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Nutrients Sep 2022Pectin is a dietary fiber, and its health effects have been described extensively. Although there are limited clinical studies, there is a growing body of evidence from... (Review)
Review
Pectin is a dietary fiber, and its health effects have been described extensively. Although there are limited clinical studies, there is a growing body of evidence from in vitro studies investigating the effect of pectin on human gut microbiota. This comprehensive review summarizes the findings of gut microbiota modulation in vitro as assessed by 16S rRNA gene-based technologies and elucidates the potential structure-activity relationships. Generally, pectic substrates are slowly but completely fermented, with a greater production of acetate compared with other fibers. Their fermentation, either directly or by cross-feeding interactions, results in the increased abundances of gut bacterial communities such as the family of , the and genera, and species such as and , where the specific stimulation of and is unique to pectic substrates. Furthermore, the degree of methyl esterification, the homogalacturonan-to-rhamnogalacturonan ratio, and the molecular weight are the most influential structural factors on the gut microbiota. The latter particularly influences the growth of spp. The prebiotic potential of pectin targeting specific gut bacteria beneficial for human health and well-being still needs to be confirmed in humans, including the relationship between its structural features and activity.
Topics: Bacteria; Clostridiales; Feces; Fermentation; Gastrointestinal Microbiome; Humans; Pectins; Prebiotics; RNA, Ribosomal, 16S
PubMed: 36079886
DOI: 10.3390/nu14173629 -
Revista Espanola de Quimioterapia :... Apr 2023The objective of this study was to perform a systematic review of the characteristics, causative microorganisms and outcome of brain abscesses caused by anaerobic...
The objective of this study was to perform a systematic review of the characteristics, causative microorganisms and outcome of brain abscesses caused by anaerobic bacteria over the past 25 years. We reviewed studies on brain abscesses which included infection due to anaerobic microorganisms published between 1998 and 2022. We excluded reports with polymicrobial infections (more than 2 anaerobic bacteria isolated) and those that do not provide enough information to make comparisons, the reports with only one case of brain abscess due to anaerobes, as well as those focused on an only anaerobic bacterium. Also, we have excluded the cases in pediatric population. We searched the scientific literature through the Cochrane Library, EMBASE and PubMed/MEDLINE databases for studies of this condition. We finally included 28 studies with 6,167 patients, of which 715 (11.5%) were cases caused by anaerobic bacteria. There was a male predominance (70%) and mean age of 40.3 years. Most infections were monomicrobial (59.4%). The most common anaerobic microorganisms isolated were Bacteroides spp (43.4%) and Gram-positive anaerobic cocci (35.1%). Cases of brain abscesses caused by anaerobic bacteria were most frequent in Asia and Europe. The source of infection most frequent was otogenic in 84.6% followed by a neurosurgery procedure infection in 23% of patients. The main symptom observed was headache in 95.6% of patients followed by fever (69.5%). Surgical treatment was performed in 48 % of patients and the percentage of patients in whom antibiotic treatment was applied range 88.8% to 100%. The main limitation of this review is the non-inclusion of studies published before of 1998 in which MALDI-TOF MS system had not been introduced in the majority of laboratories for routine identification. The patient rate with isolation of anaerobic bacteria in brain abscesses is low, but these data could be underestimated mainly due to the fastidious nature of these microorganisms and the difficulties in the identification of some anaerobes.
