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The American Journal of Clinical... Apr 2019Irritable bowel syndrome (IBS) and other functional bowel disorders (FBDs) are prevalent disorders with altered microbiota. Prebiotics positively augment gut microbiota... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Irritable bowel syndrome (IBS) and other functional bowel disorders (FBDs) are prevalent disorders with altered microbiota. Prebiotics positively augment gut microbiota and may offer therapeutic potential.
OBJECTIVES
The aim of this study was to investigate the effect of prebiotics compared with placebo on global response, gastrointestinal symptoms, quality of life (QoL), and gut microbiota, via systematic review and meta-analysis of randomized controlled trials (RCTs) in adults with IBS and other FBDs.
METHODS
Studies were identified using electronic databases, back-searching reference lists, and hand-searching abstracts. RCTs that compared prebiotics to placebo in adults with IBS or other FBDs were included. Two reviewers independently performed screening, data extraction, and bias assessment. Outcome data were synthesized as ORs, weighted mean differences (WMDs) or standardized mean differences (SMDs) with the use of a random-effects model. Subanalyses were performed for type of FBD and dose, type, and duration of prebiotic.
RESULTS
Searches identified 2332 records, and 11 RCTs were eligible (729 patients). The numbers responding were 52/97 (54%) for prebiotic and 59/94 (63%) for placebo, with no difference between groups (OR: 0.62; 95% CI: 0.07, 5.69; P = 0.67). Similarly, no differences were found for severity of abdominal pain, bloating and flatulence, and QoL score between prebiotics and placebo. However, flatulence severity was improved by prebiotics at doses ≤6 g/d (SMD: -0.35; 95% CI: -0.71, 0.00; P = 0.05) and by non-inulin-type fructan prebiotics (SMD: -0.34; 95% CI: -0.66, -0.01; P = 0.04), while inulin-type fructans worsened flatulence (SMD: 0.85; 95% CI: 0.23, 1.47; P = 0.007). Prebiotics increased absolute abundance of bifidobacteria (WMD: 1.16 log10 copies of the 16S ribosomal RNA gene; 95% CI: 0.06, 2.26; P = 0.04). No studies were at low risk of bias across all bias categories.
CONCLUSIONS
Prebiotics do not improve gastrointestinal symptoms or QoL in patients with IBS or other FBDs, but they do increase bifidobacteria. Variations in prebiotic type and dose impacted symptom improvement or exacerbation. This review was registered at PROSPERO as CRD42017074072.
Topics: Adult; Female; Gastrointestinal Microbiome; Humans; Intestinal Diseases; Irritable Bowel Syndrome; Male; Middle Aged; Prebiotics; Quality of Life; Randomized Controlled Trials as Topic; Young Adult
PubMed: 30949662
DOI: 10.1093/ajcn/nqy376 -
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 Genetics 2018This present research work reports the comparative analysis of the entire nucleotide sequence of mitochondrial genomes of and and phylogenetic analyses of their...
This present research work reports the comparative analysis of the entire nucleotide sequence of mitochondrial genomes of and and phylogenetic analyses of their protein-coding genes in order to establish their phylogenetic relationship within Cichlids. The mitochondrial genomes of and are 16,583 and 16,580 base pairs long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region (D-loop) which is 888 and 887 base pairs long, respectively, showing the same gene order and identical number of gene or regions with other well-elucidated mitogenomes of Cichlids. However, with exception of cytochrome-c oxidase subunit-1 () gene, all the identified PCGs were initiated by ATG-codons. Structurally, 11 tRNA genes in species and 9 tRNA genes in species, folded into typical clover-leaf secondary structure created by the regions of self-complementarity within tRNA. All the 22 tRNA genes in both species lack variable loop. Moreover, 28 genes which include 12-protein-coding genes are encoded on the H-strand and the remaining 9 genes including one protein-coding gene are encoded on the L-strand. Thirteen sequences of concatenated mitochondrial protein-coding genes were aligned using MUSCLE, and the phylogenetic analyses performed using maximum likelihood and Bayesian inference showed that and had a broad phylogenetic relationship. These results may be a useful tool in resolving higher-level relationships in organisms and a useful dataset for studying the evolution of the Cichlidae mitochondrial genome, since Cichlids are well-known model species in the study of evolutionary biology, because of their extreme morphological, biogeographical, parental care behavior for eggs and larvae and phylogenetic diversities.
