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Application of Microbiome in Disease Diagnosis and Treatment
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Application of Microbiome in Disease Diagnosis and Treatment

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

Deadline for manuscript submissions: closed (20 July 2023) | Viewed by 18375

Special Issue Editors

Dr. Pablo Román-López

E-Mail Website
Guest Editor
Faculty of Health Sciences, Department of Nursing Science, Physiotherapy and Medicine, University of Almeria, 04120 Almeria, Spain
Interests: gastrointestinal microbiome; dysbiosis; probiotics; prebiotics; microbiota; clinical trial
Special Issues, Collections and Topics in MDPI journals
Dr. Lola Rueda-Ruzafa

E-Mail Website
Guest Editor
Faculty of Health Sciences, Department of Nursing Science, Physiotherapy and Medicine, University of Almeria, 04120 Almeria, Spain
Interests: gastrointestinal microbiome; neuroscience; dysbiosis; probiotics; prebiotics

Special Issue Information

Dear Colleagues,

There is currently growing research into the impact of the gut microbiome on human homeostasis and how its alteration may influence the development of certain diseases via the gut–brain axis. In relation to this, it has been suggested that modification of microbial community members leads to intestinal dysbiosis, a phenomenon characterized by a loss of balance between pathogenic and beneficial microorganisms, which could contribute to the development of gastrointestinal, neurological, or metabolic disorders. Determining the levels of certain intestinal strains in diseases is becoming of great diagnostic value in the clinic, especially through 16S ribosomal RNA (rRNA) gene sequencing, quantitative polymerase chain reaction (qPCR), metabolomics, and metagenomic sequencing. The information provided by these analyses is extensive, including relative and absolute abundance, diversity, and microbial richness that can support diagnosis. Different strategies based on bidirectional communication between microbiota and brain can be used to restore the affected gut microbiota such as probiotics, prebiotics, and recently fecal microbiota transplantation. Thus, their use appears to have beneficial effects on individuals with autism, obesity, anxiety, depression, and hepatic encephalopathy. We thank you for considering this invitation and are available for any inquiries.

Dr. Pablo Román-López
Dr. Lola Rueda-Ruzafa
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Personalized Medicine is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gastrointestinal microbiome
  • gut–brain axis
  • neuroscience
  • probiotics
  • prebiotics
  • fecal microbiota transplantation
  • 16S ribosomal RNA

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Published Papers (4 papers)

