Targeting the Microbiome for Disease Diagnosis and Therapy: New Frontiers for Personalized Medicine

A special issue of Journal of Personalized Medicine (ISSN 2075-4426). This special issue belongs to the section "Mechanisms of Diseases".

Deadline for manuscript submissions: closed (10 September 2021) | Viewed by 58080

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Special Issue Editor

Division of Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
Interests: inflammatory bowel disease; irritable bowel syndrome; microbiome and probiotics

Special Issue Information

Dear Colleagues,

Background: The gut microbiota is emerging as a pivotal player in the pathogenesis of many non-communicable diseases. Thus, it has been proposed as a new diagnostic and therapeutic target.
Aim and scope: This Special Issue will focus on the microbiome as a potential target of new personalized therapies or diagnostic tools.
History: In the last decades, the gut microbiome has been deeply investigated, and many studies have provided new information on the role of dysbiosis in many gastrointestinal and extra-gastrointestinal diseases. Recently, in addition to its phylogenetic characterization, new information has become available regarding the function of the gut microbiota, thanks to proteomic and metabolomic analyses.
Cutting-edge researches: The therapeutic modulation of the gut microbiota based on different strategies, including diet modification, antibiotics, prebiotics, probiotics, and, last but not least, fecal microbiota transplantation, has been tested for the treatment of various diseases. Recently, the possible applications and modalities of gut microbiota modulation have been increasingly expanding.
We are looking for original clinical or pre-clinical research papers and reviews focusing on the use of the microbiome for disease diagnosis, monitoring, or therapy and suggesting new possible gut microbiota-based approaches for personalized care.

Dr. Lucrezia Laterza
Guest Editor

Manuscript Submission Information

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Keywords

  • gut microbiome
  • probiotics
  • prebiotics
  • diet
  • fecal microbiota transplantation
  • metabolomics
  • proteomics

Published Papers (18 papers)

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Editorial

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4 pages, 201 KiB  
Editorial
The Microbiome Revolution: New Insights for Personalized Medicine
by Lucrezia Laterza and Irene Mignini
J. Pers. Med. 2022, 12(9), 1520; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12091520 - 16 Sep 2022
Cited by 2 | Viewed by 1360
Abstract
The availability of new culture-independent techniques to study microbes led to the explosion of the gut microbiota revolution in recent decades [...] Full article

