Bacterial contamination in the different parts of household air conditioners: a comprehensive evaluation from Chengdu, Southwest China.

Introduction: Air flow driven by air-conditioner has a significant impact on the indoor environment, however, the bacterial contamination conditions in the different parts of air-conditioners have not been fully elucidated. Methods: In this study, we assessed the bacterial pollution in the four parts, including air outlet, filter net, cooling fin and water sink, of ten household air-conditioners quantitatively and qualitatively from Chengdu, southwestern China. Results: The microbial cultivation results showed the large total bacterial counts of 5042.0, 9127.6, 6595.1, and 12296.2 CFU/cm2 in air outlet, filter net, cooling fin, and water sink. Furthermore, the sequencing data showed that these four parts displayed different bacterial characteristics. At the level of genus, Caproiciproducens and Acidipropionibacterium were predominant in air outlet. Bacillus, Acinetobacter, Paracoccus, and Corynebacterium were detected as the characteristic bacteria in filter net. For cooling fin, Rhodococcus, Achromobacter, and Nocardioides were the dominant bacteria. The genera of Methylobacterium-Methylorubrum, Brevibacterium, Stenotrophomonas, and Psychrobacter were identified as the bioindicators in water sink. The bioinformatic analysis on the sequencing data illustrated that the bacteria from air-conditioners were associated with metabolic disturbance. Discussion: This study reveals the distinct bacterial compositions in the different parts of air-conditioner, and provides new clues for the non-negligible bacterial pollution in this common appliance from Chinese households.

Unveiling the gut microbiota and metabolite profiles in guinea pigs with form deprivation myopia through 16S rRNA gene sequencing and untargeted metabolomics.

Aim: The aim of this study was to confirm the presence of the form deprivation myopia (FDM) guinea pig eye-gut axis and investigate the relationship between serum vasoactive intestinal peptide (VIP), lipopolysaccharides (LPS), specific gut microbiota and their metabolites. Method: 20 specific-pathogen-free (SPF) guinea pigs were divided into the FDM and the control(Con) group. Following model induction, serum levels of VIP and LPS were quantified. A combination of 16S ribosomal ribosomal Ribonucleic Acid (rRNA) gene sequencing, non-targeted metabolomics and bioinformatics analysis were employed to identify disparities in gut microbiota and metabolites between the two groups of guinea pigs. Result: Compared to the control group, FDM guinea pigs exhibited a significant trend towards myopia, along with significantly elevated concentrations of LPS and VIP (p < 0.0001). Furthermore, Ruminococcus_albus emerged as the predominant bacterial community enriched in FDM (p < 0.05), and demonstrated positive correlations with 10 metabolites, including l-Glutamic acid, Additionally, Ruminococcus_albus exhibited positive correlations with VIP and LPS levels (p < 0.05). Conclusion: The findings suggest that the Ruminococcus_Albus and glutamate metabolic pathways play a significant role in myopia development, leading to concurrent alterations in serum VIP and LPS levels in FDM guinea pigs. This underscores the potential of specific gut microbiota and their metabolites as pivotal biomarkers involved in the pathogenesis of myopia.

Pasteurella bettyae infection requiring finger amputation due to rapid deterioration and tissue damage.

We report a case of infection of the middle finger of a 69-year-old man who visited our hospital. Pus was collected from the erythematous and swollen area of the nail cage of the left-hand middle finger and evaluated in our microbiology laboratory. Gram staining of the specimen revealed multinucleated leukocytes and abundant gram-negative bacilli. Isolated colonies were identified as Pasteurella bettyae using VITEK MS and 16 S ribosomal RNA (rRNA) gene sequencing. The patient's blood test results improved after treatment with penicillin, but the local factors affecting the finger did not improve, and amputation of the middle finger had to be performed. This case represents a report of a very rare hand infection caused by P. bettyae. Polymorphic identification methods, such as MALDI-TOF MS and 16 S rRNA gene sequencing, are needed for members of the genus Pasteurella isolated from severe infections and abnormal sites, and further studies are warranted.

The relationship between menopausal syndrome and gut microbes.

