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Journal articles on the topic '16S Rdna Sequencing of P'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Drancourt, Michel, Claude Bollet, Antoine Carlioz, Rolland Martelin, Jean-Pierre Gayral, and Didier Raoult. "16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates." Journal of Clinical Microbiology 38, no. 10 (2000): 3623–30. http://dx.doi.org/10.1128/jcm.38.10.3623-3630.2000.

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Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmen

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Lawton, Samantha J., Allison M. Weis, Barbara A. Byrne, et al. "Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing." Journal of Veterinary Diagnostic Investigation 30, no. 3 (2018): 354–61. http://dx.doi.org/10.1177/1040638718762562.

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI

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Gu, F., Y. Li, C. Zhou, et al. "Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva." Open Dentistry Journal 3, no. 1 (2009): 80–84. http://dx.doi.org/10.2174/1874210600903010080.

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Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of sal

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Girsova, Natalya, Denis Erokhin, Dmitriy Vorobyov, Damir Bogoutdinov, and Tatyana Kastalyeva. "Identification of 16SrXII-A and 16SrXII-H Phytoplasma Subgroup in Russia, Using 16S rDNA NGS Analysis." Ratarstvo i povrtarstvo, no. 00 (2025): 8. https://doi.org/10.5937/ratpov61-51638.

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The RFLP analysis of the 16S rDNA revealed two distinct phytoplasma groups, 16SrXII-A and 16SrXII-H, suggesting the presence of diverse phytoplasma strains within the analyzed isolates from the Russian State Collection of Pathogenic Microorganisms. Partial 16S rDNA sequences of four phytoplasma, 'Candidatus Phytoplasma', isolates belonging to the 16SrXII group from the three plant species: common hop (Humulus lupulus L.), Indian datura (Datura metel L.) and grapevine (Vitis vinifera L.) are presented. DNA of gene coding 16S rRNA was amplified, using nested PCR with primers P1/16Sr-SR and R16F2

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Iliyasu, M. Y., R. A. Bamanga, A. F. Umar, E. B. Agbo, and A. Uba. "16S rDNA Sequencing analysis in identification of some multidrug resistant (MDR) bacterial isolates from clinical specimens." Nigerian Journal of Biotechnology 36, no. 2 (2020): 158–66. http://dx.doi.org/10.4314/njb.v36i2.16.

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Accurate identification of bacterial pathogens from clinical specimens and Multidrug Resistant (MDR) characterization is a key to empirical therapy. Twelve (12) bacteria isolates from blood, urine and faecal samples were selected based on the ability to grow on Luria Bertani (LB) agar medium containing 100μg/ml ampicillin, identified by 16S rDNA PCR and sequencing. Identified isolates tagged; U01, U02, U03, U04, S08, U10 and U11 were from urine specimens, S05, S06, S07 and S12 from stool, while B09 was from blood. The isolates were screened for MDR pattern according to Kirby-Bauer disc diffusi

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Li, Xu-Ming, Qing Lv, Ya-Jun Chen, Lu-Biao Yan, and Xin Xiong. "Association between childhood obesity and gut microbiota: 16S rRNA gene sequencing-based cohort study." World Journal of Gastroenterology 30, no. 16 (2024): 2249–57. http://dx.doi.org/10.3748/wjg.v30.i16.2249.

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BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children (8-12 years old) using 16S rDNA sequencing. The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity. Thirty normal-weight and thirty age- and sex-matched obese children were included. Questionnaires and body measurements were collected, and fecal samples underwent 16S rDNA sequencing. Significant differences in body mass index (BMI) and body-fat percentage were observed between the groups. Analysis of gut microbiota diversity revealed lowe

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Li, Juan, Yanchen Wen, and Xiangdong Yang. "Understanding the Responses of Soil Bacterial Communities to Long-Term Fertilization Regimes Using DNA and RNA Sequencing." Agronomy 11, no. 12 (2021): 2425. http://dx.doi.org/10.3390/agronomy11122425.

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Studies of soil DNA-based and RNA-based bacterial communities under contrasting long-term fertilization regimes can provide valuable insights into how agricultural management affects soil microbial structure and functional diversity. In this study, soil bacterial communities subjected to six fertility treatments in an alkaline soil over 27 years were investigated by 454 pyrosequencing based on 16S rDNA and 16S rRNA. Long-term fertilization showed significant influences on the diversity of the soil DNA-based bacteria, as well as on their RNA-based members. The top five phyla (Proteobacteria, Ac

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Fosch, Sonia E., Cecilia A. Ficoseco, Antonella Marchesi, Silvina Cocucci, Maria E. F. Nader-Macias, and Beatriz E. Perazzi. "Contraception: Influence on Vaginal Microbiota and Identification of Vaginal Lactobacilli Using MALDI-TOF MS and 16S rDNA Sequencing." Open Microbiology Journal 12, no. 1 (2018): 218–29. http://dx.doi.org/10.2174/1874285801812010218.

