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Journal of Zhejiang University.... Dec 2022: Osteoporosis (OP) has become a major public health issue, threatening the bone health of middle-aged and elderly people from all around the world. Changes in the gut... (Meta-Analysis)
Meta-Analysis
: Osteoporosis (OP) has become a major public health issue, threatening the bone health of middle-aged and elderly people from all around the world. Changes in the gut microbiota (GM) are correlated with the maintenance of bone mass and bone quality. However, research results in this field remain highly controversial, and no systematic review or meta-analysis of the relationship between GM and OP has been conducted. This paper addresses this shortcoming, focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA (rRNA) gene sequencing results, in order to provide new clinical reference information for future customized prevention and treatment options of OP. : According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we comprehensively searched the databases of PubMed, Web of Science, Embase, Cochrane Library, and China National Knowledge Infrastructure (CNKI). In addition, we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis. We also implemented the Newcastle-Ottawa Scale (NOS), funnel plot analysis, sensitivity analysis, Egger's test, and Begg's test to assess the risk of bias. : This research ultimately considered 12 studies, which included the fecal GM data of 2033 people (604 with OP and 1429 healthy controls). In the included research papers, it was observed that the relative abundance of and increased in the OP group, while the relative abundance for of Bacteroidetes increased (except for Ireland). Meanwhile, Firmicutes, , , , and showed reduced relative abundance in Chinese studies. In the linear discriminant analysis Effect Size (LEfSe) analysis, certain bacteria showed statistically significant results consistently across different studies. : This observational meta-analysis revealed that changes in the GM were correlated with OP, and variations in some advantageous GM might involve regional differences.
Topics: Aged; Humans; Middle Aged; Feces; Gastrointestinal Microbiome; Genes, rRNA; Osteoporosis; RNA, Ribosomal, 16S
PubMed: 36518053
DOI: 10.1631/jzus.B2200344 -
International Journal of Antimicrobial... Aug 2023Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing... (Meta-Analysis)
Meta-Analysis Review
Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.
Topics: Humans; Aeromonas; Wastewater; Global Health; One Health; RNA, Ribosomal, 16S; Drug Resistance, Bacterial; Anti-Bacterial Agents; Anti-Infective Agents
PubMed: 37201798
DOI: 10.1016/j.ijantimicag.2023.106848 -
Clinical and Experimental Dental... Dec 2022Diet is one of the main factors influencing the diversity and interactions of the oral microbiota. The purpose of this study is to determine the impact of sugar intake... (Review)
Review
OBJECTIVES
Diet is one of the main factors influencing the diversity and interactions of the oral microbiota. The purpose of this study is to determine the impact of sugar intake on the microbial diversity and bacteria that predominate under these conditions.
MATERIAL AND METHODS
A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guide, using the PubMed, Scopus, and Science Direct databases and combinations of the words "microbiota," "microbiology," "bacteria," "sugars," "dysbiosis," "caries," "microbiome," "oral microbial," and "oral microbiota profile pattern." The selection criteria included year, language, type of publication, comparison of microbiota during low and high sugar intake, and bacterial identification by molecular sequencing of the 16S subunit of ribosomal RNA.
RESULTS
Out of a total of 374 papers that came up after the initial search, 8 met the criteria for this review. The papers included research on populations comprising children, young adults, and adults, with most of the studies reporting selection criteria for the participants and using validated instruments to determine sugar intake. Apart from one study, all others reported for high sugar intake conditions a significant decrease in microbial diversity of the oral microbiome and the predominance of several bacterial genera or species, including Streptococcus, Scardovia, Veillonella, Rothia, Actinomyces, and Lactobacillus.
CONCLUSIONS
Sugar-rich diets have a significantly unfavorable effect on the diversity and balance of oral microbiota; however, further studies are required to determine the exact role of sugar in microbial interactions.
