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Gut Microbes Dec 2023Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been... (Review)
Review
Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.
Topics: Humans; Gastrointestinal Microbiome; Inflammatory Bowel Diseases; Feces; Fecal Microbiota Transplantation; Biomarkers
PubMed: 38044504
DOI: 10.1080/19490976.2023.2287073 -
Cancers Aug 2023Cancer is the leading cause of death worldwide, with the most frequent being breast cancer in women, prostate cancer in men and colon cancer in both sexes. The use of... (Review)
Review
INTRODUCTION
Cancer is the leading cause of death worldwide, with the most frequent being breast cancer in women, prostate cancer in men and colon cancer in both sexes. The use of metabolomics to find new biomarkers can provide knowledge about possible interventions based on the presence of oncometabolites in different cancer types.
OBJECTIVES
The primary purpose of this review is to analyze the characteristic metabolome of three of the most frequent cancer types. We further want to identify the existence and success rate of metabolomics-based intervention in patients suffering from those cancer types. Our conclusions are based on the analysis of the methodological quality of the studies.
METHODS
We searched for studies that investigated the metabolomic characteristics in patients suffering from breast cancer, prostate cancer or colon cancer in clinical trials. The data were analyzed, as well as the effects of specific interventions based on identified metabolomics and one or more oncometabolites. The used databases were PubMed, Virtual Health Library, Web of Science, EBSCO and Cochrane Library. Only nine studies met the selection criteria. Study bias was analyzed using the Cochrane risk of bias tool. This systematic review protocol was registered at the International Prospective Register of Systematic Reviews (PROSPERO: CRD42023401474).
RESULTS
Only nine studies about clinical trials were included in this review and show a moderate quality of evidence. Metabolomics-based interventions related with disease outcome were conflictive with no or small changes in the metabolic characteristics of the different cancer types.
CONCLUSIONS
This systematic review shows some interesting results related with metabolomics-based interventions and their effects on changes in certain cancer oncometabolites. The small number of studies we identified which fulfilled our inclusion criteria in this systematic review does not allow us to draw definitive conclusions. Nevertheless, some results can be considered as promising although further research is needed. That research must focus not only on the presence of possible oncometabolites but also on possible metabolomics-based interventions and their influence on the outcome in patients suffering from breast cancer, prostate cancer or colon cancer.
PubMed: 37686573
DOI: 10.3390/cancers15174297 -
Medical Mycology Aug 2023Intestinal fungi play an important role in the health-disease process. We observed that in liver diseases, fungal infections lead to high mortality. In this review, we...
Intestinal fungi play an important role in the health-disease process. We observed that in liver diseases, fungal infections lead to high mortality. In this review, we were able to gather and evaluate the available scientific evidence on intestinal mycobiota and liver diseases. We searched PubMed and Embase, using a combination of several entry terms. Only studies in adults ≥ 18 years old with liver disease and published after 2010 were included. We observed that individuals with liver disease have an altered intestinal mycobioma, which accompanies the progression of these diseases. In cirrhotic patients, there are a high number of Candida sp. strains, especially Candida albicans. In early chronic liver disease, there is an increase in alpha diversity at the expense of Candida sp. and conversely, in advanced liver disease, there is a negative correlation between alpha diversity and model for end-stage liver disease score. On the other hand, patients with non-alcoholic fatty liver disease demonstrate greater diversity compared to controls. Our study concluded that the evidence on the subject is sparse, with few studies and a lack of standardization of outcome measures and reporting, and it was not possible to perform a meta-analysis capable of synthesizing relevant parameters of the human mycobiotic profile. However, certain fungal genera such as Candida play an important role in the context of liver disease and that adults with liver disease have a distinct gut mycobiotic profile from healthy controls.