PubMed: 30894873
DOI: 10.3389/fgene.2018.00651 -
Clinical and Translational... Feb 2019Alterations of gut microbiota have been thought to be associated with irritable bowel syndrome (IBS). Many studies have reported significant alterations of gut...
INTRODUCTION
Alterations of gut microbiota have been thought to be associated with irritable bowel syndrome (IBS). Many studies have reported significant alterations of gut microbiota in patients with IBS based on 16S ribosomal RNA-targeted sequencing. However, results from these studies are inconsistent or even contradictory. We performed a systematic review to explore the alterations of gut microbiota in patients with IBS compared with healthy controls (HCs).
METHODS
The databases PubMed, Cochrane Library, Web of Science, and Embase were searched for studies published until February 28, 2018, for case-control studies detecting gut microbiota in patients with IBS. Methodological quality was assessed using the Newcastle-Ottawa Scale. The α-diversity and alterations of gut microbiota in patients with IBS compared with HCs were analyzed.
RESULTS
Sixteen articles involving 777 patients with IBS and 461 HCs were included. Quality assessment scores of the studies ranged from 5 to 7. For most studies, patients with IBS had a lower α-diversity than HCs in both fecal and mucosal samples. Relatively consistent changes in fecal microbiota for patients with IBS included increased Firmicutes, decreased Bacteroidetes, and increased Firmicutes:Bacteroidetes ratio at the phylum level, as well as increased Clostridia and Clostridiales, decreased Bacteroidia and Bacteroidales at lower taxonomic levels. Results for mucosal microbiota were inconsistent.
CONCLUSIONS
Alterations of gut microbiota exist in patients with IBS and have significant association with the development of IBS. Further studies are needed to draw conclusions about gut microbiota changes in patients with IBS.
TRANSLATIONAL IMPACT
This knowledge might improve the understanding of microbial signatures in patients with IBS and would guide future therapeutic strategies.
Topics: Bacteria; DNA, Bacterial; Feces; Gastrointestinal Microbiome; Humans; Irritable Bowel Syndrome; RNA, Ribosomal, 16S
PubMed: 30829919
DOI: 10.14309/ctg.0000000000000012 -
Scientific Reports Feb 2019Microsporidia are a diverse parasite phylum infecting host from all major taxa in all global biomes. This research was conducted to conclude the prevalence of... (Meta-Analysis)
Meta-Analysis
Microsporidia are a diverse parasite phylum infecting host from all major taxa in all global biomes. This research was conducted to conclude the prevalence of microsporidia in China. All published articles up to February 16, 2018 were considered, including descriptive, cross-sectional, case-control and epidemiology studies. A total of 1052 articles were separated after literature search. After a strict selection according to our criteria, 82 articles were included in qualitative synthesis and ultimately 52 studies were included in quantitative synthesis. Three species of microsporidia were confirmed to exist in China, including Enterocytozoon bieneusi (E. bieneusi), Nosema and Encephalitozoon cuniculi (E. cuniculi). The highest overall estimated prevalence of E. bieneusi in humans was 8.1%, which was observed in acquired immunodeficiency syndrome patients (AIDS). Moreover, the prevalence of E. bieneusi in animals including the cattle, dogs, pigs, deer, sheep and goats were analyszed in this study. The overall estimated prevalence of E. bieneusi acquired by using the random effects model in meta-analysis in cattle, dogs, pigs, sheep and goats and deer was 20.0% (95% confidence intervals: 0.133-0.266, I = 98.031%, p < 0.0001), 7.8% (95% CI: 0.050-0.106, I = 60.822%, p = 0.0537), 45.1% (95% CI: 0.227-0.674, I = 98.183%, p < 0.0001), 28.1% (95% CI: 0.146-0.415, I = 98.716%, p < 0.0001) and 19.3% (95% CI: 0.084-0.303, I = 96.995%, p < 0.0001) respectively. The overall detection rate of E. bieneusi in water acquired by using the random effects model in meta-analysis was 64.5% (95% CI: 0.433-0.857, I = 98.486%, p < 0.0001). Currently, 221 genotypes of E. bieneusi, 1 genotype of E. cuniculi and 6 Nosema were detected in China. The most prevalent genotype of E. bieneusi was genotype D, followed by BEB6 and EbpC.
