16S rRNA Gene-based Identification and Antibiotic Resistance Profiling ofAcinetobacter baumanniifrom River Water Isolate, Dehradun, India

2014 ◽  
Vol 3 (3) ◽  
pp. 157
Author(s):  
Sadar Ali ◽  
Rakesh Kumar Gupta ◽  
Heena Shoket ◽  
Vinod Kumar Mishra
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
River Water ◽  
Rrna Gene

scholarly journals Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing

2020 ◽  
Vol 8 (8) ◽  
pp. 604
Author(s):  
Meng-Qi Ye ◽  
Guan-Jun Chen ◽  
Zong-Jun Du
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Antibiotic Resistance Genes ◽  
Control Group ◽  
Rrna Gene ◽  
Metabolic Functions ◽  
Culture Dependent

The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem.

scholarly journals Manure-based amendments influence surface-associated bacteria and markers of antibiotic resistance on radishes grown in different soil textures

2021 ◽  
Author(s):  
Giselle K. P. Guron ◽  
Chaoqi Chen ◽  
Pang Du ◽  
Amy Pruden ◽  
Monica A. Ponder
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dairy Cattle ◽  
Soil Texture ◽  
Antibiotic Use ◽  
Chemical Fertilizer ◽  
Plate Count ◽  
Rrna Gene ◽  
Greenhouse Study

A controlled greenhouse study was performed to determine the effect of manure or compost amendments, derived during or in absence of antibiotic treatment of beef and dairy cattle, on radish taproot-associated microbiota and indicators of antibiotic resistance when grown in different soil textures. Bacterial beta-diversity, determined by 16S rRNA gene amplicon sequencing, bifurcated according to soil texture (p<0.001, R=0.501). There was a striking cross-effect in which raw manure from antibiotic-treated and antibiotic-free beef and dairy cattle added to loamy sand (LS) elevated relative (16S rRNA gene-normalized) (by 0.9-1.9 log10) and absolute (per radish) (by 1.1-3.0 log10) abundances of intI1 (an integrase gene and indicator of mobile multi-antibiotic resistance) on radishes at harvest compared to chemical fertilizer only control conditions (p<0.001). Radishes tended to carry fewer copies of intI1 and sul1 when grown in silty clay loam than LS. Composting reduced relative abundance of intI1 on LS-grown radishes (0.6-2.4 log10 decrease vs corresponding raw manure; p<0.001). Effects of antibiotic use were rarely discernable. Heterotrophic plate count bacteria capable of growth on media containing tetracycline, vancomycin, sulfamethazine, or erythromycin tended to increase on radishes grown in turned composted antibiotic-treated dairy or beef control (no antibiotics) manures relative to the corresponding raw manure in LS (0.8-2.3 log10 increase; p<0.001), suggesting that composting sometimes enriches cultivable bacteria with phenotypic resistance. This study demonstrates that combined effects of soil texture and manure-based amendments influence the microbiota of radish surfaces and markers of antibiotic resistance illuminating future research directions for reducing agricultural sources of antibiotic resistance. Importance In working towards a comprehensive strategy to combat the spread of antibiotic resistance, potential farm-to-fork routes of dissemination are gaining attention. The effects of pre-harvest factors on the microbiota and corresponding antibiotic resistance indicators on the surfaces of produce commonly eaten raw is of special interest. Here we conducted a controlled greenhouse study, using radishes as a root vegetable grown in direct contact with soil, and compared the effects of manure-based soil amendments, antibiotic use in the cattle from which the manure was sourced, composting of the manure, and soil texture, with chemical fertilizer only as a control. We noted significant effects of amendment type and soil texture on the composition of the microbiota and genes used as indicators of antibiotic resistance on radish surfaces. The findings take a step towards identifying agricultural practices that aid in reducing carriage of antibiotic resistance and corresponding risks to consumers.

scholarly journals The Role of Biofilm Formation in Antibiotic Resistance of Bacteria Isolated from Saliva of Patients with Dental Caries

2021 ◽  
pp. 40-49
Author(s):  
Merriam Ghadhanfar Alwan ◽  
Hadeel Adil Al Rubaye ◽  
Noor Adil Abood ◽  
Hind Tahseen Ibrahem ◽  
Hamiza Bt Hamidon ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Antibiotic Resistance ◽  
Dental Caries ◽  
Antimicrobial Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Rrna Gene ◽  
Tissue Culture Plate

