for Streptococcus dysgalactiae (p < 0.001; OR = 9.92; 95% CI 3.87-25.44) and a seven fold higher risk for Proteus mirabilis (p < 0.001; OR = 7.43; 95% CI 3.13-17.67) and Klebsiella pneumoniae (p < 0.001; OR = 6.9; 95% CI 2.47-19.31). Furthermore, polymicrobial infections (p < 0.001; OR = 2.17; 95% CI 1.50-3.15) were found to be significantly more prevalent in patients with a BMI ≥ 40. CONCLUSION Obese patients (BMI ≥ 30) displayed a distinct microorganism profile in hip PJIs, mainly dominated by Firmicutes and Proteobacteria. Comorbidities such as diabetes, hypertension, and hyperlipidaemia may contribute to a leaky gut syndrome, increasing PJI risk caused by gut microorganisms. Optimizing comorbidities may help reduce the risk of hip PJI. Further research is needed to clarify the relationship between obesity, gut microbiome alterations and hip PJI development.
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Dörr AK, Imangaliyev S, Karadeniz U, Schmidt T, Meyer F, Kraiselburd I. Distinguishing critical microbial community shifts from normal temporal variability in human and environmental ecosystems. Sci Rep 2025; 15:16934. [PMID: 40374711 DOI: 10.1038/s41598-025-01781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 05/08/2025] [Indexed: 05/17/2025] Open
Abstract
Differentiating significant microbial community changes from normal fluctuations is vital for understanding microbial dynamics in human and environmental ecosystems. This knowledge could enable early warning systems to monitor critical changes affecting human or environmental health. We applied 16S rRNA gene sequencing and time-series analysis to model bacterial abundance trajectories in human gut and wastewater microbiomes. We evaluated various model architectures using datasets from two human studies and five wastewater settings. Long short-term memory (LSTM) models consistently outperformed other models in predicting bacterial abundances and detecting outliers, as measured by multiple metrics. Prediction intervals for each genus allowed us to identify significant changes and signaling shifts in community states. This study proposes a machine learning model capable of monitoring microbial communities and providing insights into their responses to internal and external factors in medical and environmental settings.
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Affiliation(s)
- Ann-Kathrin Dörr
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Sultan Imangaliyev
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Utku Karadeniz
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Tina Schmidt
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, 45128, Essen, Germany
| | - Folker Meyer
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Computer Science, University of Duisburg-Essen, Essen, Germany
| | - Ivana Kraiselburd
- Department of Medicine, Institute for Artificial Intelligence in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Wang L, Ding Y, Tang Y, Yang M, Yang Z, Yang X, Xia J. Association between sphingomyelin levels and gut microbiota abundance in Alzheimer's disease: a two-sample Mendelian randomization study. BMC Neurol 2025; 25:191. [PMID: 40307740 PMCID: PMC12044981 DOI: 10.1186/s12883-025-04207-3] [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: 03/07/2024] [Accepted: 04/24/2025] [Indexed: 05/02/2025] Open
Abstract
BACKGROUND Several previous observational studies have shown that abnormal sphingomyelin metabolism may be implicated in the pathogenesis of Alzheimer's disease. To determine the causal relationship between sphingolipid abundance and gut microbiota abundance at the genetic level, we conducted a Mendelian randomization (MR) investigation. METHODS We first used the TwoSampleMR and MRPRESSO packages for conducting two-sample MR studies. Second, we utilized random effect inverse variance weighting (IVW) as the principal method of analysis and used MR‒Egger, the weighted median, the simple mode and the weighted mode as supplementary methods. Finally, we performed tests for heterogeneity and horizontal pleiotropy. These analyses were also conducted to evaluate the impact of individual SNPs on the outcomes of our analysis. A Bonferroni-corrected threshold of p = 2.4e-4(0.05/211) was considered significant, and p values less than 0·05 were considered to be suggestive of an association. RESULTS The results showed that sphingolipid levels were suggestively associated with the abundance of 6 gut microbiota taxa. Specifically, two taxa were positively correlated with sphingolipid levels, including the family Alcaligenaceae (p = 0.006, OR 95% CI = 1.109 [1.030-1.194]) and the species Ruminococcus callidus (p = 0.034, OR 95% CI = 1.217 [1.015-1.460]). In contrast, negative correlations were observed with the abundances of 4 gut microbiota taxa, including the genus Flavonifractor (p = 0.026, OR 95% CI = 0.804 [0.663-0.974]), the genus Streptococcus (p = 0.014, OR 95% CI = 0.909 [0.842-0.981]), the species Bacteroides caccae (p = 0.037, OR 95% CI = 0.870 [0.763-0.992]), and the species Haemophilus parainfluenzae (p = 0.006, beta 95% CI = -0.269 [-0.462, -0.076]). The results presented a normal distribution, with no anomalous values, heterogeneity, or horizontal pleiotropic effects detected. CONCLUSIONS This two-sample MR study revealed a potential causal relationship between sphingomyelin levels and gut microbiota abundance.
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Affiliation(s)
- Liping Wang
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China
| | - Yuyan Ding
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China
| | - Yu Tang
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China
| | - Mengqi Yang
- Department of General Surgery, The Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Zhihui Yang
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China
| | - Xiao Yang
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China
| | - Jiazeng Xia
- Department of General Surgery, Institute of General Surgical Research, Jiangnan University Medical Center, Wuxi, China.
- Department of General Surgery, The Affiliated Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China.
- Wuxi Clinical College, Nantong University, Wuxi, China.
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Wang H, Ali M, Zhu Y, Chen X, Lu D, Liu Y, Li K, Zhang C. Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County. Sci Rep 2025; 15:14317. [PMID: 40274860 PMCID: PMC12022119 DOI: 10.1038/s41598-025-95357-4] [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: 01/01/2025] [Accepted: 03/20/2025] [Indexed: 04/26/2025] Open
Abstract
Gut microbiota variations in response to environmental and nutritional factors are of great significance as gut microbiota plays an integral role in nutrient metabolism, immunity, health, and disease conditions. In this context, limited studies investigated variations of gut microbiota in response to different feeding systems and environmental conditions. The current study obtained fresh fecal samples from house-fed (LS) and grazing yaks (LF) from Linzhou County. 16 S rRNA amplicon sequencing of the V3-V4 and internal transcribed spacer 2 (ITS2) domains generated 16,332 bacterial and 2345 fungus amplicon sequence variants (ASVs). Alpha and beta diversity indices revealed significant variations (p > 0.05) in gut microflora between the two groups. At the phylum level, Firmicutes, Actinobacteriota, Bacteroidota, and Patescibacteria regarding bacteria, and Ascomycota and Basidiomycota regarding fungi dominated. At the genus level, UCG-005, Rikenellaceae_RC9_gut_group, Clostridium_sensu_stricto_1, g__Muribaculaceae, UCG-010, [Eubacterium]_coprostanoligenes_group, Turicibacter, Alistipes, Prevotellaceae_UCG-003, UCG-009, Blautia, dgA-11_gut_group, Candidatus_Saccharimonas dominated in LS, while Anthrobacter and Terrisporobacter dominated in the LF group. Fungal genera like Myrothecium and Plectosphaerella dominated the LS group, while Neoascochyta, Paraphaeosphaeria, and Hypocreales dominated the LF group. Also, significant variations (p > 0.05) in gene expressions were found between the two groups. These findings provide insights into yak gut microbiota adaptations and metabolic changes in response to varied environmental conditions and can provide valuable information, optimizing feeding strategies after identifying specific differences between grazing and house-fed yaks, reducing environmental impacts, and improving yaks' health and productivity in specific geographical settings.
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Affiliation(s)
- Hongzhuang Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Munwar Ali
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Xiaoying Chen
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Dongyang Lu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Yang Liu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Kun Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengfu Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China.
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El Jaddaoui I, Sehli S, Al Idrissi N, Bakri Y, Belyamani L, Ghazal H. The Gut Mycobiome for Precision Medicine. J Fungi (Basel) 2025; 11:279. [PMID: 40278100 PMCID: PMC12028274 DOI: 10.3390/jof11040279] [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: 03/08/2025] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/26/2025] Open
Abstract
The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.
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Affiliation(s)
- Islam El Jaddaoui
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, University Mohammed V, Rabat 10000, Morocco; (I.E.J.); (Y.B.)
- Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat 10000, Morocco
- Laboratory of Precision Medicine & One Health (MedPreOne), School of Medicine, Mohammed VI University of Sciences & Health, Casablanca 82403, Morocco; (S.S.); (N.A.I.)
| | - Sofia Sehli
- Laboratory of Precision Medicine & One Health (MedPreOne), School of Medicine, Mohammed VI University of Sciences & Health, Casablanca 82403, Morocco; (S.S.); (N.A.I.)
| | - Najib Al Idrissi
- Laboratory of Precision Medicine & One Health (MedPreOne), School of Medicine, Mohammed VI University of Sciences & Health, Casablanca 82403, Morocco; (S.S.); (N.A.I.)
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, University Mohammed V, Rabat 10000, Morocco; (I.E.J.); (Y.B.)
- Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat 10000, Morocco
| | - Lahcen Belyamani
- School of Medicine, Mohammed VI University of Sciences & Health, Casablanca 82403, Morocco;
| | - Hassan Ghazal
- Laboratory of Precision Medicine & One Health (MedPreOne), School of Medicine, Mohammed VI University of Sciences & Health, Casablanca 82403, Morocco; (S.S.); (N.A.I.)
- Laboratory of Sports Sciences and Performance Optimization, Royal Institute of Executive Management, Salé 10102, Morocco
- National Center for Scientific and Technical Research, Rabat 10102, Morocco
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Park Y, Lee JY, Lee ES. A retrospective study on blood microbiota as a marker for cognitive decline: implications for detecting Alzheimer's disease and amnestic mild cognitive impairment in Republic of Korea. Osong Public Health Res Perspect 2025; 16:141-151. [PMID: 40122583 PMCID: PMC12066232 DOI: 10.24171/j.phrp.2024.0329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 12/24/2024] [Accepted: 02/12/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND This study aimed to investigate the relationship between blood microbiota, specifically bacterial DNA, and cognitive decline in individuals with subjective cognitive decline (SCD) and amnestic mild cognitive impairment (aMCI). The objective was to identify potential microbial signatures that could serve as biomarkers for cognitive deterioration. METHODS Forty-seven participants were recruited, including 13 with aMCI, 20 with SCD, and 14 normal cognition (NC). Blood samples were collected, and microbial DNA was analyzed using 16S rRNA sequencing on the Illumina MiSeq platform. Bioinformatics analyses-including α- and β-diversity measures and differential abundance testing (using edgeR)-were employed to assess microbial diversity and differences in bacterial composition among groups. Logistic regression models were used to evaluate the predictive impact of the microbiota on cognitive decline. RESULTS Microbial diversity differed significantly between groups, with NC exhibiting the highest α-diversity. Both the aMCI and SCD groups showed reduced diversity. Taxa such as Bacteroidia, Alphaproteobacteria, and Clostridia were significantly decreased in the aMCI group compared to NC (p< 0.05). In contrast, Gammaproteobacteria increased significantly in the aMCI group compared to both NC and SCD, indicating progressive microbial changes from SCD to aMCI. No significant differences were found between the NC and SCD groups. CONCLUSION Distinct bacterial taxa-particularly the increase in Gammaproteobacteria along with decreases in Bacteroidia, Alphaproteobacteria, and Clostridia-are associated with the progression of cognitive decline. These findings suggest that blood microbiota could serve as potential biomarkers for the early detection of aMCI. However, the small sample size and the lack of control for confounding factors such as diet and medication limit the findings. Larger studies are needed to validate these results and further explore the role of microbiota in neurodegeneration.