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Background:The vaginal microbiome is influenced by a wide variety of factors, including contraceptive methods.Aim:To evaluate the effect of contraceptive methods on vaginal microbiota and to compare MALDI-TOF MS and 16S rDNA sequencing for lactobacilli identification.Patients and Methods:One hundred and one (101) women consulting for birth control were included in a prospective study. Their vaginal content was sampled and analyzed once before they started using the contraceptive method of their choice, and twice after the initiation of contraception, at three months (94/101 women attended) and

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Liu, Lou, Jiale Chen, Yu Chen, et al. "Characterization of Vaginal Microbiota in Third Trimester Premature Rupture of Membranes Patients through 16S rDNA Sequencing." Pathogens 11, no. 8 (2022): 847. http://dx.doi.org/10.3390/pathogens11080847.

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In China, premature rupture of membranes (PROM) counts as a major pregnancy complication in China and usually results into adverse pregnancy outcomes. We analysed the vagina microbiome composition using 16S rDNA V3–V4 amplicon sequencing technology, in this prospective study of 441 women in their third trimester of pregnancy. We first divided all subjects into PROM and HC (healthy control) groups, in order to investigate the correlation of vagina microbiome composition and the development of PROM. We found that seven pathogens were higher in the PROM group as compared to the HC group with stat

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de Vries, Jacob, Faizan Saleem, Enze Li, et al. "Comparative Analysis of Metagenomic (Amplicon and Shotgun) DNA Sequencing to Characterize Microbial Communities in Household On-Site Wastewater Treatment Systems." Water 15, no. 2 (2023): 271. http://dx.doi.org/10.3390/w15020271.

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The performance of on-site wastewater treatment systems (OWTSs) can be improved by altering digester design and by manipulating environmental variables that affect microbial community composition. Community composition can potentially be assessed using high-throughput DNA sequencing, but the two most common methods of community DNA sequencing (16S and shotgun sequencing) generally yield different taxonomic identification profiles and can perform differently according to the sampled environment. To evaluate the use of these two approaches in monitoring OWTS operation, we conducted a comparative

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Pardhi, Dimple, Khushbu Rabadiya, Rushikesh Joshi, Vikram Raval, Rakeshkumar Panchal, and Kiransinh Rajput. "EXPLORING THE POTENTIAL OF SHOUCHELLA OSHIMENSIS P-106 FOR CYCLODEXTRIN GLUCANOTRANSFERASE PRODUCTION." VIDYA - A JOURNAL OF GUJARAT UNIVERSITY 4, no. 1 (2025): 1–9. https://doi.org/10.47413/03szp371.

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Cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19) is an enzyme that utilizes starch by promoting an intramolecular transglycosylation reaction to produce cyclodextrins. An alkaliphilic, spore-forming, Gram-positive, potential CGTase producing bacteria was isolated from maize field and was identified as Shouchella oshimensis P-106 by 16S rDNA sequencing. The isolate P-106 efficiently produced 1.37 U/ml of β-CGTase as a major product and showed little existence of α- and γ-CGTase production. Optimization by one-factor-at-a-time (OFAT) approach significantly enhanced the β-CGTase production t

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Scortichini, Marco, Maria Pia Rossi, Stefania Loreti, et al. "Pseudomonas syringae pv. coryli, the Causal Agent of Bacterial Twig Dieback of Corylus avellana." Phytopathology® 95, no. 11 (2005): 1316–24. http://dx.doi.org/10.1094/phyto-95-1316.

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Thirty-eight bacterial strains isolated from hazelnut (Corylus avellana) cv. Tonda Gentile delle Langhe showing a twig dieback in Piedmont and Sardinia, Italy, were studied by a polyphasic approach. All strains were assessed by fatty acids analysis and repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using BOX and ERIC primer sets. Representative strains also were assessed by sequencing the 16S rDNA and hrpL genes, determining the presence of the syrB gene, testing their biochemical and nutritional characteristics, and determining their pathogenicity to hazelnut and oth

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Liu, Zerui, Yu Guo, Chuanxin Qin, Xiaohui Mu, and Jia Zhang. "High-Throughput Sequencing Analysis Revealed a Preference for Animal-Based Food in Purple Sea Urchins." Biology 13, no. 8 (2024): 623. http://dx.doi.org/10.3390/biology13080623.

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Sea urchins play an important role in marine ecosystems. Owing to limitations in previous research methods, there has been insufficient understanding of the food sources and ecological functional value of purple sea urchins, leading to considerable controversy regarding their functional positioning. We focused on Daya Bay as the research area, utilizing stable isotope technology and high-throughput sequencing of 16S rDNA and 18S rDNA to analyze sea urchins and their potential food sources in stone and algae areas. The results showed that the δ13C range of purple sea urchins in the stone area i

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Ram, Nanda, Vishal Sharma, Indu Singh Sankhla, and Kailash Agrawal. "Association of Pseudomonas syringae pv. apii with the Seed of Ajwain (Trachyspermum ammi L.)." Journal of Plant Science Research 38, no. 2 (2023): 883–92. http://dx.doi.org/10.32381/jpsr.2022.38.02.42.

