Application of 16S rDNA Sequencing Technology in the Analysis of Pathogenic Bacteria in Sputum of Severe Pneumonia

Background. Stress ulcer (SU) is a serious gastrointestinal mucosal lesion under acute stress. Huanglian decoction is a famous traditional Chinese medicine prescription, which has been used to treat digestive system diseases for thousands of years. Many clinical cases have proved that Huanglian decoction has a good effect on SU. Some studies have shown that the intestinal bacteria will be changed accordingly when the gastrointestinal mucosa is damaged. However, there are few published reports on the effect of the intestinal microbiome with SU mice that were treated by Huanglian decoction. In this study, we investigated the effect of the fecal microbiome in mice with SU by the 16S rDNA sequencing technology. Methods. Male KM mice were induced by cold-restraint stress except for the normal control group and then treated by Huanglian decoction (Group HD) and Esomeprazole magnesium solution (Group ES) separately for 7 days. 16S rDNA sequencing technology analysis was applied to evaluate the changes of bacterial flora in mice feces. And, histopathological methods and molecular biological detection methods were also performed. Results. Huanglian decoction could help to repair the gastric mucosal injury and regulate the relative content of TNF-α and IL-1β. Moreover, Huanglian decoction could increase the relative abundance of intestinal probiotics in the intestine of mice with SU, especially in Verrucomicrobiae and Akkermansia. Conclusions. Huanglian decoction might effectively promote the repair of gastrointestinal mucosal injury and regulate the number and species of intestinal bacteria to maintain the stability of gastrointestinal microecology.

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Application of 16s rDNA Sequencing in the Analysis of Pathogenic Bacteria in Sputum of Severe Bacterial Pneumonia

Advances in Microbiology ◽

10.4236/aim.2021.112008 ◽

2021 ◽

Vol 11 (02) ◽

pp. 109-116

Author(s):

Juncheng Zheng ◽

Juan Zhu ◽

Bin Chen ◽

Lingxiu Chen ◽

Tian Gao ◽

...

Keyword(s):

16S Rdna ◽

Bacterial Pneumonia ◽

Pathogenic Bacteria ◽

16S Rdna Sequencing ◽

Rdna Sequencing

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Profiling of Diagnostic Information of and Latent Susceptibility to Bacterial Keratitis From the Perspective of Ocular Bacterial Microbiota

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.645907 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhichao Ren ◽

Qing Liu ◽

Wenfeng Li ◽

Xian Wu ◽

Yanling Dong ◽

...

Keyword(s):

Healthy Volunteers ◽

16S Rdna ◽

High Throughput ◽

Pathogenic Bacteria ◽

Bacterial Culture ◽

Diagnostic Information ◽

Bacterial Keratitis ◽

16S Rdna Sequencing ◽

Bacterial Microbiota ◽

Rdna Sequencing

The ocular surface possesses its own bacterial microbiota. Once given a chance, opportunistic pathogens within ocular microbiota may lead to corneal infection like bacterial keratitis (BK). To reveal the possible factor that makes people vulnerable to BK from the perspective of ocular bacterial microbiota, as well as to compare diagnostic information provided by high-throughput 16S rDNA sequencing and bacterial culture, 20 patients with BK and 42 healthy volunteers were included. Conjunctival swabs and corneal scrapings collected from the diseased eyes of BK patients were subjected for both high-throughput 16S rDNA sequencing and bacterial culture. Conjunctival swabs collected from the normal eyes of BK patients and healthy volunteers were sent only for sequencing. For identifying the pathogens causing BK, high-throughput 16S rDNA sequencing presented a higher positive rate than bacterial culture (98.04% vs. 17.50%), with 92.11% reaching the genus level (including 10.53% down to the species level). However, none of the sequencing results was consistent with the cultural results. The sequencing technique appears to challenge culture, and could be a complement for pathogen identification. Moreover, compared to the eyes of healthy subjects, the ocular microbiota of three sample groups from BK patients contained significantly less Actinobacteria and Corynebacteria (determinate beneficial symbiotic bacteria), but significantly more Gammaproteobacteria, Pseudomonas, Bacteroides, and Escherichia-Shigella (common ocular pathogenic bacteria). Therefore, it is speculated that the imbalance of protective and aggressive bacteria in the ocular microbiota of healthy people may trigger susceptibility to BK. Based on this speculation, it seems promising to prevent and treat infectious oculopathy through regulating ocular microbiota.

