Search

Background: Variability in recanalization success during endovascular treatment for acute ischemic stroke (AIS) has led to increased interests in thrombus composition and associated cellular materials. While evidence suggests that bacteria may influence thrombus characteristics, limited data exist on microbiological profiles of thrombi in stroke patients. Objectives: Characterization of bacterial communities present in thrombi of AIS patients undergoing mechanical thrombectomy, providing insights into microbial contributions to stroke pathogenesis and treatment outcomes. Methods: Thrombi were collected from 20 AIS patients. After extracting metagenome, 16S rDNA sequencing was performed. Bioinformatic analysis included taxonomy and diversity assessments. The presence of bacterial DNA and viable bacteria in thrombi was validated using polymerase chain reaction (PCR) and bacterial culturing followed by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) analysis, respectively. Results: 16S rDNA was amplified in 19/20 thrombi (95%). Analysis identified a diverse microbial community, with Corynebacterium spp. as the most prevalent genus, followed by Staphylococcus spp., Bifidobacterium spp., Methylobacterium spp., and Anaerococcus spp. Alpha diversity analyses (Shannon index: 4.0–6.0 and Simpson index: 0.8–1.0) revealed moderate to high microbial diversity across samples; beta diversity demonstrated distinct clustering, indicating inter-patient variability in microbial profiles. PCR confirmed the presence of DNA specific to dominant bacterial taxa identified through sequencing. Culturing showed the presence of Staphylococcus epidermidis and Enterococcus faecalis in some clots as identified through MALDI analysis. Conclusions: This study shows bacterial communities present in AIS patients' thrombi, suggesting a potential link between microbial signatures and thrombus characteristics. [ABSTRACT FROM AUTHOR]

Background: Gut microbes have been used to predict CRC risk. Fecal occult blood test (FOBT) has been recommended for population screening of CRC. Objective: To analyze the effects of fecal occult blood test (FOBT) on gut microbes. Methods: Fecal samples from 107 healthy individuals (FOBT-negative) and 111 CRC patients (39 FOBT-negative and 72 FOBT-positive) were included for 16 S ribosomal RNA sequencing. Based on the results of different FOBT, the community structure and diversity of intestinal bacteria in healthy individuals and CRC patients were analyzed. Characteristic gut bacteria were screened, and various machine learning algorithms were applied to construct CRC risk prediction models. Results: The gut microbiota of healthy people and CRC patients with different fecal occult blood were mapped. There was no statistical difference in diversity between CRC patients with negative FOBT and positive FOBT. Bacteroides, Blautia and Escherichia-Shigella were more correlated to healthy individuals, while Streptococcus showed higher correlation with CRC patients with negative FOBT. The accuracy of CRC risk prediction model based on the support vector machines (SVM) algorithm was the highest (89.71%). Subsequently, FOBT was included as a characteristic element in the model construction, and the prediction accuracy of the model was all increased. Similarly, the CRC risk prediction model based on SVM algorithm had the highest accuracy (92%). Conclusion: FOB affects the community composition of gut microbes. When predicting CRC risk based on gut microbiome, considering the influence of FOBT is expected to improve the accuracy of CRC risk prediction. Key points: The top 3 bacteria in CRC patients with FOBT-positive were Bacteroides, Blautia, Escherichia-Shigella. In the FOBT-positive group, 26 differential bacteria (Bacteroides, Parabacteroides, UCG-002, Phascolarctobacterium, Parvimonas, etc) was found. FOBT was included as a characteristic element in the construction of CRC risk prediction models , and the prediction accuracy of the model was all increased. [ABSTRACT FROM AUTHOR]

Background: Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication. Methods: Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3–V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe). Results: While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase. Conclusions: Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments. [ABSTRACT FROM AUTHOR]

ABSTRACT Aims Materials and Methods Results Conclusion To determine the relationship between microbiome dysbiosis indices and biofilm immunogenicity and their prognostic implications on periodontal treatment response.Thirty periodontally healthy controls and 30 periodontitis cases (stage III) were recruited. Cases received non‐surgical periodontal therapy (NSPT), and their treatment response at 6 months was evaluated using a treat‐to‐target endpoint (≤ 4 sites with probing depths ≥ 5 mm). Pooled subgingival biofilm samples were obtained from controls and cases. The V3–4 hypervariable region of the 16S rRNA gene was sequenced and two compositional indices (subgingival microbiome dysbiosis index, SMDI, and dysbiosis ratio, DR) were calculated. Nuclear factor kappa‐B (NF‐κB) activation elicited by biofilm samples in monocytic reporter cells was quantified to assess biofilm immunogenicity.SMDI, DR and biofilm immunogenicity were highly diagnostic for periodontitis (area under curves [AUC] > 0.90, p < 0.001). Among periodontitis cases, all three microbial parameters were significantly reduced after NSPT (p < 0.001). Cases achieving the treat‐to‐target endpoint had lower pre‐treatment SMDI and biofilm immunogenicity (p < 0.05) and different microbial recolonization patterns from poor responders. Both measures predicted treatment response (AUC of 0.767 and 0.835, respectively, p < 0.05).Subgingival biofilm dysbiosis quantified using SMDI and biofilm immunogenicity was diagnostic of periodontitis and predictive of NSPT outcomes. [ABSTRACT FROM AUTHOR]