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Affiliation(s)
- Youngchan Park
- Division of Bio Bigdata, Department of Precision Medicine, Korea National Institution of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | | | - Eek-Sung Lee
- Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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Tufail MA, Schmitz RA. Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm. Probiotics Antimicrob Proteins 2025; 17:681-704. [PMID: 39377977 PMCID: PMC11925995 DOI: 10.1007/s12602-024-10370-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2024] [Indexed: 03/21/2025]
Abstract
Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.
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Affiliation(s)
- Muhammad Aammar Tufail
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany.
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany.
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Byrne SR, DeMott MS, Yuan Y, Ghanegolmohammadi F, Kaiser S, Fox JG, Alm EJ, Dedon PC. Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome. MICROBIOME 2025; 13:81. [PMID: 40128848 PMCID: PMC11931770 DOI: 10.1186/s40168-025-02071-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 02/24/2025] [Indexed: 03/26/2025]
Abstract
BACKGROUND Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications. RESULTS Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m6dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.
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Affiliation(s)
- Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yifeng Yuan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Stefanie Kaiser
- Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - James G Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore, Singapore
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore, Singapore.
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11
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Li C, Cheng D, Ren H, Zhang T. Unraveling the gut microbiota's role in PCOS: a new frontier in metabolic health. Front Endocrinol (Lausanne) 2025; 16:1529703. [PMID: 40171188 PMCID: PMC11958223 DOI: 10.3389/fendo.2025.1529703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Accepted: 02/27/2025] [Indexed: 04/03/2025] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder affecting reproductive-age women, characterized primarily by hyperandrogenism, ovulatory dysfunction, and metabolic abnormalities. In recent years, the gut microbiota has garnered widespread attention for its potential role as a key regulator of host metabolism in the pathogenesis of PCOS. Studies have shown that PCOS patients exhibit dysbiosis in their gut microbiota, characterized by reduced microbial diversity, an imbalance in the ratio of Firmicutes to Bacteroidetes, changes in the abundance of specific taxa, and abnormal levels of metabolic products. These alterations may exacerbate metabolic dysfunction in PCOS through multiple mechanisms, including influencing host energy metabolism, disrupting lipid and bile acid metabolism, and inducing chronic inflammation. Addressing gut dysbiosis through the modulation of patients' microbiomes-such the use of, prebiotics, fecal microbiota transplantation, and optimizing diet lifestyle-may offer strategies for improving metabolic abnormalities and alleviating clinical symptoms in PCOS. Additionally, the gut microbiome promises as a potential marker, aiding in the precise diagnosis and personalization of PCOS. Although our current understanding of how the gut microbiota influences PCOS is still limited, research is needed to explore the causal relationships and mechanisms involved, providing a more reliable theoretical basis for clinical. This review aims summarize the research progress on the relationship between gut microbiota and PCOS, and to suggest future directions to promote the development of prevention and treatment strategies for PCOS.
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Affiliation(s)
- Caihong Li
- Department of Assisted Reproductive Laboratory, Shenyang Jinghua Hospital, Shenyang, China
| | - Dongkai Cheng
- Department of Assisted Reproductive Laboratory, Shenyang Jinghua Hospital, Shenyang, China
| | - Haiqin Ren
- Department of Assisted Reproductive Laboratory, Shenyang Jinghua Hospital, Shenyang, China
| | - Tao Zhang
- Department of Stem Cells and Regenerative Medicine, Shenyang Key Laboratory of Stem Cell and Regenerative Medicine, China Medical University, Shenyang, China
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12
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Ribeiro G, Schellekens H, Cuesta-Marti C, Maneschy I, Ismael S, Cuevas-Sierra A, Martínez JA, Silvestre MP, Marques C, Moreira-Rosário A, Faria A, Moreno LA, Calhau C. A menu for microbes: unraveling appetite regulation and weight dynamics through the microbiota-brain connection across the lifespan. Am J Physiol Gastrointest Liver Physiol 2025; 328:G206-G228. [PMID: 39811913 DOI: 10.1152/ajpgi.00227.2024] [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: 07/26/2024] [Revised: 08/14/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]
Abstract
Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior. Therefore, the role of the microbiota-gut-brain axis in appetite and obesity is receiving increased attention. Omics approaches such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics in appetite and weight regulation offer new opportunities for featuring obesity phenotypes. Furthermore, gut-microbiota-targeted approaches such as pre-, pro-, post-, and synbiotic, personalized nutrition, and fecal microbiota transplantation are novel avenues for precision treatments. The aim of this narrative review is 1) to provide an overview of the role of the microbiota-gut-brain axis in appetite regulation across the lifespan and 2) to discuss the potential of omics and gut microbiota-targeted approaches to deepen understanding of appetite regulation and obesity.
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Affiliation(s)
- Gabriela Ribeiro
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Harriët Schellekens
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Cristina Cuesta-Marti
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ivie Maneschy
- Growth, Exercise, Nutrition and Development Research Group, Instituto Agroalimentario de Aragón, University of Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón, University of Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Shámila Ismael
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Amanda Cuevas-Sierra
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- Precision Nutrition and Cardiometabolic Health, IMDEA-Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM+CSIC, Spanish National Research Council, Madrid, Spain
| | - J Alfredo Martínez
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
- Precision Nutrition and Cardiometabolic Health, IMDEA-Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM+CSIC, Spanish National Research Council, Madrid, Spain
| | - Marta P Silvestre
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Cláudia Marques
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - André Moreira-Rosário
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Ana Faria
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CINTESIS - Comprehensive Health Research Centre, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Luis A Moreno
- Growth, Exercise, Nutrition and Development Research Group, Instituto Agroalimentario de Aragón, University of Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón, University of Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Conceição Calhau
- Metabolism and Nutrition Department, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- CHRC - Center for Health Technology and Services Research, Faculdade de Ciências Médicas, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
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13
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Santangelo BE, Bada M, Hunter LE, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. Sci Rep 2025; 15:6905. [PMID: 40011529 PMCID: PMC11865272 DOI: 10.1038/s41598-025-91230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 02/19/2025] [Indexed: 02/28/2025] Open
Abstract
Knowledge graphs have been a useful tool for many biomedical applications because of their effective representation of biological concepts. Plentiful evidence exists linking the gut microbiome to disease in a correlative context, but uncovering the mechanistic explanation for those associations remains a challenge. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. We have constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink, and, using a shortest path or template-based search through the graph and a novel path-prioritization methodology based on the structure of the knowledge graph, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.
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Affiliation(s)
- Brook E Santangelo
- Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA.
| | - Michael Bada
- Department of Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
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14
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Fliegerová KO, Mahayri TM, Sechovcová H, Mekadim C, Mrázek J, Jarošíková R, Dubský M, Fejfarová V. Diabetes and gut microbiome. Front Microbiol 2025; 15:1451054. [PMID: 39839113 PMCID: PMC11747157 DOI: 10.3389/fmicb.2024.1451054] [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: 06/18/2024] [Accepted: 12/17/2024] [Indexed: 01/23/2025] Open
Abstract
Diabetes mellitus represents a significant global health problem. The number of people suffering from this metabolic disease is constantly rising and although the incidence is heterogeneous depending on region, country, economic situation, lifestyle, diet and level of medical care, it is increasing worldwide, especially among youths and children, mainly due to lifestyle and environmental changes. The pathogenesis of the two most common subtypes of diabetes mellitus, type 1 (T1DM) and type 2 (T2DM), is substantially different, so each form is characterized by a different causation, etiology, pathophysiology, presentation, and treatment. Research in recent decades increasingly indicates the potential role of the gut microbiome in the initiation, development, and progression of this disease. Intestinal microbes and their fermentation products have an important impact on host metabolism, immune system, nutrient digestion and absorption, gut barrier integrity and protection against pathogens. This review summarizes the current evidence on the changes in gut microbial populations in both types of diabetes mellitus. Attention is focused on changes in the abundance of specific bacterial groups at different taxonomic levels in humans, and microbiome shift is also assessed in relation to geographic location, age, diet and antidiabetic drug. The causal relationship between gut bacteria and diabetes is still unclear, and future studies applying new methodological approaches to a broader range of microorganisms inhabiting the digestive tract are urgently needed. This would not only provide a better understanding of the role of the gut microbiome in this metabolic disease, but also the use of beneficial bacterial species in the form of probiotics for the treatment of diabetes.
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Affiliation(s)
- Kateřina Olša Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Prague, Czechia
| | - Tiziana Maria Mahayri
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Prague, Czechia
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Hana Sechovcová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Prague, Czechia
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Prague, Czechia
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, CAS, Prague, Czechia
| | - Radka Jarošíková
- Institute for Clinical and Experimental Medicine, Diabetes Centre, Prague, Czechia
- Department of Internal Medicine, Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Michal Dubský
- Institute for Clinical and Experimental Medicine, Diabetes Centre, Prague, Czechia
| | - Vladimíra Fejfarová
- Institute for Clinical and Experimental Medicine, Diabetes Centre, Prague, Czechia
- Department of Internal Medicine, Second Faculty of Medicine, Charles University, Prague, Czechia
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15
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Palmas V, Deledda A, Heidrich V, Sanna G, Cambarau G, Fosci M, Puglia L, Cappai EA, Lai A, Loviselli A, Manzin A, Velluzzi F. Impact of Ketogenic and Mediterranean Diets on Gut Microbiota Profile and Clinical Outcomes in Drug-Naïve Patients with Diabesity: A 12-Month Pilot Study. Metabolites 2025; 15:22. [PMID: 39852366 PMCID: PMC11766981 DOI: 10.3390/metabo15010022] [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: 11/11/2024] [Revised: 12/18/2024] [Accepted: 12/28/2024] [Indexed: 01/26/2025] Open
Abstract
Background/Objectives: Managing type 2 diabetes mellitus (T2DM) and obesity requires a multidimensional, patient-centered approach including nutritional interventions (NIs) and physical activity. Changes in the gut microbiota (GM) have been linked to obesity and the metabolic alterations typical of T2DM and obesity, and they are strongly influenced by diet. However, few studies have evaluated the effects on the GM of a very-low-calorie ketogenic diet (VLCKD) in patients with T2DM, especially in the mid-term and long-term. This longitudinal study is aimed at evaluating the mid-term and long-term impact of the VLCKD and Mediterranean diet (MD) on the GM and on the anthropometric, metabolic, and lifestyle parameters of 11 patients with T2DM and obesity (diabesity). This study extends previously published results evaluating the short-term (three months) impact of these NIs on the same patients. Methods: At baseline, patients were randomly assigned to either a VLCKD (KETO group) or a Mediterranean diet (MEDI group). After two months, the KETO group gradually shifted to a Mediterranean diet (VLCKD-MD), according to current VLCKD guidelines. From the fourth month until the end of the study both groups followed a similar MD. Previous published results showed that VLCKD had a more beneficial impact than MD on several variables for 3 months of NI. In this study, the analyses were extended until six (T6) and twelve months (T12) of NI by comparing data prospectively and against baseline (T0). The GM analysis was performed through next-generation sequencing. Results: Improvements in anthropometric and metabolic parameters were more pronounced in the KETO group at T6, particularly for body mass index (-5.8 vs. -1.7 kg/m2; p = 0.006) and waist circumference (-15.9 vs. -5.2 cm; p = 0.011). At T6, a significant improvement in HbA1c (6.7% vs. 5.5% p = 0.02) and triglyceride (158 vs. 95 mg/dL p = 0.04) values compared to T0 was observed only in the KETO group, which maintained the results achieved at T3. The VLCKD-MD had a more beneficial impact than the MD on the GM phenotype. A substantial positive modulatory effect was observed especially up to the sixth month of the NI in KETO due to the progressive increase in bacterial markers of human health. After the sixth month, most markers of human health decreased, though they were still increased compared with baseline. Among them, the Verrucomicrobiota phylum was identified as the main biomarker in the KETO group, together with its members Verrucomicrobiae, Akkermansiaceae, Verrucomicrobiales, and Akkermansia at T6 compared with baseline. Conclusions: Both dietary approaches ameliorated health status, but VLCKD, in support of the MD, has shown greater improvements on anthropometric and metabolic parameters, as well as on GM profile, especially up to T6 of NI.