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Present study aimed to isolate, identify and characterize the bacterial pathogens associated with ajwain seeds using biochemical and molecular methods. One hundred thirty-nine seed samples of ajwain were collected from various districts of Rajasthan. Twenty-four bacterial isolates were isolated and purified from collected seed samples. All strains were characterised for their biochemical activity. All isolates were tested for genetic diversity by using amplified rDNA restriction analysis (ARDRA). Selective strains were subjected for 16S rDNA sequencing and molecular phylogeny study. Most strai

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Li, Binbin, Shuji Liu, Xiaoting Chen, et al. "Dynamic Changes in the Microbial Composition and Spoilage Characteristics of Refrigerated Large Yellow Croaker (Larimichthys crocea) during Storage." Foods 12, no. 21 (2023): 3994. http://dx.doi.org/10.3390/foods12213994.

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The quality changes, dynamic changes in microbial composition, and diversity changes in large yellow croaker (Larimichthys crocea) during 4 °C refrigeration were studied using 16S rDNA high-throughput sequencing technology, and the total viable count (TVC), total volatile basic nitrogen (TVB-N), and thiobarbituric acid-reactive substances (TBARS) were determined. The results revealed a consistent increase in TVC, TVB-N, and TBARS levels over time. On the 9th day, TVC reached 7.43 lg/(CFU/g), while on the 15th day, TVB-N exceeded the upper limit for acceptable quality, reaching 42.56 mg/100 g.

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Marques, Eder, Rafaela CF Borges, and Carlos H. Uesugi. "Identification and pathogenicity of Pseudomonas cichorii associated with a bacterial blight of gerbera in the Federal District." Horticultura Brasileira 34, no. 2 (2016): 244–48. http://dx.doi.org/10.1590/s0102-053620160000200015.

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ABSTRACT: In 2013, leaf samples of gerbera plants showing symptoms of bacterial blight were collected in cut-flower high tunnels, in the settlement of núcleo rural alexandre gusmão, located in brazlândia, distrito federal, brazil. seven isolates obtained were subjected to phenotypic and molecular characterization, including pathogenicity tests, lopat, and partial sequencing of the 16s rdna gene. all isolates were gram-negative, aerobic, oxidase-positive, produced fluorescent pigment, induced hypersensitivity in tobacco leaves, used sorbitol and glutamate and were pathogenic to 24 different pla

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Usta, Mustafa, and Abdullah Güller. "Detection and Molecular Characterization of ‘Candidatus Phytoplasma Trifolii’, a Member of the Clover Proliferation Grup, Infecting Tomato Plants from Iğdır Province in Turkey." Turkish Journal of Agriculture - Food Science and Technology 8, no. 12 (2020): 2533–40. http://dx.doi.org/10.24925/turjaf.v8i12.2533-2540.3592.

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The tomato plant exhibiting leaf rolling, witches’ broom, distorted and elongated ﬂower’s sepals in Iğdır province, Turkey, was observed. Total DNA extraction was performed from the symtomatic fresh tomato sample. All DNAs were subjected to Direct and Nested polymerase chain reaction (PCR) with universal primer sets that amplified the 16S rRNA of phytoplasmas. PCR products were purified from agarose gel and cloned into the pGEM T-Easy cloning vector. Recombinant plasmids were introduced into the prokaryotic cloning bacteria by electroporation. Plasmid isolation was performed by selecting one o

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Zhao, Tianyuan, Jianing Ma, Meiwei Lin, et al. "Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances." International Journal of Molecular Sciences 25, no. 4 (2024): 2195. http://dx.doi.org/10.3390/ijms25042195.

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screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and B

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Lian, Qiuhua, Hengyue Ding, Huiping Zhu, et al. "Study of Jianpi Mixture on Intestinal Microbiota of Diarrhea Irritable Bowel Syndrome Mice." Evidence-Based Complementary and Alternative Medicine 2020 (April 30, 2020): 1–19. http://dx.doi.org/10.1155/2020/5241308.

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To investigate the differences in intestinal microbiota between diarrhea irritable bowel syndrome mice (IBS-D) and healthy mice and to explore the effects of Jianpi mixture on intestinal microbes’ changes in IBS-D mice based on 16S rDNA sequencing analysis. 48 young ICR male mice were randomly divided into four groups (n = 12): (1) control group, (2) IBS-D group fed with distilled water, (3) IBS-D group fed with lactic acid bacteria compound, and (4) IBS-D group fed with Jianpi mixture for 14 days. At the end of the treatment period, 5 mice were randomly selected from each group, and then the

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Chen, Mei-Feng, Chih-Hsiang Chang, Chuan Chiang-Ni, et al. "Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing." Bone & Joint Research 8, no. 8 (2019): 367–77. http://dx.doi.org/10.1302/2046-3758.88.bjr-2019-0003.r2.