Research

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17 pages, 1787 KiB  
Article
Intestinal Permeability and Dysbiosis in Female Patients with Recurrent Cystitis: A Pilot Study
by Cristina Graziani, Lucrezia Laterza, Claudia Talocco, Marco Pizzoferrato, Nicoletta Di Simone, Silvia D’Ippolito, Caterina Ricci, Jacopo Gervasoni, Silvia Persichilli, Federica Del Chierico, Valeria Marzano, Stefano Levi Mortera, Aniello Primiano, Andrea Poscia, Francesca Romana Ponziani, Lorenza Putignani, Andrea Urbani, Valentina Petito, Federica Di Vincenzo, Letizia Masi, Loris Riccardo Lopetuso, Giovanni Cammarota, Daniela Romualdi, Antonio Lanzone, Antonio Gasbarrini and Franco Scaldaferriadd Show full author list remove Hide full author list
J. Pers. Med. 2022, 12(6), 1005; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12061005 - 20 Jun 2022
Cited by 3 | Viewed by 2706
Abstract
Recurrent cystitis (RC) is a common disease, especially in females. Anatomical, behavioral and genetic predisposing factors are associated with the ascending retrograde route, which often causes bladder infections. RC seems to be mainly caused by agents derived from the intestinal microbiota, and most [...] Read more.
Recurrent cystitis (RC) is a common disease, especially in females. Anatomical, behavioral and genetic predisposing factors are associated with the ascending retrograde route, which often causes bladder infections. RC seems to be mainly caused by agents derived from the intestinal microbiota, and most frequently by Escherichia coli. Intestinal contiguity contributes to the etiopathogenesis of RC and an alteration in intestinal permeability could have a major role in RC. The aim of this pilot study is to assess gut microbiome dysbiosis and intestinal permeability in female patients with RC. Patients with RC (n = 16) were enrolled and compared with healthy female subjects (n = 15) and patients with chronic gastrointestinal (GI) disorders (n = 238). We calculated the Acute Cystitis Symptom Score/Urinary Tract Infection Symptom Assessment (ACSS/UTISA) and Gastrointestinal Symptom Rating Scale (GSRS) scores and evaluated intestinal permeability and the fecal microbiome in the first two cohorts. Patients with RC showed an increased prevalence of gastrointestinal symptoms compared with healthy controls. Of the patients with RC, 88% showed an increased intestinal permeability with reduced biodiversity of gut microbiota compared to healthy controls, and 68% of the RC patients had a final diagnosis of gastrointestinal disease. Similarly, GI patients reported a higher incidence of urinary symptoms with a diagnosis of RC in 20%. Gut barrier impairment seems to play a major role in the pathogenesis of RC. Further studies are necessary to elucidate the role of microbiota and intestinal permeability in urinary tract infections. Full article
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18 pages, 4716 KiB  
Article
Gut Microbiota as Early Predictor of Infectious Complications before Cardiac Surgery: A Prospective Pilot Study
by Ekaterina Chernevskaya, Evgenii Zuev, Vera Odintsova, Anastasiia Meglei and Natalia Beloborodova
J. Pers. Med. 2021, 11(11), 1113; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11111113 - 29 Oct 2021
Cited by 4 | Viewed by 2354
Abstract
Cardiac surgery remains a field of medicine with a high percentage of postoperative complications, including infectious ones. Modern data indicate a close relationship of infectious disorders with pathological changes in the composition of the gut microbiome; however, the extent of such changes in [...] Read more.
Cardiac surgery remains a field of medicine with a high percentage of postoperative complications, including infectious ones. Modern data indicate a close relationship of infectious disorders with pathological changes in the composition of the gut microbiome; however, the extent of such changes in cardiac surgery patients is not fully clarified. In this prospective, observational, single center, pilot study, 72 patients were included, 12 among them with the infectious complications. We analyzed the features of the fecal microbiota before and in the early postoperative period, as one of the markers for predicting the occurrence of bacterial infection. We also discovered the significant change in microbial composition in the group of patients with infectious complications compared to the non-infectious group before and after cardiac surgery, despite the intra-individual variation in composition of gut microbiome. Our study demonstrated that the group of patients that had a bacterial infection in the early postoperative period already had an altered microbial composition even before the surgery. Further studies will evaluate the clinical significance of the identified proportions of individual taxa of the intestinal microbiota and consider the microbiota as a novel target for reducing the risk of infectious complications. Full article