BACKGROUND: Gut microbes were closely related to women's health. Previous studies reported that the gut microbes of premenopausal women were different from those of postmenopausal women. However, little was known about the relationship between gut microbiota dysbiosis and menopausal syndrome (MPS). The aim of this study was to explore the relationship between MPS and gut microbes. METHODS: Patients with MPS (P group, n = 77) and healthy women (H group, n = 24) at menopause were recruited in this study. The stool specimen and clinical parameters (demographic data, follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), et al) of participants' were collected. We evaluated the differences in gut microbes by 16S ribosomal RNA gene sequencing. We used LEfSe to identify gut microbes with varying abundances in different groups. The Spearman correlation coefficients of clinical parameters and gut microbes were calculated. PICRUSt was used to predict the potential KEGG Ortholog functional profiles of microbial communities. RESULTS: The abundance of 14 species differed substantially between the MPS and menopausal healthy women (LDA significance threshold > 2.0) according to LEfSe analysis. Using Spearman's correlation analysis, it was discovered that E2 had a positive correlation with Aggregatibacter segnis, Bifidobacterium animalis, Acinetobacter guillouiae (p < 0.05, these three species were enriched in menopausal healthy women), while FSH and LH had a negative correlation with them (p < 0.05). KEGG level3 metabolic pathways relevant to cardiovascular disease and carbohydrate metabolism were enriched in the MPS (p < 0.05), according to functional prediction by PICRUST and analyzed by Dunn test. CONCLUSION: There was gut microbiota dysbiosis in MPS, which is reflected in the deficiency of the abundance of Aggregatibacter segnis, Bifidobacterium animalis and Acinetobacter guillouiae related to the level of sex hormones. In MPS individuals, species with altered abundances and unique functional pathways were found.

Characteristics of the sputum microbiome in COPD exacerbations and correlations between clinical indices.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a prevalent, progressive respiratory disease, and acute exacerbations of COPD (AECOPD) can accelerate the deterioration of the disease. Increasing evidence suggests that airway bacterial dysbiosis is associated with AECOPD. However, the exact relationship between changes in the sputum microbiome during AECOPD and clinical indices remains unclear. METHODS: In this study, a total of 76 sputum samples were collected from patients with AECOPD (n = 28), stable COPD (n = 23), recovery (n = 15) and healthy controls (HCs; n = 10). The sputum microbiome profile was analysed by sequencing the V3­V4 amplicon of the 16S rRNA (ribosomal RNA) gene. RESULTS: The bacterial diversity (Shannon and Simpson's index) was found to be significantly decreased in the AECOPD and recovery groups when compared to that in the stable COPD and HC groups. The most dominant phylum identified in the sputum samples of AECOPD patients was Proteobacteria, accounting for 30% of the microbiome. Compared to the stable COPD groups, the relative abundances of Firmicutes and Bacteroidetes were decreased, whereas those of Proteobacteria and Actinobacteria were increased in AECOPD patients. Furthermore, discriminative bacteria, such as Haemophilus, were identified as being specific taxa in AECOPD patients. Functional analysis showed that genes involved in membrane transport and signal transduction metabolism were enriched in the AECOPD group. Importantly, the proportions of Veillonella were positively correlated with lung function, and Staphylococcus was positively correlated with inflammatory indices. CONCLUSION: Our study revealed variations in the sputum microbiome of AECOPD (based on composition and function) in a Chinese cohort and highlighted its correlation to clinical indices. These results indicated that microbial dysbiosis may contribute to disease progression and provide microbial biomarkers for the diagnosis of AECOPD.

A case of Bordetella trematum and Kerstersia gyiorum infections in a patient with congestive dermatitis.