Topics: Humans; Animals; Fungi; End Stage Liver Disease; Gastrointestinal Microbiome; Mycobiome; Severity of Illness Index; Candida albicans; Liver Diseases
PubMed: 37463798
DOI: 10.1093/mmy/myad071 -
Journal of Gastroenterology and... Jul 2023The role of the microbiota in diverticulosis and diverticular disease is underexplored. This systematic review aimed to assess all literature pertaining to the... (Review)
Review
BACKGROUND AND AIMS
The role of the microbiota in diverticulosis and diverticular disease is underexplored. This systematic review aimed to assess all literature pertaining to the microbiota and metabolome associations in asymptomatic diverticulosis, symptomatic uncomplicated diverticular disease (SUDD), and diverticulitis pathophysiology.
METHODS
Seven databases were searched for relevant studies published up to September 28, 2022. Data were screened in Covidence and extracted to Excel. Critical appraisal was undertaken using the Newcastle Ottawa Scale for case/control studies.
RESULTS
Of the 413 papers screened by title and abstract, 48 full-text papers were reviewed in detail with 12 studies meeting the inclusion criteria. Overall, alpha and beta diversity were unchanged in diverticulosis; however, significant changes in alpha diversity were evident in diverticulitis. A similar Bacteroidetes to Firmicutes ratio compared with controls was reported across studies. The genus-level comparisons showed no relationship with diverticular disease. Butyrate-producing microbial species were decreased in abundance, suggesting a possible contribution to the pathogenesis of diverticular disease. Comamonas species was significantly increased in asymptomatic diverticulosis patients who later developed diverticulitis. Metabolome analysis reported significant differences in diverticulosis and SUDD, with upregulated uracil being the most consistent outcome in both. No significant differences were reported in the mycobiome.
CONCLUSION
Overall, there is no convincing evidence of microbial dysbiosis in colonic diverticula to suggest that the microbiota contributes to the pathogenesis of asymptomatic diverticulosis, SUDD, or diverticular disease. Future research investigating microbiota involvement in colonic diverticula should consider an investigation of mucosa-associated microbial changes within the colonic diverticulum itself.
Topics: Humans; Diverticulum, Colon; Diverticulosis, Colonic; Microbiota; Diverticulitis; Diverticular Diseases
PubMed: 36775316
DOI: 10.1111/jgh.16142 -
American Journal of Respiratory Cell... Mar 2023Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of...
Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.
Topics: Humans; Lung; Asthma; Pulmonary Disease, Chronic Obstructive; Microbiota; Cystic Fibrosis
PubMed: 36476129
DOI: 10.1165/rcmb.2022-0208TR -
Mycoses Mar 2022Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease with an increasing prevalence worldwide. The aetiology and pathogenesis of AD have not been... (Review)
Review
Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease with an increasing prevalence worldwide. The aetiology and pathogenesis of AD have not been fully elucidated. Previous studies have suggested the role of fungi as a triggering factor in the development AD. Here we conducted a systematic review to investigate the skin mycobiome profiles in AD and to address whether there is an association between fungal dysbiosis and AD. We searched Medline/PubMed, Embase and Web of Science for research studies published in English between January 1st, 2010 and April 21st, 2021. A total of 11 human studies and 3 animal studies were included in this analysis. Fungal dysbiosis was observed in AD lesions with a depleted amount of Malassezia and a higher abundance of filamentous fungi. A positive correlation between Candida and Staphylococcus was also demonstrated in AD. We supposed that specific species of Malassezia spp. and Candida spp. may play a role in the pathogenesis of AD by interacting with the pathogenic bacteria. Topical application of emollients could improve the skin barrier function and restore the skin fungal flora by increasing the amount of Malassezia. Further studies focusing on the complex interplay between specific skin fungi and the host can provide better insight into the role of microorganisms in the pathogenesis of AD.