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13 pages, 2719 KiB  
Article
Sphingomonas and Phenylobacterium as Major Microbiota in Thymic Epithelial Tumors
by Rumi Higuchi, Taichiro Goto, Yosuke Hirotsu, Sotaro Otake, Toshio Oyama, Kenji Amemiya, Hiroshi Ohyama, Hitoshi Mochizuki and Masao Omata
J. Pers. Med. 2021, 11(11), 1092; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11111092 - 26 Oct 2021
Cited by 14 | Viewed by 1979
Abstract
The microbiota has been reported to be closely associated with carcinogenesis and cancer progression. However, its involvement in the pathology of thymoma remains unknown. In this study, we aimed to identify thymoma-specific microbiota using resected thymoma samples. Nineteen thymoma tissue samples were analyzed [...] Read more.
The microbiota has been reported to be closely associated with carcinogenesis and cancer progression. However, its involvement in the pathology of thymoma remains unknown. In this study, we aimed to identify thymoma-specific microbiota using resected thymoma samples. Nineteen thymoma tissue samples were analyzed through polymerase chain reaction amplification and 16S rRNA gene sequencing. The subjects were grouped according to histology, driver mutation status in the GTF2I gene, PD-L1 status, and smoking habits. To identify the taxa composition of each sample, the operational taxonomic units (OTUs) were classified on the effective tags with 97% identity. The Shannon Index of the 97% identity OTUs was calculated to evaluate the alpha diversity. The linear discriminant analysis effect size (LEfSe) method was used to compare the relative abundances of all the bacterial taxa. We identified 107 OTUs in the tumor tissues, which were classified into 26 genera. Sphingomonas and Phenylobacterium were identified as abundant genera in almost all the samples. No significant difference was determined in the alpha diversity within these groups; however, type A thymoma tended to exhibit a higher bacterial diversity than type B thymoma. Through the LEfSe analysis, we identified the following differentially abundant taxa: Bacilli, Firmicutes, and Lactobacillales in type A thymoma; Proteobacteria in type B thymoma; Gammaproteobacteria in tumors harboring the GTF2I mutation; and Alphaproteobacteria in tumors without the GTF2I mutation. In conclusion, Sphingomonas and Phenylobacterium were identified as dominant genera in thymic epithelial tumors. These genera appear to comprise the thymoma-specific microbiota. Full article
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8 pages, 2023 KiB  
Article
Lipid and Energy Metabolism of the Gut Microbiota Is Associated with the Response to Probiotic Bifidobacterium breve Strain for Anxiety and Depressive Symptoms in Schizophrenia
by Ryodai Yamamura, Ryo Okubo, Noriko Katsumata, Toshitaka Odamaki, Naoki Hashimoto, Ichiro Kusumi, Jinzhong Xiao and Yutaka J. Matsuoka
J. Pers. Med. 2021, 11(10), 987; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11100987 - 30 Sep 2021
Cited by 18 | Viewed by 2868
Abstract
A recent meta-analysis found that probiotics have moderate-to-large beneficial effects on depressive symptoms in patients with psychiatric disorders. However, it remains unclear how the baseline gut microbiota before probiotic administration influences the host’s response to probiotics. Therefore, we aimed to determine whether the [...] Read more.
A recent meta-analysis found that probiotics have moderate-to-large beneficial effects on depressive symptoms in patients with psychiatric disorders. However, it remains unclear how the baseline gut microbiota before probiotic administration influences the host’s response to probiotics. Therefore, we aimed to determine whether the predicted functional profile of the gut microbiota influences the effectiveness of probiotic treatment in patients with schizophrenia. A total of 29 patients with schizophrenia consumed Bifidobacterium breve A-1 (synonym B. breve MCC1274) for 4 weeks. We considered patients who showed a 25% or more reduction in the Hospital Anxiety and Depression Scale total score at 4 weeks from baseline to be “responders” and those who did not to be “non-responders”. We predicted the gut microbial functional genes based on 16S rRNA gene sequences and applied the linear discriminant analysis effect size method to determine the gut microbial functional genes most likely to explain the differences between responders and non-responders at baseline. The results showed that lipid and energy metabolism was elevated at baseline in responders (n = 12) compared to non-responders (n = 17). These findings highlight the importance of assessing the gut microbial functional genes at baseline before probiotic therapy initiation in patients with psychiatric disorders. Full article