Bordetella trematum and Kerstersia gyiorum are rare gram-negative bacilli that are not frequently detected in human infections. In this report, we describe a case of a 48-year-old man who presented to our hospital with an infected wound on his leg. Discharges from the cracks of the granulation were collected and evaluated in our microbiology laboratory. Gram staining of the specimen showed polymorphonuclear leukocytes and abundant gram-negative bacilli. Three types of colonies were isolated on blood agar and were identified as B. trematum and Alcaligenes faecalis using VITEK MS. Moreover, K. gyiorum and B. trematum were identified and confirmed via 16S ribosomal RNA (rRNA) gene sequencing. The patient successfully recovered following application of meropenem antibacterial therapy and surgical debridement. This is the first reported case of complex wound infection caused by both B. trematum and K. gyiorum. Identification of B. trematum has recently been made possible by routine bacterial identification using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, K. gyiorum isolation is still rare, and species identification requires 16S rRNA sequencing. Thus, this case highlighted the importance of using multiple methods, such as MALDI-TOF MS and 16S rRNA gene sequencing, for identification of rarely isolated species from clinical specimens.

Microbiota in Gingival Crevicular Fluid Before and After Mechanical Debridement With Antimicrobial Photodynamic Therapy in Peri-Implantitis.

OBJECTIVES: This study aims to compare the microbiota of gingival crevicular fluid (GCF) before and after mechanical debridement (MD) with antimicrobial photodynamic therapy (aPDT) and determine the core efficient microbiota in peri-implantitis after treatment. METHODS: We recruited 9 patients (14 implants) treated with MD+aPDT for peri-implantitis at our center from February 1, 2018, to February 1, 2019. GCF was collected using filter paper strip before and after the treatment. The bacterial 16S rRNA was amplified and sequenced using an Illumina MiSeq platform to characterize the GCF. Bioinformatics and statistical analyses were performed using QIIME2 and R. RESULTS: A total of 4,110,861 high-quality sequences were obtained from GCF samples. Based on the reference database, 1,120 amplicon sequence variants (ASVs) were finally harvested. Principal coordinates analysis indicated significant differences in the bacterial community structure between the 180 days after-treatment group and pre-treatment group. Difference analysis and least discriminant analysis showed that the differences were mainly reflected in non-dominant bacteria between these two groups. The non-dominant genera with significantly different distribution between the 180 days after-treatment group and the pre-treatment group included Lactobacillus, Pedobacter, Bulleidia, Centipeda, Desulfovibrio, Ochrobactrum, Staphylococcus, Microbacterium, Brevundimonas, Desulfobulbus, and Parvimonas. Moreover, a total of 29 predictive functional categories at KEGG level 2 were identified. The significant difference pathways at KEGG level 2 between after-treatment and pre-treatment were concentrated in infectious disease-related pathways. CONCLUSIONS: Patients with peri-implantitis have significant changes in the low-abundance bacteria of the GCF before and after MD+aPDT. MD+aPDT may change the composition of GCF microbiota by increasing the abundance of cluster 1 (beneficial) and decreasing that of cluster 4 (harmful), which may decrease metabolic response to infection and thus improve peri-implantitis.

Variations in fecal microbial profiles of acute exacerbations and stable chronic obstructive pulmonary disease.

AIM: Alterations in the respiratory and digestive tract microbiomes influence the occurrence and progression of chronic obstructive pulmonary disease (COPD). Here, we aimed to identify fecal microbiome profiles during COPD development. METHODS: Fecal samples were collected from 29 COPD patients with acute exacerbation (AECOPD), 29 stable COPD patients, and 22 normal subjects (NS). The fecal microbial profiles were obtained using 16S rRNA gene sequencing. KEY FINDINGS: The diversity and richness were lower and fewer variations in the taxonomic composition of fecal microbiota were observed in AECOPD patients than in stable COPD and NS. The relative abundances of Firmicutes and Actinobacteria were decreased, while those of Bacteroidetes and Proteobacteria were increased in AECOPD compared to COPD and NS. Among the top ten genera, the proportions of Lachnoclostridium and Parabacteroides significantly increased in AECOPD, whereas those of other genera decreased. Discriminative bacteria, such as p_Bacteroidetes, c_Bacteroidia, o_Bacteroidales, Lactobacillales, and Proteobacteria, were identified in AECOPD compared to stable COPD and NS. The weighted gene co-expression networks showed that Firmicutes and Actinobacteria were the main hub bacterial taxa related with lung function (FEV1% and FEV1/FVC%) and inflammatory indices (TNF-α, IL-6, IL-8, PCT, and CRP). SIGNIFICANCE: These findings emphasized the changes in the abundance and composition of the fecal microbiome in stable COPD and AECOPD. Variations in fecal microbiota may be associated with COPD progression.

Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger.

It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.

Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice.

Gut microbiota is the collection of microbes that lives in the host. Glycan is the major factor to shape the composition of microbial community. Nostoc sphaeroids Kütz (NSK) has been used as food and medicine for thousands of years in Asian countries while the bioactivity on gut microbiota is unclear till now. Here, we used NSK polysaccharide and NSK powder to investigate the bioactivity on the gut microbiota of C57BL/6j mice, respectively. By 16S ribosomal RNA gene sequencing, we found the composition of gut microbiota had been changed and differed from each other. However, the abundance of Bacteroides, Parabacteroides, Escherichia-Shigella and Parasutterella on genus level were significantly increased by NSK polysaccharide and NSK powder. In addition, Akkermansia and Rikenellaceae were enriched by NSK powder. Moreover, we found the IL-1ß and IL-6 decreased significantly while TNF-α and IL-10 increased significantly especially in NSK powder group. Intriguingly, the increased microbes were significantly positively co-related with TNF-α and IL-10 while negatively co-related with IL-1ß and IL-6 by co-relation and network analysis. The above results suggested that Nostoc sphaeroids Kütz may selectively enrich a "core bacterial community" and add new evidence to discover how Nostoc sphaeroids Kütz has biological function.

Characterization of the Esophageal Microbiota and Prediction of the Metabolic Pathways Involved in Esophageal Cancer.

Esophageal microbiota plays important roles in esophageal cancer. Esophagectomy, as the most important therapeutic way, contributes to changes of esophageal microbiome. However, there are few studies examining the esophageal microbiome and the metabolic changes before and after esophagectomy. The present study characterized the esophageal microbiome of 17 patients with esophageal squamous cell carcinoma (ESCC), 11 patients with esophagogastric junction (EGJ) cancer, 15 patients at 9-12 months after radical esophagectomy and 16 healthy controls (HC). 16S ribosomal RNA gene sequencing was used to evaluate the microbiome and predict the metabolic pathways. Our results showed that the microbial diversity was significantly lower in ESCC, EGJ and post-ESCC groups than that in the HC group. The abundance of Fusobacteria was higher (7.01 vs. 1.12%, P = 0.039) and the abundance of Actinobacteria (1.61 vs. 4.04%) was lower in the ESCC group than that in the HC group. We found significant differences in the abundance of Bacteroidetes (20.45 vs. 9.86%, P = 0.026), Fusobacteria (7.01 vs. 1.66%, P = 0.030) between ESCC and post-ESCC groups. The results of microbial composition analysis and PICRUSt demonstrated significant differences between ESCC and HC groups. The ß diversity and PICRUSt suggested that the microbial composition and metabolic pathways were similar to HC group after esophagectomy. The monitoring of the esophagus microbiota may be an essential method to predict the recurrence of tumor.

Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition.