Conjunctivitis is the most common eye disease, characterized by contextual inflammation, which can be caused by bacteria. The diagnosis of conjunctivitis is established based various factors, including the patients’s medical history, onset of eye symptoms, non-ocular symptoms, previous disease history, family medical history, allergies, and physical examination of the eyes, which may include assessments of visual acuity and vision field. Some cases of conjunctivitis require laboratory examinations to confirm the diagnosis. These may include cytological examination with Giemsa staining, Chlamydia Diagnostic Test, Nucleic acid amplification tests (NAATs) or Polymerase chain reaction (PCR), and microbiological tests. Microbiological examination helps identify the bacteria responsible for conjunctivitis and aids in treatment by prescribing antibiotics to suppress the growth of the infecting bacteria. While identification tests are not routinely performed, researchers often seek to determine the specific type of bacteria causing conjunctivitis infections, which may require several laboratory tests. Bacterial virulence plays a significant role, with genetic mutations potentially leading to severe infections of varying severity. Virulence genes encode proteins that express pathogenic properties. The species responsible for conjunctivitis can be definitively identified definitively through microbiological examination, utilizing methods such as the 16S Ribosomal RNA Sequencing (rRNA) technique, known for its accuracy and speed. This study aims to analyze the results of rRNA sequencing in cases of acute bacterial conjunctivitis caused by 16S rRNA genotyping. The research employed an exploratory metholodolot, with the results analyzed using the The Basic Local Alignment Search Tool (BLAST) tracking program database on the National Center for Biotechnology Information (NCBI) website. The findings revealed that Sphingomonas paucimobilis encoded the 16S rRNA using Universal Primary 27 F and 1492 R, obtained in a sequence size of 1351bp. The isolate demonstrated similarities to Sphingomonas paucimobilis.

Objectives: This study aimed to describe the effects of two single-file systems on the diversity of the endodontic microbiome of teeth with primary asymptomatic apical periodontitis. Materials and methods: The root canals from single-rooted teeth with apical periodontitis were prepared using either the Reciproc Blue (RB) or the XP-endo Shaper (XPS) instrument system. The latter was followed by a supplementary step with the XP-endo Finisher (XPF) instrument. For irrigation, 5.25% sodium hypochlorite was used. Root canal samples were taken at the baseline (S1), after preparation (S2), and after the supplementary step (S3). DNA was extracted and subjected to high-throughput sequencing using the MiSeq Illumina platform. Results: Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems. The most dominant phyla in S2 were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria. The same phyla were found to dominate baseline samples and samples taken after using XPF, but with differences in the ranking of the most dominant ones. At the genus level, the most dominant genera identified after RB instrumentation were Bacteroidaceae [G-1], Fusobacterium, and Staphylococcus, while the most dominant genera after XPS instrumentation were Fusobacterium and Porphyromonas. These genera were also dominant in the initial samples. Conclusions: Both treatment protocols had measurable effects on the root canal microbial diversity, with no significant differences between them. Most of the dominant taxa involved in the primary infection and probably in the aetiology of apical periodontitis were eliminated or substantially reduced. Clinical relevance: The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus, and Bacteroidaceae [G-1]. [ABSTRACT FROM AUTHOR]

Guixuan Wang,1,2 Danyang Zou,2 Xinying Lu,2 Xin Gu,2 Yuanyuan Cheng,2 Tengfei Qi,2 Yanchun Cheng,2 Junjun Yu,2 Meiping Ye,2 Pingyu Zhou1,2 1Shanghai Skin Disease Clinical College of Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, People’s Republic of China; 2STD Institute, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of ChinaCorrespondence: Pingyu Zhou, Shanghai Skin Disease Clinical College of Anhui Medical University, Shanghai Skin Disease Hospital, 1278 Bao’de Road, Shanghai, 200443, People’s Republic of China, Tel +86-18017336631, Email zpyls@yahoo.comBackground: The gut microbiota plays an important role in the development of neurological disorders such as Parkinson’s disease and Alzheimer’s disease. However, studies on the gut microbiota of patients with neurosyphilis (NS) were rarely reported.Methods: In this study, we collected fecal samples from 62 syphilis patients, including 39 with NS and 23 with non-NS. Among the NS patients, 18 were general paresis (GP). The white blood cell counts, protein concentrations, and Venereal Disease Research Laboratory test positive rates of cerebrospinal fluid from patients in NS or GP group were significantly higher than those from patients in non-NS group. 16S ribosomal RNA sequencing results revealed that the alpha and beta diversities of the gut microbiota were similar between NS and non-NS patients or GP and non-NS patients.Results: Linear discriminant analysis with effect size (LEfSe) analysis showed that some taxa, such as Coprobacter, were increased in both NS group and GP group, compared with non-NS group. Besides, the clade of Akkermansia was also overrepresented in GP Patients. Meanwhile, some taxa such as Clostridia_UCG-014 and SC-I-84 were underrepresented in NS patients. The abundances of class Bacilli and genus Alloprevotella were decreased in GP patients. Among them, the abundances of some taxa such as Coprobacter and Akkermansia have been reported to be associated with other neuropsychiatric disorders.Conclusion: Our findings suggest that the alternation of the gut microbiota in NS patients may contribute to the course of NS, which will deepen our understanding of NS.Keywords: syphilis, neurosyphilis, general paresis, gut microbiota, 16S ribosomal RNA sequencing

