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Pediatric Research Jan 2024The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated...
BACKGROUND
The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated how pre- and perinatal factors influence the composition of the meconium microbiota.
METHODS
We performed the systematic review using Covidence by searching PubMed, Scopus, and Web of Science databases with the search terms "meconium microbiome" and "meconium microbiota". In the cohort study, we performed 16 S rRNA gene sequencing on 393 meconium samples and analyzed the sequencing data using QIIME2.
RESULTS
Our systematic review identified 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition in relation to subsequent health of infants but gave only limited comparative evidence regarding factors related to the composition of the meconium microbiota. The cohort study pointed to a low-biomass microbiota consisting of the phyla Firmicutes, Proteobacteria and Actinobacteriota and the genera Staphylococcus, Escherichia-Shigella and Lactobacillus, and indicated that immediate perinatal factors affected the composition of the meconium microbiota more than did prenatal factors.
CONCLUSIONS
This finding supports the idea that the meconium microbiota mostly starts developing during delivery.
IMPACT
It is unclear when the first-pass meconium microbiota develops, and what are the sources of the colonization. In this systematic review, we found 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition relative to subsequent health of infants, but there was no consensus on the factors affecting the meconium microbiota development. In this cohort study, immediate perinatal factors markedly affected the meconium microbiota development while prenatal factors had little effect on it. As the meconium microbiota composition was influenced by immediate perinatal factors, the present study supports the idea that the initial gut microbiota develops mainly during delivery.
Topics: Infant, Newborn; Pregnancy; Infant; Female; Humans; Meconium; Cohort Studies; Microbiota; Gastrointestinal Microbiome; Bacteria; RNA, Ribosomal, 16S
PubMed: 37591927
DOI: 10.1038/s41390-023-02783-z -
Journal of Clinical Microbiology Sep 2023rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the... (Meta-Analysis)
Meta-Analysis
Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis.
rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.
Topics: Humans; Anti-Bacterial Agents; Bacteria; Genes, rRNA; Meta-Analysis as Topic; Mycoses; Polymerase Chain Reaction; RNA, Ribosomal, 16S; RNA, Ribosomal, 18S; Sensitivity and Specificity; Systematic Reviews as Topic
PubMed: 37367430
DOI: 10.1128/jcm.00338-23 -
Nutrients Nov 2022Gut microbiota (GM) after bariatric surgery (BS) has been considered as a factor associated with metabolic improvements and weight loss. In this systematic review, we... (Review)
Review
Gut microbiota (GM) after bariatric surgery (BS) has been considered as a factor associated with metabolic improvements and weight loss. In this systematic review, we evaluate changes in the GM, characterized by 16S rRNA and metagenomics techniques, in obese adults who received BS. The PubMed, Scopus, Web of Science, and LILACS databases were searched. Two independent reviewers analyzed articles published in the last ten years, using Rayyan QCRI. The initial search resulted in 1275 documents, and 18 clinical trials were included after the exclusion criteria were applied. The predominance of intestinal bacteria phyla varied among studies; however, most of them reported a greater amount of (B), (P), and diversity (D) after BS. (F), B, and the (F/B) ratio was inconsistent, increasing or decreasing after Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG) were conducted, compared to before surgery. There was a reduction in the relative proportion of F. Moreover, a higher proportion of (A) was observed after RYGB was conducted. However, the same was not identified when SG procedures were applied. Genera abundance and bacteria predominance varied according to the surgical procedure, with limited data regarding the impact on phyla. The present study was approved by PROSPERO, under registration number CRD42020209509.
Topics: Humans; RNA, Ribosomal, 16S; Bariatric Surgery; Gastric Bypass; Gastrointestinal Microbiome; Gastrectomy; Bacteria; Obesity, Morbid; Treatment Outcome
PubMed: 36501007
DOI: 10.3390/nu14234979 -
PeerJ 2021Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of (also known as...
BACKGROUND
Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes.
METHODOLOGY
A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms "vaginal microbiome", "pregnancy", and "16S rRNA sequencing". Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester.
RESULTS
Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS ( = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting.
CONCLUSION
Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.