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Isolation of pathogenic bacteria from the skin ulcerous symptomatic gourami (Colisa lalia) through 16S rDNA analysis

University Journal of Zoology Rajshahi University ◽

10.3329/ujzru.v27i0.1948 ◽

1970 ◽

Vol 27 ◽

pp. 21-24 ◽

Cited By ~ 8

Author(s):

Mosharrof Hossain

Keyword(s):

16S Rdna ◽

Pathogenic Bacteria ◽

Infected Fish ◽

Bacterial Disease ◽

16S Rdna Sequencing ◽

Aeromonas Veronii ◽

Rdna Sequencing ◽

Colisa Lalia ◽

Ulcerative Lesions ◽

Rdna Analysis

Aeromonas spp infections are probably the most common bacterial disease diagnosed in cultured warm water fish. In the present study, six strains of Aeromonas spp bacteria were isolated from the gourami (Colisa lalia) by 16S rDNA sequencing analyses that are pathogenic to freshwater fish. Among them, three were under Aeromonas veronii species, two were Aeromonas sp ATCC and one was Aeromonas hydrophila. Colisa lalia usually imported in Korea from the South and South-east Asian countries for recreational purposes. However, they are playing important role as a disease vector or carriers. The infected fish of this study frequently have hemorrhages at the base of the fins or on the skin, and gross ulcerative lesions. Internal signs include, fluid in the abdomen, swollen liver and spleen, and the intestine was distended and fluid-filled. In this study, the utility of 16S rDNA sequencing was employed to isolate Aeromonas bacteria from freshwater imported fish are important to environment, veterinary, and clinical purposes. Key word: Bacteria, Colisa lalia, 16S rDNA, Aeromonas Â doi:10.3329/ujzru.v27i0.1948 Univ. j. zool. Rajshahi Univ. Vol. 27, 2008 pp. 21-24

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Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

Current Pharmaceutical Analysis ◽

10.2174/1573412916666200206160836 ◽

2020 ◽

Vol 16 ◽

Author(s):

Nidhi Srivastava ◽

Indira P. Sarethy

Keyword(s):

Ethyl Acetate ◽

16S Rdna ◽

Retention Index ◽

Ethyl Acetate Extract ◽

Similarity Index ◽

Antimicrobial Drug ◽

16S Rdna Sequencing ◽

Metabolite Fingerprinting ◽

Streptomyces Sp ◽

Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

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2-Way k-Means as a Model for Microbiome Samples

Journal of Healthcare Engineering ◽

10.1155/2017/5284145 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Weston J. Jackson ◽

Ipsita Agarwal ◽

Itsik Pe’er

Keyword(s):

Unsupervised Learning ◽

16S Rdna ◽

Mixture Model ◽

Vaginal Microbiome ◽

16S Rdna Sequencing ◽

Sequencing Data ◽

Cluster Assignment ◽

Rdna Sequencing

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

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Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

PLoS ONE ◽

10.1371/journal.pone.0181860 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0181860 ◽

Cited By ~ 19

Author(s):

Anna Maria Timperio ◽

Susanna Gorrasi ◽

Lello Zolla ◽

Massimiliano Fenice

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Sea Water ◽

16S Rdna Sequencing ◽

Maldi Tof Mass Spectrometry ◽

Maldi Tof ◽

Rdna Sequencing ◽

Arctic Sea ◽

Maldi Biotyper ◽

Identification Of Bacteria

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Analysis of the bacterial floral structure and diversity of Xuanwei ham by 16S rDNA sequencing

Journal of Food Safety ◽

10.1111/jfs.12800 ◽

2020 ◽

Vol 40 (4) ◽

Author(s):

Luying Shan ◽

Yinjiao Li ◽

Shi Zheng ◽

Yuanmiao Wei ◽

Ying Shang

Keyword(s):

16S Rdna ◽

16S Rdna Sequencing ◽

Floral Structure ◽

Rdna Sequencing

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ISOLATION, PURIFICATION, AND CHARACTERIZATION OF LIPASE FROM BACILLUS SP. FROM KITCHEN GREASE

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2018.v11i6.24955 ◽

2018 ◽

Vol 11 (6) ◽

pp. 224

Author(s):

Jaiganesh R ◽

Jaganathan Mk

Keyword(s):

16S Rdna ◽

Solvent Tolerance ◽

16S Rdna Sequencing ◽

Bacillus Sp ◽

Purification And Characterization ◽

Lipase Enzyme ◽

Sequencing Method ◽

Rdna Sequencing ◽

Solvent Tolerant

Objective: The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. from kitchen grease for a variety of applications including organic synthetic reactions and preparation of enantiomerically pure pharmaceuticals.Methods: Lipase producing isolates were screened from kitchen grease on a selective medium rhodamine B olive oil agar, and tributyrin agar was used to screen the lipase and esterase producing an organism, respectively. The isolate identified using 16S rDNA sequencing method and enzyme activity was quantitatively assayed. Lipase production was characterized in different conditions.Results: The isolate showed highest lipase activity was which later was identified as Bacillus sp. using 16S rDNA sequencing method. The lipase was purified using ammonium sulfate precipitation. The isolate showed excellent tolerance to methanol, ethanol, acetonitrile, and moderate tolerance to butanol. The increased biomass concentration, maximum production, and activity were achieved at 37°C in 24 h incubation, then gradual reduction in production was observed. The maximum activity of lipase enzyme was obtained at pH between 6 and 9.Conclusion: The isolate produce solvent tolerance lipase enzyme and it can be a promising candidate of solvent tolerance lipase enzyme for variety of industrial applications.

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