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15 pages, 1614 KiB  
Article
Different Associations between Tonsil Microbiome, Chronic Tonsillitis, and Intermittent Hypoxemia among Obstructive Sleep Apnea Children of Different Weight Status: A Pilot Case-Control Study
by Hai-Hua Chuang, Jen-Fu Hsu, Li-Pang Chuang, Cheng-Hsun Chiu, Yen-Lin Huang, Hsueh-Yu Li, Ning-Hung Chen, Yu-Shu Huang, Chun-Wei Chuang, Chung-Guei Huang, Hsin-Chih Lai and Li-Ang Lee
J. Pers. Med. 2021, 11(6), 486; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11060486 - 28 May 2021
Cited by 8 | Viewed by 2743
Abstract
The tonsil microbiome is associated with chronic tonsillitis and obstructive sleep apnea (OSA) in children, and the gut microbiome is associated with host weight status. In this study, we hypothesized that weight status may be associated with clinical profiles and the tonsil microbiome [...] Read more.
The tonsil microbiome is associated with chronic tonsillitis and obstructive sleep apnea (OSA) in children, and the gut microbiome is associated with host weight status. In this study, we hypothesized that weight status may be associated with clinical profiles and the tonsil microbiome in children with OSA. We prospectively enrolled 33 non-healthy-weight (cases) and 33 healthy-weight (controls) pediatric OSA patients matched by the proportion of chronic tonsillitis. Differences in the tonsil microbiome between the non-healthy-weight and healthy-weight subgroups and relationships between the tonsil microbiome and clinical variables were investigated. Non-healthy weight was associated with significant intermittent hypoxemia (oxygen desaturation index, mean blood saturation (SpO2), and minimal SpO2) and higher systolic blood pressure percentile, but was not related to the tonsil microbiome. However, chronic tonsillitis was related to Acidobacteria in the non-healthy-weight subgroup, and oxygen desaturation index was associated with Bacteroidetes in the healthy-weight subgroup. In post hoc analysis, the children with mean SpO2 ≤ 97% had reduced α and β diversities and a higher abundance of Bacteroidetes than those with mean SpO2 > 97%. These preliminary findings are novel and provide insights into future research to understand the pathogenesis of the disease and develop personalized treatments for pediatric OSA. Full article
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8 pages, 1520 KiB  
Article
Rifaximin as a Potential Treatment for IgA Nephropathy in a Humanized Mice Model
by Vincenzo Di Leo, Patrick J. Gleeson, Fabio Sallustio, Carine Bounaix, Jennifer Da Silva, Gesualdo Loreto, Sanae Ben Mkaddem and Renato C. Monteiro
J. Pers. Med. 2021, 11(4), 309; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11040309 - 16 Apr 2021
Cited by 15 | Viewed by 3351
Abstract
IgA Nephropathy (IgAN) is the most common glomerulonephritis worldwide, characterized by the mesangial deposition of abnormally glycosylated IgA1 (Gd-IgA). The production of Gd-IgA occurs in mucose-associated lymphoid tissue (MALT). The microbiota plays a role in MALT modulation. Rifaximin (NORMIX®), a non-absorbable [...] Read more.
IgA Nephropathy (IgAN) is the most common glomerulonephritis worldwide, characterized by the mesangial deposition of abnormally glycosylated IgA1 (Gd-IgA). The production of Gd-IgA occurs in mucose-associated lymphoid tissue (MALT). The microbiota plays a role in MALT modulation. Rifaximin (NORMIX®), a non-absorbable oral antibiotic, induces positive modulation of the gut microbiota, favoring the growth of bacteria beneficial to the host. Here, we evaluate the effect of rifaximin on a humanized mice model of IgAN (α1KI-CD89Tg). Methods: The α1KI-CD89Tg mice were treated by the vehicle (olive oil) or rifaximin (NORMIX®). Serum levels of hIgA, hIgA1–sCD89, and mIgG–hIgA1 immune complexes were determined. Glomerular hIgA1 deposit and CD11b+ cells recruitment were revealed using confocal microscopy. Furthermore, the mRNA of the B-Cell Activating Factor (BAFF), polymeric immunoglobulin receptor (pIgR), and Tumor Necrosing Factor-α (TNF-α) in gut samples were detected by qPCR. Results: Rifaximin treatment decreased the urinary protein-to-creatinine ratio, serum levels of hIgA1–sCD89 and mIgG–hIgA1 complexes, hIgA1 glomerular deposition, and CD11b+ cell infiltration. Moreover, rifaximin treatment decreased significantly BAFF, pIgR, and TNF-α mRNA expression. Conclusions: Rifaximin decreased the IgAN symptoms observed in α1KI-CD89Tg mice, suggesting a possible role for it in the treatment of the disease. Full article