PubMed: 34046261
DOI: 10.7717/peerj.11437 -
Animals : An Open Access Journal From... May 2023Florfenicol is a broad-spectrum bacteriostatic antibiotic used exclusively in veterinary medicine in order to treat the pathology of farm and aquatic animals. It is a... (Review)
Review
Florfenicol is a broad-spectrum bacteriostatic antibiotic used exclusively in veterinary medicine in order to treat the pathology of farm and aquatic animals. It is a synthetic fluorinated analog of thiamphenicol and chloramphenicol that functions by inhibiting ribosomal activity, which disrupts bacterial protein synthesis and has shown over time a strong activity against Gram-positive and negative bacterial groups. Florfenicol was also reported to have anti-inflammatory activity through a marked reduction in immune cell proliferation and cytokine production. The need for improvement came from (1) the inappropriate use (to an important extent) of this antimicrobial, which led to serious concerns about florfenicol-related resistance genes, and (2) the fact that this antibiotic has a low water solubility making it difficult to formulate an aqueous solution in organic solvents, and applicable for different routes of administration. This review aims to synthesize the various applications of florfenicol in veterinary medicine, explore the potential use of nanotechnology to improve its effectiveness and analyze the advantages and limitations of such approaches. The review is based on data from scientific articles and systematic reviews identified in several databases.
PubMed: 37238125
DOI: 10.3390/ani13101695 -
Microbiology Spectrum Jun 2023Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using... (Meta-Analysis)
Meta-Analysis
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that changed significantly and decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C ( = 0.220 and = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
Topics: Humans; Gastrointestinal Microbiome; Preservation, Biological; Feces; Ethanol; Specimen Handling; Biodiversity; Nitrogen; RNA, Ribosomal, 16S
PubMed: 37093040
DOI: 10.1128/spectrum.04297-22 -
Genes & Nutrition Jul 2021Peripheral blood mononuclear cells (PBMCs) have shown promise as a tissue sensitive to subtle and possibly systemic transcriptomic changes, and as such may be useful in... (Review)
Review
BACKGROUND AND OBJECTIVES
Peripheral blood mononuclear cells (PBMCs) have shown promise as a tissue sensitive to subtle and possibly systemic transcriptomic changes, and as such may be useful in identifying responses to weight loss interventions. The primary aim was to comprehensively evaluate the transcriptomic changes that may occur during weight loss and to determine if there is a consistent response across intervention types in human populations of all ages.
METHODS
Included studies were randomised control trials or cohort studies that administered an intervention primarily designed to decrease weight in any overweight or obese human population. A systematic search of the literature was conducted to obtain studies and gene expression databases were interrogated to locate corresponding transcriptomic datasets. Datasets were normalised using the ArrayAnalysis online tool and differential gene expression was determined using the limma package in R. Over-represented pathways were explored using the PathVisio software. Heatmaps and hierarchical clustering were utilised to visualise gene expression.
RESULTS
Seven papers met the inclusion criteria, five of which had raw gene expression data available. Of these, three could be grouped into high responders (HR, ≥ 5% body weight loss) and low responders (LR). No genes were consistently differentially expressed between high and low responders across studies. Adolescents had the largest transcriptomic response to weight loss followed by adults who underwent bariatric surgery. Seven pathways were altered in two out of four studies following the intervention and the pathway 'cytoplasmic ribosomal proteins' (WikiPathways: WP477) was altered between HR and LR at baseline in the two datasets with both groups. Pathways related to 'toll-like receptor signalling' were altered in HR response to the weight loss intervention in two out of three datasets.
CONCLUSIONS
Transcriptomic changes in PBMCs do occur in response to weight change. Transparent and standardised data reporting is needed to realise the potential of transcriptomics for investigating phenotypic features.
REGISTRATION NUMBER
PROSPERO: CRD42019106582.
PubMed: 34281497
DOI: 10.1186/s12263-021-00692-6 -
Frontiers in Cellular and Infection... 2021The development of periodontitis is associated with an imbalanced subgingival microbial community enriched with species such as the traditionally classified red-complex... (Meta-Analysis)
Meta-Analysis
The development of periodontitis is associated with an imbalanced subgingival microbial community enriched with species such as the traditionally classified red-complex bacteria (, , and ). Saliva has been suggested as an alternative to subgingival plaque for the microbial analysis due to its easy and non-invasive collection. This systematic review aims to determine whether the levels of red-complex bacteria assessed using saliva reflect those in subgingival plaque from periodontitis patients. The MEDLINE, EMBASE, and Cochrane Library databases were searched up to April 30, 2021. Studies were considered eligible if microbial data of at least one of the red-complex species were reported in both saliva and subgingival plaque from periodontitis patients, based on DNA-based methods. Of the 17 included studies, 4 studies used 16S rRNA gene sequencing techniques, and the rest used PCR-based approaches. The detection frequency of each red-complex species in periodontitis patients was reported to be > 60% in most studies, irrespective of samples types. Meta-analyses revealed that both detection frequencies and relative abundances of red-complex bacteria in saliva were significantly lower than those in subgingival plaque. Moreover, the relative abundances of all 3 bacterial species in saliva showed significantly positive correlation with those in subgingival plaque. In conclusion, current evidence suggests that one-time saliva sampling cannot replace subgingival plaque for microbial analysis of the red-complex bacteria in periodontitis patients. Given the positive microbial associations between saliva and subgingival plaque, a thorough review of longitudinal clinical studies is needed to further assess the role of saliva.