Topics: Animals; Cattle; China; DNA, Ribosomal Spacer; Deer; Dogs; Encephalitozoon cuniculi; Enterocytozoon; Genetic Variation; Genotype; Goats; Humans; Microsporidia; Microsporidiosis; Nosema; Phylogeny; Sheep; Swine
PubMed: 30816168
DOI: 10.1038/s41598-019-39290-3 -
PLoS Neglected Tropical Diseases Feb 2018Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people. Unfortunately, its... (Review)
Review
BACKGROUND
Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people. Unfortunately, its diagnosis is hampered by the lack of a gold standard, as the sensitivity of traditional parasitological tests (including microscopic examination of stool samples and coproculture) is low. Hence, alternative diagnostic methods, such as molecular biology techniques (mostly polymerase chain reaction, PCR) have been implemented. However, there are discrepancies in the reported accuracy of PCR.
METHODOLOGY
A systematic review with meta-analysis was conducted in order to evaluate the accuracy of PCR for the diagnosis of S. stercoralis infection. The protocol was registered with PROSPERO International Prospective Register of Systematic Reviews (record: CRD42016054298). Fourteen studies, 12 of which evaluating real-time PCR, were included in the analysis. The specificity of the techniques resulted high (ranging from 93 to 95%, according to the reference test(s) used). When all molecular techniques were compared to parasitological methods, the sensitivity of PCR was assessed at 71.8% (95% CI 52.2-85.5), that decreased to 61.8% (95% CI 42.0-78.4) when serology was added among the reference tests. Similarly, sensitivity of real-time PCR resulted 64.4% (95% CI 46.2-77.7) when compared to parasitological methods only, 56.5% (95% CI 39.2-72.4) including serology.
CONCLUSIONS
PCR might not be suitable for screening purpose, whereas it might have a role as a confirmatory test.
Topics: Animals; DNA, Helminth; Databases, Factual; Humans; Meta-Analysis as Topic; Molecular Diagnostic Techniques; RNA, Ribosomal, 18S; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Strongyloides stercoralis; Strongyloidiasis
PubMed: 29425193
DOI: 10.1371/journal.pntd.0006229 -
Asian Pacific Journal of Tropical... Sep 2017To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various... (Review)
Review
OBJECTIVE
To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.
METHODS
We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.
RESULTS
T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F) was from low to high values (0.02433-0.41892). The statistically F points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates.
CONCLUSIONS
An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.
PubMed: 29080613
DOI: 10.1016/j.apjtm.2017.08.011 -
Microbiome Mar 2017Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.
METHODS AND RESULTS
Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).
CONCLUSIONS
Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
Topics: Bacteria; Bacteroides; Dysbiosis; Enterocolitis, Necrotizing; Feces; Firmicutes; Gastrointestinal Microbiome; Humans; Infant, Newborn; Infant, Premature; Infant, Premature, Diseases; Intestines; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 28274256
DOI: 10.1186/s40168-017-0248-8 -
Trends in Genetics : TIG Feb 2017Our understanding of gene expression has come far since the 'one-gene one-polypeptide' hypothesis proposed by Beadle and Tatum. In this review, we address the gradual... (Review)
Review
Our understanding of gene expression has come far since the 'one-gene one-polypeptide' hypothesis proposed by Beadle and Tatum. In this review, we address the gradual recognition that a growing number of polycistronic genes, originally discovered in viruses, are being identified within the mammalian genome, and that these may provide new insights into disease mechanisms and treatment. We carried out a systematic literature review identifying 13 mammalian genes for which there is evidence for polycistronic expression via translation through an internal ribosome entry site (IRES). Although the canonical mechanism of translation initiation has been studied extensively, here we highlight a process of noncanonical translation, IRES-mediated translation, that is a growing source for understanding complex inheritance, the elucidation of disease mechanisms, and the discovery of novel therapeutic targets. Identification of additional polycistronic genes may provide new insights into disease therapy and allow for new discoveries of both translational and disease mechanisms.