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9 pages, 1210 KiB  
Article
Streptococcus australis and Ralstonia pickettii as Major Microbiota in Mesotheliomas
by Rumi Higuchi, Taichiro Goto, Yosuke Hirotsu, Sotaro Otake, Toshio Oyama, Kenji Amemiya, Hitoshi Mochizuki and Masao Omata
J. Pers. Med. 2021, 11(4), 297; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11040297 - 14 Apr 2021
Cited by 14 | Viewed by 2344
Abstract
The microbiota has been reported to be correlated with carcinogenesis and cancer progression. However, its involvement in the pathology of mesothelioma remains unknown. In this study, we aimed to identify mesothelioma-specific microbiota using resected or biopsied mesothelioma samples. Eight mesothelioma tissue samples were [...] Read more.
The microbiota has been reported to be correlated with carcinogenesis and cancer progression. However, its involvement in the pathology of mesothelioma remains unknown. In this study, we aimed to identify mesothelioma-specific microbiota using resected or biopsied mesothelioma samples. Eight mesothelioma tissue samples were analyzed via polymerase chain reaction (PCR) amplification and 16S rRNA gene sequencing. The operational taxonomic units (OTUs) of the effective tags were analyzed in order to determine the taxon composition of each sample. For the three patients who underwent extra pleural pneumonectomy, normal peripheral lung tissues adjacent to the tumor were also included, and the same analysis was performed. In total, 61 OTUs were identified in the tumor and lung tissues, which were classified into 36 species. Streptococcus australis and Ralstonia pickettii were identified as abundant species in almost all tumor and lung samples. Streptococcus australis and Ralstonia pickettii were found to comprise mesothelioma-specific microbiota involved in tumor progression; thus, they could serve as targets for the prevention of mesothelioma. Full article
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18 pages, 1279 KiB  
Article
Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients
by Irina Grigor’eva, Tatiana Romanova, Natalia Naumova, Tatiana Alikina, Alexey Kuznetsov and Marsel Kabilov
J. Pers. Med. 2021, 11(4), 294; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11040294 - 12 Apr 2021
Cited by 9 | Viewed by 1967
Abstract
The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota [...] Read more.
The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females. Full article
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24 pages, 5014 KiB  
Article
‘Statistical Irreproducibility’ Does Not Improve with Larger Sample Size: How to Quantify and Address Disease Data Multimodality in Human and Animal Research
by Abigail R. Basson, Fabio Cominelli and Alexander Rodriguez-Palacios
J. Pers. Med. 2021, 11(3), 234; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11030234 - 23 Mar 2021
Cited by 4 | Viewed by 2059
Abstract
Poor study reproducibility is a concern in translational research. As a solution, it is recommended to increase sample size (N), i.e., add more subjects to experiments. The goal of this study was to examine/visualize data multimodality (data with >1 data peak/mode) as cause [...] Read more.
Poor study reproducibility is a concern in translational research. As a solution, it is recommended to increase sample size (N), i.e., add more subjects to experiments. The goal of this study was to examine/visualize data multimodality (data with >1 data peak/mode) as cause of study irreproducibility. To emulate the repetition of studies and random sampling of study subjects, we first used various simulation methods of random number generation based on preclinical published disease outcome data from human gut microbiota-transplantation rodent studies (e.g., intestinal inflammation and univariate/continuous). We first used unimodal distributions (one-mode, Gaussian, and binomial) to generate random numbers. We showed that increasing N does not reproducibly identify statistical differences when group comparisons are repeatedly simulated. We then used multimodal