Topics: Aggregatibacter actinomycetemcomitans; Humans; Periodontitis; Porphyromonas gingivalis; RNA, Ribosomal, 16S; Saliva; Treponema denticola
PubMed: 34692561
DOI: 10.3389/fcimb.2021.727732 -
Autoimmunity Reviews Mar 2020The discovery of autoantibodies to ribosomal proteins (anti-RibP) dates back more than fifty years when antibodies to ribosomes were identified in systemic lupus... (Meta-Analysis)
Meta-Analysis
The discovery of autoantibodies to ribosomal proteins (anti-RibP) dates back more than fifty years when antibodies to ribosomes were identified in systemic lupus erythematosus (SLE) sera. Over the years, anti-RibP autoantibodies have been the subject of extensive study and became known as a highly specific biomarker for the diagnosis of SLE and were associated with neuropsychiatric SLE (NPSLE), lupus nephritis (LN) and hepatitis (LH). As demonstrated by studies on cultured human cells and of murine models, there is evidence to suggest that anti-RibP may have a pathogenic role in LN and NPSLE. Despite a wealth of evidence, in comparison to other SLE autoantibodies such as anti-Sm and anti-dsDNA, anti-RibP has not been included in classification criteria for SLE. A significant challenge is the variability of assays used to detect anti-RibP, including the antigens and diagnostic platforms employed. This may account for the marked variation in frequencies (10-47%) in SLE and its association with clinical and demographic features reported in SLE cohorts. We performed a systematic literature review and meta-analysis to help clarify its prevalence, various clinical and serological associations in SLE based on the different RibP antigens and assay platforms used.
Topics: Animals; Autoantibodies; Humans; Lupus Erythematosus, Systemic; Lupus Nephritis; Lupus Vasculitis, Central Nervous System; Mice; Ribosomal Proteins
PubMed: 31927088
DOI: 10.1016/j.autrev.2020.102463 -
Journal of Reproductive Immunology Feb 2022To assess the available scientific evidence regarding the placental microbial composition of a healthy pregnancy, the quality of this evidence, and the potential...
OBJECTIVE
To assess the available scientific evidence regarding the placental microbial composition of a healthy pregnancy, the quality of this evidence, and the potential relation between placental and oral microbiome.
MATERIALS AND METHODS
Data sources: MEDLINE and EMBASE up to August 1, 2019.
STUDY ELIGIBILITY CRITERIA
Human subjects; healthy women; term deliveries; healthy normal birth weight; assessment of microorganisms (bacteria) in placental tissue; full research papers in English. The quality of the included studies was assessed by a modified Joanna Briggs Institute checklist for analytical cross-sectional studies.
RESULTS
57 studies passed the inclusion criteria. Of these, 33 had a high risk of quality bias (e.g., insufficient infection control, lack of negative controls, poor description of the healthy cases). The remaining 24 studies had a low (N = 12) to moderate (N = 12) risk of bias and were selected for in-depth analysis. Of these 24 studies, 22 reported microorganisms in placental tissues, where Lactobacillus (11 studies), Ureaplasma (7), Fusobacterium (7), Staphylococcus (7), Prevotella (6) and Streptococcus (6) were among the most frequently identified genera. Methylobacterium (4), Propionibacterium (3), Pseudomonas (3) and Escherichia (2), among others, although frequently reported in placental samples, were often reported as contaminants in studies that used negative controls.
CONCLUSIONS
The results support the existence of a low biomass placental microbiota in healthy pregnancies. Some of the microbial taxa found in the placenta might have an oral origin. The high risk of quality bias for the majority of the included studies indicates that the results of individual papers should be interpreted with caution.
Topics: Adult; Animals; Female; Fusobacterium; Healthy Volunteers; Humans; Lactobacillus; Microbiota; Placenta; Pregnancy; RNA, Ribosomal, 16S; Ureaplasma
PubMed: 34883392
DOI: 10.1016/j.jri.2021.103455