What are the different features of the vaginal microbiome (VMB) between patients with polycystic ovary syndrome (PCOS) and healthy women? A cross-sectional study was conducted at a single academic university-affiliated centre. A total of 1446 participants were recruited (PCOS group, n =713, control group, n = 733). Vaginal swabs were analysed using 16S rRNA gene sequencing. The diversity and composition of the microbiome were compared between the PCOS group and the control group. Microbial interaction networks and functional prediction were investigated. The PCOS group had a higher alpha diversity than the control group (Shannon P = 0.03, Simpson P = 0.02), and higher intra-group variability was observed in PCOS group (P < 2.2E-16). At the genus level, the proportion of Lactobacillus decreased (85.1% versus 89.3%, false discovery rate [FDR] = 0.02), whereas the proportion of Gardnerella vaginalis and Ureaplasma increased in the PCOS group (5.1% versus 3.3%, FDR = 0.006; 1.2% versus 0.6%, FDR = 0.002, respectively). Lactobacillus acidophilus, Prevotella buccalis and G. vaginalis were identified as the main differential species. L. acidophilus was positively correlated with serum levels of anti-Müllerian hormone (AMH), and triglyceride (P = 2.01E-05, P = 0.004, respectively). P. buccalis was negatively correlated with serum levels of AMH and testosterone (P = 0.002, P = 0.003, respectively). G. vaginalis was positively correlated with serum levels of AMH, oestradiol and progesterone (P = 0.004, P = 0.005, P = 0.03, respectively). The VMB interaction network indicated that Lactobacillus crispus, Prevotella timonensis, and P. buccalis could be key drivers in the PCOS group. Overall, 55 predicted genes were found to be differentially abundant between PCOS and the control (FDRs < 0.25). The PCOS group had a higher diversity of vaginal microbiome and showed an enhanced level of heterogeneity. The proportion of Lactobacillus in the PCOS group decreased, whereas the proportions of Gardnerella and Ureaplasma increased. These results warrant further research that can validate the correlation between PCOS and VMB. [ABSTRACT FROM AUTHOR]

Objectives: To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm. Materials and methods: Root canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0. Results: Within the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group. Conclusions: A few taxa were differentially abundant within either the PEI or SEI group. Clinical relevance: Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections. [ABSTRACT FROM AUTHOR]

The successional dynamics of microbial communities are influenced by the synergistic interactions of physical and biological factors. In our motivating data, ocean microbiome samples were collected from the Santa Cruz Municipal Wharf, Monterey Bay at multiple time points and then 16S ribosomal RNA (rRNA) sequenced. We develop a Bayesian semiparametric regression model to investigate how microbial abundance and succession change with covarying physical and biological factors including algal bloom and domoic acid concentration level using 16S rRNA sequencing data. A generalized linear regression model is built using the Laplace prior, a sparse inducing prior, to improve estimation of covariate effects on mean abundances of microbial species represented by operational taxonomic units (OTUs). A nonparametric prior model is used to facilitate borrowing strength across OTUs, across samples and across time points. It flexibly estimates baseline mean abundances of OTUs and provides the basis for improved quantification of covariate effects. The proposed method does not require prior normalization of OTU counts to adjust differences in sample total counts. Instead, the normalization and estimation of covariate effects on OTU abundance are simultaneously carried out for joint analysis of all OTUs. Using simulation studies and a real data analysis, we demonstrate improved inference compared to an existing method.

Abstract Background Staphylococcus schleiferi is a gram-positive pathogenic coccus which causes canine skin and ear infections. Only four cases of human infection caused by Staphylococcus schleiferi subspecies coagulans have been reported. Herein, we present the first case of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. Case presentation A 62-year-old Japanese man was admitted to our hospital for examination of sigmoid colon tumor. During hospitalization, he had fever, shaking chills, and swelling at the peripheral venous catheter insertion site. Two sets of blood cultures were positive for S. schleiferi subspecies coagulans which was confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), 16S ribosomal RNA sequencing and the coagulase test. The patient was successfully treated without relapse. Conclusion To our knowledge, this is the first report of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. S. schleiferi subsp. coagulans can be pathogenic in humans, and MALDI-TOF MS can contribute to accurate identification of S. schleiferi subspecies coagulans.

Advanced DNA sequencing technology allows more detailed analysis and description of the endodontic microbiome. This study used the MiSeq high-throughput sequencing platform (Illumina, San Diego, CA) to describe the endodontic microbiome of teeth with primary asymptomatic apical periodontitis with no sinus tract. Root canal samples from 25 patients were prepared for DNA sequencing analysis. Bacterial diversity of the microbiome was identified and compared between cases and according to the size of the related apical periodontitis lesions. Statistical analyses of the operational taxonomic unit distribution was performed using principal component analysis with the Bray-Curtis distance and a principal coordinate analysis, 2-way permutational multivariate analysis of variance. The chi-square or Fisher exact test was used to evaluate the prevalence of different operational taxonomic units related to small and large apical periodontitis lesions. Although there was a very high bacterial diversity in the microbiome of teeth with asymptomatic apical periodontitis, 4 phyla dominated the microbiome: Firmicutes (27%), Bacteroidetes (21%), Proteobacteria (21%), and Actinobacteria (12%). There was high variability in species composition between root canal samples with no common species pattern for the cases. Large lesions showed a higher number of species but did not significantly differ from small lesions in bacterial diversity indexes. Bacteroidaceae [G-1] bacterium HMT 272, a previously uncultivated but still unnamed and uncharacterized taxon, was the most prevalent and abundant phylotype. High-throughput sequencing technology confirmed the complexity of the endodontic microbiome and revealed that microbial heterogeneity is a feature between cases. This indicates that various microbial combinations of the endodontic microbiome are able to illicit periapical inflammatory diseases. [ABSTRACT FROM AUTHOR]

Stroke (ST), endangering human health due to its high incidence and high mortality, is a global public health problem. There is increasing evidence that there is a link between the gut microbiota (GM) and neuropsychiatric diseases. We aimed to find the GM of ST, post-ST cognitive impairment (PSCI), and post-ST affective disorder (PSTD). GM composition was analyzed, followed by GM identification. Alpha diversity estimation showed microbiota diversity in ST patients. Beta diversity analysis showed that the bacterial community structure segregated differently between different groups. At the genus level, ST patients had a significantly higher proportion of Enterococcus and lower content of Bacteroides, Escherichia-Shigella, and Megamonas. PSCI patients had a significantly higher content of Enterococcus, Bacteroides, and Escherichia-Shigella and a lower proportion of Faecalibacterium compared with patients with ST. Patients with PSTD had a significantly higher content of Bacteroides and Escherichia-Shigella and lower content of Enterococcus and Faecalibacterium. Parabacteroides and Lachnospiraceae were associated with Montreal cognitive assessment score of ST patients. Our study indicated that the characteristic GM, especially Bacteroidetes, could be used as clinical biomarkers of PSCI and PSTD.