BACKGROUND: The human gut microbiome is recognized as an important determinant of human health, yet little is known about how dietary habits are related to the microbiome in post-weaned, pre-pubescent children. OBJECTIVE: The goal of this work was to link quantitative dietary intake with microbiome features in a diverse population of children consuming a predominantly Western diet. DESIGN: This was a cross-sectional study. PARTICIPANTS/SETTINGS: English- or Spanish-speaking families with healthy children between the ages of 2 and 9 years were recruited from a community-based, early childhood learning center in suburban Los Angeles, California between June and September 2014. MAIN OUTCOME MEASURES: Children included in the analyses (n=75) contributed three fecal samples and three quantitative 24-hour dietary recalls using the multiple-pass method with an average of 5.7 days between samples. Microbial communities of each fecal sample were characterized using Illumina sequencing of the 16S ribosomal RNA gene. Dietary recalls were analyzed using the Automated Self-Administered 24-Hour Recall Dietary Assessment Tool. STATISTICAL ANALYSIS PERFORMED: Associations between dietary factors and microbiome features were assessed using the Kruskal-Wallis test, Spearman rank correlations, or permutational multivariate analysis of variance. For demographic and health-related variables, χ2 analyses were used to test for differences between age groups for categorical variables. RESULTS: Our results show that age is correlated with three metrics of microbiome diversity (P<0.05) and is associated with both community structure (P=0.0488) and membership (P=0.0002). Several dietary food groups and nutrients were likewise associated with microbiome features. For example, consumption of non-whole-grain foods was associated with community structure (P=0.0089) and membership (P=0.0057), but not diversity (P>0.05). Likewise, the relative abundance of several bacterial taxa were linked to consumption of particular food groups and/or nutrients, as illustrated by the positive associations between total fruit (Pfalsediscovery rate<0.05) and fiber (Pfalsediscovery rate<0.05) consumption with the relative abundance of the Lachnospira genera. CONCLUSIONS: This hypothesis-generating study demonstrates that the composition of the child gut microbiome remains dynamic beyond the age of 3 years and responds to dietary differences across individuals. In particular, non-whole-grain foods fortified with vitamins and minerals appear to be associated with the composition of the microbiome. Future interventional or model organism-based studies will be needed to test these associations between diet and microbiome composition.

Filifactor alocis brain abscess identified by 16S ribosomal RNA gene sequencing: A case report.

We report a clinical case of Filifactor alocis brain abscess in an 85-year-old man who had decayed teeth 1 week prior. In this case, the abscess was surgically drained after empirical antibiotics had been initiated. Although the causative organism could not be identified by culture, F. alocis was detected via 16S ribosomal RNA (16S rRNA) gene sequencing of the pus isolated from the abscess. The patient recovered without serious sequelae after surgical drainage and prolonged antibiotic treatment, including metronidazole, ceftriaxone and meropenem for 8 weeks. The findings in this case emphasize that 16S rRNA gene sequencing allows bacterial diagnosis of brain abscess when phenotypic identification fails, such as in cases where patients are undergoing antimicrobial treatment at the time of sampling or where patients are infected with fastidious organisms.

Endometriosis and the microbiome: a systematic review.

BACKGROUND: The aetiology and pathogenesis of endometriosis are still under investigation. There is evidence that there is a complex bidirectional interaction between endometriosis and the microbiome. OBJECTIVE: To systematically review the available literature on the endometriosis-microbiome interaction, with the aim of guiding future inquiries in this emerging area of endometriosis research. SEARCH STRATEGY: MEDLINE, Embase, Scopus and Web of Science were searched through May 2019. A manual search of reference lists of relevant studies was also performed. SELECTION CRITERIA: Published and unpublished literature in any language describing a comparison of the microbiome state in mammalian hosts with and without endometriosis. DATA COLLECTION AND ANALYSIS: Identified studies were screened and assessed independently by two authors. Data were extracted and compiled in a qualitative synthesis of the evidence. MAIN RESULTS: Endometriosis appears to be associated with an increased presence of Proteobacteria, Enterobacteriaceae, Streptococcus spp. and Escherichia coli across various microbiome sites. The phylum Firmicutes and the genus Gardnerella also appear to have an association; however, this remains unclear. CONCLUSIONS: The complex bidirectional relationship between the microbiome and endometriosis has begun to be characterised by the studies highlighted in this systematic review. Laboratory and clinical studies demonstrate that there are indeed differences in the microbiome composition of hosts with and without endometriosis. TWEETABLE ABSTRACT: Review findings show endometriosis associated with increased Proteobacteria, Enterobacteriaceae, Streptococcus and Escherichia coli across various microbiome sites.