Topics: Child; Young Adult; Humans; Microbiota; Bacteria; Dental Caries; Dysbiosis; Sugars
PubMed: 35946056
DOI: 10.1002/cre2.640 -
Frontiers in Cellular and Infection... 2023is a Gram-negative oral anaerobic bacterium that plays a key role in the pathogenesis of periodontitis. expresses a variety of virulence factors that disrupt innate... (Review)
Review
is a Gram-negative oral anaerobic bacterium that plays a key role in the pathogenesis of periodontitis. expresses a variety of virulence factors that disrupt innate and adaptive immunity, allowing to survive and multiply in the host and destroy periodontal tissue. In addition to periodontal disease, is also associated with systemic diseases, of which insulin resistance is an important pathological basis. causes a systemic inflammatory response, disrupts insulin signaling pathways, induces pancreatic β-cell hypofunction and reduced numbers, and causes decreased insulin sensitivity leading to insulin resistance (IR). In this paper, we systematically review the studies on the mechanism of insulin resistance induced by , discuss the association between and systemic diseases based on insulin resistance, and finally propose relevant therapeutic approaches. Overall, through a systematic review of the mechanisms related to systemic diseases caused by through insulin resistance, we hope to provide new insights for future basic research and clinical interventions for related systemic diseases.
Topics: Humans; Porphyromonas gingivalis; Insulin Resistance; Base Composition; RNA, Ribosomal, 16S; Phylogeny; Sequence Analysis, DNA; Insulin
PubMed: 37520442
DOI: 10.3389/fcimb.2023.1209381 -
Nutrients Sep 2022Necrotizing enterocolitis (NEC) is the most devastating gastrointestinal emergency in preterm neonates. Research on early predictive biomarkers is fundamental. This is a... (Review)
Review
Necrotizing enterocolitis (NEC) is the most devastating gastrointestinal emergency in preterm neonates. Research on early predictive biomarkers is fundamental. This is a systematic review of studies applying untargeted metabolomics and gut microbiota analysis to evaluate the differences between neonates affected by NEC (Bell’s stage II or III), and/or by spontaneous intestinal perforation (SIP) versus healthy controls. Five studies applying metabolomics (43 cases, 95 preterm controls) and 20 applying gut microbiota analysis (254 cases, 651 preterm controls, 22 term controls) were selected. Metabolomic studies utilized NMR spectroscopy or mass spectrometry. An early urinary alanine/histidine ratio >4 showed good sensitivity and predictive value for NEC in one study. Samples collected in proximity to NEC diagnosis demonstrated variable pathways potentially related to NEC. In studies applying untargeted gut microbiota analysis, the sequencing of the V3−V4 or V3 to V5 regions of the 16S rRNA was the most used technique. At phylum level, NEC specimens were characterized by increased relative abundance of Proteobacteria compared to controls. At genus level, pre-NEC samples were characterized by a lack or decreased abundance of Bifidobacterium. Finally, at the species level Bacteroides dorei, Clostridium perfringens and perfringens-like strains dominated early NEC specimens, whereas Clostridium butyricum, neonatale and Propionibacterium acnei those at disease diagnosis. Six studies found a lower Shannon diversity index in cases than controls. A clear separation of cases from controls emerged based on UniFrac metrics in five out of seven studies. Importantly, no studies compared NEC versus SIP. Untargeted metabolomics and gut microbiota analysis are interrelated strategies to investigate NEC pathophysiology and identify potential biomarkers. Expression of quantitative measurements, data sharing via biorepositories and validation studies are fundamental to guarantee consistent comparison of results.