Topics: Animals; Dermatitis, Atopic; Dysbiosis; Eczema; Humans; Malassezia; Mycobiome; Skin
PubMed: 34817898
DOI: 10.1111/myc.13402 -
International Journal of Molecular... Aug 2021Down syndrome (DS) is a genetic disorder associated with early-onset periodontitis and other periodontal diseases (PDs). The present work aimed to systematically review... (Meta-Analysis)
Meta-Analysis
Down syndrome (DS) is a genetic disorder associated with early-onset periodontitis and other periodontal diseases (PDs). The present work aimed to systematically review the scientific literature reporting studies in vivo on oral microbiota features in subjects with DS and related periodontal health and to highlight any correlation and difference with subjects not affected by DS, with and without PDs. PubMed, Web of Science, Scopus and Cochrane were searched for relevant studies in May 2021. The participants were subjects affected by Down syndrome (DS) with and without periodontal diseases; the study compared subjects with periodontal diseases but not affected by DS, and DS without periodontal diseases; the outcomes were the differences in oral microbiota/periodontopathogen bacterial composition among subjects considered; the study design was a systematic review. Study quality was assessed with risk of bias in non-randomized studies of interventions (ROBINS-I). Of the 954 references retrieved, 26 studies were considered. The conclusions from the qualitative assessment of the papers revealed an increasing knowledge over the last years of the microbiota associated with DS and their periodontal diseases, in comparison with healthy subjects and subjects with other kinds of mental disabilities. Few data have emerged on the mycobiome and virobiome of DS, hence, further investigations are still necessary.
Topics: Biofilms; Dental Plaque; Down Syndrome; Gingivitis; Humans; Microbiota; Mouth; Periodontal Diseases
PubMed: 34502159
DOI: 10.3390/ijms22179251 -
PloS One 2021Fungal infections are common on oral mucosae, but their role in other oral sites is ill defined. Over the last few decades, numerous studies have reported the presence... (Meta-Analysis)
Meta-Analysis
Fungal infections are common on oral mucosae, but their role in other oral sites is ill defined. Over the last few decades, numerous studies have reported the presence of fungi, particularly Candida species in endodontic infections, albeit in relatively small numbers in comparison to its predominant anaerobic bacteriome. Here, we review the fungal biome of primary and secondary endodontic infections, with particular reference to the prevalence and behavior of Candida species. Meta-analysis of the available data from a total of 39 studies fitting the inclusion criteria, indicate the overall weighted mean prevalence (WMP) of fungal species in endodontic infections to be 9.11% (from a cumulative total of 2003 samples), with 9.0% in primary (n = 1341), and 9.3% in secondary infections (n = 662). Nevertheless, WMP for fungi in primary and secondary infections which were 6.3% and 7.5% for culture-based studies, increased to 12.5% and 16.0% in molecular studies, respectively. The most prevalent fungal species was Candida spp. The high heterogeneity in the reported fungal prevalence suggests the need for standardized sampling, and speciation methods. The advent of the new molecular biological analytical platforms, such as the next generation sequencing (NGS), and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF), that enables identification and quantitation of a broad spectrum of hitherto unknown organisms in endodontic infections should radically alter our understanding of the endodontic mycobiome in the future. Candida spp. appear to be co-pathogens with bacteria in approximately one in ten patients with endodontic infections. Hence, clinicians should comprehend the importance and the role of fungi in endodontic infections and be cognizant of the need to eradicate both bacteria and fungi for successful therapy.
Topics: Bacteria; Bacterial Infections; Candida; Candidiasis; Dental Pulp Diseases; Humans
PubMed: 34293029
DOI: 10.1371/journal.pone.0255003 -
Journal of Oral Microbiology Aug 2020Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for... (Review)
Review
INTRODUCTION
Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis.
METHODS
A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients.
RESULTS
21 studies were included and the most identified species was . The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21).
CONCLUSIONS
Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.
PubMed: 32944157
DOI: 10.1080/20002297.2020.1807179 -
Microbial Cell (Graz, Austria) Jan 2020Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of... (Review)
Review
Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of delivery and breastfeeding may have impact on the oral bacterial colonization, however, the influence on oral fungal colonization is still unknown. We performed a systematic literature review on mother to child oral fungi transmission, namely regarding the association between the mode of delivery and breastfeeding in oral yeast colonization. Our analysis revealed no significant differences between the oral mycobiome of breastfed and bottle-fed children. As for the delivery mode, the majority of studies found a relation between fungal colonization and vaginal delivery. was the most commonly isolated fungi species. Our analysis suggests that maternal breastfeeding does not seem to influence oral mycology, but vaginal delivery appears to promote oral yeast colonization in early life.
PubMed: 32025512
DOI: 10.15698/mic2020.02.706