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ObjectivesProsthetic joint infection (PJI) is the most common cause of arthroplasty failure. However, infection is often difficult to detect by conventional bacterial cultures, for which false-negative rates are 23% to 35%. In contrast, 16S rRNA metagenomics has been shown to quantitatively detect unculturable, unsuspected, and unviable pathogens. In this study, we investigated the use of 16S rRNA metagenomics for detection of bacterial pathogens in synovial fluid (SF) from patients with hip or knee PJI.MethodsWe analyzed the bacterial composition of 22 SF samples collected from 11 patients wi

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Fu, Yimin, Yong Yang, Keyun Mu, Yuye Zhou, and Hui Chai. "Efficacy of toothpaste containing OPTIMEALTH® OR in inhibiting dental plaque and gingivitis: A randomized controlled trial." Medicine 104, no. 5 (2025): e41225. https://doi.org/10.1097/md.0000000000041225.

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Background: This randomized double-blind, placebo-controlled clinical trial evaluated the effects of 2% OPTIMEALTH® OR toothpaste in regulating dental plaque microbiota and alleviating gingivitis. Methods: Subjects were randomly assigned to the placebo group and test group. They were instructed to brush their teeth with placebo toothpaste (placebo group) or OPTIMEALTH® OR toothpaste (test group) for a continuous 4 weeks. Clinical indices of plaque index, gingival index, and bleeding on probe (%) were examined, and images of dental plaque staining were captured at baseline and after 2 and 4 wee

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Akhtar, Khalid Pervaiz, Muhammad Yussouf Saleem, Sumaira Yousaf, Najeeb Ullah, Ghulam Rasool, and Nighat Sarwar. "Occurrence, identification and transmission of the phytoplasma associated with tomato big bud disease and identification of its vector and weed host in Pakistan." Archives of Phytopathology and Plant Protection 51, no. 7 (2018): 387–98. http://dx.doi.org/10.1080/03235408.2018.1485827.

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Tomato (Solanum lycopersicum L.) plants showing stunting, big bud, leaves yellowing or reddening and witches’-broom symptoms were observed since 2009 in Pakistan. A weed Parthenium hysterophorus grown in and around tomato fields also exhibited witches’-broom like symptoms. Fluorescence light microscopy of hand-cut stem stalk sections treated with Dienes’ stain showed blue areas in the phloem region of both tomato and P. hysterophorus symptomatic plants that indicated the association of phytoplasma with the complex. Amplification of 1.2 kb 16S rDNA fragment in nested PCR confirmed that the symp

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Xu, Zheng, Britton Lance, Claudia Vargas, et al. "Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool." Genetics 163, no. 4 (2003): 1299–313. http://dx.doi.org/10.1093/genetics/163.4.1299.

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Abstract A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data inte

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Gumtow, R. L., A. A. Khan, A. M. Bocsanczy, J. M. F. Yuen, A. J. Palmateer, and D. J. Norman. "First Report of a Leaf Spot Disease of Golden Dewdrop (Duranta erecta) Caused by Pseudomonas cichorii and a Xanthomonas Species in Florida." Plant Disease 97, no. 6 (2013): 836. http://dx.doi.org/10.1094/pdis-12-12-1117-pdn.

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Duranta erecta (Verbenaceae) is used extensively in southern states as an ornamental shrub and has replaced boxwood as the most common short hedge accenting flower beds. Over the past 2 years, during warm wet periods, dark necrotic leaf spots have been observed on golden dewdrop plants in Florida. Isolations from these spots on Difco nutrient agar (NA) consistently yielded two types of bacterial colonies that were not always simultaneously present: 1) round butyrous, bright yellow and 2) flat cream-colored. Both were 2 mm in size after 48 h, gram-negative, and produced a hypersensitivity react

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Rodríguez-Verdugo, Alejandra, Valeria Souza, Luis E. Eguiarte, and Ana E. Escalante. "Diversity across Seasons of CulturablePseudomonasfrom a Desiccation Lagoon in Cuatro Cienegas, Mexico." International Journal of Microbiology 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/201389.

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Cuatro Cienegas basin (CCB) is a biodiversity reservoir within the Chihuahuan desert that includes several water systems subject to marked seasonality. While several studies have focused on biodiversity inventories, this is the first study that describes seasonal changes in diversity within the basin. We sampledPseudomonaspopulations from a seasonally variable water system at four different sampling dates (August 2003, January 2004, January 2005, and August 2005). A total of 70Pseudomonasisolates across seasons were obtained, genotyped by fingerprinting (BOX-PCR), and taxonomically characteriz

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Febriansyah, E., I. Saskiawan, R. Riffiani, R. R. Elfirta, R. H. Setyawan, and Kasirah. "Effect of Bacillus aryabhattai extract addition on growth and productivity of Pleurotus ostreatus ((Jacq ex Fr.) P. Kumm)." Food Research 8, Supplementary 2 (2024): 46–49. http://dx.doi.org/10.26656/fr.2017.8(s2).17.