Topics: Alanine; Biomarkers; Enterocolitis, Necrotizing; Gastrointestinal Microbiome; Histidine; Humans; Infant, Newborn; Infant, Newborn, Diseases; Intestinal Perforation; Metabolome; RNA, Ribosomal, 16S
PubMed: 36145235
DOI: 10.3390/nu14183859 -
International Journal of Environmental... Sep 2022Recent advances in the development of next-generation sequencing (NGS) technologies, such as the 16S rRNA gene sequencing, have enabled significant progress in... (Review)
Review
Recent advances in the development of next-generation sequencing (NGS) technologies, such as the 16S rRNA gene sequencing, have enabled significant progress in characterizing the architecture of the oral microbiome. Understanding the taxonomic and functional components of the oral microbiome, especially during early childhood development, is becoming critical for identifying the interactions and adaptations of bacterial communities to dynamic conditions that may lead to the dysfunction of the host environment, thereby contributing to the onset and/or progression of a wide range of pathological conditions. We aimed to provide a comprehensive overview of the most recent evidence from studies of the oral microbiome of infants and young children, focusing on the development of oral microbiome in the window of birth to 18 years, focusing on infants. A systematic literature search was conducted in , , , and the WHO clinical trial website for relevant articles published between 2006 to 2022 to identify studies that examined genome-wide transcriptome of the oral microbiome in birth, early childhood, and adolescence performed via 16s rRNA sequence analysis. In addition, the references of selected articles were screened for other relevant studies. This systematic review was performed in accordance PRISMA guidelines. Data extraction and quality assessment were independently conducted by two authors, and a third author resolved discrepancies. Overall, 34 studies were included in this systematic review. Due to a considerable heterogeneity in study population, design, and outcome measures, a formal meta-analysis was not carried out. The current evidence indicates that a core microbiome is present in newborns, and it is stable in species number. Disparity about delivery mode influence are found. Further investigations are needed.
Topics: Adolescent; Bacteria; Child; Child, Preschool; High-Throughput Nucleotide Sequencing; Humans; Infant; Infant, Newborn; Microbiota; RNA, Ribosomal, 16S
PubMed: 36141674
DOI: 10.3390/ijerph191811403 -
Archives of Oral Biology Sep 2021To review published oral microbiome studies and create a comprehensive list of bacterial species found in saliva and dental plaque among healthy children and adults... (Review)
Review
OBJECTIVE
To review published oral microbiome studies and create a comprehensive list of bacterial species found in saliva and dental plaque among healthy children and adults associated with presence of carious lesions and caries-free state (oral health).
DESIGN
This review followed PRISMA-ScR guidelines. We searched published studies querying PUBMED and EMBASE using the following keywords: (plaque OR saliva) AND caries AND (next generation sequencing OR checkerboard OR 16s rRNA or qPCR). Studies were limited to human studies published in English between January 1, 2010 and June 24, 2020 that included > 10 caries-active and > 10 caries-free participants, and assessed the entire bacterial community.
RESULTS
Our search strategy identified 298 articles. After exclusion criteria, 22 articles remained; we considered 2 studies that examined saliva and plaque as separate studies, for a total of 24 studies. Species associated with caries or oral health varied widely among studies reviewed, with notable differences by age and biologic sample type. No bacterial species was associated with caries in all studies. Streptococcus mutans was found more frequently among those with caries (14/24 (58.3 %)) and Fusobacterium periodonticum was found more frequently among those that were caries-free (5/24 (20.8 %)).
CONCLUSION
No bacterial species was associated with caries or oral health across all studies supporting multiple pathways to cariogenesis. However, the variation may be due to sampling at different time points during caries development, varying methods of specimen sampling, storage, sequencing or analysis or differences in host factors such as age.
Topics: Adult; Child; Dental Caries; Fusobacterium; Humans; Mouth; Oral Health; RNA, Ribosomal, 16S; Saliva; Streptococcus mutans
PubMed: 34246103
DOI: 10.1016/j.archoralbio.2021.105204 -
American Journal of Rhinology & Allergy 2016Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are... (Review)
Review
BACKGROUND
Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS).
OBJECTIVES
To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date.
METHODS
A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored.
RESULTS
A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses.
CONCLUSION
The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.
Topics: Animals; Bacteria; Biodiversity; Chronic Disease; Homeostasis; Humans; Microbiota; Paranasal Sinuses; RNA, Ribosomal, 16S; Rhinitis, Allergic; Sinusitis
PubMed: 26867525
DOI: 10.2500/ajra.2016.30.4255 -
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 -
Frontiers in Bioengineering and... 2020Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of...
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used -based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use but are equally applicable to the systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
PubMed: 33117774
DOI: 10.3389/fbioe.2020.01031