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Affiliation(s)
- Vanessa Palmas
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (V.P.); (G.S.)
| | - Andrea Deledda
- Obesity Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy; (A.D.); (G.C.); (E.A.C.); (F.V.)
| | - Vitor Heidrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil;
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (V.P.); (G.S.)
| | - Giulia Cambarau
- Obesity Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy; (A.D.); (G.C.); (E.A.C.); (F.V.)
| | - Michele Fosci
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (M.F.); (L.P.); (A.L.)
| | - Lorenzo Puglia
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (M.F.); (L.P.); (A.L.)
| | - Enrico Antonio Cappai
- Obesity Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy; (A.D.); (G.C.); (E.A.C.); (F.V.)
| | - Alessio Lai
- Diabetologia, P.O. Binaghi, ASSL Cagliari, 09126 Cagliari, Italy;
| | - Andrea Loviselli
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (M.F.); (L.P.); (A.L.)
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy; (V.P.); (G.S.)
| | - Fernanda Velluzzi
- Obesity Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy; (A.D.); (G.C.); (E.A.C.); (F.V.)
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16
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Todorov SD, Tagg J, Algburi A, Tiwari SK, Popov I, Weeks R, Mitrokhin OV, Kudryashov IA, Kraskevich DA, Chikindas ML. The Hygienic Significance of Microbiota and Probiotics for Human Wellbeing. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10419-9. [PMID: 39688648 DOI: 10.1007/s12602-024-10419-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2024] [Indexed: 12/18/2024]
Abstract
The human body can be viewed as a combination of ecological niches inhabited by trillions of bacteria, viruses, fungi, and parasites, all united by the microbiota concept. Human health largely depends on the nature of these relationships and how they are built and maintained. However, personal hygiene practices have historically been focused on the wholesale elimination of pathogens and "hygiene-challenging microorganisms" without considering the collateral damage to beneficial and commensal species. The microbiota can vary significantly in terms of the qualitative and quantitative composition both between different people and within one person during life, and the influence of various environmental factors, including age, nutrition, bad habits, genetic factors, physical activity, medication, and hygienic practices, facilitates these changes. Disturbance of the microbiota is a predisposing factor for the development of diseases and also greatly influences the course and severity of potential complications. Therefore, studying the composition of the microbiota of the different body systems and its appropriate correction is an urgent problem in the modern world. The application of personal hygiene products or probiotics must not compromise health through disruption of the healthy microbiota. Where changes in the composition or metabolic functions of the microbiome may occur, they must be carefully evaluated to ensure that essential biological functions are unaffected. As such, the purpose of this review is to consider the microbiota of each of the "ecological niches" of the human body and highlight the importance of the microbiota in maintaining a healthy body as well as the possibility of its modulation through the use of probiotics for the prevention and treatment of certain human diseases.
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Affiliation(s)
- Svetoslav D Todorov
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos E Nutrição Experimental, Food Research Center, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
- Instituto Politécnico de Viana Do Castelo, 4900-347, Viana Do Castelo, Portugal.
| | - John Tagg
- Blis Technologies, South Dunedin, 9012, New Zealand
| | - Ammar Algburi
- Department of Microbiology, College of Veterinary Medicine, University of Diyala, Baqubah, Iraq
| | - Santosh Kumar Tiwari
- Department of Genetics, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Igor Popov
- Center for Agrobiotechnology, Don State Technical University, Gagarina Sq., 1344002, Rostov-On-Don, Russia
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, Federal Territory Sirius, Olimpijskij Ave., 1, Federal Territory Sirius, Sirius, 354340, Russia
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University-Campus Venlo, Villafloraweg, 1, 5928 SZ, Venlo, The Netherlands
| | - Richard Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Oleg V Mitrokhin
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, Moscow, 119435, Russia
| | - Ilya A Kudryashov
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, Moscow, 119435, Russia
| | - Denis A Kraskevich
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, Moscow, 119435, Russia
| | - Michael L Chikindas
- Center for Agrobiotechnology, Don State Technical University, Gagarina Sq., 1344002, Rostov-On-Don, Russia.
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, Moscow, 119435, Russia.
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17
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Chaudhari DS, Francescutti DM, Winters AD, Koka O, Kracht DJ, Greenberg JM, Theis KR, Angoa-Perez M. Contributions of the gut microbiota to Gulf War Illness susceptibility: Findings from a mouse model. Life Sci 2024; 359:123244. [PMID: 39551360 DOI: 10.1016/j.lfs.2024.123244] [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: 08/26/2024] [Revised: 11/01/2024] [Accepted: 11/11/2024] [Indexed: 11/19/2024]
Abstract
AIMS In light of the evidence supporting a significant role of the gut microbiome in Gulf War Illness (GWI) pathology, we sought to examine its contribution to GWI susceptibility in a mouse model. We also aimed to identify bacterial taxa and microbially-derived metabolites associated with disease susceptibility. MAIN METHODS Male mice receiving pyridostigmine bromide (PB) orally, and controls were evaluated for symptoms of GWI at 8 weeks post-treatment. The Kansas criteria were adapted to assess behaviors associated with the following domains: gastrointestinal alterations, pain, mood, cognitive function, skin and respiratory disturbances. PB-treated subjects were classified into susceptible (GWI-S) or resilient (GWI-R). The status of the gut microbiome was assessed via analyses of the 16S rRNA gene and microbial-derived metabolites were evaluated with metabolomics tools. KEY FINDINGS Our results indicate that application of the Kansas criteria to behavioral outcomes in PB-treated mice resulted in a GWI susceptibility rate of ~35 %, similar to the one reported in humans. The composition and structure of the gut microbiome was different in GWI-S subjects compared to both control and GWI-R mice at 8 weeks but differences in microbial community structure were observed prior to PB treatment between GWI-R and GWI-S mice. GWI-S subjects exhibited a pattern of differentially abundant bacterial taxa and microbial metabolites. SIGNIFICANCE To our knowledge, this is the first preclinical report in which a stratification by susceptibility to GWI and its association with the gut microbiome is described. In light of the research conundrum that vulnerability to GWI represents, the use of tools that could provide further insight into this complex factor should be considered.
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Affiliation(s)
- Diptaraj S Chaudhari
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Dina M Francescutti
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Andrew D Winters
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Orena Koka
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - David J Kracht
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA
| | - Jonathan M Greenberg
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Mariana Angoa-Perez
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA.
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18
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Malcomson FC, Louca P, Nelson A, Willis ND, McCallum I, Xie L, Ouwehand AC, Stowell JD, Preston T, Morrison DJ, Kelly SB, Bradburn DM, Belshaw NJ, Johnson IT, Corfe BM, Stewart CJ, Mathers JC. Effects of non-digestible carbohydrates on gut microbiota and microbial metabolites: a randomised, controlled dietary intervention in healthy individuals. Br J Nutr 2024; 132:1433-1445. [PMID: 39494600 PMCID: PMC7616798 DOI: 10.1017/s000711452400271x] [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: 04/22/2024] [Revised: 10/16/2024] [Accepted: 10/18/2024] [Indexed: 11/05/2024]
Abstract
The gut microbiome is impacted by certain types of dietary fibre. However, the type, duration and dose needed to elicit gut microbial changes and whether these changes also influence microbial metabolites remain unclear. This study investigated the effects of supplementing healthy participants with two types of non-digestible carbohydrates (resistant starch (RS) and polydextrose (PD)) on the stool microbiota and microbial metabolite concentrations in plasma, stool and urine, as secondary outcomes in the Dietary Intervention Stem Cells and Colorectal Cancer (DISC) Study. The DISC study was a double-blind, randomised controlled trial that supplemented healthy participants with RS and/or PD or placebo for 50 d in a 2 × 2 factorial design. DNA was extracted from stool samples collected pre- and post-intervention, and V4 16S rRNA gene sequencing was used to profile the gut microbiota. Metabolite concentrations were measured in stool, plasma and urine by high-performance liquid chromatography. A total of fifty-eight participants with paired samples available were included. After 50 d, no effects of RS or PD were detected on composition of the gut microbiota diversity (alpha- and beta-diversity), on genus relative abundance or on metabolite concentrations. However, Drichlet's multinomial mixture clustering-based approach suggests that some participants changed microbial enterotype post-intervention. The gut microbiota and fecal, plasma and urinary microbial metabolites were stable in response to a 50-d fibre intervention in middle-aged adults. Larger and longer studies, including those which explore the effects of specific fibre sub-types, may be required to determine the relationships between fibre intake, the gut microbiome and host health.
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Affiliation(s)
- Fiona C. Malcomson
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
- Centre for Cancer, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Panayiotis Louca
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
| | - Andrew Nelson
- Department of Applied Science, Northumbria University, Newcastle upon TyneNE1 8ST, UK
| | - Naomi D. Willis
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
| | - Iain McCallum
- Northumbria Healthcare NHS Foundation Trust, North Tyneside General Hospital, Rake Lane, North ShieldsNE29 8NH, UK
| | - Long Xie
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
| | | | | | - Tom Preston
- Scottish Universities Environmental Research Centre, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - Douglas J. Morrison
- Scottish Universities Environmental Research Centre, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - Seamus B. Kelly
- Northumbria Healthcare NHS Foundation Trust, North Tyneside General Hospital, Rake Lane, North ShieldsNE29 8NH, UK
| | - D. Michael Bradburn
- Northumbria Healthcare National Health Service Foundation Trust, Ashington, UK
| | - Nigel J. Belshaw
- University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, UK
| | - Ian T. Johnson
- Quadram Institute, Norwich Research Park, Norwich, NorfolkNR4 7UQ, UK
| | - Bernard M. Corfe
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
| | - Christopher J. Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
| | - John C. Mathers
- Human Nutrition and Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, UK
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19
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Bradford LM, Carrillo C, Wong A. Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets. BMC Bioinformatics 2024; 25:372. [PMID: 39627685 PMCID: PMC11613480 DOI: 10.1186/s12859-024-05952-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/07/2024] [Indexed: 12/08/2024] Open
Abstract
BACKGROUND Culture-independent diagnostic tests are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communities, but the challenge is in analyzing large and complex sequencing datasets with a high degree of both sensitivity and specificity. Falsely classifying sequencing reads as originating from pathogens can lead to unnecessary food recalls or production shutdowns, while low sensitivity resulting in false negatives could lead to preventable illness. RESULTS We used simulated and published shotgun sequencing datasets containing Salmonella-derived reads to explore the appearance and mitigation of false positive results using the popular taxonomic annotation softwares Kraken2 and Metaphlan4. Using default parameters, Kraken2 is sensitive but prone to false positives, while Metaphlan4 is more specific but unable to detect Salmonella at low abundance. We then developed a bioinformatic pipeline for identifying and removing reads falsely identified as Salmonella by Kraken2 while retaining high sensitivity. Carefully considering software parameters and database choices is essential to avoiding false positive sample calls. With well-chosen parameters plus additional steps to confirm the taxonomic origin of reads, it is possible to detect pathogens with very high specificity and sensitivity.