Topics: Humans; Male; Child; Adult; Female; Anaerobiosis; Base Composition; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Brain Abscess; Bacteria, Anaerobic; Gram-Positive Cocci
PubMed: 36733997
DOI: 10.37201/req/114.2022 -
Frontiers in Public Health 2020The emergence and dissemination of antibiotic resistance genes (ARGs) in the environment poses a huge global health hazard. Hospital wastewater (HWW), in which a high... (Meta-Analysis)
Meta-Analysis
The emergence and dissemination of antibiotic resistance genes (ARGs) in the environment poses a huge global health hazard. Hospital wastewater (HWW), in which a high density of antibiotic residues and antibiotic-resistant bacteria are present, may be a reservoir of ARGs dissemination into the environment. Our meta-analysis comprehensively analyzes the prevalence of ARGs in HWW, as well as the influencing factors in ARGs distribution. Online databases were used to search for literature using the subject terms: "Drug Resistance" AND "Genes" AND "Hospitals" AND "Wastewater." Two reviewers independently applied predefined criteria to assess the literature and extract data including "relative abundance of ARGs," "title," "authors," "country," "location," "sampling year," and "sampling seasons." The median values and 95% confidence intervals of ARGs abundance were calculated by Wilcox.test function in R. Temporal trends, spatial differences, seasonal variations and removal efficiency of ARGs were analyzed by Pearson correlation analysis and Kruskal-Wallis H test. Resistance genes to carbapenems, sulfonamides, tetracyclines and mobile genetic elements were found at high relative abundance (>10 gene copies/16S rRNA gene copies) in HWW. The abundance of resistance genes to extended-spectrum β-lactams, carbapenems, sulfonamides and glycopeptide significantly decreased, while tetracycline resistance genes abundance increased from 2014 to 2018. The abundance of ARGs was significantly different by country but not by season. ARGs could not be completely removed by on-site HWW treatments and the removal efficiency varies for different ARGs. HWW presents more types of ARGs, and their abundance is higher than those in most wastewater systems. HWW may be a reservoir of ARGs and play an important role in the dissemination of ARGs.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; Hospitals; RNA, Ribosomal, 16S; Wastewater
PubMed: 33194975
DOI: 10.3389/fpubh.2020.574968 -
Clinical Pharmacology and Therapeutics Feb 2022Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity)....
Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity). MT-RNR1 is a gene that encodes the 12s rRNA subunit and is the mitochondrial homologue of the prokaryotic 16s rRNA. Some MT-RNR1 variants (i.e., m.1095T>C; m.1494C>T; m.1555A>G) more closely resemble the bacterial 16s rRNA subunit and result in increased risk of aminoglycoside-induced hearing loss. Use of aminoglycosides should be avoided in individuals with an MT-RNR1 variant associated with an increased risk of aminoglycoside-induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for the use of aminoglycosides based on MT-RNR1 genotype (updates at https://cpicpgx.org/guidelines/ and www.pharmgkb.org).
Topics: Aminoglycosides; Anti-Bacterial Agents; Clinical Decision-Making; Genotype; Hearing Loss, Sensorineural; Humans; Ototoxicity; Patient Safety; Pharmacogenetics; Pharmacogenomic Testing; Pharmacogenomic Variants; Predictive Value of Tests; RNA, Ribosomal; Risk Assessment; Risk Factors
PubMed: 34032273
DOI: 10.1002/cpt.2309 -
Parasites & Vectors Mar 2024The study of parasites provides insight into intricate ecological relationships in ecosystem dynamics, food web structures, and evolution on multiple scales. Hepatozoon... (Review)
Review
BACKGROUND
The study of parasites provides insight into intricate ecological relationships in ecosystem dynamics, food web structures, and evolution on multiple scales. Hepatozoon Eucoccidiorida: Hepatozoidae) is a genus of protozoan hemoparasites with heteroxenous life cycles that switch infections between vertebrates and blood-feeding invertebrates. The most comprehensive review of the genus was published 26 years ago, and currently there are no harmonized data on the epizootiology, diagnostics, genotyping methods, evolutionary relationships, and genetic diversity of Hepatozoon in the Americas.
METHODS
Here, we provide a comprehensive review based on the PRISMA method regarding Hepatozoon in wild mammals within the American continent, in order to generate a framework for future research.
RESULTS
11 out of the 35 countries of the Americas (31.4%) had data on Hepatozoon, with Carnivora and Rodentia orders having the most characterizations. Bats, ungulates, and shrews were the least affected groups. While Hepatozoon americanum, H. americanum-like, H. canis, H. didelphydis, H. felis, H. milleri, H. griseisciuri, and H. procyonis correspond to the identified species, a plethora of genospecies is pending for a formal description combining morphology and genetics. Most of the vectors of Hepatozoon in the Americas are unknown, but some flea, mite, and tick species have been confirmed. The detection of Hepatozoon has relied mostly on conventional polymerase chain reaction (PCR), and the implementation of specific real time PCR for the genus needs to be employed to improve its diagnosis in wild animals in the future. From a genetic perspective, the V4 region of the 18S rRNA gene has been widely sequenced for the identification of Hepatozoon in wild animals. However, mitochondrial and apicoplast markers should also be targeted to truly determine different species in the genus. A phylogenetic analysis of herein retrieved 18S ribosomal DNA (rDNA) sequences showed two main clades of Hepatozoon: Clade I associated with small mammals, birds, and herpetozoa, and Clade II associated with Carnivora. The topology of the tree is also reflected in the haplotype network.