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Pleurotus ostreatus (White oyster mushroom) is one of the most widely cultivated mushrooms in the world. Nutrients provided in the media are one of the most important factors affecting the growth of mushrooms. The present study mainly focuses on the isolation of mushroom growth-promoting (MGP) bacteria and studies its effects on the growth of mushroom fruiting bodies. Bacillus aryabhattai was isolated from the growth media of Pleurotus ostreatus, identified based on 16S rDNA sequencing and phylogenetic tree construction by the neighbor-joining method using MEGA version 6.06 and its effect on f

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Yamanouchi, K., T. Tsujiguchi, Y. Shiroma, et al. "COMPARISON OF BACTERIAL FLORA IN RIVER SEDIMENTS FROM FUKUSHIMA AND AOMORI PREFECTURES BY 16S RDNA SEQUENCE ANALYSIS." Radiation Protection Dosimetry 184, no. 3-4 (2019): 504–9. http://dx.doi.org/10.1093/rpd/ncz114.

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AbstractMonitoring of radioactive materials has been reported in rivers and soil in Fukushima post the Fukushima Daiichi Nuclear Power Plant accident in March 2011. However, there are few reports on the influence of this event on bacteria in forest soils and rivers. Therefore, through amplicon sequencing of 16S rDNA we compared the bacterial flora in river sediment soils from Fukushima prefecture and from an area not exposed to radioactive contamination, Aomori prefecture. The bacterial composition in the Aomori prefecture soil and Fukushima soil were found to be very similar at the phylum lev

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Castellana, Stefano, Vittoriana De Laurentiis, Angelica Bianco, et al. "Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients." Microorganisms 12, no. 4 (2024): 799. http://dx.doi.org/10.3390/microorganisms12040799.

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This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylo

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Hao, Xiaoxia, Xingru Shang, Yiwen Zhang, et al. "Effects of Exercise on Gut Microbiome and Serum Metabolomics in Post-Traumatic Osteoarthritis Rats." Metabolites 15, no. 5 (2025): 341. https://doi.org/10.3390/metabo15050341.

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Objective: The aim of this work is to investigate the impact of exercise on gut microbiome composition, serum metabolites, and their correlation with osteoarthritis (OA) severity. Methods: Thirty-six Sprague-Dawley (SD) rats were randomly divided into four groups: Sham rats without treadmill walking (Sham/Sed group, n = 9), Sham rats with treadmill walking 2 months (Sham/TW2M group, n = 9), PTOA rats without treadmill walking (PTOA/Sed group, n = 9), and PTOA rats with treadmill walking 2 months (PTOA/TW2M group, n = 9). The PTOA model was induced by transection of the anterior cruciate ligame

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Sharma, Garima, Shweta Dang, Sanjay Gupta, and Reema Gabrani. "IDENTIFICATION AND MOLECULAR CHARACTERIZATION OF BACTERIA HAVING ANTIMICROBIAL AND ANTIBIOFILM ACTIVITY." International Journal of Pharmacy and Pharmaceutical Sciences 8, no. 10 (2016): 111. http://dx.doi.org/10.22159/ijpps.2016v8i10.12338.

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<p><strong>Objective:</strong> The aim of the current study was to isolate and identify the bacteriocinogenic strain exhibiting broad range antimicrobial activity and antibiofilm activity from soil of animal farms.</p><p><strong>Methods:</strong> In the current study, bacterial strains were isolated from soil of twelve different regions of animal farm all over India and screened for antimicrobial activity against<em> Staphylococcus epidermidis</em>, <em>Micrococcus luteus, Pseudomonas fluorescence</em> and <em>Escherichia

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Chen, Xiaowei, Haixiang Sun, Fei Jiang, et al. "Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing." PeerJ 8 (January 14, 2020): e8317. http://dx.doi.org/10.7717/peerj.8317.

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Background Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods According to the inclusion criteria and exclusion criteria, twenty-three normal weight and

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Zhang, Ruifang, Chun Xiao, Tianqiao Yong, et al. "Grifola frondosa Polysaccharide F2 Ameliorates Disordered Glucose and Lipid Metabolism in Prediabetic Mice by Modulating Bile Acids." Foods 14, no. 6 (2025): 955. https://doi.org/10.3390/foods14060955.