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Affiliation(s)
| | - Catherine Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada.
- Institute for Advancing Health Through Agriculture, Texas A & M University, College Station, USA.
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20
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Ferrara KM, Gupta KR, Pi H. Bacterial Organelles in Iron Physiology. Mol Microbiol 2024; 122:914-928. [PMID: 39545931 DOI: 10.1111/mmi.15330] [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: 06/06/2024] [Revised: 10/26/2024] [Accepted: 10/29/2024] [Indexed: 11/17/2024]
Abstract
Bacteria were once thought to be simple organisms, lacking the membrane-bound organelles found in eukaryotic cells. However, recent advancements in microscopy have changed this view, revealing a diverse array of organelles within bacterial cells. These organelles, surrounded by lipid bilayers, protein-lipid monolayers, or proteinaceous shells, play crucial roles in facilitating biochemical reactions and protecting cells from harmful byproducts. Unlike eukaryotic organelles, which are universally present, bacterial organelles are species-specific and induced only under certain conditions. This review focuses on the bacterial organelles that contain iron, an essential micronutrient for all life forms but potentially toxic when present in excess. To date, three types of iron-related bacterial organelles have been identified: two membrane-bound organelles, magnetosomes and ferrosomes, and one protein-enclosed organelle, the encapsulated ferritin-like proteins. This article provides an updated overview of the genetics, biogenesis, and physiological functions of these organelles. Furthermore, we discuss how bacteria utilize these specialized structures to adapt, grow, and survive under various environmental conditions.
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Affiliation(s)
- Kristina M Ferrara
- Department of Microbial Pathogenesis, Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kuldeepkumar R Gupta
- Department of Microbial Pathogenesis, Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hualiang Pi
- Department of Microbial Pathogenesis, Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
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21
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Lu R, Luo XM. The role of gut microbiota in different murine models of systemic lupus erythematosus. Autoimmunity 2024; 57:2378876. [PMID: 39014962 DOI: 10.1080/08916934.2024.2378876] [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: 04/30/2024] [Accepted: 07/07/2024] [Indexed: 07/18/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune system dysfunction that can lead to serious health issues and mortality. Recent investigations highlight the role of gut microbiota alterations in modulating inflammation and disease severity in SLE. This review specifically summaries the variations in gut microbiota composition across various murine models of lupus. By focusing on these differences, we aim to elucidate the intricate relationship between gut microbiota dysbiosis and the development and progression of SLE in preclinical settings.
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Affiliation(s)
- Ran Lu
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
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22
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López-Tenorio II, Aguilar-Villegas ÓR, Espinoza-Palacios Y, Segura-Real L, Peña-Aparicio B, Amedei A, Aguirre-García MM. Primary Prevention Strategy for Non-Communicable Diseases (NCDs) and Their Risk Factors: The Role of Intestinal Microbiota. Biomedicines 2024; 12:2529. [PMID: 39595097 PMCID: PMC11591598 DOI: 10.3390/biomedicines12112529] [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: 09/11/2024] [Revised: 10/22/2024] [Accepted: 11/01/2024] [Indexed: 11/28/2024] Open
Abstract
Non-communicable diseases (NCDs) are the leading cause of morbidity and mortality worldwide. These conditions have numerous health consequences and significantly impact patients' lifestyles. Effective long-term treatment is essential since NCDs are irreversible. Therefore, primary healthcare must be both exclusive and of the highest quality, ensuring comprehensive care. The primary goal should be to improve quality of life with a focus on patients, families, and communities, as most of these diseases can be prevented and controlled, although not cured. Several factors have been linked to individual health, including social, cultural, and economic aspects, lifestyle, and certain environmental factors, including work, that can have positive or negative effects. More of these variables may contribute to the onset of NCDs, which are defined by their chronic nature, propensity for prolongation, and generally slow rate of progression. Examples of NCDs include hypertension, type 2 diabetes (T2D), dyslipidemia, and fatty liver disease linked to metabolic dysfunction. The onset of these diseases has been associated with an imbalance in certain microbial niches, such as the gut, which hosts billions of microorganisms performing multiple metabolic functions, such as the production of metabolites like bile acids (BAs), short-chain fatty acids (SCFAs), and trimethylamine N-oxide (TMAO). Therefore, lifestyle changes and personal habits can significantly impact the gut microbiota (GM), potentially preventing chronic diseases associated with metabolism. NCDs are highly prevalent worldwide, prompting increased attention to strategies for modifying the intestinal microbiota (IM). Approaches such as probiotics, prebiotics, synbiotics, and fecal transplantation (FMT) have demonstrated improvements in the quality of life for individuals with these conditions. Additionally, lifestyle changes and the adoption of healthy habits can significantly impact IM and may help prevent chronic diseases related to metabolism. Therefore, the main aim of this review is to analyze and understand the importance of microbiota intervention in the prevention of non-communicable diseases. R3:A1.
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Affiliation(s)
- Itzel Ivonn López-Tenorio
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina UNAM, Instituto Nacional de Cardiología Ignacio Cháve, Mexico City 14080, Mexico; (I.I.L.-T.); (Ó.R.A.-V.); (Y.E.-P.); (L.S.-R.)
| | - Óscar Rodrigo Aguilar-Villegas
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina UNAM, Instituto Nacional de Cardiología Ignacio Cháve, Mexico City 14080, Mexico; (I.I.L.-T.); (Ó.R.A.-V.); (Y.E.-P.); (L.S.-R.)
| | - Yoshua Espinoza-Palacios
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina UNAM, Instituto Nacional de Cardiología Ignacio Cháve, Mexico City 14080, Mexico; (I.I.L.-T.); (Ó.R.A.-V.); (Y.E.-P.); (L.S.-R.)
| | - Lorena Segura-Real
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina UNAM, Instituto Nacional de Cardiología Ignacio Cháve, Mexico City 14080, Mexico; (I.I.L.-T.); (Ó.R.A.-V.); (Y.E.-P.); (L.S.-R.)
| | - Berenice Peña-Aparicio
- Consulta Externa Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico;
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), 50134 Florence, Italy
| | - María Magdalena Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina UNAM, Instituto Nacional de Cardiología Ignacio Cháve, Mexico City 14080, Mexico; (I.I.L.-T.); (Ó.R.A.-V.); (Y.E.-P.); (L.S.-R.)
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23
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Ma BDY, Chan TYH, Lo BWY. Unveiling the hidden culprit: How the brain-gut axis fuels neuroinflammation in ischemic stroke. Surg Neurol Int 2024; 15:394. [PMID: 39640340 PMCID: PMC11618647 DOI: 10.25259/sni_703_2024] [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: 08/17/2024] [Accepted: 09/25/2024] [Indexed: 12/07/2024] Open
Abstract
Background The brain-gut axis represents a bidirectional communication network between the gut microbiome and the central nervous system that plays an important role in homeostasis. Compelling evidence now confirms that ischemic stroke disrupts this delicate balance by inducing gut dysbiosis. Methods A comprehensive literature search was performed in PubMed, Web of Science, and Google Scholar for articles published between January 2000 and January 2023 using relevant keywords. Studies were limited to English and included original studies, literature, and systematic reviewers from peer-reviewed journals which discussed gut microbiota composition in models/subjects with ischemic stroke or assessed stroke impact on gut microbiota. Comments, meeting abstracts, and case reports were excluded. From the 80 relevant articles, we summarized key findings related to gut microbiota changes after stroke and their association with stroke outcomes. Results Emerging preclinical evidence underscores the pivotal role of the gut microbiome in glial cell development and function. Germ-free models exhibit compromised microglial activation and impaired cellular debris clearance, exacerbating tissue damage following ischemic stroke. Targeted interventions, including prebiotics, probiotics, and fecal microbiota transplantation, have demonstrated efficacy in rescuing glial phenotypes in preclinical stroke models. Beyond its local effects, the gut microbiome significantly influences systemic immunity. Ischemic stroke polarizes pro-inflammatory phenotypes of neutrophils and T cells, amplifying neurovascular inflammation. Microbiota manipulation modulates leukocyte trafficking and metabolic signaling, offering potential avenues to mitigate infarct pathology. Conclusion Our review demonstrates that in preclinical stroke models, modulating the lipopolysaccharide, short-chain fatty acid, and trimethylamine N-oxide pathways through the gut-brain axis reduces infarct sizes and edema and improves functional recovery after ischemic stroke. Further exploration of this important axis may unveil additional adjunctive stroke therapies by elucidating the complex interplay between the microbiome and the brain. Rigorously controlled clinical studies are now warranted to translate these promising preclinical findings and investigate whether manipulating the microbiome-brain relationship can help improve outcomes for stroke patients. Overall, continued research on the gut-brain axis holds exciting possibilities for developing novel treatment strategies that may enhance recovery after stroke.
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Affiliation(s)
- Brian D. Y. Ma
- Department of Neurosurgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Travis Y. H. Chan
- Department of Neurosurgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Benjamin W. Y. Lo
- Department of Neurosurgery, Queen Mary Hospital, Pok Fu Lam, Hong Kong Hospital Authority, Hong Kong
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24
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Soe Thu M, Sawaswong V, Chanchaem P, Klomkliew P, Campbell BJ, Hirankarn N, Fothergill JL, Payungporn S. Optimization of a DNA extraction protocol for improving bacterial and fungal classification based on Nanopore sequencing. Access Microbiol 2024; 6:000754.v3. [PMID: 39376590 PMCID: PMC11457918 DOI: 10.1099/acmi.0.000754.v3] [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: 11/21/2023] [Accepted: 06/03/2024] [Indexed: 10/09/2024] Open
Abstract
Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimized protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and full-length amplicon PCR-based approaches using Nanopore sequencing. Three lysis conditions were applied to a mock microbial community, including known bacterial and fungal species: ZymoBIOMICS lysis buffer (ML) alone, incorporating bead-beating (MLB) or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). In profiling of bacteria in comparison to reference data, MLB had more statistically different bacterial phyla and genera than the other two conditions. In fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, a principal coordinates analysis plot by the Bray-Curtis metric showed a significant difference among groups for bacterial (P=0.033) and fungal (P=0.012) profiles, highlighting the importance of understanding the biases present in pretreatment. Overall, microbial profiling and diversity analysis revealed that ML and MLBE are more similar than MLB for both bacteria and fungi; therefore, using this specific pipeline, bead-beating is not recommended for whole gene amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, taxonomic classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human bacterial and fungal microbiome studies.