distributions (>1-modes and Markov chain Monte Carlo methods of random sampling) to simulate similar multimodal datasets A and B (t-test-p = 0.95; N = 100,000), and confirmed that increasing N does not improve the ‘reproducibility of statistical results or direction of the effects’. Data visualization with violin plots of categorical random data simulations with five-integer categories/five-groups illustrated how multimodality leads to irreproducibility. Re-analysis of data from a human clinical trial that used maltodextrin as dietary placebo illustrated multimodal responses between human groups, and after placebo consumption. In conclusion, increasing N does not necessarily ensure reproducible statistical findings across repeated simulations due to randomness and multimodality. Herein, we clarify how to quantify, visualize and address disease data multimodality in research. Data visualization could facilitate study designs focused on disease subtypes/modes to help understand person–person differences and personalized medicine. Full article
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16 pages, 1393 KiB  
Article
Differences in the Microbial Composition of Hemodialysis Patients Treated with and without β-Blockers
by Yi-Ting Lin, Ting-Yun Lin, Szu-Chun Hung, Po-Yu Liu, Wei-Chun Hung, Wei-Chung Tsai, Yi-Chun Tsai, Rachel Ann Delicano, Yun-Shiuan Chuang, Mei-Chuan Kuo, Yi-Wen Chiu and Ping-Hsun Wu
J. Pers. Med. 2021, 11(3), 198; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11030198 - 12 Mar 2021
Cited by 3 | Viewed by 2428
Abstract
β-blockers are commonly prescribed to treat cardiovascular disease in hemodialysis patients. Beyond the pharmacological effects, β-blockers have potential impacts on gut microbiota, but no study has investigated the effect in hemodialysis patients. Hence, we aim to investigate the gut microbiota composition difference between [...] Read more.
β-blockers are commonly prescribed to treat cardiovascular disease in hemodialysis patients. Beyond the pharmacological effects, β-blockers have potential impacts on gut microbiota, but no study has investigated the effect in hemodialysis patients. Hence, we aim to investigate the gut microbiota composition difference between β-blocker users and nonusers in hemodialysis patients. Fecal samples collected from hemodialysis patients (83 β-blocker users and 110 nonusers) were determined by 16S ribosomal RNA amplification sequencing. Propensity score (PS) matching was performed to control confounders. The microbial composition differences were analyzed by the linear discriminant analysis effect size, random forest, and zero-inflated Gaussian fit model. The α-diversity (Simpson index) was greater in β-blocker users with a distinct β-diversity (Bray–Curtis Index) compared to nonusers in both full and PS-matched cohorts. There was a significant enrichment in the genus Flavonifractor in β-blocker users compared to nonusers in full and PS-matched cohorts. A similar finding was demonstrated in random forest analysis. In conclusion, hemodialysis patients using β-blockers had a different gut microbiota composition compared to nonusers. In particular, the Flavonifractor genus was increased with β-blocker treatment. Our findings highlight the impact of β-blockers on the gut microbiota in hemodialysis patients. Full article
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19 pages, 5305 KiB  
Article
Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components
by Zahra A. Barandouzi, Joochul Lee, Kendra Maas, Angela R. Starkweather and Xiaomei S. Cong
J. Pers. Med. 2021, 11(1), 35; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11010035 - 08 Jan 2021
Cited by 28 | Viewed by 6436
Abstract
The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as [...] Read more.
The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study. Full article
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13 pages, 10623 KiB  
Article
Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study
by Isabel Cornejo-Pareja, Patricia Ruiz-Limón, Ana M. Gómez-Pérez, María Molina-Vega, Isabel Moreno-Indias and Francisco J. Tinahones
J. Pers. Med. 2020, 10(4), 192; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm10040192 - 26 Oct 2020
Cited by 31 | Viewed by 3176
Abstract
The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the [...] Read more.
The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto’s thyroiditis (HT), nine Graves–Basedow’s disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens. Full article
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Review