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Prediabetes (pre-DM) is the buffer period before developing overt type 2 diabetes (T2DM), and the search for novel food agents to protect against pre-DM is in high demand. Our team previously reported that the Grifola frondosa (maitake mushroom) polysaccharide F2 reduced insulin resistance in T2DM rats induced by streptozocin (STZ) combined with a high-fat diet (HFD). This study aimed to evaluate the effects of G. frondosa polysaccharide F2 on disordered lipid and glucose metabolism and to investigate its mechanisms in pre-DM mice. F2 (30 and 60 mg/kg/d) was administered (i.g.) for 5 weeks to

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Jia, Mingyang, Qiang Ma, Hongjun Wang, et al. "Exploring the Effects of Gracilaria lemaneiformis Polysaccharides on the Fecal Microbiota and Fecal Metabolites of Fattening Pigs Based on 16S rDNA and Metabolome Sequencing." Animals 15, no. 2 (2025): 153. https://doi.org/10.3390/ani15020153.

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Sixty Duroc × (Landrace × Yorkshire) castrated male finishing pigs were randomly divided into negative control (NC) and gracilaria lemaneiformis polysaccharides (GLP) groups to study the effects of GLP on the fecal microbiota and fecal metabolites of fattening pigs. The NC group was fed a basic diet, and the GLP group was fed a basic diet supplemented with 0.1% GLP. The diversity of the species and the fecal metabolites were analyzed using 16S rDNA sequencing and metabolome sequencing, respectively. The serum immune and antioxidant indices were analyzed using the ELISA assay. The abundances of

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Li, Chongbi, S. N. Liang, F. Y. Gao, et al. "Isolation of Endophytic Bacteria and Amplification of 16SrDNA on Citrus in Zhaoqing Districts." Journal of Agricultural Science 7, no. 12 (2015): 198. http://dx.doi.org/10.5539/jas.v7n12p198.

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<p>Zhaoqing is the main source of Citrus in China. However, the reason of citrus Huanglongbing (HLB) is unclear and may be from endophyte. Therefore, the study of citrus endophyte is necessary. The experiment would be carried out by endophyte being isolated from citrus plant and amplifying the specific 16SrDNA fragment from endogenous bacteria to know the relation of citrus HLB to 16S rDNA of endogenous bacteria. The results showed that total 55 strains of endophytic bacteria were identified. And one specific fragment long of 1261 nt was got. Sequencing analysis showed for 91.3% homology

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Nygren, Erik, Lucia Gonzales Strömberg, Jenny Logenius, Ulrika Husmark, Charlotta Löfström, and Birgitta Bergström. "Potential sources of contamination on textiles and hard surfaces identified as high-touch sites near the patient environment." PLOS ONE 18, no. 7 (2023): e0287855. http://dx.doi.org/10.1371/journal.pone.0287855.

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The hospital environment represents an important mediator for the transmission of healthcare-associated infections through direct and indirect hand contact with hard surfaces and textiles. In this study, bacteria on high-touch sites, including textiles and hard surfaces in two care wards in Sweden, were identified using microbiological culture methods and 16S rDNA sequencing. During a cross-sectional study, 176 high-touch hard surfaces and textiles were identified and further analysed using microbiological culture for quantification of total aerobic bacteria, Staphylococcus aureus, Clostridium

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Jin, Xun, Yanting Guan, Hua Bai, Yan Liu, and Xing Lv. "Effects of sEA on Slow Transit Constipation through the Microbiota-Gut-Brain Axis in Rats." Evidence-Based Complementary and Alternative Medicine 2020 (December 14, 2020): 1–13. http://dx.doi.org/10.1155/2020/8828846.

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To investigate the effect of sacral electroacupuncture (sEA) on the microbiota-gut-brain axis in the treatment of slow transit constipation, this study established a drug-induced model of slow transit constipation in rats and carried out sEA at the Baliao acupoints (BL31-BL34). On the 14th day of the therapeutic period (24 h fecal pellets), the aquaporin 3 (AQP3), 5-hydroxytryptamine (5-HT), and substance P (SP) transcripts from the distal colon and hypothalamus were analyzed. 16S rDNA has been widely used to analyze the diversity of the microbial communities. Therefore, in the present study,

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Terlizzi, F., A. R. Babini, C. Lanzoni та ін. "First Report of a γ 3-Proteobacterium Associated with Diseased Strawberries in Italy". Plant Disease 91, № 12 (2007): 1688. http://dx.doi.org/10.1094/pdis-91-12-1688b.

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During the fall seasons of 2005 and 2006, diseased strawberry plants (Fragaria × ananassa Duch.) were observed in nurseries and production fields in Ferrara, Forli-Cesena, and Ravenna provinces (Emilia-Romagna region, northern Italy). Symptoms consisted of a conspicuous plant stunting with a poor root system. Older leaves rolled upward and displayed a marked premature purplish discoloration, while young leaves were cupped, chlorotic, generally reduced in size, and had shortened petioles. This strawberry disorder was similar to “marginal chlorosis”, an infectious disease occurring in France tha

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Nilsson, Hans-Olof, Jalal Taneera, Maria Castedal, Elisabeth Glatz, Rolf Olsson, and Torkel Wadström. "Identification of Helicobacter pylori and OtherHelicobacter Species by PCR, Hybridization, and Partial DNA Sequencing in Human Liver Samples from Patients with Primary Sclerosing Cholangitis or Primary Biliary Cirrhosis." Journal of Clinical Microbiology 38, no. 3 (2000): 1072–76. http://dx.doi.org/10.1128/jcm.38.3.1072-1076.2000.