Topics: Animals; Genetic Diseases, Inborn; Humans; Internal Ribosome Entry Sites; Mammals; Molecular Targeted Therapy; Protein Biosynthesis; RNA, Messenger
PubMed: 28012572
DOI: 10.1016/j.tig.2016.11.007 -
BMC Cancer Nov 2016Mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase responsible for regulating ribosomal biogenesis and protein synthesis. Dysregulation of mTOR... (Meta-Analysis)
Meta-Analysis Review
Clinicopathological and prognostic significance of mTOR and phosphorylated mTOR expression in patients with esophageal squamous cell carcinoma: a systematic review and meta-analysis.
BACKGROUND
Mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase responsible for regulating ribosomal biogenesis and protein synthesis. Dysregulation of mTOR contributes to tumorigenesis, angiogenesis, cellular growth and metastasis but its roles in esophageal squamous cell carcinoma (ESCC) are controversial. Therefore, the objective of this study is to evaluate the prognostic and clinicopathological significance of mTOR/p-mTOR expression in ESCC.
METHODS
Literature retrieval was conducted by searching PubMed, EMBASE and the Web of Science for full-text papers that met our eligibility criteria. Odds ratio (OR) and hazard ratio (HR) with 95 % confidence interval (CI) served as the appropriate summarized statistics for assessments of clinicopathological and prognostic significance, respectively. Cochrane Q-test and I-statistic were adopted to estimate the heterogeneity level between studies. Potential publication bias was detected by Begg's test and Egger's test.
RESULTS
A total of 915 ESCC patients from nine original articles were included into this meta-analysis. The pooled analyses suggested that mTOR/p-mTOR expression was significantly correlated with the unfavorable outcomes of differentiation degree (OR: 2.63; 95 % CI: 1.71-4.05; P = 0.001), tumor invasion (OR: 1.48; 95 % CI: 1.02-2.13; P = 0.037), TNM stage (OR: 2.25; 95 % CI: 1.05-4.82; P = 0.037) and lymph node metastasis (OR: 1.82; 95 % CI: 1.06-3.11; P = 0.029), but had no significant relationship to the genders (OR: 0.81; 95 % CI: 0.50-1.32; P = 0.396). Moreover, mTOR/p-mTOR expression could independently predict the worse overall survival (HR: 2.04; 95 % CI: 1.58-2.62; P < 0.001), disease-free survival (HR: 2.39; 95 % CI: 1.64-3.49; P < 0.001) and cancer-specific survival (HR: 1.62; 95 % CI: 1.18-2.23; P = 0.003) of patients with ESCC. Such prognostic value of mTOR was not substantially altered by further subgroup analyses.
CONCLUSIONS
Positive expression of mTOR and p-mTOR was significantly associated with the unfavorable conditions on the depth of tumor invasion, TNM stage, differentiation degree and lymph node metastasis. mTOR and p-mTOR could serve as a valuable predictor for the poor prognosis of ESCC. More high-quality worldwide studies performing a multivariate analysis based on larger sample size are urgently required for further verifying and modifying our findings in the future.
Topics: Biomarkers, Tumor; Carcinoma, Squamous Cell; Esophageal Neoplasms; Humans; Lymphatic Metastasis; Neoplasm Invasiveness; Phosphoproteins; Phosphorylation; Prognosis; Protein Processing, Post-Translational; Survival Analysis; TOR Serine-Threonine Kinases
PubMed: 27835987
DOI: 10.1186/s12885-016-2940-7