CONCLUSIONS
Finally, our review emphasizes Hepatozoon as a potential disease agent in threatened wild mammals and the role of wild canids as spreaders of Hepatozoon infections in the Americas.
Topics: Animals; Cats; Ecosystem; Phylogeny; Chiroptera; Eucoccidiida; Shrews; Animals, Wild; Canidae
PubMed: 38444020
DOI: 10.1186/s13071-024-06154-3 -
Disease Markers 2020The gut microbiota has been presumed to have a role in the pathogenesis of type 1 diabetes (T1D). Significant changes in the microbial composition of T1D patients have... (Review)
Review
The gut microbiota has been presumed to have a role in the pathogenesis of type 1 diabetes (T1D). Significant changes in the microbial composition of T1D patients have been reported in several case-control studies. This study is aimed at systematically reviewing the existing literature, which has investigated the alterations of the intestinal microbiome in T1D patients compared with healthy controls (HCs) using 16S ribosomal RNA-targeted sequencing. The databases of MEDLINE, EMBASE, Web of Science, and the Cochrane Library were searched until April 2019 for case-control studies comparing the composition of the intestinal microbiome in T1D patients and HCs based on 16S rRNA gene sequencing techniques. The Newcastle-Ottawa Scale was used to assess the methodological quality. Ten articles involving 260 patients with T1D and 276 HCs were included in this systematic review. The quality scores of all included studies were 6-8 points. In summary, a decreased microbiota diversity and a significantly distinct pattern of clustering with regard to -diversity were observed in T1D patients when compared with HCs. At the phylum level, T1D was characterised by a reduced ratio of in the structure of the gut community, although no consistent conclusion was reached. At the genus or species level, T1D patients had a reduced abundance of and compared with HCs, whereas and were found to be more enriched in T1D patients. This systematic review identified that there is a close association between the gut microbiota and development of T1D. Moreover, gut dysbiosis might be involved in the pathogenesis of T1D, although the causative role of gut microbiota remains to be established. Further well-controlled prospective studies are needed to better understand the role of the intestinal microbiome in the pathogenesis of T1D, which may help explore novel microbiota-based strategies to prevent and treat T1D.
Topics: Bacteria; DNA, Bacterial; DNA, Ribosomal; Diabetes Mellitus, Type 1; Gastrointestinal Microbiome; Humans; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32908614
DOI: 10.1155/2020/3936247 -
PloS One 2022The incidence of women developing gestational diabetes mellitus (GDM) is increasing, which is associated with an increased risk of type 2 diabetes mellitus (T2DM) for...
BACKGROUND
The incidence of women developing gestational diabetes mellitus (GDM) is increasing, which is associated with an increased risk of type 2 diabetes mellitus (T2DM) for both mother and child. Gut microbiota dysbiosis may contribute to the pathogenesis of both GDM and the accompanying risk of T2DM. Thus, a better understanding of the microbial communities associated with GDM could offer a potential target for intervention and treatment in the future. Therefore, we performed a systematic review to investigate if the GDM women have a distinct gut microbiota composition compared to non-GDM women.
METHODS
We identified 21 studies in a systematic literature search of Embase and PubMed up to February 24, 2021. Data on demographics, methodology and identified microbial metrics were extracted. The quality of each study was assessed according to the Newcastle-Ottawa Scale.
RESULTS
Sixteen of the studies did find a GDM-associated gut microbiota, although no consistency could be seen. Only Collinsella and Blautia showed a tendency to be increased in GDM women, whereas the remaining genera were significantly different in opposing directions.
CONCLUSION
Although most of the studies found an association between GDM and gut microbiota dysbiosis, no overall GDM-specific gut microbiota could be identified. All studies in the second trimester found a difference between GDM and non-GDM women, indicating that dysbiosis is present at the time of diagnosis. Nevertheless, it is still unclear when the dysbiosis develops, as no consensus could be seen between the studies investigating the gut microbiota in the first trimester of pregnancy. However, studies varied widely concerning methodology and study design, which might explain the highly heterogeneous gut microbiota compositions between studies. Therefore, future studies need to include multiple time points and consider possible confounding factors such as ethnicity, pre-pregnancy body mass index, and GDM treatment.