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Helicobacter pylori was identified in human liver tissue by PCR, hybridization, and partial DNA sequencing. Liver biopsies were obtained from patients with primary sclerosing cholangitis (n = 12), primary biliary cirrhosis (n = 12), and noncholestatic liver cirrhosis (n = 13) and (as controls) normal livers (n = 10). PCR analyses were carried out using primers for the Helicobacter genus, Helicobacter pylori(the gene encoding a species-specific 26-kDa protein and the 16S rRNA),Helicobacter bilis, Helicobacter pullorum, andHelicobacter hepaticus. Samples from patients with primary biliary cirrho

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Aravena, Pamela, Rodrigo Pulgar, Javiera Ortiz-Severín, et al. "PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples." Pathogens 9, no. 5 (2020): 358. http://dx.doi.org/10.3390/pathogens9050358.

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Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR

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Fu, Yan-Mei, Hong-Bin Liu, and Xiao-Qin Wu. "Diversity and Function of Endo-Bacteria in Bursaphelenchus xylophilus from Pinus massoniana Lamb. in Different Regions." Forests 11, no. 5 (2020): 487. http://dx.doi.org/10.3390/f11050487.

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The pine wood nematode (PWN) Bursaphelenchus xylophilus is the pathogen that causes pine wilt disease (PWD), a devastating forest disease. PWN-associated bacteria may play a role in PWD. However, little is known about the endo-bacteria in PWN. We analyzed the diversity of endo-bacteria in nine isolates of PWNs from Pinus massoniana Lamb. in nine epidemic areas from three Chinese provinces by high-throughput sequencing of 16S rDNA and isolated and identified culturable endo-bacteria through construction of a 16S rDNA phylogenetic tree and Biolog microbial identification. We also examined the ef

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Said, Layla Abdulhamed, Sawsan Saeed Hasan, and Saad L. Hamed. "Identification of Clinical Pseudomonas spp. by VITEK 2 Compact System and Species-specific Polymerase Chain Reaction Assay for Identification of Pseudomonas aeruginosa." International Journal of Drug Delivery Technology 10, no. 03 (2020): 383–88. http://dx.doi.org/10.25258/ijddt.10.3.14.

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The objective of this study was to isolate, identify, and diagnose Pseudomonas spp. from different clinical sources in Baghdad, Iraq. VITEK 2 compact system identification gram-negative bacteria (ID gNB) cards were used to confirm the identification. Polymerase chain reaction (PCR) technique and sequencing were used for recognition of the 16S rDNA gene, by two pairs of primers, universal primers (930 bp fragments) for recognition of Pseudomonas spp., and Pseudomonas aeruginosa specific species (PASS) primers (956 bp fragments) for differentiation of P. aeruginosa from other species. Amplified

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Teethaisong, Yothin, Kittipot Sirichaiwetchakoon, Peerapat Krittanan, et al. "Detection of Carbapenemase Producers and Inhibitory Activity of Pediococcus pentosaceus YTPP 02 against Carbapenemase-Producing Bacteria." Trends in Sciences 22, no. 1 (2024): 8766. http://dx.doi.org/10.48048/tis.2024.8766.

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Carbapenem resistance caused by carbapenemase enzymes is of serious public health concerns globally, resulting in limited options for effective treatment. Rapid detection and exploring new agents are urgently required. This study aims to detect carbapenemase producers and to investigate the antibacterial potential of Pediococcus pentosaceus YTPP 02 against carbapenemase-producing Acinetobacter baumannii and Klebsiella pneumoniae. The carbapenemase producers were detected by a Nitro-beta test (NBT), a novel and rapid method, as well as by a combined disc with resazurin assay (CRA), and multiple

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Koike, Steven T., Jeri D. Barak, Diana M. Henderson, and Robert L. Gilbertson. "Bacterial Blight of Leek: A New Disease in California Caused by Pseudomonas syringae." Plant Disease 83, no. 2 (1999): 165–70. http://dx.doi.org/10.1094/pdis.1999.83.2.165.

