Comparison of the automated Phoenix with the Vitek 2 for the identification of Streptococcus pneumoniaePortions of this study were presented at the 2007 American Society of Microbiology 107th General Meeting in Toronto, Ontario, Canada.

Rapid and accurate identification of Streptococcus pneumoniae is a critical component in the optimal management of infected patients. The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was evaluated for identification of S. pneumoniae (n = 311) and was compared to the Vitek 2 (bioMérieux, Marcy l’Étoile, France). Strains with discordant identification between methods were resolved with 16S rRNA gene sequencing as the gold standard. The Phoenix and the Vitek 2 correctly identified 96.8% (n = 301) and 95.2% (n = 296) of S. pneumoniae strains, respectively. Overall, there was no statistically significant difference in the performance of the 2 automated systems for the identification of S. pneumoniae in this study. The Vitek 2 mean time-to-results for all streptococcal identification was 1.5 h faster than that for the Phoenix. We conclude that the automated Phoenix and the Vitek 2 systems are comparable in their ability to identify S. pneumoniae and are preferable to the use of routine biochemical assays, which have delayed time-to-results and are not dependably accurate.

Download Full-text

Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

Download Full-text

Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.605825 ◽

2021 ◽

Vol 11 ◽

Author(s):

Shiju Xiao ◽

Guangzhong Zhang ◽

Chunyan Jiang ◽

Xin Liu ◽

Xiaoxu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Target Genes ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Phosphotransferase System ◽

Microbial Composition ◽

Kegg Pathways ◽

Significant Difference ◽

Rrna Gene Sequencing ◽

Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

Download Full-text

Comparison of VITEK 2, MALDI-TOF MS, 16S rRNA gene sequencing, and whole-genome sequencing for identification of Roseomonas mucosa

Microbial Pathogenesis ◽

10.1016/j.micpath.2019.103576 ◽

2019 ◽

Vol 134 ◽

pp. 103576 ◽

Cited By ~ 1

Author(s):

Wolfram W. Rudolph ◽

Florian Gunzer ◽

Melanie Trauth ◽

Boyke Bunk ◽

Richard Bigge ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Whole Genome ◽

Vitek 2 ◽

Rrna Gene Sequencing ◽

Roseomonas Mucosa ◽

Tof Ms

Download Full-text

Biological Removal and Fate Assessment of Diclofenac Using Bacillus subtilis and Brevibacillus laterosporus Strains and Ecotoxicological Effects of Diclofenac and 4′-Hydroxy-diclofenac

Journal of Chemistry ◽

10.1155/2020/9789420 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12 ◽

Cited By ~ 4

Author(s):

Camille Grandclément ◽

Anne Piram ◽

Marie-Eléonore Petit ◽

Isabelle Seyssiecq ◽

Isabelle Laffont-Schwob ◽

...

Keyword(s):

Vibrio Fischeri ◽

High Resolution Mass Spectrometry ◽

Parent Compound ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Consortia ◽

Brevibacillus Laterosporus ◽

Emerging Pollutant ◽

Significant Difference ◽

Rrna Gene Sequencing

Since bacterial consortia involved in conventional wastewater treatment processes are not efficient in removing diclofenac (DCF), an emerging pollutant frequently detected in water bodies, the identification of microorganisms able to metabolise this pharmaceutical compound is relevant. Thus, DCF removal was investigated using bacteria isolated from aqueous stock solutions of this micropollutant and identified as Bacillus and Brevibacillus species using 16S rRNA gene sequencing. A 100% DCF removal was achieved after 17 hours of experiment at 20°C in a nutrient medium; the biodegradation kinetic followed a pseudo-first order (kbiol = 11 L·gSS−1·d−1). Quantitative assessment of DCF removal showed that its main route was biotic degradation. The main degradation product of DCF, 4′-hydroxy-diclofenac (4′-OH-DCF), was identified using liquid chromatography-electrospray ionisation high-resolution mass spectrometry. Since the ecotoxicological impact of 4′-hydroxy-diclofenac was not reported in the literature, the ecotoxicity of DCF and its metabolite were tentatively evaluated using Vibrio fischeri bioassays. Results from these tests showed that this metabolite is not more toxic than its parent compound and may hopefully be an intermediate product in the DCF transformation. Indeed, no significant difference in ecotoxicity was observed after 30 min between DCF (50 should be writtten in subscript all along the manuscript in EC50 = 23 ± 4 mg·L−1) and 4′-hydroxy-diclofenac (EC50 = 19 ± 2 mg·L−1). Besides, the study highlighted a limit of the Microtox® bioassay, which is largely used to assess ecotoxicity. The bioluminescence of Vibrio fischeri was impacted due to the production of microbial activity and the occurrence of some carbon source in the studied medium.