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Research

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11 pages, 306 KiB  
Article
Influence of Shift Work on The Health of Nursing Professionals
by Pablo Roman, Isabel Perez-Cayuela, Esther Gil-Hernández, Miguel Rodriguez-Arrastia, Adrian Aparicio-Mota, Carmen Ropero-Padilla and Lola Rueda-Ruzafa
J. Pers. Med. 2023, 13(4), 627; https://doi.org/10.3390/jpm13040627 - 2 Apr 2023
Cited by 10 | Viewed by 6614
Abstract
Shift work is increasingly common in health services, subjecting healthcare professionals to work schedules that can alter circadian rhythms and eating habits with consequent repercussions for the intestinal homeostasis. The objective of this study was to describe the relationship of rotating work shifts [...] Read more.
Shift work is increasingly common in health services, subjecting healthcare professionals to work schedules that can alter circadian rhythms and eating habits with consequent repercussions for the intestinal homeostasis. The objective of this study was to describe the relationship of rotating work shifts with the intestinal health, sleep quality, and emotional dimension of nursing professionals. In March and May 2019, an observational and comparative study was conducted among 380 nursing professionals from different Spanish cities and divided into fixed shift (n = 159) and rotating shift (n = 221). To carry out the present work, the variables measured were gastrointestinal symptoms, stool consistency and shape, anxiety, depression, sleep, as well as stress and work environment. Nurses with rotating shifts reported more abdominal pain and symptoms of depersonalization, as well as worse sleep efficiency and worse nursing practice environment. In addition, overall scores of the Gastrointestinal Symptom Rating Scale and Hospital Anxiety and Depression Scale were found to be significantly worse in nurses with these shifts. Rotating shift work by nursing staff may be associated with the occurrence of gastrointestinal and anxiety-related symptoms. These findings, together with the presence of negative and insensitive attitudes towards patients by nurses on rotating shifts, should be considered to maintain the quality of healthcare. Full article
(This article belongs to the Special Issue Application of Microbiome in Disease Diagnosis and Treatment)
16 pages, 337 KiB  
Article
Mental Health Symptom Reduction Using Digital Therapeutics Care Informed by Genomic SNPs and Gut Microbiome Signatures
by Inti Pedroso, Shreyas Vivek Kumbhare, Bharat Joshi, Santosh K. Saravanan, Dattatray Suresh Mongad, Simitha Singh-Rambiritch, Tejaswini Uday, Karthik Marimuthu Muthukumar, Carmel Irudayanathan, Chandana Reddy-Sinha, Parambir S. Dulai, Ranjan Sinha and Daniel Eduardo Almonacid
J. Pers. Med. 2022, 12(8), 1237; https://doi.org/10.3390/jpm12081237 - 28 Jul 2022
Cited by 2 | Viewed by 5220
Abstract
Neuropsychiatric diseases and obesity are major components of morbidity and health care costs, with genetic, lifestyle, and gut microbiome factors linked to their etiology. Dietary and weight-loss interventions can help improve mental health, but there is conflicting evidence regarding their efficacy; and moreover, [...] Read more.
Neuropsychiatric diseases and obesity are major components of morbidity and health care costs, with genetic, lifestyle, and gut microbiome factors linked to their etiology. Dietary and weight-loss interventions can help improve mental health, but there is conflicting evidence regarding their efficacy; and moreover, there is substantial interindividual heterogeneity that needs to be understood. We aimed to identify genetic and gut microbiome factors that explain interindividual differences in mental health improvement after a dietary and lifestyle intervention for weight loss. We recruited 369 individuals participating in Digbi Health’s personalized digital therapeutics care program and evaluated the association of 23 genetic scores, the abundance of 178 gut microbial genera, and 42 bacterial pathways with mental health. We studied the presence/absence of anxiety or depression, or sleep problems at baseline and improvement on anxiety, depression, and insomnia after losing at least 2% body weight. Participants lost on average 5.4% body weight and >95% reported improving mental health symptom intensity. There were statistically significant correlations between: (a) genetic scores with anxiety or depression at baseline, gut microbial functions with sleep problems at baseline, and (b) genetic scores and gut microbial taxa and functions with anxiety, depression, and insomnia improvement. Our results are concordant with previous findings, including the association between anxiety or depression at baseline with genetic scores for alcohol use disorder and major depressive disorder. As well, our results uncovered new associations in line with previous epidemiological literature. As evident from previous literature, we also observed associations of gut microbial signatures with mental health including short-chain fatty acids and bacterial neurotoxic metabolites specifically with depression. Our results also show that microbiome and genetic factors explain self-reported mental health status and improvement better than demographic variables independently. The genetic and microbiome factors identified in this study provide the basis for designing and personalizing dietary interventions to improve mental health. Full article
(This article belongs to the Special Issue Application of Microbiome in Disease Diagnosis and Treatment)
12 pages, 20272 KiB  
Article
Metagenomic Analysis of Plasma Microbial Extracellular Vesicles in Patients Receiving Mechanical Ventilation: A Pilot Study
by Jinkyeong Park, Jae Jun Lee, Yoonki Hong, Hochan Seo, Tae-Seop Shin and Ji Young Hong
J. Pers. Med. 2022, 12(4), 564; https://doi.org/10.3390/jpm12040564 - 2 Apr 2022
Cited by 2 | Viewed by 2150
Abstract
Background: Previous studies reported a significant association between pneumonia outcome and the respiratory microbiome. There is increasing interest in the roles of bacterial extracellular vesicles (EVs) in various diseases. We studied the composition and function of microbiota-derived EVs in the plasma of patients [...] Read more.
Background: Previous studies reported a significant association between pneumonia outcome and the respiratory microbiome. There is increasing interest in the roles of bacterial extracellular vesicles (EVs) in various diseases. We studied the composition and function of microbiota-derived EVs in the plasma of patients receiving mechanical ventilation to evaluate whether they can be used as a diagnostic marker and to predict clinical outcomes. Methods: Plasma samples (n = 111) from 59 mechanically ventilated patients (41 in the pneumonia group; 24 in the nursing home and hospital-associated infection [NHAI] group) were prospectively collected on days one and seven. After isolating the bacterial EVs from plasma samples, nucleic acid was extracted for 16S rRNA gene pyrosequencing. The samples were evaluated to determine the α and β diversity, bacterial composition, and predicted functions. Results: Principal coordinates analysis revealed significantly different clustering of microbial EVs between the pneumonia and non-pneumonia groups. The proportions of Lactobacillus, Cutibacterium, and Sphingomonas were significantly different between the pneumonia and non-pneumonia groups. In addition, the abundances of Lactobacillus and Bifidobacterium were significantly higher in the non-NHAI than the NHAI group. In the analysis of β diversity, the structure of microbial EVs differed significantly different between 28-day survivors and non-survivors (Bray-Curtis distance, p = 0.014). Functional profiling revealed significant differences between the pneumonia and non-pneumonia groups. The longitudinal change in predicted functions of microbial EV genes showed a significant difference between 28-day survivors and non-survivors. Conclusions: Bacterial microbiota–derived EVs in the plasma have potential as diagnostic and prognostic markers for patients receiving mechanical ventilation. Further large prospective studies are needed to determine the clinical utility of plasma microbiota-EVs in intubated patients. Full article
(This article belongs to the Special Issue Application of Microbiome in Disease Diagnosis and Treatment)
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Review