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27 pages, 1174 KiB  
Review
Gut and Endometrial Microbiome Dysbiosis: A New Emergent Risk Factor for Endometrial Cancer
by Soukaina Boutriq, Alicia González-González, Isaac Plaza-Andrades, Aurora Laborda-Illanes, Lidia Sánchez-Alcoholado, Jesús Peralta-Linero, María Emilia Domínguez-Recio, María José Bermejo-Pérez, Rocío Lavado-Valenzuela, Emilio Alba and María Isabel Queipo-Ortuño
J. Pers. Med. 2021, 11(7), 659; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11070659 - 14 Jul 2021
Cited by 16 | Viewed by 4995
Abstract
Endometrial cancer is one of the most common gynaecological malignancies worldwide. Histologically, two types of endometrial cancer with morphological and molecular differences and also therapeutic implications have been identified. Type I endometrial cancer has an endometrioid morphology and is estrogen-dependent, while Type II [...] Read more.
Endometrial cancer is one of the most common gynaecological malignancies worldwide. Histologically, two types of endometrial cancer with morphological and molecular differences and also therapeutic implications have been identified. Type I endometrial cancer has an endometrioid morphology and is estrogen-dependent, while Type II appears with non-endometrioid differentiation and follows an estrogen-unrelated pathway. Understanding the molecular biology and genetics of endometrial cancer is crucial for its prognosis and the development of novel therapies for its treatment. However, until now, scant attention has been paid to environmental components like the microbiome. Recently, due to emerging evidence that the uterus is not a sterile cavity, some studies have begun to investigate the composition of the endometrial microbiome and its role in endometrial cancer. In this review, we summarize the current state of this line of investigation, focusing on the relationship between gut and endometrial microbiome and inflammation, estrogen metabolism, and different endometrial cancer therapies. Full article
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15 pages, 17973 KiB  
Review
Exploring the Oral Microbiome in Rheumatic Diseases, State of Art and Future Prospective in Personalized Medicine with an AI Approach
by Silvia Bellando-Randone, Edda Russo, Vincenzo Venerito, Marco Matucci-Cerinic, Florenzo Iannone, Sabina Tangaro and Amedeo Amedei
J. Pers. Med. 2021, 11(7), 625; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11070625 - 30 Jun 2021
Cited by 17 | Viewed by 4522
Abstract
The oral microbiome is receiving growing interest from the scientific community, as the mouth is the gateway for numerous potential etiopathogenetic factors in different diseases. In addition, the progression of niches from the mouth to the gut, defined as “oral–gut microbiome axis”, affects [...] Read more.
The oral microbiome is receiving growing interest from the scientific community, as the mouth is the gateway for numerous potential etiopathogenetic factors in different diseases. In addition, the progression of niches from the mouth to the gut, defined as “oral–gut microbiome axis”, affects several pathologies, as rheumatic diseases. Notably, rheumatic disorders (RDs) are conditions causing chronic, often intermittent pain affecting the joints or connective tissue. In this review, we examine evidence which supports a role for the oral microbiome in the etiology and progression of various RDs, including rheumatoid arthritis (RA), Sjogren’s syndrome (SS), and systemic lupus erythematosus (SLE). In addition, we address the most recent studies endorsing the oral microbiome as promising diagnostic biomarkers for RDs. Lastly, we introduce the concepts of artificial intelligence (AI), in particular, machine learning (ML) and their general application for understanding the link between oral microbiota and rheumatic diseases, speculating the application of a possible AI approach-based that can be applied to personalized medicine in the future. Full article
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10 pages, 3521 KiB  
Review
Gut Microbiota and Acute Diverticulitis: Role of Probiotics in Management of This Delicate Pathophysiological Balance
by Andrea Piccioni, Laura Franza, Mattia Brigida, Christian Zanza, Enrico Torelli, Martina Petrucci, Rebecca Nicolò, Marcello Covino, Marcello Candelli, Angela Saviano, Veronica Ojetti and Francesco Franceschi
J. Pers. Med. 2021, 11(4), 298; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11040298 - 14 Apr 2021
Cited by 15 | Viewed by 5891
Abstract
How can the knowledge of probiotics and their mechanisms of action be translated into clinical practice when treating patients with diverticular disease and acute diverticulitis? Changes in microbiota composition have been observed in patients who were developing acute diverticulitis, with a reduction of [...] Read more.