Background: Staphylococcus schleiferi is a gram-positive pathogenic coccus which causes canine skin and ear infections. Only four cases of human infection caused by Staphylococcus schleiferi subspecies coagulans have been reported. Herein, we present the first case of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. Case presentation: A 62-year-old Japanese man was admitted to our hospital for examination of sigmoid colon tumor. During hospitalization, he had fever, shaking chills, and swelling at the peripheral venous catheter insertion site. Two sets of blood cultures were positive for S. schleiferi subspecies coagulans which was confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), 16S ribosomal RNA sequencing and the coagulase test. The patient was successfully treated without relapse. Conclusion: To our knowledge, this is the first report of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. S. schleiferi subsp. coagulans can be pathogenic in humans, and MALDI-TOF MS can contribute to accurate identification of S. schleiferi subspecies coagulans. [ABSTRACT FROM AUTHOR]

ObjectiveAccumulative evidence suggests that gut microbiota play an important role in bone remodeling and hence bone health maintenance. This study aimed to explore the association of gut microbiota with the risk of osteoporosis and to identify potential disease-related taxa, which may be promising targets in osteoporosis prevention and treatment in the future.MethodsAbsolute quantification 16S ribosomal RNA gene sequencing was used to detect absolute and relative abundances of gut microbiota in 44 patients with osteoporosis and 64 controls. In combination with one of our previous studies, a total of 175 samples were involved in the relative abundance analysis.ResultsCompared with the controls, the patients with osteoporosis had higher absolute and relative abundances of Bacteroidetes phylum, and Bacteroides and Eisenbergiella genera. The absolute abundances of Clostridium_XlVa, Coprococcus, Lactobacillus, and Eggerthella genera increased, and that of the Veillonella genus decreased in the osteoporosis group. As for relative abundance, that of the Parabacteroides and Flavonifractor genera increased, whereas that of the Raoultella genus decreased in the osteoporosis group. Controlling for potential confounders, the associations of Clostridium_XlVa, Coprococcus, and Veillonella genera with the risk of osteoporosis did not maintain significance. Ridge regression analysis suggested that Bacteroides is associated with reduced bone mineral density (BMD) and T-score at lumbar spines, and Anaerovorax is associated with increased BMD at the femoral neck. Functional predictions revealed that 10 Kyoto Encyclopedia of Genes and Genomes pathways were enriched in the osteoporosis group.ConclusionsGut microbiota compositions may contribute to the risk of osteoporosis. Several specific taxa and functional pathways are identified to associate with reduced bone density, thus providing epidemiologic evidence for the potential role of aberrant gut microbiota in osteoporosis pathogenesis.

Objective: Accumulative evidence suggests that gut microbiota play an important role in bone remodeling and hence bone health maintenance. This study aimed to explore the association of gut microbiota with the risk of osteoporosis and to identify potential disease-related taxa, which may be promising targets in osteoporosis prevention and treatment in the future. Methods: Absolute quantification 16S ribosomal RNA gene sequencing was used to detect absolute and relative abundances of gut microbiota in 44 patients with osteoporosis and 64 controls. In combination with one of our previous studies, a total of 175 samples were involved in the relative abundance analysis. Results: Compared with the controls, the patients with osteoporosis had higher absolute and relative abundances of Bacteroidetes phylum, and Bacteroides and Eisenbergiella genera. The absolute abundances of Clostridium_XlVa , Coprococcus , Lactobacillus , and Eggerthella genera increased, and that of the Veillonella genus decreased in the osteoporosis group. As for relative abundance, that of the Parabacteroides and Flavonifractor genera increased, whereas that of the Raoultella genus decreased in the osteoporosis group. Controlling for potential confounders, the associations of Clostridium_XlVa , Coprococcus , and Veillonella genera with the risk of osteoporosis did not maintain significance. Ridge regression analysis suggested that Bacteroides is associated with reduced bone mineral density (BMD) and T-score at lumbar spines, and Anaerovorax is associated with increased BMD at the femoral neck. Functional predictions revealed that 10 Kyoto Encyclopedia of Genes and Genomes pathways were enriched in the osteoporosis group. Conclusions: Gut microbiota compositions may contribute to the risk of osteoporosis. Several specific taxa and functional pathways are identified to associate with reduced bone density, thus providing epidemiologic evidence for the potential role of aberrant gut microbiota in osteoporosis pathogenesis. [ABSTRACT FROM AUTHOR]

Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections. Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4–V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P <.05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis. Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P <.05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis , Tannerella forsythia , Alloprevotella tannerae , Prevotella intermedia , Pseudoramibacter alactolyticus , Olsenella sp. HMT 809 , Olsenella sp. HMT 939, Olsenella uli , and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1). The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections. [ABSTRACT FROM AUTHOR]