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Affiliation(s)
- May Soe Thu
- Joint Chulalongkorn University–University of Liverpool Doctoral Program in Biomedical Sciences and Biotechnology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 3GE, UK
- Center of Excellence in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prangwalai Chanchaem
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Barry J. Campbell
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 3GE, UK
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Joanne L. Fothergill
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, L69 3GE, UK
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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25
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Dabboussi N, Debs E, Bouji M, Rafei R, Fares N. Balancing the mind: Toward a complete picture of the interplay between gut microbiota, inflammation and major depressive disorder. Brain Res Bull 2024; 216:111056. [PMID: 39182696 DOI: 10.1016/j.brainresbull.2024.111056] [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: 06/03/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
The intricate interplay existing between gut microbiota and homeostasis extends to the realm of the brain, where emerging research underscores the significant impact of the microbiota on mood regulation and overall neurological well-being and vice-versa, with inflammation playing a pivotal role in mediating these complex interactions. This comprehensive review explores the complex interplay between inflammation, alterations in gut microbiota, and their impact on major depressive disorder (MDD). It provides a cohesive framework for the puzzle pieces of this triad, emphasizing recent advancements in understanding the gut microbiota and inflammatory states' contribution to the depressive features. Two directions of communication between the gut and the brain in depression are discussed, with inflammation serving as a potential modulator. Therapeutic implications were discussed as well, drawing insights from interventional studies on the effects of probiotics on gut bacterial composition and depressive symptoms. Ultimately, this review will attempt to provide a complete and valuable framework for future research and therapeutic interventions in MDD.
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Affiliation(s)
- Nour Dabboussi
- Laboratory of Research in Physiology and pathophysiology, Faculty of Medicine, Saint Joseph University of Beirut, POBox. 17-5208 - Mar Mikhaël, Beirut 1104 2020, Lebanon; Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| | - Espérance Debs
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O. Box 100, Tripoli, Lebanon.
| | - Marc Bouji
- Faculté des Sciences, Université Saint-Joseph de Beyrouth-Liban, Mar Roukos, Beirut, Lebanon.
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Nassim Fares
- Laboratory of Research in Physiology and pathophysiology, Faculty of Medicine, Saint Joseph University of Beirut, POBox. 17-5208 - Mar Mikhaël, Beirut 1104 2020, Lebanon.
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26
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Gindt ME, Lück R, Deppenmeier U. Genetic optimization of the human gut bacterium Phocaeicola vulgatus for enhanced succinate production. Appl Microbiol Biotechnol 2024; 108:465. [PMID: 39283347 PMCID: PMC11405475 DOI: 10.1007/s00253-024-13303-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/22/2024]
Abstract
The demand for sustainably produced bulk chemicals is constantly rising. Succinate serves as a fundamental component in various food, chemical, and pharmaceutical products. Succinate can be produced from sustainable raw materials using microbial fermentation and enzyme-based technologies. Bacteroides and Phocaeicola species, widely distributed and prevalent gut commensals, possess enzyme sets for the metabolization of complex plant polysaccharides and synthesize succinate as a fermentative end product. This study employed novel molecular techniques to enhance succinate yields in the natural succinate producer Phocaeicola vulgatus by directing the metabolic carbon flow toward succinate formation. The deletion of the gene encoding the methylmalonyl-CoA mutase (Δmcm, bvu_0309-0310) resulted in a 95% increase in succinate production, as metabolization to propionate was effectively blocked. Furthermore, deletion of genes encoding the lactate dehydrogenase (Δldh, bvu_2499) and the pyruvate:formate lyase (Δpfl, bvu_2880) eliminated the formation of fermentative end products lactate and formate. By overproducing the transketolase (TKT, BVU_2318) in the triple deletion mutant, succinate production increased from 3.9 mmol/g dry weight in the wild type to 10.9 mmol/g dry weight. Overall, succinate yield increased by 180% in the new mutant strain P. vulgatus Δmcm Δldh Δpfl pG106_tkt relative to the parent strain. This approach is a proof of concept, verifying the genetic accessibility of P. vulgatus, and forms the basis for targeted genetic optimization. The increase of efficiency highlights the huge potential of P. vulgatus as a succinate producer with applications in sustainable bioproduction processes. KEY POINTS: • Deleting methylmalonyl-CoA mutase gene in P. vulgatus doubled succinate production • Triple deletion mutant with transketolase overexpression increased succinate yield by 180% • P. vulgatus shows high potential for sustainable bulk chemical production via genetic optimization.
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Affiliation(s)
- Mélanie E Gindt
- Institute of Microbiology and Biotechnology, University of Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Rebecca Lück
- Institute of Microbiology and Biotechnology, University of Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology, University of Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.
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27
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Ng HM, Maggo J, Wall CL, Bayer SB, McNabb WC, Mullaney JA, Foster M, Cabrera DL, Fraser K, Cooney J, Trower T, Günther CS, Frampton C, Gearry RB, Roy NC. Effects of Defatted Rice Bran-Fortified Bread on the Gut Microbiota Composition of Healthy Adults With Low Dietary Fiber Intake: Protocol for a Crossover Randomized Controlled Trial. JMIR Res Protoc 2024; 13:e59227. [PMID: 39207833 PMCID: PMC11393501 DOI: 10.2196/59227] [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: 04/05/2024] [Accepted: 07/17/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Inadequate dietary fiber (DF) intake is associated with several human diseases. Bread is commonly consumed, and its DF content can be increased by incorporating defatted rice bran (DRB). OBJECTIVE This first human study on DRB-fortified bread primarily aims to assess the effect of DRB-fortified bread on the relative abundance of a composite of key microbial genera and species in fecal samples. Secondary outcomes include clinical (cardiovascular risk profile), patient-reported (daily bread consumption and bowel movement, gut comfort, general well-being, and total DF intake), biological (fecal microbiota gene abundances, and fecal and plasma metabolites), and physiome (whole-gut and regional transit time and gas fermentation profiles) outcomes in healthy adults with low DF intake. METHODS This is a 2-armed, placebo-controlled, double-blinded, crossover randomized controlled trial. The study duration is 14 weeks: 2 weeks of lead-in, 4 weeks of intervention per phase, 2 weeks of washout, and 2 weeks of follow-up. Overall, 60 healthy adults with low DF intake (<18 g [female individuals] or <22 g [male individuals] per day) were recruited in Christchurch, New Zealand, between June and December 2022. Randomly assigned participants consumed 3 (female individuals) or 4 (male individuals) slices of DRB-fortified bread per day and then placebo bread, and vice versa. The DRB-fortified bread provided 8 g (female individuals) or 10.6 g (male individuals) of total DF, whereas the placebo (a matched commercial white toast bread) provided 2.7 g (female individuals) or 3.6 g (male individuals) of total DF. Before and after each intervention phase, participants provided fecal and blood samples to assess biological responses; completed a 3-day food diary to assess usual intakes and web-based questionnaires to assess gut comfort, general and mental well-being, daily bread intake, and bowel movement via an app; underwent anthropometry and blood pressure measurements; and drank blue food dye to assess whole-gut transit time. Additionally, 25% (15/60) of the participants ingested Atmo gas-sensing capsules to assess colonic gas fermentation profile and whole-gut and regional transit time. Mean differences from baseline will be compared between the DRB and placebo groups, as well as within groups (after the intervention vs baseline). For metabolome analyses, comparisons will be made within and between groups using postintervention values. RESULTS Preliminary analysis included 56 participants (n=33, 59% female; n=23, 41% male). Due to the large dataset, data analysis was planned to be fully completed by the last quarter of 2024, with full results expected to be published in peer-reviewed journals by the end of 2024. CONCLUSIONS This first human study offers insights into the prospect of consuming DRB-fortified bread to effectively modulate health-promoting gut microbes, their metabolism, and DF intake in healthy adults with low DF intake. TRIAL REGISTRATION Australian New Zealand Clinical Trials Registry ACTRN12622000884707; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=383814. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/59227.
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Affiliation(s)
- Hwei Min Ng
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Jasjot Maggo
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Catherine Louisa Wall
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Simone Brigit Bayer
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Warren C McNabb
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jane Adair Mullaney
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- AgResearch Grasslands, Palmerston North, New Zealand
| | - Meika Foster
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Edible Research, Christchurch, New Zealand
| | - Diana L Cabrera
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Plant and Food Research, Palmerston North, New Zealand
| | - Karl Fraser
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- AgResearch Grasslands, Palmerston North, New Zealand
| | - Janine Cooney
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Plant and Food Research, Ruakura Research Centre, Hamilton, New Zealand
| | - Tania Trower
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Plant and Food Research, Ruakura Research Centre, Hamilton, New Zealand
| | - Catrin S Günther
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Plant and Food Research, Ruakura Research Centre, Hamilton, New Zealand
| | - Chris Frampton
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, Christchurch, New Zealand
| | - Richard Blair Gearry
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole Clemence Roy
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
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Chupp DP, Rivera CE, Zhou Y, Xu Y, Ramsey PS, Xu Z, Zan H, Casali P. A humanized mouse that mounts mature class-switched, hypermutated and neutralizing antibody responses. Nat Immunol 2024; 25:1489-1506. [PMID: 38918608 PMCID: PMC11291283 DOI: 10.1038/s41590-024-01880-3] [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: 11/20/2023] [Accepted: 05/18/2024] [Indexed: 06/27/2024]
Abstract
Humanized mice are limited in terms of modeling human immunity, particularly with regards to antibody responses. Here we constructed a humanized (THX) mouse by grafting non-γ-irradiated, genetically myeloablated KitW-41J mutant immunodeficient pups with human cord blood CD34+ cells, followed by 17β-estradiol conditioning to promote immune cell differentiation. THX mice reconstitute a human lymphoid and myeloid immune system, including marginal zone B cells, germinal center B cells, follicular helper T cells and neutrophils, and develop well-formed lymph nodes and intestinal lymphoid tissue, including Peyer's patches, and human thymic epithelial cells. These mice have diverse human B cell and T cell antigen receptor repertoires and can mount mature T cell-dependent and T cell-independent antibody responses, entailing somatic hypermutation, class-switch recombination, and plasma cell and memory B cell differentiation. Upon flagellin or a Pfizer-BioNTech coronavirus disease 2019 (COVID-19) mRNA vaccination, THX mice mount neutralizing antibody responses to Salmonella or severe acute respiratory syndrome coronavirus 2 Spike S1 receptor-binding domain, with blood incretion of human cytokines, including APRIL, BAFF, TGF-β, IL-4 and IFN-γ, all at physiological levels. These mice can also develop lupus autoimmunity after pristane injection. By leveraging estrogen activity to support human immune cell differentiation and maturation of antibody responses, THX mice provide a platform to study the human immune system and to develop human vaccines and therapeutics.
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Affiliation(s)
- Daniel P Chupp
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
- Invivyd, Waltham, MA, USA
| | - Carlos E Rivera
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Yulai Zhou
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Yijiang Xu
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Patrick S Ramsey
- Department of Obstetrics & Gynecology, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Zhenming Xu
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
| | - Hong Zan
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA
- Prellis Biologics, Berkeley, CA, USA
| | - Paolo Casali
- The Antibody Laboratory, Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Long School of Medicine, San Antonio, TX, USA.
- Department of Medicine, The University of Texas Long School of Medicine, San Antonio, TX, USA.
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Wosinska L, Walsh LH, Walsh CJ, Cotter PD, Guinane CM, O’Sullivan O. Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome. MICROBIOME RESEARCH REPORTS 2024; 3:41. [PMID: 39741946 PMCID: PMC11684919 DOI: 10.20517/mrr.2023.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/15/2024] [Accepted: 07/03/2024] [Indexed: 01/03/2025]
Abstract
Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns. Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation. Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota, Candidatus Melainabacteria, Elusimicrobia, Firmicutes, Lentisphaerae, Proteobacteria, Tenericutes, and Verrucomicrobiota. Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.