Linderae radix ethanol extract attenuates alcoholic liver injury via attenuating inflammation and regulating gut microbiota in rats

This study aimed to explore the influence of gut microbiota alterations induced by Linderae radix ethanol extract (LREE) on alcoholic liver disease (ALD) in rats and to study the anti-inflammatory effect of LREE on ALD through the lipopolysaccharide (LPS) toll-like receptor 4 (TLR4)-nuclear factor kappa B (NF-κB) pathway. ALD rat models were established by intragastric liquor [50% (v/v) ethanol] administration at 10 mL/kg body weight for 20 days. Rats were divided into six groups: normal group (no treatment), model group (ALD rats), Essentiale group (ALD rats fed with Essentiale, 137 mg/kg), and LREE high/moderate/low dose groups (ALD rats fed with 4, 2, or 1 g LREE/kg). NF-κB and LPS levels were evaluated. Liver pathological changes and intestinal ultrastructure were examined by hematoxylin and eosin staining and transmission electron microscopy. The gut microbiota composition was evaluated by 16S rDNA sequencing. Expression levels of TLR4 and CD68 in liver tissue, and occludin and claudin-1 in intestinal tissue were measured. LREE treatment significantly reduced NF-κB and LPS levels, improved liver pathological changes, and ameliorated intestinal ultrastructure injury. Meanwhile, LREE-fed groups showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than the rats in the model group. Administration of LREE suppressed TLR4 overexpression and promoted the expression of occludin and claudin-1 in intestine tissue. Thus, LREE could partly ameliorate microflora dysbiosis, suppress the inflammatory response, and attenuate liver injury in ALD rats. The protective effect of LREE might be related to the LPS-TLR4-NF-κB pathway.

Association Between Gut Microbiota and Helicobacter pylori-Related Gastric Lesions in a High-Risk Population of Gastric Cancer.

Eradication of Helicobacter pylori has been found to be effective for gastric cancer prevention, but uncertainties remain about the possible adverse consequences such as the potential microbial dysbiosis. In our study, we investigated the association between gut microbiota and H. pylori-related gastric lesions in 47 subjects by deep sequencing of microbial 16S ribosomal RNA (rRNA) gene in fecal samples. The dominant phyla in fecal samples were Bacteroidetes, Firmicutes, and Proteobacteria with average relative abundances of 54.77, 31.37 and 12.91%, respectively. Microbial diversity analysis showed that observed species and Shannon index were increased in subjects with past or current H. pylori infection compared with negative subjects. As for the differential bacteria, the average relative abundance of Bacteroidetes was found to significantly decrease from H. pylori negative (66.16%) to past infection group (33.01%, p = 0.007), as well as from normal (76.49%) to gastritis (56.04%) and metaplasia subjects (46.83%, p = 0.027). For Firmicutes and Proteobacteria, the average relative abundances showed elevated trends in the past H. pylori infection group (47.11, 20.53%) compared to negative group (23.44, 9.05%, p = 0.068 and 0.246, respectively), and similar increased trends were also found from normal (18.23, 5.05%) to gastritis (35.31, 7.23%, p = 0.016 and 0.294, respectively) or metaplasia subjects (32.33, 20.07%, both p < 0.05). These findings suggest that the alterations of fecal microbiota, especially the dominant phyla of Bacteroidetes, Firmicutes and Proteobacteria, may be involved in the process of H. pylori-related gastric lesion progression and provide hints for future evaluation of microbial changes after H. pylori eradication.

Omeprazole Minimally Alters the Fecal Microbial Community in Six Cats: A Pilot Study.

Although they have historically been thought of as safe medications, proton pump inhibitors such as omeprazole have been associated with an increased risk of enteric, particularly Clostridium difficile, infections in people. In cats, omeprazole is often the first choice acid suppressant prescribed for the treatment of upper gastrointestinal (GI) ulceration and bleeding. Despite this, no studies to date have explored the effect of omeprazole on the feline fecal microbiome and metabolome. Therefore, the purpose of this pilot study was to evaluate the effect of prolonged omeprazole administration on the fecal microbiome and metabolome in healthy cats to identify targets for analysis in a larger subset of cats with GI disease. A within-subjects, before and after, pilot study was performed whereby six healthy adult cats received 60 days of placebo (250 mg lactose PO q 12 h) followed by 5 mg (0.83-1.6 mg/kg PO q 12 h) omeprazole. On days 0, 30, and 60 of placebo and omeprazole therapy, the fecal microbiome and metabolome were characterized utilizing 16S ribosomal RNA sequencing by Illumina and untargeted mass spectrometry-based methods, respectively. Omeprazole administration resulted in no significant changes in the global microbiome structure or richness. However, transient changes were noted in select bacterial groups with omeprazole administration resulting in an increased sequence percentage of Streptococcus, Lactobacillus, Clostridium, and Faecalibacterium spp. and a decreased sequence percentage of Bifidobacterium spp. Significance was lost for all of these bacterial groups after adjustment for multiple comparisons. The fecal concentration of O-acetylserine and aminomalonate decreased with omeprazole therapy, but significance was lost after adjustment for multiple comparisons. The results of this pilot study conclude that omeprazole has a mild and transient impact on the fecal microbiome and metabolome when orally administered to healthy cats for 60 days. Based on the findings of this pilot study, evaluation of the effect of omeprazole specifically on Streptococcus, Lactobacillus, Clostridium, Faecalibacterium, and Bifidobacterium spp. is warranted in cats with primary GI disease.