Aim: This study was aimed at identifying Indian field isolates of Avibacterium paragallinarum on both molecular as well as serological levels that cause infectious coryza in chickens. Materials and Methods: Species-specific polymerase chain reaction (HPG-2 PCR), and 16S ribosomal RNA (rRNA) sequencing were employed for molecular identification. Whereas, multiplex PCR technique was used for serological identification of Indian field isolates of A. paragallinarum. Results: All three field isolates were identified as A. paragallinarum using HPG-2 PCR. The species-specific PCR results were validated using 16S rRNA sequencing. The partial 16S rRNA sequences obtained from all three isolates showed 96-99% homology with the NCBI database reference strains of A. paragallinarum. The aligned partial sequences of 16S rRNA were submitted to GenBank, and accession numbers were obtained. Multiplex PCR-based molecular serotyping showed that there are three serotypes of field isolates of A. paragallinarum, namely, strain IND101 is serovar A, strain IND102 is serovar B, and strain IND103 is serovar C. Conclusion: HPG-2 PCR, 16S rRNA sequencing, and multiplex PCR are proved to be more accurate, sensitive, and reliable diagnostic tools for molecular and serological identification of A. paragallinarum field isolates. These diagnostic methods can substitute conventional cultural characterization and would be much valuable to formulate quick and correct prevention and control measures against this detrimental poultry pathogen.

The genus Nocardia usually infect immunocompromised patients. Pulmonary nocardiosis is the most common Nocardia-induced infection while central nervous system (CNS) is the most common extrapulmonary site to develop nocardial disease. Approximately 54 % cases of previously reported nocardial brain abscesses were solitary lesions, while 38 % cases had multiple lesions; but miliary-like ring enhancing lesions have not been reported previously.We present a case of immunocompetent patient with miliary-like cerebrospinal lesions caused by Nocardia beijingensis. A 68-year-old Japanese man presented with acute-onset headache, vomiting, and progressive disturbance of consciousness. A contrasted magnetic resonance imaging (MRI) scan showed countless miliary-like ring-shaped enhancing lesions on the patient’s whole brain, brain stem, and cervical spinal cord. A brain biopsy was performed and Kinyoun stain suggested that the brain lesions were abscesses caused by Nocardia species. 16S ribosomal RNA sequencing identified Nocardia beijingensis as the causative microorganism. The trimethoprim/sulfamethoxazole regimen was continued for 7 months and the patient showed good improvement with recovery of consciousness.Clinical manifestation of Nocardia beijingensis infection is poorly studied. Further cases are needed to be accumulated.

Emerging evidence suggests that gut microbiota dysbiosis plays a role in neurodegenerative disorders. However, whether the composition and diversity of the gut microbiota are altered in tauopathies remains largely unknown. This study was aimed to examine the diversity and composition of the gut microbiota in tauopathies, as well as the correlation with pathological changes in the brain. We collected fecal samples from 32 P301L tau transgenic mice and 32 age- and gender-matched littermate mice at different ages. The 16S ribosomal RNA sequencing technique was used to analyze the microbiota composition in feces. Brain tau pathology levels were measured by immunohistochemistry. The diversity and composition of the gut microbiota significantly changed with aging. At the phylum level, the relative abundance of Bacteroidetes was increased, while Firmicutes were decreased in P301L mice compared with that in Wt mice after 3 months of age. In addition, Actinobacteria was decreased in P301L mice at 3 and 6 months of age, meanwhile Tenericutes was decreased in P301L mice at 10 months of age. Moreover, several specific macrobiota were highly associated with the levels of AT8-tau or pT231-tau protein in the brain. Our findings suggest that gut microbiota changed with aging, as well as in the tauopathy mice model. Modulation of the gut microbiota may be a potential strategy for treatment of tauopathy. [ABSTRACT FROM AUTHOR]

What are the different characteristics of vaginal microbial composition between patients with endometrial polypoid lesions and controls? This cohort study compared the pre-operative microbial compositions of vaginal samples in a cohort of 703 women with endometrial polypoid lesions [293 and 410 women diagnosed and not diagnosed with polyps pathologically (polyps group and not-polyps group, respectively] and 703 women in the control group. Bacterial abundance, diversity, differential taxa and microbial network structure were assessed using 16S rRNA gene sequencing. Predictive algorithms were used to determine the functional pathways of vaginal microbiota within the cohort. The control group exhibited higher relative abundance of Lactobacillus crispatus in comparison with the polypoid lesions group (P = 0.0427). Beta diversity of vaginal microbiota differed significantly between the groups (P < 0.05). Comparing the polyps group with the not-polyps group, Leptotrichia spp. and Cutibacterium spp. were more abundant in the polyps group, and Fannyhessea spp. , Acinetobacter spp. and Achromobacter spp. were more abundant in the not-polyps group. The control group exhibited higher abundance of Bifidobacterium spp., Achromobacter spp. and Escherichia/Shigella spp. (false discovery rate < 0.05). Furthermore, the polyps group and not-polyps group displayed more complex co-occurrence networks compared with the control group. The results of this study provide compelling evidence supporting associations between vaginal microbiota and endometrial polypoid lesions, highlighting the potential relationship between a well-balanced vaginal microbial ecosystem and a healthy intrauterine environment. [ABSTRACT FROM AUTHOR]