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Affiliation(s)
- Laura Wosinska
- Department of Biological Sciences, Munster Technological University, Cork Campus, Cork T12 P928, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
- APC Microbiome Ireland, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Liam H. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
- APC Microbiome Ireland, Cork T12 YT20, Ireland
- Authors contributed equally
| | - Calum J. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
- APC Microbiome Ireland, Cork T12 YT20, Ireland
- VistaMilk, Fermoy, Cork P61 C996, Ireland
| | - Caitriona M. Guinane
- Department of Biological Sciences, Munster Technological University, Cork Campus, Cork T12 P928, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
- APC Microbiome Ireland, Cork T12 YT20, Ireland
- VistaMilk, Fermoy, Cork P61 C996, Ireland
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30
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Jang Y, Nyamjav I, Kim HR, Suh DE, Park N, Lee YE, Lee S. Identification of plastic-degrading bacteria in the human gut. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172775. [PMID: 38670383 DOI: 10.1016/j.scitotenv.2024.172775] [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: 03/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Environmental pollution caused by the excessive use of plastics has resulted in the inflow of microplastics into the human body. However, the effects of microplastics on the human gut microbiota still need to be better understood. To determine whether plastic-degrading bacteria exist in the human gut, we collected the feces of six human individuals, did enrichment cultures and screened for bacterial species with a low-density polyethylene (LDPE) or polypropylene (PP)-degrading activity using a micro-spray method. We successfully isolated four bacterial species with an LDPE-degrading activity and three with a PP-degrading activity. Notably, all bacterial species identified with an LDPE or PP-degrading activity were opportunistic pathogens. We analyzed the microbial degradation of the LDPE or PP surface using scanning electron microscopy and confirmed that each bacterial species caused the physical changes. Chemical structural changes were further investigated using X-ray photoelectron spectroscopy and Fourier-transform-infrared spectroscopy, confirming the oxidation of the LDPE or PP surface with the formation of carbonyl groups (C=O), ester groups (CO), and hydroxyl groups (-OH) by each bacterial species. Finally, high temperature gel permeation chromatography (HT-GPC) analysis showed that these bacterial species performed to a limited extent depolymerization. These results indicate that, as a single species, these opportunistic pathogens in the human gut have a complete set of enzymes and other components required to initiate the oxidation of the carbon chains of LDPE or PP and to degrade them. Furthermore, these findings suggest that these bacterial species can potentially biodegrade and metabolize microplastics in the human gut.
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Affiliation(s)
- Yejin Jang
- School of Undergraduate Studies, College of Transdisciplinary Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Indra Nyamjav
- Department of Brain Sciences, Graduate School, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Hong Rae Kim
- Department of Research and Development, Repla Inc., Suwon 16679, Republic of Korea
| | - Dong-Eun Suh
- Department of Research and Development, Repla Inc., Suwon 16679, Republic of Korea
| | - Nohyoon Park
- School of Undergraduate Studies, College of Transdisciplinary Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Ye Eun Lee
- Department of Brain Sciences, Graduate School, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Sukkyoo Lee
- Department of Brain Sciences, Graduate School, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea.
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31
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Ross PA, Xu W, Jalomo-Khayrova E, Bange G, Gumerov VM, Bradley PH, Sourjik V, Zhulin IB. Framework for exploring the sensory repertoire of the human gut microbiota. mBio 2024; 15:e0103924. [PMID: 38757952 PMCID: PMC11237719 DOI: 10.1128/mbio.01039-24] [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: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, bacteria employ various sensors feeding into multiple signal transduction pathways. Signal recognition by bacterial sensors is studied mainly in a few model organisms, but advances in genome sequencing and analysis offer new ways of exploring the sensory repertoire of many understudied organisms. The human gut is a natural target of this line of study: it is a nutrient-rich and dynamic environment and is home to thousands of bacterial species whose activities impact human health. Many gut commensals are also poorly studied compared to model organisms and are mainly known through their genome sequences. To begin exploring the signals human gut commensals sense and respond to, we have designed a framework that enables the identification of sensory domains, prediction of signals that they recognize, and experimental verification of these predictions. We validate this framework's functionality by systematically identifying amino acid sensors in selected bacterial genomes and metagenomes, characterizing their amino acid binding properties, and demonstrating their signal transduction potential.IMPORTANCESignal transduction is a central process governing how bacteria sense and respond to their environment. The human gut is a complex environment with many living organisms and fluctuating streams of nutrients. One gut inhabitant, Escherichia coli, is a model organism for studying signal transduction. However, E. coli is not representative of most gut microbes, and signaling pathways in the thousands of other organisms comprising the human gut microbiota remain poorly understood. This work provides a foundation for how to explore signals recognized by these organisms.
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Affiliation(s)
- Patricia A. Ross
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ekaterina Jalomo-Khayrova
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Patrick H. Bradley
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
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Filippo D, Guardone L, Listorti V, Elisabetta R. Microbiome in cancer: A comparative analysis between humans and dogs. Vet J 2024; 305:106145. [PMID: 38788999 DOI: 10.1016/j.tvjl.2024.106145] [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: 09/18/2023] [Revised: 04/22/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a major cause of death in humans and animals worldwide. While cancer survival rates have increased over recent decades, further research to identify risk factors for the onset and progression of disease, and safe and highly efficacious treatments, is needed. Spontaneous tumours in pets represent an excellent model for neoplastic disease in humans. In this regard, dogs are an interesting species, as the divergence between the dog and human genome is low, humans and dogs have important similarities in the development and functioning of the immune system, and both species often share the same physical environment. There is also a higher homology between the canine and human microbiome than murine model. This review aims to describe and organize recently published information on canine microbiome assemblages and their relationship with the onset and progression of colorectal cancer, breast cancer and lymphoma, and to compare this with human disease. In both species, dysbiosis can induce variations in the gut microbiota that strongly influence shifts in status between health and disease. This can produce an inflammatory state, potentially leading to neoplasia, especially in the intestine, thus supporting canine studies in comparative oncology. Intestinal dysbiosis can also alter the efficacy and side effects of cancer treatments. Fewer published studies are available on changes in the relevant microbiomes in canine lymphoma and mammary cancer, and further research in this area could improve our understanding of the role of microbiota in the development of these cancers.
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Affiliation(s)
- Dell'Anno Filippo
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy; Department of Public Health, Experimental and Forensic Medicine, Section of Biostatistics and Clinical Epidemiology, University of Pavia, Pavia, Italy
| | - Lisa Guardone
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Valeria Listorti
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Razzuoli Elisabetta
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy.
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Kandalgaonkar MR, Kumar V, Vijay‐Kumar M. Digestive dynamics: Unveiling interplay between the gut microbiota and the liver in macronutrient metabolism and hepatic metabolic health. Physiol Rep 2024; 12:e16114. [PMID: 38886098 PMCID: PMC11182692 DOI: 10.14814/phy2.16114] [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: 04/11/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Although the liver is the largest metabolic organ in the body, it is not alone in functionality and is assisted by "an organ inside an organ," the gut microbiota. This review attempts to shed light on the partnership between the liver and the gut microbiota in the metabolism of macronutrients (i.e., proteins, carbohydrates, and lipids). All nutrients absorbed by the small intestines are delivered to the liver for further metabolism. Undigested food that enters the colon is metabolized further by the gut microbiota that produces secondary metabolites, which are absorbed into portal circulation and reach the liver. These microbiota-derived metabolites and co-metabolites include ammonia, hydrogen sulfide, short-chain fatty acids, secondary bile acids, and trimethylamine N-oxide. Further, the liver produces several compounds, such as bile acids that can alter the gut microbial composition, which can in turn influence liver health. This review focuses on the metabolism of these microbiota metabolites and their influence on host physiology. Furthermore, the review briefly delineates the effect of the portosystemic shunt on the gut microbiota-liver axis, and current understanding of the treatments to target the gut microbiota-liver axis.
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Affiliation(s)
- Mrunmayee R. Kandalgaonkar
- Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOhioUSA
| | - Virender Kumar
- College of Pharmacy and Pharmaceutical SciencesUniversity of ToledoToledoOhioUSA
| | - Matam Vijay‐Kumar
- Department of Physiology and PharmacologyUniversity of Toledo College of Medicine and Life SciencesToledoOhioUSA
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Byrne SR, DeMott MS, Yuan Y, Ghanegolmohammadi F, Kaiser S, Fox JG, Alm EJ, Dedon PC. Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596306. [PMID: 38854053 PMCID: PMC11160787 DOI: 10.1101/2024.05.29.596306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically-reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications. Results Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m6dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Firmicutes, Actinobacteria, and Proteobacteria, which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Conclusions The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically-reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.
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Affiliation(s)
- Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yifeng Yuan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Farzan Ghanegolmohammadi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kaiser
- Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Singapore
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Panaitescu PȘ, Răzniceanu V, Mocrei-Rebrean ȘM, Neculicioiu VS, Dragoș HM, Costache C, Filip GA. The Effect of Gut Microbiota-Targeted Interventions on Neuroinflammation and Motor Function in Parkinson's Disease Animal Models-A Systematic Review. Curr Issues Mol Biol 2024; 46:3946-3974. [PMID: 38785512 PMCID: PMC11120577 DOI: 10.3390/cimb46050244] [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: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Gut microbiome-targeted interventions such as fecal transplant, prebiotics, probiotics, synbiotics, and antibiotic gut depletion are speculated to be of potential use in delaying the onset and progression of Parkinson's disease by rebalancing the gut microbiome in the context of the gut-brain axis. Our study aims to organize recent findings regarding these interventions in Parkinson's disease animal models to identify how they affect neuroinflammation and motor outcomes. A systematic literature search was applied in PubMed, Web of Science, Embase, and SCOPUS for gut microbiome-targeted non-dietary interventions. Studies that investigated gut-targeted interventions by using in vivo murine PD models to follow dopaminergic cell loss, motor tests, and neuroinflammatory markers as outcomes were considered to be eligible. A total of 1335 studies were identified in the databases, out of which 29 were found to be eligible. A narrative systematization of the resulting data was performed, and the effect direction for the outcomes was represented. Quality assessment using the SYRCLE risk of bias tool was also performed. Out of the 29 eligible studies, we found that a significant majority report that the intervention reduced the dopaminergic cell loss (82.76%, 95% CI [64.23%, 94.15%]) produced by the induction of the disease model. Also, most studies reported a reduction in microglial (87.5%, 95% CI [61.65%, 98.45%]) and astrocytic activation (84,62%, 95% CI [54.55%, 98.08%]) caused by the induction of the disease model. These results were also mirrored in the majority (96.4% 95% CI [81.65%, 99.91%]) of the studies reporting an increase in performance in behavioral motor tests. A significant limitation of the study was that insufficient information was found in the studies to assess specific causes of the risk of bias. These results show that non-dietary gut microbiome-targeted interventions can improve neuroinflammatory and motor outcomes in acute Parkinson's disease animal models. Further studies are needed to clarify if these benefits transfer to the long-term pathogenesis of the disease, which is not yet fully understood. The study had no funding source, and the protocol was registered in the PROSPERO database with the ID number CRD42023461495.
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Affiliation(s)
- Paul-Ștefan Panaitescu
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (P.-Ș.P.); (Ș.-M.M.-R.)