Objectives: This study aim to determine the bacterial diversity, biofilm forming ability and the antimicrobial resistance of bacteria isolated from saliva of patients with dental caries conditions with the using of 16S rRNA gene sequencing technique for identification of the most virulent isolates. Methods: Isolation and identification of microorganisms were done employing standard bacteriologic techniques, followed by biofilm detection using tissue culture plate method. The strong biofilm forming isolates were selected for antibiotic susceptibility test against selected antibiotics using disk diffusion technique. In order to identify the selected isolates. The genomic DNA obtained following the extraction process were used for the amplification of the bacterial 16S rRNA gene. Results: A total of 137 bacterial isolates were obtained and identified as belonging to 21 genera. Tissue culture plate (TCP) method were employed for screening the isolates according to its biofilm forming ability, its showed that 55 (40.1%) of the total isolates were strong, 57 (41.6%) were moderate and 25 (18.3%) were weak biofilm producers. The antimicrobial susceptibility test showed the multi antibiotics resistance of the strong biofilm former isolates to the conventional antibiotics. Enterococcus faecalis isolates showed the highest biofilm formation and antibiotic resistance. The 16S rRNA gene for two of these isolates have been amplified using PCR and the product sequenced, analyzed and registered in the National Center for Biotechnology Information (NCBI) as UKMS1 and UKMS2 and the accession numbers KX960104.1 and KX960105.1 respectively. Conclusion: The study has revealed that antimicrobial resistance of bacteria isolates from saliva of patients with dental caries conditions is associated with biofilm formation. Other uncommon pathogenic bacteria were also isolated in this study as a result of the use of non-selective enrichment medium for culturing. Enterococcus faecalis isolates indicated the highest biofilm formation and antibiotic resistance.

scholarly journals Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Egija Zaura ◽  
Bernd W. Brandt ◽  
M. Joost Teixeira de Mattos ◽  
Mark J. Buijs ◽  
Martien P. M. Caspers ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Antibiotic Treatment ◽  
Gut Microbiome ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Fecal Microbiome ◽  
The Impact

ABSTRACT Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body. IMPORTANCE Many health care professionals use antibiotic prophylaxis strategies to prevent infection after surgery. This practice is under debate since it enhances the spread of antibiotic resistance. Another important reason to avoid nonessential use of antibiotics, the impact on our microbiome, has hardly received attention. In this study, we assessed the impact of antibiotics on the human microbial ecology at two niches. We followed the oral and gut microbiomes in 66 individuals from before, immediately after, and up to 12 months after exposure to different antibiotic classes. The salivary microbiome recovered quickly and was surprisingly robust toward antibiotic-induced disturbance. The fecal microbiome was severely affected by most antibiotics: for months, health-associated butyrate-producing species became strongly underrepresented. Additionally, there was an enrichment of genes associated with antibiotic resistance. Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome.

scholarly journals Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments

2006 ◽  
Vol 72 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Hiroyuki Kimura ◽  
Maki Sugihara ◽  
Kenji Kato ◽  
Satoshi Hanada
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
River Water ◽  
Clone Library ◽  
Hot Spring ◽  
Drilling Fluid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Deep Subsurface

ABSTRACT Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

scholarly journals IDENTIFICATION OF BACTERIA CAUSING NECROTIC PULP WITH 16S rRNA GENE POLYMERASE CHAIN REACTION AND ANTIBIOTIC RESISTANCE TESTING AT THE DENTAL HOSPITAL IN SEKELOA, BANDUNG, INDONESIA

2017 ◽  
Vol 10 (6) ◽  
pp. 284
Author(s):  
Tina Rostinawati ◽  
Sulistiyaningsih Hadisoebroto ◽  
Yoppi Iskandar ◽  
Prasetyo Hadi Nugroho ◽  
Audria Amanda Tara
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Inhibition Zone ◽  
Resistance Testing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Study Results ◽  
Dental Hospital ◽  
Polymerase Chain

Objective: This study aims to identify the bacteria that cause necrotic pulp in teeth of dental patients and test resistance of the bacteria found to antibiotics. Methods: Bacteria were taken with paper points that were inserted into the root canal of patients at the Dental Hospital of the Faculty of Dentistry, Universitas Padjadjaran, Sekeloa, Bandung. Bacteria were cultured and Gram-stained. Bacterial DNA was isolated to be identified by polymerase chain reactions 16S rRNA method against known sequences of bacterial DNA. Then, identified bacteria were tested for antibiotic resistance to tetracycline (30 μg), clindamycin (2 μg), amoxicillin (10 μg), and ampicillin (10 μg). Results: The 16s rRNA gene fragment of the main bacterium found was in 98% homology with 16S rRNA gene database in http://blast.ncbi.nlm. nih.gov, i.e., Pseudomonas aeruginosa and Acinetobacter schindleri. The results from inhibition zone of each antibiotic were 20.12 mm, 8.97 mm, 8.12 mm, and 8.03 mm for tetracycline, clindamycin, amoxicillin, and ampicillin, respectively, to P. aeruginosa. While inhibition zone of tetracycline to A. schindleri was 37.7 mm. Conclusion: Based on the study results, P. aeruginosa from patients with necrotic pulp samples were resistant to clindamycin, amoxicillin, ampicillin, and decreased activity to tetracycline. While Acinetobacter schindleri was still sensitive to tetracycline.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

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