Background: Ultrasonic scaler is a preferential treatment modality among the clinicians. However, the aerosol/splatter generated is a concern for patients and practitioners. Therefore, the purpose of this study was to evaluate contamination of contact lenses of the dentist after scaling and root planing using ultrasonic scalers with and without protective eyewear. Materials and Methods: Thirty patients were randomly selected for scaling and root planing and divided into 2 groups of 15 each. Group A - dentist wearing contact lenses and protective eyewear. Group B - dentist wearing only contact lenses. After scaling and root planing using ultrasonic scalers, the lenses were subjected to culture and 16S rRNA (16S ribosomal RNA) gene sequencing. Results: In Group A – 15 out of thirty samples were contaminated, in Group B – all the thirty samples were contaminated. Most of the samples showed Gram-positive bacteria and 5 samples were contaminated with fungi. 16S rRNA gene sequencing of forty contaminated samples showed that 31 were contaminated with Streptococcus mutans and 9 with Staphylococcus aureus. Conclusion: Keeping in mind the limitation of the study for the absence of negative control, we would like to conclude that dental practitioners should better avoid contact lenses in a dental setup because of the risk of contamination of the contact lenses from the various dental procedures which can produce aerosol/splatter and if worn, it is recommended to wear protective eyewear.

Previous studies suggest that gut microbiota is associated with neuropsychiatric disorders, such as Parkinson's disease, amyotrophic lateral sclerosis, and depression. However, whether the composition and diversity of gut microbiota is altered in patients with Alzheimer's disease (AD) remains largely unknown. In the present study, we collected fecal samples from 43 AD patients and 43 age- and gender-matched cognitively normal controls. 16S ribosomal RNA sequencing technique was used to analyze the microbiota composition in feces. The composition of gut microbiota was different between the two groups. Several bacteria taxa in AD patients were different from those in controls at taxonomic levels, such as Bacteroides, Actinobacteria, Ruminococcus, Lachnospiraceae, and Selenomonadales. Our findings suggest that gut microbiota is altered in AD patients and may be involved in the pathogenesis of AD. [ABSTRACT FROM AUTHOR]

Introduction: Escherichia coli is one of the most common bacteria causing urinary tract infection. Accurate identification of urinary isolates is highly desirable and frequently challenging. Our study aims at identifying the “atypical” phenotype of E. coli by conventional, automated, and molecular methods and studying its prevalence among all the urinary isolates of E. coli. Materials and Methods: The present prospective study was conducted in the Department of Microbiology of a teaching tertiary care hospital of Central India for 6 months during the year 2014–2015. A total of 592 urine samples were processed. Identification of different urinary isolates was done by conventional and automated methods and by molecular method in special cases. Results: Two hundred and sixty-one uropathogens were isolated during the study. Among these, 110 (42.1%) isolates were E. coli, of which 4 (3.6%) isolates were confirmed as “atypical” E. coli by automated and molecular method. Conclusions: Our study highlights the challenges in the identification of atypical urinary isolates of E. coli. Accurate identification is essential for implicating proper antibiotic treatment.

Alteration of microbiota has been associated with intestinal, inflammatory and neurological diseases. An abundance of 'good bacteria,' such as Bifidobacterium, or their products has been generally believed to be beneficial for any diseases, whereas 'bad bacteria,' such as pathogenic Helicobacter pylori, are assumed to be always detrimental for hosts. However, this is not the case when we compare and contrast the association of the gut microbiota with two neurological diseases, multiple sclerosis and Alzheimer's disease. After H. pylori infection, pro-inflammatory T helper (Th)1 and Th17 immune responses are initially induced to eradicate bacteria. However, H. pylori evades the host immune response by inducing Th2 cells and regulatory T cells that produce anti-inflammatory interleukin-10. Suppression of anti-bacterial Th1/Th17 cells by regulatory T cells might enhance gastric H. pylori propagation , followed by a cascade reaction involving vitamin B12 and folic acid malabsorption, plasma homocysteine elevation, and reactive oxygen species induction. This can damage the blood-brain barrier, leading to accumulation of amyloid-β in the brain, a hallmark of Alzheimer's disease. In contrast, this suppression of pro-inflammatory Th1/Th17 responses to H. pylori has protective effects on the hosts, as it prevents uncontrolled gastritis as well as suppresses the induction of encephalitogenic Th1/Th17 cells, which can mediate neuroinflammation in multiple sclerosis. The above scenario might explain why chronic H. pylori infection is positively associated with Alzheimer's disease, whereas it is negatively associated with multiple sclerosis. Finally, we list '10 pitfalls of microbiota studies,' which will be useful for evaluating and designing clinical and experimental microbiota studies. [ABSTRACT FROM AUTHOR]