Topics: Adult; Body Mass Index; Diabetes Mellitus, Type 2; Diabetes, Gestational; Dysbiosis; Female; Gastrointestinal Microbiome; Humans; Microbiota; Pregnancy; RNA, Ribosomal, 16S
PubMed: 35025980
DOI: 10.1371/journal.pone.0262618 -
Clinical Infectious Diseases : An... Feb 2020Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and metadata from published studies to examine α-diversity measures between HIV-uninfected (HIV-) and HIV-infected (HIV+) individuals.
METHODS
We conducted a systematic review and individual level meta-analysis by searching Embase, Medline, and Scopus for original research studies (inception to 31 December 2017). Included studies reported 16S rRNA gene sequences of fecal samples from HIV+ patients. Raw sequence reads and metadata were obtained from public databases or from study authors. Raw reads were processed through standardized pipelines with use of a high-resolution taxonomic classifier. The χ2 test, paired t tests, and generalized linear mixed models were used to relate α-diversity measures and clinical metadata.
RESULTS
Twenty-two studies were identified with 17 datasets available for analysis, yielding 1032 samples (311 HIV-, 721 HIV+). HIV status was associated with a decrease in measures of α-diversity (P < .001). However, in stratified analysis, HIV status was associated with decreased α-diversity only in women and in men who have sex with women (MSW) but not in men who have sex with men (MSM). In analyses limited to women and MSW, controlling for HIV status, women displayed increased α-diversity compared with MSW.
CONCLUSIONS
Our study suggests that HIV status, sexual risk category, and gender impact gut microbial community α-diversity. Future studies should consider MSM status in gut microbiome analyses.
Topics: Female; Gastrointestinal Microbiome; HIV Infections; Homosexuality, Male; Humans; Male; RNA, Ribosomal, 16S; Sexual and Gender Minorities
PubMed: 30921452
DOI: 10.1093/cid/ciz258 -
Frontiers in Microbiology 2024The is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a...
The is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
PubMed: 38855772
DOI: 10.3389/fmicb.2024.1415698 -
Medicine Aug 2021Plenty of studies have showed matrix metalloproteinase 14 (MMP14) expression might be associated with the prognosis of gastric cancer (GC). However, no definite... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Plenty of studies have showed matrix metalloproteinase 14 (MMP14) expression might be associated with the prognosis of gastric cancer (GC). However, no definite conclusion has been obtained for the contradictory results.
METHODS
We searched PubMed, Web of science, Embase, and Cochrane library for eligible studies. The association between MMP14 expression and prognostic outcomes of GC was evaluated. Hazard ratio (HR) and 95% confidence interval (CI) were integrated to show the effect of MMP14 expression on the overall survival (OS) or recurrence-free survival (RFS). Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used to validate the association of MMP14 expression with OS or RFS in GC. A brief bioinformatics analysis was also performed to determine the prognostic role of MMP14 expression in GC.
RESULTS
High MMP14 expression was associated with shorter OS compared to low MMP14 expression in GC (HR = 1.95, P < .01). Patients with high MMP14 expression tended to have worse differentiation (P = .03), deeper tumor invasion (P < .01), earlier lymph node metastasis (P < .01), earlier distant metastasis (P < .01) and more advanced clinical stage (P < .01) compared to those with low MMP14 expression. The data from TCGA and GEO showed MMP14 was overexpressed in tumor tissues compared to normal tissues (P < .05), and high MMP14 expression was significantly related to shorter OS (HR = 1.70, 95% CI = 1.32-2.20, P < .01) and RFS (HR = 1.45, 95% CI = 1.15-1.83, P < .01) compared to low MMP14 expression in GC. Expression of MMP14 was linked to functional networks involving the biological process, metabolic process, response to stimulus, cell communication and so on. Functional network analysis suggested that MMP14 regulated the protein digestion and absorption, extracellular matrix receptor interaction, focal adhesion, ribosome, spliceosome, and so on.
CONCLUSION
High MMP14 expression was associated with worse prognosis of GC compared to low MMP14 expression. MMP14 expression could serve as a prognostic factor and potential therapeutic target of GC.
Topics: Biomarkers, Tumor; DNA, Neoplasm; Disease Progression; Gene Expression Regulation, Neoplastic; Humans; Matrix Metalloproteinase 14; Prognosis; Stomach Neoplasms
PubMed: 34397871
DOI: 10.1097/MD.0000000000026545