Pulmonary Reinfection by Nocardia in an Immunocompetent Patient with Bronchiectasis.

Pulmonary reinfection by Nocardia has been rarely reported. We describe a case of pulmonary reinfection by Nocardia in an immunocompetent patient. An 82-year-old immunocompetent woman with bronchiectasis presented with exacerbation of cough. She had a history of pulmonary nocardiosis three years earlier. At that time, Nocardia species were cultured from the sputum and identified as N. cyriacigeorgica with 16S ribosomal RNA gene sequencing. In the present episode, cultures of sputum and bronchial washing specimens grew N. beijingensis, which was identified with 16S ribosomal RNA gene sequencing. Pulmonary reinfection by different Nocardia species can occur in immunocompetent patients.

16S Ribosomal RNA Gene Sequencing to Evaluate the Effects of 6 Commonly Prescribed Antibiotics.

INTRODUCTION: The rapid antibiotic sensitivity test (RAST) is a novel in-office culture and sensitivity system for endodontic infections. The purpose of this research was to validate the RAST system as a viable, in-office alternative to antibiotic sensitivity testing using turbidity to determine antibiotic sensitivities of endodontic infections. METHODS: Aspirates were taken from the root canals of 9 necrotic human teeth at the initiation of root canal therapy. These samples were cultured in the RAST medium, and antibiotic sensitivity to 6 antibiotics was tested. Further analysis was performed using 16S ribosomal RNA (rRNA) gene sequencing. RESULTS: Thirty-one bacterial phyla were identified as well as 2 phyla of the kingdom Archaea. Augmentin (Dr. Reddy's Laboratories Ltd, Hyderabad, India) and ampicillin performed identically at 24 hours, inhibiting turbidity in 100% of the samples. At 48 hours in anaerobic conditions, Augmentin outperformed ampicillin by 13%. Ciprofloxacin was the least efficacious antibiotic. At 48 hours, only 22% of anaerobic ciprofloxacin cultures affectively inhibited bacterial growth. CONCLUSIONS: The RAST medium is a viable in-office alternative to antibiotic susceptibility testing in an off-site laboratory. It is able to support the growth of a wide variety of microorganisms in both aerobic and anaerobic environments, and, in combination with 16S rRNA gene sequencing, it led to the identification of a new archaebacterial phylum, Crenarchaeota, as part of the endodontic infection microbiome.

A case of relapsed lung abscess caused by Eubacterium brachy infection following an initial diagnosis of pulmonary actinomycosis.

We report a rare case of lung abscess due to Eubacterium brachy. In this case, an analysis of the aspirate from frank pus revealed Gram-positive coccobacilli. We initially strongly suspected lung abscess associated with actinomycosis because of the chronic/recurrent clinical course and radio-pathological findings such as a granuloma lesion. Although a biochemical analysis revealed Actinomyces sp., 16S rRNA gene sequencing and a phylogenetic tree analysis of the isolated strain confirmed the presence of E. brachy. Some cases previously diagnosed as actinomycosis might be correctly diagnosed as E. brachy infection. Clinicians should be aware that additional studies using 16S rRNA gene sequencing are needed to clarify whether pulmonary infection associated with E. brachy is a similar entity to that of chronic granulomatous infection disease in pulmonary actinomycosis.