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.S.N.)
| | - Vlad Răzniceanu
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (P.-Ș.P.); (Ș.-M.M.-R.)
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.S.N.)
| | - Ștefania-Maria Mocrei-Rebrean
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (P.-Ș.P.); (Ș.-M.M.-R.)
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.S.N.)
| | - Vlad Sever Neculicioiu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.S.N.)
| | - Hanna-Maria Dragoș
- Department of Neurology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Carmen Costache
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (V.S.N.)
| | - Gabriela Adriana Filip
- Department of Physiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (P.-Ș.P.); (Ș.-M.M.-R.)
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Bedu-Ferrari C, Biscarrat P, Pepke F, Vati S, Chaudemanche C, Castelli F, Chollet C, Rué O, Hennequet-Antier C, Langella P, Cherbuy C. In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential. mSystems 2024; 9:e0140123. [PMID: 38441031 PMCID: PMC11019791 DOI: 10.1128/msystems.01401-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
The microbial utilization of dietary carbohydrates is closely linked to the pivotal role of the gut microbiome in human health. Inherent to the modulation of complex microbial communities, a prebiotic implies the selective utilization of a specific substrate, relying on the metabolic capacities of targeted microbes. In this study, we investigated the metabolic capacities of 17 commensal bacteria of the human gut microbiome toward dietary carbohydrates with prebiotic potential. First, in vitro experiments allowed the classification of bacterial growth and fermentation profiles in response to various carbon sources, including agave inulin, corn fiber, polydextrose, and citrus pectin. The influence of phylogenetic affiliation appeared to statistically outweigh carbon sources in determining the degree of carbohydrate utilization. Second, we narrowed our focus on six commensal bacteria representative of the Bacteroidetes and Firmicutes phyla to perform an untargeted high-resolution liquid chromatography-mass spectrometry metabolomic analysis: Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Subdoligranulum variabile, Roseburia intestinalis, and Eubacterium rectale exhibited distinct metabolomic profiles in response to different carbon sources. The relative abundance of bacterial metabolites was significantly influenced by dietary carbohydrates, with these effects being strain-specific and/or carbohydrate-specific. Particularly, the findings indicated an elevation in short-chain fatty acids and other metabolites, including succinate, gamma-aminobutyric acid, and nicotinic acid. These metabolites were associated with putative health benefits. Finally, an RNA-Seq transcriptomic approach provided deeper insights into the underlying mechanisms of carbohydrate metabolization. Restricting our focus on four commensal bacteria, including B. xylanisolvens, B. thetaiotaomicron, S. variabile, and R. intestinalis, carbon sources did significantly modulate the level of bacterial genes related to the enzymatic machinery involved in the metabolization of dietary carbohydrates. This study provides a holistic view of the molecular strategies induced during the dynamic interplay between dietary carbohydrates with prebiotic potential and gut commensal bacteria. IMPORTANCE This study explores at a molecular level the interactions between commensal health-relevant bacteria and dietary carbohydrates holding prebiotic potential. We showed that prebiotic breakdown involves the specific activation of gene expression related to carbohydrate metabolism. We also identified metabolites produced by each bacteria that are potentially related to our digestive health. The characterization of the functional activities of health-relevant bacteria toward prebiotic substances can yield a better application of prebiotics in clinical interventions and personalized nutrition. Overall, this study highlights the importance of identifying the impact of prebiotics at a low resolution of the gut microbiota to characterize the activities of targeted bacteria that can play a crucial role in our health.
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Affiliation(s)
- Cassandre Bedu-Ferrari
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- General Mills France, Boulogne Billancourt, France
| | - Paul Biscarrat
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Frederic Pepke
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sarah Vati
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Florence Castelli
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Céline Chollet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Christelle Hennequet-Antier
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Straub TJ, Lombardo MJ, Bryant JA, Diao L, Lodise TP, Freedberg DE, Wortman JR, Litcofsky KD, Hasson BR, McGovern BH, Ford CB, Henn MR. Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection. Clin Infect Dis 2024; 78:833-841. [PMID: 37823484 PMCID: PMC11006105 DOI: 10.1093/cid/ciad636] [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] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores [VOS], formerly SER-109]; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI). METHODS Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment. RESULTS Baseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non-spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated. CONCLUSIONS This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.
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Affiliation(s)
| | | | | | - Liyang Diao
- Seres Therapeutics, Cambridge, Massachusetts, USA
| | - Thomas P Lodise
- Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center–New York Presbyterian Hospital, New York, New York, USA
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Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol 2024; 15:1351678. [PMID: 38638909 PMCID: PMC11024261 DOI: 10.3389/fmicb.2024.1351678] [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: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/20/2024] Open
Abstract
Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.
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Affiliation(s)
- Brook E. Santangelo
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Madison Apgar
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Casey G. Martin
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - John Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, CO, United States
| | - Elena Wall
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcin P. Joachimiak
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Biosystems Data Science Department, Berkeley, CA, United States
| | - Lawrence E. Hunter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
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Nikoloudaki O, Pinto D, Acin Albiac M, Celano G, Da Ros A, De Angelis M, Rinaldi F, Gobbetti M, Di Cagno R. Exploring the Gut Microbiome and Metabolome in Individuals with Alopecia Areata Disease. Nutrients 2024; 16:858. [PMID: 38542770 PMCID: PMC10975414 DOI: 10.3390/nu16060858] [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: 01/30/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 11/12/2024] Open
Abstract
In recent years, heightened attention has been devoted to unravelling the intricate interplay between genetic and environmental factors shaping the gut microbiota and its significance for human health. This study delves into exploring the plausible connection between Alopecia Areata (AA), an autoimmune disease, and the dynamics of the gut microbiome. Examining a cohort of healthy adults and individuals with AA, both the gut microbiota composition and volatile organic compound (VOC) metabolites from faeces and urine were analysed. While overall microbiota composition showed no significant differences, intra-individual variability revealed distinctions related to age, gender, and pathology status, with AA individuals exhibiting reduced species richness and evenness. Differential abundance analysis identified microbial biomarkers for AA, notably Firmicutes, Lachnospirales, and Blautia, while Coprococcus stood out for healthy individuals. The Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) method further supported these findings including metabolite biomarkers, such as esters of branched chain fatty acids and branched chain amino acids as predictors for AA, suggesting potential links to oxidative stress. Despite certain limitations, the study highlights the complexity of the gut microbiome and its metabolites in the context of AA, while the biomarkers identified could be useful starting points for upcoming studies.
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Affiliation(s)
- Olga Nikoloudaki
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy (M.G.); (R.D.C.)
| | - Daniela Pinto
- Human Microbiome Advanced Project (HMAP), Giuliani S.p.A, 20129 Milan, Italy; (D.P.); (F.R.)
| | - Marta Acin Albiac
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy (M.G.); (R.D.C.)
| | - Giuseppe Celano
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70121 Bari, Italy; (G.C.); (M.D.A.)
| | - Alessio Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy (M.G.); (R.D.C.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70121 Bari, Italy; (G.C.); (M.D.A.)
| | - Fabio Rinaldi
- Human Microbiome Advanced Project (HMAP), Giuliani S.p.A, 20129 Milan, Italy; (D.P.); (F.R.)
| | - Marco Gobbetti
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy (M.G.); (R.D.C.)
| | - Raffaella Di Cagno
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy (M.G.); (R.D.C.)
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Langford L, Shah DD. Bioinformatic Analysis of Sulfotransferases from an Unexplored Gut Microbe, Sutterella wadsworthensis 3_1_45B: Possible Roles towards Detoxification via Sulfonation by Members of the Human Gut Microbiome. Int J Mol Sci 2024; 25:2983. [PMID: 38474230 DOI: 10.3390/ijms25052983] [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: 01/19/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Sulfonation, primarily facilitated by sulfotransferases, plays a crucial role in the detoxification pathways of endogenous substances and xenobiotics, promoting metabolism and elimination. Traditionally, this bioconversion has been attributed to a family of human cytosolic sulfotransferases (hSULTs) known for their high sequence similarity and dependence on 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfo donor. However, recent studies have revealed the presence of PAPS-dependent sulfotransferases within gut commensals, indicating that the gut microbiome may harbor a diverse array of sulfotransferase enzymes and contribute to detoxification processes via sulfation. In this study, we investigated the prevalence of sulfotransferases in members of the human gut microbiome. Interestingly, we stumbled upon PAPS-independent sulfotransferases, known as aryl-sulfate sulfotransferases (ASSTs). Our bioinformatics analyses revealed that members of the gut microbial genus Sutterella harbor multiple asst genes, possibly encoding multiple ASST enzymes within its members. Fluctuations in the microbes of the genus Sutterella have been associated with various health conditions. For this reason, we characterized 17 different ASSTs from Sutterella wadsworthensis 3_1_45B. Our findings reveal that SwASSTs share similarities with E. coli ASST but also exhibit significant structural variations and sequence diversity. These differences might drive potential functional diversification and likely reflect an evolutionary divergence from their PAPS-dependent counterparts.
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Affiliation(s)
- Lauryn Langford
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281, USA
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
| | - Dhara D Shah
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85281, USA
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
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Liu X, Yu J, Huan Z, Xu M, Song T, Yang R, Zhu W, Jiang J. Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors. BMC Genomics 2024; 25:148. [PMID: 38321370 PMCID: PMC10848473 DOI: 10.1186/s12864-024-10041-7] [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: 08/31/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.
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Affiliation(s)
- Xuanzhen Liu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Jianqiu Yu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Zongjin Huan
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Mei Xu
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ting Song
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Ruilin Yang
- Chengdu Zoo & Chengdu Research Institute of Wildlife, 610081, Chengdu, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
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Verma B, Parkinson J. HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads. BIOINFORMATICS ADVANCES 2024; 4:vbae016. [PMID: 38371920 PMCID: PMC10873905 DOI: 10.1093/bioadv/vbae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024]
Abstract
Motivation Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining the functional roles of microbial communities. A key challenge in analyzing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxa of origin. While still performing worse relative to reference-based short-read tools in species classification, ML algorithms have shown promising results in taxonomic classification at higher ranks. A recent approach exploited to enhance the performance of ML tools, which can be translated to reference-dependent classifiers, has been to integrate the hierarchical structure of taxonomy within the tool's predictive algorithm. Results Here, we introduce HiTaxon, an end-to-end hierarchical ensemble framework for taxonomic classification. HiTaxon facilitates data collection and processing, reference database construction and optional training of ML models to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. In addition, through exploring hierarchical methods for HiTaxon, we highlight that our custom approach to hierarchical ensembling improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensembles over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally derived reads. Availability and implementation HiTaxon is available at: https://github.com/ParkinsonLab/HiTaxon.
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Affiliation(s)
- Bhavish Verma
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front Mol Biosci 2024; 10:1337373. [PMID: 38313584 PMCID: PMC10834744 DOI: 10.3389/fmolb.2023.1337373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024] Open
Abstract
The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.
