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International Journal of Antimicrobial... Feb 2022Global antibiotic use has been increasing for decades. The gut microbiome, a key contributor to health, can be altered by antibiotics, which have been associated with... (Review)
Review
BACKGROUND
Global antibiotic use has been increasing for decades. The gut microbiome, a key contributor to health, can be altered by antibiotics, which have been associated with both short- and long-term effects on the intestinal microbiome. The aim of this study was to summarize the effects of antibiotics on the diversity and composition of the human microbiota at different anatomical sites.
METHODS
A systematic review was conducted according to PRISMA guidelines. PubMed, Scopus and Web of Science online databases were searched for studies that described the microbiome of any human bodily site pre- and post-antibiotic treatment using 16S rRNA gene sequencing. Increases or decreases in diversity, dissimilarity of microbial communities, and changes in taxonomic composition following antibiotic treatment were recorded as outcome measures.
RESULTS
The review identified consistent changes in the microbiota following quinolone and metronidazole treatment, and showed that combination treatment may result in longer-term dysbiosis. The importance of longitudinal analysis, and a lack of studies in paediatric populations was highlighted. Heterogeneity in the methodology of included studies could have contributed to the inconsistent findings regarding the effect of most antibiotic classes on the microbiome.
CONCLUSIONS
It is recommended that studies investigating the effect of antibiotics on the microbiome need to exclude participants exposed to antibiotics within 4 months preceding collection and analysis of baseline samples, and to include longitudinal analysis, particularly in the longer term. Further explorations need to be made into the functional implications of antibiotic-induced dysbiosis in the microbiome.
SYSTEMATIC REVIEW REGISTRATION
PROSPERO (https://www.crd.york.ac.uk/prospero; Registration:CRD42020168991).
Topics: Anti-Bacterial Agents; Child; Dysbiosis; Gastrointestinal Microbiome; Humans; Microbiota; RNA, Ribosomal, 16S
PubMed: 34929293
DOI: 10.1016/j.ijantimicag.2021.106502 -
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 -
BMC Microbiology Nov 2021Although recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory diseases, the association... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Although recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory diseases, the association between the lung microbiome and lung cancer has not been extensively studied. Conflicting reports of individual studies on respiratory microbiome alterations in lung cancer complicate the matter for specifying how the lung microbiome is linked to lung cancer. Consequently, as the first meta-analysis on this topic, we integrate publicly available 16S rRNA gene sequence data on lung tissue samples of lung cancer patients to identify bacterial taxa which differ consistently between case and control groups.
RESULTS
The findings of the current study suggest that the relative abundance of several bacterial taxa including Actinobacteria phylum, Corynebacteriaceae and Halomonadaceae families, and Corynebacterium, Lachnoanaerobaculum, and Halomonas genera is significantly decreased (p < 0.05) in lung tumor tissues of lung cancer patients in comparison with tumor-adjacent normal tissues.
CONCLUSIONS
Despite the underlying need for scrutinizing the findings further, the present study lays the groundwork for future research and adds to our limited understanding of the key role of the lung microbiome and its complex interaction with lung cancer. More data on demographic factors and tumor tissue types would help establish a greater degree of accuracy in characterizing the lung microbial community which accords with subtypes and stages of the disease and fully capturing the changes of the lung microbiome in lung cancer.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; DNA, Bacterial; Female; Humans; Lung; Lung Neoplasms; Male; Microbiota; RNA, Ribosomal, 16S
PubMed: 34763672
DOI: 10.1186/s12866-021-02375-z -
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 -
Acta Clinica Belgica Oct 2022Rat bite fever is a rare disease with a challenging differential diagnosis. The zoonosis has a potentially lethal course in a vulnerable population (children and low...
CONTEXT
Rat bite fever is a rare disease with a challenging differential diagnosis. The zoonosis has a potentially lethal course in a vulnerable population (children and low socioeconomic class) and a commonly available standard therapy (penicillin). This case report review outlines common epidemiological and clinical factors to improve clinical awareness and timely response to therapeutic actions.
METHODS
A systematic literature review was conducted in the PubMed database looking for English language European case reports of rat bite fever from 2000 to 2021.
RESULTS
In 17 out of 20 selected cases, the condition of the index patient was identified as an infectious syndrome. Thanks to the almost omnisensitive susceptibility pattern of , timely antibiotic administration prevented an unfavorable outcome in all these cases. However, in the three remaining cases, the initial diagnoses were arthritis (on autoimmune basis and gout) and viral syndrome. Due to delayed antibiotic administration, one case suffered persistent harm, while the other two cases encountered prolonged illness.
CONCLUSION AND RECOMMENDATIONS
Rat bite fever is a diagnosis that can be easily missed from both a clinical and a microbiological point of view. As such, rat bite fever becomes part of the differential diagnosis whenever a patient presents with a fever syndrome after being in contact with rodents. In the case of persistent fever, blood culture sampling should be performed even in the absence of a systemic inflammatory response. A bacterial 16S ribosomal RNA PCR on blood or joint aspiration (cultures) is an even more sensitive diagnostic test. Since most transmissions occurred in a domestic setting, keeping rats as pets cannot be recommended.
Topics: Animals; Anti-Bacterial Agents; Humans; Penicillins; RNA, Ribosomal, 16S; Rat-Bite Fever; Rats; Streptobacillus; Zoonoses
PubMed: 34672901
DOI: 10.1080/17843286.2021.1992940 -
Microbial Genomics Aug 2021Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota... (Meta-Analysis)
Meta-Analysis
Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA =0.005, pseudo-=2.643, =0.001). A sparse partial least squares - discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.
Topics: China; Ethnicity; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; India; Indonesia; Malaysia; RNA, Ribosomal, 16S
PubMed: 34463609
DOI: 10.1099/mgen.0.000619 -
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 -
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 -
Acta Dermato-venereologica Jul 2021Advances in technology have led to an increased number of studies investigating the microbiome in patients with psoriasis. This systematic review examined data regarding...
Advances in technology have led to an increased number of studies investigating the microbiome in patients with psoriasis. This systematic review examined data regarding the oral and gut microbiota in patients with psoriasis and/or psoriatic arthritis and the effect of probiotics on the microbiota and severity of psoriasis. Of 1,643 studies, 23 were included (22 observational, 1 interventional). Studies examined the microbiota using culture or 16S rRNA gene sequencing analysis. All culture-based studies identified an increased presence of oral Candida in patients with psoriasis, whereas small variations in the oral microbiota were found in a 16S rRNA gene-based study. All 16S rRNA gene sequencing based studies agreed that the gut microbiota of patients with psoriatic disease differed from that of healthy controls, but the results were heterogeneous. Probiotics were associated with a significant improvement in the severity of psoriasis, but did not change microbiota. Overall, studies lacked relevant inclusion criteria and baseline information. In conclusion, the role of the microbiota in patients with psoriasis requires further investigation using more robust methods.
Topics: Arthritis, Psoriatic; Gastrointestinal Microbiome; Humans; Microbiota; Psoriasis; RNA, Ribosomal, 16S
PubMed: 34263334
DOI: 10.2340/00015555-3882 -
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