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During 1996 and 1997, a new and damaging disease of leek (Allium porrum) was observed on greenhouse-produced transplants and field-grown plants in California. Symptoms were water-soaked lesions at leaf tips, which eventually expanded down the length of the leaf and resulted in brown, elongated, stripe-like lesions with yellow margins. Diseased leaves eventually wilted. A blue fluorescent pseudomonad was consistently recovered from lesions, and biochemical and physiological tests indicated that it was Pseudomonas syringae. Pathogenicity tests established that representative strains of this P. s

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Trivedi, Mahendra Kumar, Alice Branton, Dahryn Trivedi, Gopal Nayak, Sambhu Charan Mondal, and Snehasis Jana. "Phenotyping and Genotyping Characterization of Proteus vulgaris After Biofield Treatment." International Journal of Genetics and Genomics 3, no. 6 (2015): 66–73. https://doi.org/10.11648/j.ijgg.20150306.12.

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Proteus vulgaris (P. vulgaris) is widespread in nature, mainly found in flora of human gastrointestinal tract. The current study was attempted to investigate the effects of Mr. Trivedi’s biofield treatment on lyophilized as well as revived state of P. vulgaris for antimicrobial susceptibility pattern, biochemical characteristics, and biotype. P. vulgaris cells were procured from Micro BioLogics Inc., USA, in sealed pack bearing the American Type Culture Collection (ATCC 33420) number and stored according to the recommended storage protocol until needed for experiments. Lyophilized vial o

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Trivedi, Mahendra Kumar, Alice Branton, Dahryn Trivedi, Gopal Nayak, Sambhu Charan Mondal, and Snehasis Jana. "Phenotyping and Genotyping Characterization of Proteus vulgaris After Biofield Treatment." International Journal of Genetics and Genomics 3, no. 6 (2015): 66–73. https://doi.org/10.5281/zenodo.191284.

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Proteus vulgaris (P. vulgaris) is widespread in nature, mainly found in flora of human gastrointestinal tract. The current study was attempted to investigate the effects of Mr. Trivedi’s biofield treatment on lyophilized as well as revived state of P. vulgaris for antimicrobial susceptibility pattern, biochemical characteristics, and biotype. P. vulgaris cells were procured from Micro BioLogics Inc., USA, in sealed pack bearing the American Type Culture Collection (ATCC 33420) number and stored according to the recommended storage protocol until needed for experiments. Lyophilized vial o

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Zheng, Pengfei, Chuantao Wang, Xiaoli Zhang, and Jun Gong. "Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites." Archaea 2019 (November 18, 2019): 1–11. http://dx.doi.org/10.1155/2019/5108012.

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Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accountin

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Wang, Lu, Xia Liu, and Yongming Ruan. "Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA." PeerJ 11 (August 14, 2023): e15843. http://dx.doi.org/10.7717/peerj.15843.

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The ability of Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) to utilize a wide range of host plants is closely related to the symbiotic bacteria within its body. This study investigated the diversity of symbiotic microorganisms associated with the sap-sucking hemipteran insect. Using deep sequencing of the 16S rDNA gene and subsequent analysis with the Qiime software package, we constructed a comprehensive library of bacterial operational taxonomic units (OTUs). We compared the microbial communities of female and male adult mealybugs. Our results showed significant differences in

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Song, Hang, Kang Xiao, Hanyi Min, Zhengyu Chen, and Qin Long. "Characterization of Conjunctival Sac Microbiome from Patients with Allergic Conjunctivitis." Journal of Clinical Medicine 11, no. 4 (2022): 1130. http://dx.doi.org/10.3390/jcm11041130.

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Conjunctival sac microbiome alterations have been reported to be closely associated with many ocular diseases. However, the characteristic of conjunctival sac microbiome in allergic conjunctivitis (AC) was scarcely described. In this study, we aimed to identify the differences of the conjunctival sac microbiome composition in AC patients compared with normal controls (NCs) using high-throughput 16S rDNA sequencing metagenomic analysis. The conjunctival sac microbiome samples from 28 AC patients and 39 NC patients were collected. The V3-V4 region of 16S rRNA gene high-throughput sequencing was

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Jiang, Jing, Hao Liu, Zidong Wang, et al. "Electroacupuncture could balance the gut microbiota and improve the learning and memory abilities of Alzheimer’s disease animal model." PLOS ONE 16, no. 11 (2021): e0259530. http://dx.doi.org/10.1371/journal.pone.0259530.

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Alzheimer’s disease (AD), as one of most common dementia, mainly affects older people from the worldwide. In this study, we intended to explore the possible mechanism of improving cognitive function and protecting the neuron effect by electroacupuncture. Method: We applied senescence-accelerated mouse prone 8 (SAMP8) mice as AD animal model, used Morris water maze, HE staining, 16S rDNA amplicon sequencing of gut microbiota and ELISA to demonstrate our hypothesis. Results: electroacupuncture improved the learning and memory abilities in SAMP8 mice (P<0.05) and could protect the frontal lobe

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Ursenbach, Axel, Frédéric Schramm, François Séverac, et al. "Impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study." BMC Infectious Diseases 21, no. 1 (2021). http://dx.doi.org/10.1186/s12879-021-05892-4.

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Abstract Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was ratio

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