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34 pages, 2445 KiB  
Review
Probiotics and Probiotic-like Agents against Chemotherapy-Induced Intestinal Mucositis: A Narrative Review
by Laura López-Gómez, Alexandra Alcorta and Raquel Abalo
J. Pers. Med. 2023, 13(10), 1487; https://doi.org/10.3390/jpm13101487 - 12 Oct 2023
Cited by 9 | Viewed by 3681
Abstract
Cancer chemotherapy has allowed many patients to survive, but not without risks derived from its adverse effects. Drugs, such as 5-fluorouracil, irinotecan, oxaliplatin, methotrexate, and others, as well as different drug combinations trigger intestinal mucositis that may cause or contribute to anorexia, pain, [...] Read more.
Cancer chemotherapy has allowed many patients to survive, but not without risks derived from its adverse effects. Drugs, such as 5-fluorouracil, irinotecan, oxaliplatin, methotrexate, and others, as well as different drug combinations trigger intestinal mucositis that may cause or contribute to anorexia, pain, diarrhea, weight loss, systemic infections, and even death. Dysbiosis is a hallmark of chemotherapy-induced intestinal mucositis and diarrhea, and, therefore, strategies aimed at modulating intestinal microbiota may be useful to counteract and prevent those dreadful effects. This narrative review offers an overview of the studies performed to test the efficacy of probiotics and probiotic-like agents against chemotherapy-induced intestinal mucositis and its consequences. Microbiota modulation through the oral administration of different probiotics (mainly strains of Lactobacillus and Bifidobacterium), probiotic mixtures, synbiotics, postbiotics, and paraprobiotics has been tested in different animal models and in some clinical trials. Regulation of dysbiosis, modulation of epithelial barrier permeability, anti-inflammatory effects, modulation of host immune response, reduction of oxidative stress, or prevention of apoptosis are the main mechanisms involved in their beneficial effects. However, the findings are limited by the great heterogeneity of the preclinical studies and the relative lack of studies in immunocompromised animals, as well as the scarce availability of results from clinical trials. Despite this, the results accumulated so far are promising. Hopefully, with the aid of these agents, intestinal mucositis will be less impactful to the cancer patient in the near future. Full article
(This article belongs to the Special Issue Application of Microbiome in Disease Diagnosis and Treatment)
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