Background: While microbiome and host regulation contribute independently to many disease states, it is unclear how circumcision in pediatric population influences subsequent changes in penile microbiome., Objective: Our study aims to analyze jointly paired taxonomic profiles and assess pathways implicated in inflammation, barrier protection, and energy metabolism., Design, Setting, and Participants: We analyzed 11 paired samples, periurethral collection, before and after circumcision, to generate microbiome and mycobiome profiling. Sample preparation of 16S ribosomal RNA and internal transcribed spacer sequencing was adapted from the methods developed by the National Institutes of Health Human Microbiome Project., Outcome Measurements and Statistical Analysis: We obtained the predictive functional attributes of the microbial communities between samples using Silva-Tax4Fun and the Greengenes-Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) approach. The predictive functioning of the microbial communities was determined by linearly combining the normalized taxonomic abundances into the precomputed association matrix of Kyoto Encyclopedia of Genes and Genomes orthology reference profiles., Results and Limitations: Several notable microbiome and mycobiome compositional differences were observed between pre- and postcircumcision patients. Pairwise comparisons across taxa revealed a significant decrease (p < 0.05, false discovery rate corrected) of microbiome organisms (Clostridiales, Bacteroidales, and Campylobacterales) and mycobiome (Saccharomycetales and Pleosporales) following circumcision. A total of 14 pathways were found to differ in abundance between the pre- and postcircumcision groups (p < 0.005, false discovery rate <0.1 and linear discriminant analysis score >3; five enriched and nine depleted). The pathways reduced after circumcision were mostly involved with amino acid and glucose metabolism, while pathways prior to circumcision were enriched in genetic information processing and transcription processes. As expected, enrichment in methyl-accepting chemotaxis protein, an integral membrane protein involved in directed motility of microbes to chemical cues and environment, occurred prior to circumcision, while the filamentous hemagglutinin pathway (a strong immunogenic protein) was depleted after circumcision CONCLUSIONS: Our results offer greater insight into the host-microbiota relationship of penile circumcision and may serve to lay the groundwork for future studies focused on drivers of inflammation, infection, and oncogenesis., Patient Summary: Our study showed a significant reduction in bacteria and fungi after circumcision, particularly anaerobic bacteria, which are known to be potential inducers of inflammation and cancer. This is the first study of its kind showing the changes in microbiome after circumcision, and some of the changes that occur in healthy infants after circumcision that may explain the differences in cancer and inflammatory disorders in adulthood., (Copyright © 2022 European Association of Urology. Published by Elsevier B.V. All rights reserved.)

Background: Ultrasonic scaler is a preferential treatment modality among the clinicians. However, the aerosol/splatter generated is a concern for patients and practitioners. Therefore, the purpose of this study was to evaluate contamination of contact lenses of the dentist after scaling and root planing using ultrasonic scalers with and without protective eyewear. Materials and Methods: Thirty patients were randomly selected for scaling and root planing and divided into 2 groups of 15 each. Group A - dentist wearing contact lenses and protective eyewear. Group B - dentist wearing only contact lenses. After scaling and root planing using ultrasonic scalers, the lenses were subjected to culture and 16S rRNA (16S ribosomal RNA) gene sequencing. Results: In Group A - 15 out of thirty samples were contaminated, in Group B - all the thirty samples were contaminated. Most of the samples showed Gram-positive bacteria and 5 samples were contaminated with fungi. 16S rRNA gene sequencing of forty contaminated samples showed that 31 were contaminated with Streptococcus mutans and 9 with Staphylococcus aureus. Conclusion: Keeping in mind the limitation of the study for the absence of negative control, we would like to conclude that dental practitioners should better avoid contact lenses in a dental setup because of the risk of contamination of the contact lenses from the various dental procedures which can produce aerosol/splatter and if worn, it is recommended to wear protective eyewear. [ABSTRACT FROM AUTHOR]

Bordetella holmesii is a recently recognized Gram-negative bacterium causing both pertussis-like respiratory symptoms and invasive infections, such as bacteremia, pneumonia, meningitis, arthritis, pericarditis and endocarditis. Few data are available on its epidemiological characteristics, mostly related to respiratory infections. However, these are frequently misdiagnosed as a Bordetella pertussis infection as most diagnostic tests routinely used are not species-specific, thus biasing the epidemiological studies of both strains, as well as the efficacy studies on pertussis vaccination. There is no accepted agreement on treatment and it remains unknown if antimicrobial prophylaxis is indicated in certain clinical settings. We review here the current knowledge on B. holmesii and the need for further research. [ABSTRACT FROM AUTHOR]

Some lipid hydrolysis products such as medium-chained NEFA (MC-NEFA), sphingosine and monoacylglycerols (MAG) possess antibacterial activity, while others, including oleic acid, are essential for the optimal growth of Lactobacillus species. Thus, changes in the concentrations of NEFA and MAG in the distal ileum and colon can potentially selectively modulate the composition of the gut microbiota, especially in early life when lipid absorption efficacy is reduced. As medium-chained fatty acids are enriched in mothers' milk, such effects may be highly relevant during gut colonisation. In the present study, we examined the effect of selected NEFA, MAG and sphingosine on the composition of faecal microbial communities derived from infants aged 2-5 months during a 24 h anaerobic in vitro fermentation. We tested lipid mixtures in the concentration range of 0-200 μM, either based on MC-NEFA (10 : 0 to 14 : 0 and MAG 12 : 0) or long-chained NEFA (LC-NEFA; 16 : 0 to 18 : 1 and MAG 16 : 0) with and without sphingosine, representing lipid hydrolysis products characteristic for intestinal hydrolysis of breast milk lipids. Ion Torrent sequencing of the bacterial 16S ribosomal RNA gene revealed that the relative abundance of lactic acid-producing genera, including Lactobacillus and Bifidobacterium, was generally increased in the presence of 50μM or higher concentrations of MC-NEFA. For Bifidobacterium, the same effect was also observed in the presence of a mixture containing LC-NEFA with sphingosine. On the contrary, the relative abundance of Enterobacteriaceae was significantly decreased in the presence of both lipid mixtures. Our findings suggest that the high concentration of medium-chained fatty acids in breast milk might have functional effects on the establishment of the gut microbiota in early life. [ABSTRACT FROM AUTHOR]