How can the knowledge of probiotics and their mechanisms of action be translated into clinical practice when treating patients with diverticular disease and acute diverticulitis? Changes in microbiota composition have been observed in patients who were developing acute diverticulitis, with a reduction of taxa with anti-inflammatory activity, such as Clostridium cluster IV, Lactobacilli and Bacteroides. Recent observations supported that a dysbiosis characterised by decreased presence of anti-inflammatory bacterial species might be linked to mucosal inflammation, and a vicious cycle results from a mucosal inflammation driving dysbiosis at the same time. An alteration in gut microbiota can lead to an altered activation of nerve fibres, and subsequent neuronal and muscular dysfunction, thus favoring abdominal symptoms’ development. The possible role of dysbiosis and mucosal inflammation in leading to dysmotility is linked, in turn, to bacterial translocation from the lumen of the diverticulum to perivisceral area. There, a possible activation of Toll-like receptors has been described, with a subsequent inflammatory reaction at the level of the perivisceral tissues. Being aware that bacterial colonisation of diverticula is involved in the pathogenesis of acute diverticulitis, the rationale for the potential role of probiotics in the treatment of this disease becomes clearer. For this review, articles were identified using the electronic PubMed database through a comprehensive search conducted by combining key terms such as “gut microbiota”, “probiotics and gut disease”, “probiotics and acute diverticulitis”, “probiotics and diverticular disease”, “probiotics mechanism of action”. However, the amount of data present on this matter is not sufficient to draw robust conclusions on the efficacy of probiotics for symptoms’ management in diverticular disease. Full article
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13 pages, 1745 KiB  
Brief Report
Intestinal Dysbiosis in Young Cystic Fibrosis Rabbits
by Xiubin Liang, Mohamad Bouhamdan, Xia Hou, Kezhong Zhang, Jun Song, Ke Hao, Jian-Ping Jin, Zhongyang Zhang and Jie Xu
J. Pers. Med. 2021, 11(2), 132; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11020132 - 16 Feb 2021
Cited by 6 | Viewed by 2311
Abstract
Individuals with cystic fibrosis (CF) often experience gastrointestinal (GI) abnormalities. In recent years, the intestinal microbiome has been postulated as a contributor to the development of CF-associated GI complications, hence representing a potential therapeutic target for treatment. We recently developed a rabbit model [...] Read more.
Individuals with cystic fibrosis (CF) often experience gastrointestinal (GI) abnormalities. In recent years, the intestinal microbiome has been postulated as a contributor to the development of CF-associated GI complications, hence representing a potential therapeutic target for treatment. We recently developed a rabbit model of CF, which is shown to manifest many human patient-like pathological changes, including intestinal obstruction. Here, we investigated the feces microbiome in young CF rabbits in the absence of antibiotics treatment. Stool samples were collected from seven- to nine-week-old CF rabbits (n = 7) and age-matched wild-type (WT) rabbits (n = 6). Microbiomes were investigated by iTag sequencing of 16S rRNA genes, and functional profiles were predicted using PICRUSt. Consistent with reports of those in pediatric CF patients, the fecal microbiomes of CF rabbits are of lower richness and diversity than that of WT rabbits, with a marked taxonomic and inferred functional dysbiosis. Our work identified a new CF animal model with the manifestation of intestinal dysbiosis phenotype. This model system may facilitate the research and development of novel treatments for CF-associated gastrointestinal diseases. Full article
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14 pages, 751 KiB  
Systematic Review
Fecal Microbiota Transplantation in Allogeneic Hematopoietic Stem Cell Transplantation Recipients: A Systematic Review
by Andrea Pession, Daniele Zama, Edoardo Muratore, Davide Leardini, Davide Gori, Federica Guaraldi, Arcangelo Prete, Silvia Turroni, Patrizia Brigidi and Riccardo Masetti
J. Pers. Med. 2021, 11(2), 100; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm11020100 - 04 Feb 2021
Cited by 17 | Viewed by 2961
Abstract
The disruption of gut microbiota eubiosis has been linked to major complications in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. Various strategies have been developed to reduce dysbiosis and related complications. Fecal microbiota transplantation (FMT) consists of the infusion of fecal matter from [...] Read more.
The disruption of gut microbiota eubiosis has been linked to major complications in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. Various strategies have been developed to reduce dysbiosis and related complications. Fecal microbiota transplantation (FMT) consists of the infusion of fecal matter from a healthy donor to restore impaired intestinal homeostasis, and could be applied in the allo-HSCT setting. We conducted a systematic review of studies addressing the use of FMT in allo-HSCT patients. In the 23 papers included in the qualitative synthesis, FMT was used for the treatment of recurrent Clostridioides difficile infections or as a therapeutic strategy for steroid-resistant gut aGvHD. FMT was also performed with a preventive aim (e.g., to decolonize from antibiotic-resistant bacteria). Additional knowledge on the biological mechanisms underlying clinical findings is needed in order to employ FMT in clinical practice. There is also concern regarding the administration of microbial consortia in immune-compromised patients with altered gut permeability. Therefore, the safety profile and efficacy of the procedure must be determined to better assess the role of FMT in allo-HSCT recipients. Full article
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