Download Full-text

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

The Open Microbiology Journal ◽

10.2174/1874285801004010123 ◽

2010 ◽

Vol 4 (1) ◽

pp. 123-131 ◽

Cited By ~ 6

Author(s):

Jens JØrgen Christensen ◽

Brita Bruun ◽

Ute Wolff Sönksen ◽

Lisbeth Nielsen ◽

Annemarie Hesselbjerg ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Sequencing Analysis ◽

Vitek 2 ◽

Rrna Gene Sequencing

Download Full-text

Effects of Giardia lamblia Colonization and Fenbendazole Treatment on Canine Fecal Microbiota

Journal of the American Association for Laboratory Animal Science ◽

10.30802/aalas-jaalas-19-000113 ◽

2020 ◽

Author(s):

Naomi N Lee ◽

Willie A Bidot ◽

Aaron C Ericsson ◽

Craig L Franklin

Keyword(s):

Giardia Lamblia ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Limited Information ◽

Sample Collection ◽

Minimal Impact ◽

Clinically Normal ◽

Significant Difference ◽

Rrna Gene Sequencing

The gut microbiota (GM) is the sum of hundreds of distinct microbial species that can equal or outnumber their host’ssomatic cells. The GM influences a multitude of physiologic and immunologic processes in the host, and changes in the GM have been shown to alter the phenotypes of animal models. Previous studies using rodents have also shown that the composition of the GM is affected by many factors, including diet, husbandry, housing, and the genetic background of the animals. However, limited information exists about factors that may modulate GM in other laboratory species, such as dogs. We sought to eliminate sporadic Giardia colonization of dogs using fenbendazole (FBZ), an antiprotozoal widely used in biomedical research dog colonies. Concerns that FBZ could have inadvertent effects on the canine GM led us to assess GM over the course of treatment. FBZ (50 mg/kg) was given orally to all dogs in 3 different facilities (n = 19 to 25) for 10 consecutive days. Fecal samples were obtained 2 d before the initiation of treatment, on the last day of treatment, and 2 wk after the completion of treatment. Targeted 16S rRNA gene sequencing was used to analyze fecal microbiota. All dogs were clinically normal throughout the sample collection period. Statistical analyses of data showed significant differences between dogs housed in the 3 different facilities, further emphasizing the effect of housing and husbandry factors on the GM. However,negligible differences were seen between time points, indicating that FBZ did not significantly alter the canine GM. Comparison of the GM of Giardia lamblia positive and negative dogs revealed no significant difference between the 2 groups. These findings suggest that FBZ can be used therapeutically in dogs with minimal impact on the GM. Furthermore, the presence ofG. lamblia in clinically normal animals may not be sufficient to influence the normal canine microbiota.

Download Full-text

Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

Animals ◽

10.3390/ani10122245 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2245

Author(s):

Yiping Zhu ◽

Wuyan Jiang ◽

Reed Holyoak ◽

Bo Liu ◽

Jing Li

Keyword(s):

Dental Treatment ◽

16S Rrna Gene Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Microbial Composition ◽

Dental Procedures ◽

Significant Difference ◽

Dental Diseases ◽

Rrna Gene Sequencing ◽

The Impact

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

Download Full-text

Septic arthritis due to Roseomonas gilardii in an immunocompetent adolescent

Journal of Medical Microbiology ◽

10.1099/jmm.0.011106-0 ◽

2009 ◽

Vol 58 (11) ◽

pp. 1514-1516 ◽

Cited By ~ 14

Author(s):

Sergio Fanella ◽

Daryl Schantz ◽

James Karlowsky ◽

Ethan Rubinstein

Keyword(s):

Septic Arthritis ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Sports Injury ◽

Bordetella Bronchiseptica ◽

Rrna Gene ◽

First Case ◽

Vitek 2 ◽

Rrna Gene Sequencing ◽

Slow Growing

The genus Roseomonas comprises groups of slow-growing, Gram-negative coccobacilli, which only infrequently cause infection in humans. When identified, they are associated with immunocompromised adults, often causing bacteraemia. Due to their rarity, members of this genus can be overlooked or misidentified using automated laboratory identification systems. We report on an immunocompetent adolescent patient who developed septic arthritis due to Roseomonas gilardii following surgery for a sports injury. The isolate was initially misidentified as Bordetella bronchiseptica using the Vitek 2 system, but confirmed as R. gilardii based on 16S rRNA gene sequencing. To the best of our knowledge, this is the first case of a healthy paediatric patient with septic arthritis due to R. gilardii.

Download Full-text