This study was aimed at characterizing microbiologically Gilthead sea bream (Sparus aurata) and Sea bass (Dicentrarchus labrax) produced in two estuarine ecosystems in Andalusia (Spain): the estuary of the river Guadalquivir (La Puebla del Río, Sevilla) (A), and the estuary of the river Guadiana (Ayamonte, Huelva) (B). The collected fish individuals and water were analysed for hygiene indicator microorganisms and pathogens. The statistical analysis of results revealed that microbial counts for the different microbiological parameters were not statistically different for fish type. On the contrary, considering anatomic part, viscera showed significantly higher concentrations for Enterobacteriaceae , total coliforms and for Staphylococcus spp. coagulase +. Furthermore, location A showed in water and fish higher levels for lactic acid bacteria, aerobic mesophilic bacteria, Enterobacteriaceae , total coliforms and Staphylococcus spp. coagulase +. Neither Listeria monocytogenes , nor Salmonella spp. were detected, though Vibrio parahaemolyticus was identified, molecularly, in estuarine water in location B. The predictive analysis demonstrated that the initial microbiological quality could have an impact on product shelf-life, being longer for location B, with better microbiological quality. Results stress the relevance of preventing the microbiological contamination of water in estuary production systems in order to assure the quality and safety of Gilthead sea bream and Sea bass. • Microbial counts were statistically similar in Gilthead sea bream and Sea bass. • Vibrio parahaemolyticus was isolated from estuarine water. • Neither Listeria monocytogenes nor Salmonella spp. were detected in fish and water. • Higher microbial levels were found in fish viscera in comparison with skin. • The initial microbiological quality could have impact on the product shelf-life. [ABSTRACT FROM AUTHOR]

Background: With the development of next generation sequencing technology, a lot of research has focused on the role of human microbiome in regulating immunity. The present study evaluated microbiome changes of colorectal cancer patients who received XELOX regimen (capecitabine plus oxaliplatin) without requiring antimicrobials., Methods: Stool samples from 7 patients (3 females/4 males) after screening of 11 patients before and after XELOX chemotherapy were subjected to 16S ribosomal RNA (rRNA) sequencing and flora dynamics compared at baseline and after 8 weeks of chemotherapy. Enrolled patients were newly diagnosed with stage IV colorectal cancer and had not received antimicrobial therapy or surgery. XELOX was administered for 2 cycles or 2-weekly treatments for 3 cycles., Results: The patterns of relative abundance of all bacteria isolated from stool samples before or after chemotherapy treatment appeared to be different, but there were no significant differences in the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolism pathway between the two groups. The top five pathways in patients were the two-component system, phenylalanine metabolism, degradation of aromatic compounds, beta-lactam resistance and folate biosynthesis. More than 99.6% intestinal flora isolates were bacteria, <0.4% were viruses and Archaea . The relative abundances of the 5 most common bacterial phyla in fecal samples before chemotherapy were Bacteroides, Firmicutes, Proteobacteria, Actinobacteria and Verrucomicrobia . The abundance of Actinomycetes in stools after chemotherapy was increased to 2.5 fold higher than before chemotherapy. Bifidobacterium longum species were significantly elevated in stools after chemotherapy (P<0.05), and changes of relative abundance of Bifidobacterium longum species after chemotherapy from baseline in favorable outcome population (stable disease) was significant higher than them in unfavorable outcome population (progressive disease, PD) (P=0.023)., Conclusions: The results indicated that Actinomyces in the gut might have a positive clinical outcome for colorectal cancer patients. This idea needs further studies to examine the actions of Actinomyces on inhibition of tumor growth., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tcr.2020.03.33). The authors have no conflicts of interest to declare., (2020 Translational Cancer Research. All rights reserved.)

Background Early life acute respiratory infection (ARI) with respiratory syncytial virus (RSV) has been strongly associated with the development of childhood wheezing illnesses, but the pathways underlying this association are poorly understood. Objective To examine the role of the nasopharyngeal microbiome in the development of childhood wheezing illnesses following RSV ARI in infancy. Methods We conducted a nested cohort study of 118 previously healthy, term infants with confirmed RSV ARI by RT-PCR. We used next-generation sequencing of the V4 region of the 16S ribosomal RNA gene to characterize the nasopharyngeal microbiome during RSV ARI. Our main outcome of interest was 2-year subsequent wheeze. Results Of the 118 infants, 113 (95.8%) had 2-year outcome data. Of these, 46 (40.7%) had parental report of subsequent wheeze. There was no association between the overall taxonomic composition, diversity, and richness of the nasopharyngeal microbiome during RSV ARI with the development of subsequent wheeze. However, the nasopharyngeal detection and abundance of Lactobacillus was consistently higher in infants who did not develop this outcome. Lactobacillus also ranked first among the different genera in a model distinguishing infants with and without subsequent wheeze. Conclusions The nasopharyngeal detection and increased abundance of Lactobacillus during RSV ARI in infancy are associated with a reduced risk of childhood wheezing illnesses at age 2 years. [ABSTRACT FROM AUTHOR]

The successional dynamics of microbial communities are influenced by the synergistic interactions of physical and biological factors. In our motivating data, ocean microbiome samples were collected from the Santa Cruz Municipal Wharf, Monterey Bay at multiple time points and then 16S ribosomal RNA (rRNA) sequenced. We develop a Bayesian semiparametric regression model to investigate how microbial abundance and succession change with covarying physical and biological factors including algal bloom and domoic acid concentration level using 16S rRNA sequencing data. A generalized linear regression model is built using the Laplace prior, a sparse inducing prior, to improve estimation of covariate effects on mean abundances of microbial species represented by operational taxonomic units (OTUs). A nonparametric prior model is used to facilitate borrowing strength across OTUs, across samples and across time points. It flexibly estimates baseline mean abundances of OTUs and provides the basis for improved quantification of covariate effects. The proposed method does not require prior normalization of OTU counts to adjust differences in sample total counts. Instead, the normalization and estimation of covariate effects on OTU abundance are simultaneously carried out for joint analysis of all OTUs. Using simulation studies and a real data analysis, we demonstrate improved inference compared to an existing method.