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Affiliation(s)
- Jingyue Wu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Stephanie S. Singleton
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Urnisha Bhuiyan
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lori Krammer
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC, United States
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Kandari A, Odat MA, Alzaid F, Scott KP. Biotics and bacterial function: impact on gut and host health. THE ISME JOURNAL 2024; 18:wrae226. [PMID: 39499657 PMCID: PMC11631128 DOI: 10.1093/ismejo/wrae226] [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: 08/22/2024] [Revised: 10/08/2024] [Accepted: 11/04/2024] [Indexed: 11/07/2024]
Abstract
The human gut microbiota, the vast community of microbes inhabiting the gastrointestinal tract, plays a pivotal role in maintaining health. Bacteria are the most abundant organism, and the composition of bacterial communities is strongly influenced by diet. Gut bacteria can degrade complex dietary carbohydrates to produce bioactive compounds such as short-chain fatty acids. Such products influence health, by acting on systemic metabolism, or by virtue of anti-inflammatory or anti-carcinogenic properties. The composition of gut bacteria can be altered through overgrowth of enteropathogens (e.g. Campylobacter, Salmonella spp.), leading to dysbiosis of the gut ecosystem, with some species thriving under the altered conditions whereas others decline. Various "biotics" strategies, including prebiotics, probiotics, synbiotics, and postbiotics, contribute to re-establishing balance within the gut microbial ecosystem conferring health benefits. Prebiotics enhance growth of beneficial members of the resident microbial community and can thus prevent pathogen growth by competitive exclusion. Specific probiotics can actively inhibit the growth of pathogens, either through the production of bacteriocins or simply by reducing the gastrointestinal pH making conditions less favorable for pathogen growth. This review discusses the importance of a balanced gut ecosystem, and strategies to maintain it that contribute to human health.
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Affiliation(s)
- Anwar Kandari
- Dasman Diabetes Institute, Al-Soor Street, Dasman, 15462, Kuwait
- Ministry of Health, Sulaibkhat, Jamal Abdel Nasser Street, PO Box 5, 13001, Kuwait
| | - Ma’en Al Odat
- Medical Laboratory Science, Mutah University, Mutah, Karak 61710, Jordan
| | - Fawaz Alzaid
- Dasman Diabetes Institute, Al-Soor Street, Dasman, 15462, Kuwait
- INSERM UMR-S1151, CNRS UMR-S8253, Université Paris Cité, Institut Necker Enfants Malades, Paris, France
| | - Karen P Scott
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen AB25 2ZD, UK
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Wheeler R, Gomperts Boneca I. The hidden base of the iceberg: gut peptidoglycome dynamics is foundational to its influence on the host. Gut Microbes 2024; 16:2395099. [PMID: 39239828 PMCID: PMC11382707 DOI: 10.1080/19490976.2024.2395099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/01/2024] [Accepted: 08/16/2024] [Indexed: 09/07/2024] Open
Abstract
The intestinal microbiota of humans includes a highly diverse range of bacterial species. All these bacteria possess a cell wall, composed primarily of the macromolecule peptidoglycan. As such, the gut also harbors an abundant and varied peptidoglycome. A remarkable range of host physiological pathways are regulated by peptidoglycan fragments that originate from the gut microbiota and enter the host system. Interactions between the host system and peptidoglycan can influence physiological development and homeostasis, promote health, or contribute to inflammatory disease. Underlying these effects is the interplay between microbiota composition and enzymatic processes that shape the intestinal peptidoglycome, dictating the types of peptidoglycan generated, that subsequently cross the gut barrier. In this review, we highlight and discuss the hidden and emerging functional aspects of the microbiome, i.e. the hidden base of the iceberg, that modulate the composition of gut peptidoglycan, and how these fundamental processes are drivers of physiological outcomes for the host.
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Affiliation(s)
- Richard Wheeler
- Institut Pasteur, Université Paris Cité, Paris, France
- Hauts-de-Seine, Arthritis Research and Development, Neuilly-sur-Seine, France
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Singhal S, Rani V. Therapeutic Potential of Syzygium aromaticum in Gut Dysbiosis via TMAO Associated Diabetic Cardiomyopathy. Cardiovasc Hematol Agents Med Chem 2024; 22:441-455. [PMID: 37608671 DOI: 10.2174/1871525721666230822100142] [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: 04/07/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Dysbiosis of the gastrointestinal microbiota is not only related to the pathogenesis of intestinal disorders but also associated with extra-intestinal diseases. Various studies have revealed the role of an imbalance of intestinal microbiota and their metabolites including bile acids, indole derivatives, polyamines, and trimethylamine in the progression of various diseases. The elevated plasma level of the oxidized form of trimethylamine is associated with the increased risk of cardiovascular diseases. Literature supports that herbal medicines can modulate human health by altering the diversity of gut microbiota and their metabolites and proposes the use of prebiotics to improve dysbiotic conditions as a new way of therapeutic strategy. METHODS In silico studies including drug likeliness, toxicity prediction, and molecular interaction of phytochemicals against trimethylamine lyase enzyme have been done. Antimicrobial activity of extracts of selected plant i.e. Syzygium aromaticum was done by disc diffusion and the protective effects of plant compounds were examined on trimethylamine-n-oxide a bacterial metabolic product and high glucose induced toxicity. RESULTS The current study has found that the phytochemicals of S. aromaticum identified as nontoxic and followed the standard rules of drug likeliness and showed a significant binding affinity against trimethylamine-n-oxide producing enzymes. Furthermore, S. aromaticum extract was found to have antimicrobial potential and cardioprotective effects by reducing the production of intracellular reactive oxygen species and correcting the distorted nuclear morphology in the presence of high trimethylamine-n-oxide. CONCLUSION Conclusively, our study explored the herbal intervention in intestinal dysbiosis and suggested a natural therapy against dysbiosis associated with cardiac disease, and S, aromaticum was found to have exceptional cardioprotective potential against TMAO induced gut dysbiosis, which provides a novel future therapeutic intervention for treating cardiovascular complications.
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Affiliation(s)
- Shivani Singhal
- Department of Biotechnology, Center for Emerging Diseases, Jaypee Institute of Information Technology, A-10, Sector- 62, Noida, 201307, Uttar Pradesh, India
| | - Vibha Rani
- Department of Biotechnology, Center for Emerging Diseases, Jaypee Institute of Information Technology, A-10, Sector- 62, Noida, 201307, Uttar Pradesh, India
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Tikunov AY, Fedorets VA, Shrainer EV, Morozov VV, Bystrova VI, Tikunova NV. Intestinal Microbiome Changes and Clinical Outcomes of Patients with Ulcerative Colitis after Fecal Microbiota Transplantation. J Clin Med 2023; 12:7702. [PMID: 38137770 PMCID: PMC10743744 DOI: 10.3390/jcm12247702] [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: 11/09/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND AND AIMS Ulcerative colitis (UC) is a chronic inflammatory disease that affects many people. One of the possible ways to treat UC is fecal microbiota transplantation (FMT). In this study, changes in the intestinal microbiome and clinical outcomes of 20 patients with UC after FMT were estimated. METHODS FMT enemas were administrated ten times, once a day, and fecal microbiota from three donors was used for each enema. The clinical outcomes were assessed after eight weeks and then via a patient survey. The 16S rRNA profiles of the gut microbiota were compared between three samplings: samples from 20 patients with UC before and after FMT and samples from 18 healthy volunteers. RESULTS Clinical remission was achieved in 19 (95%) patients at week 8. Adverse events occurred in five patients, including one non-responder. A significant increase in average biodiversity was shown in samples after FMT compared to samples before FMT, as well as a decrease in the proportion of some potentially pathogenic bacteria. CONCLUSION The efficacy of FMT for UC treatment was confirmed; however, the duration of remission varied substantially, possibly due to different characteristics of the initial microbiota of patients. Targeted analysis of a patient's microbiome before FMT could increase the treatment efficacy.
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Affiliation(s)
- Artem Y. Tikunov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria A. Fedorets
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Evgenia V. Shrainer
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Vitaliy V. Morozov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria I. Bystrova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Nina V. Tikunova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
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Chattopadhyay A, Lee CY, Lee YC, Liu CL, Chen HK, Li YH, Lai LC, Tsai MH, Ni YH, Chiu HM, Lu TP, Chuang EY. Twnbiome: a public database of the healthy Taiwanese gut microbiome. BMC Bioinformatics 2023; 24:474. [PMID: 38097965 PMCID: PMC10722848 DOI: 10.1186/s12859-023-05585-6] [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: 05/31/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
With new advances in next generation sequencing (NGS) technology at reduced costs, research on bacterial genomes in the environment has become affordable. Compared to traditional methods, NGS provides high-throughput sequencing reads and the ability to identify many species in the microbiome that were previously unknown. Numerous bioinformatics tools and algorithms have been developed to conduct such analyses. However, in order to obtain biologically meaningful results, the researcher must select the proper tools and combine them to construct an efficient pipeline. This complex procedure may include tens of tools, each of which require correct parameter settings. Furthermore, an NGS data analysis involves multiple series of command-line tools and requires extensive computational resources, which imposes a high barrier for biologists and clinicians to conduct NGS analysis and even interpret their own data. Therefore, we established a public gut microbiome database, which we call Twnbiome, created using healthy subjects from Taiwan, with the goal of enabling microbiota research for the Taiwanese population. Twnbiome provides users with a baseline gut microbiome panel from a healthy Taiwanese cohort, which can be utilized as a reference for conducting case-control studies for a variety of diseases. It is an interactive, informative, and user-friendly database. Twnbiome additionally offers an analysis pipeline, where users can upload their data and download analyzed results. Twnbiome offers an online database which non-bioinformatics users such as clinicians and doctors can not only utilize to access a control set of data, but also analyze raw data with a few easy clicks. All results are customizable with ready-made plots and easily downloadable tables. Database URL: http://twnbiome.cgm.ntu.edu.tw/ .
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Affiliation(s)
- Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yueh Lee
- Department of Biomedical Engineering, China Medical University, Taichung, Taiwan
| | - Ya-Chin Lee
- Department of Public Health, Institute of Health Data Analytics and Statistics, National Taiwan University, Taipei, Taiwan
| | - Chiang-Lin Liu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Hsin-Kuang Chen
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yung-Hua Li
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yen-Hsuan Ni
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Han-Mo Chiu
- College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Public Health, Institute of Health Data Analytics and Statistics, National Taiwan University, Taipei, Taiwan.
- Institute of Health Data Analytics and Statistics, National Taiwan University, Taipei, Taiwan.
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan.
- Division Research and Development Center for Medical Devices, National Taiwan University, Taipei, Taiwan.
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Popov IV, Popov IV, Krikunova AA, Lipilkina TA, Derezina TN, Chikindas ML, Venema K, Ermakov AM. Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison. Int J Mol Sci 2023; 24:17301. [PMID: 38139130 PMCID: PMC10744024 DOI: 10.3390/ijms242417301] [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: 10/28/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.
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Affiliation(s)
- Igor V. Popov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Federal Territory Sirius, Russia
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University Campus Venlo, 5928 SZ Venlo, The Netherlands;
| | - Ilia V. Popov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Anastasya A. Krikunova
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Tatyana A. Lipilkina
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Tatyana N. Derezina
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Michael L. Chikindas
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08901, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University Campus Venlo, 5928 SZ Venlo, The Netherlands;
| | - Alexey M. Ermakov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
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Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569645. [PMID: 38106100 PMCID: PMC10723325 DOI: 10.1101/2023.12.01.569645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Knowledge graphs have found broad biomedical applications, providing useful representations of complex knowledge. Although plentiful evidence exists linking the gut microbiome to disease, mechanistic understanding of those relationships remains generally elusive. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. To do so, we constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink. Using a semantically constrained shortest path search through the graph and a novel path prioritization methodology based on cosine similarity, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.
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