scholarly journals An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota

2021 ◽  
Vol 15 (4) ◽  
pp. e0009331
Author(s):  
Yan-Chiao Mao ◽  
Han-Ni Chuang ◽  
Chien-Hung Shih ◽  
Han-Hsueh Hsieh ◽  
Yu-Han Jiang ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Bacterial Species ◽  
Microbial Culture ◽  
Human Pathogens ◽  
Bite Wound ◽  
Culture Methods ◽  
Therapeutic Implications ◽  
Bacterial Microbiota ◽  
Empiric Antibiotic ◽  
Naja Atra

Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wound infection. Therefore, we evaluated 16S Sanger sequencing and next-generation sequencing (NGS) to identify bacterial species in the oropharynx of N. atra. Using conventional microbial culture methods and the VITEK 2 system, we isolated nine species from snakebite wounds. On the basis of the 16S Sanger sequencing of bacterial clones from agar plates, we identified 18 bacterial species in the oropharynx of N. atra, including Morganella morganii, Proteus vulgaris, and Proteus mirabilis, which were also present in the infected bite wound. Using NGS of 16S metagenomics, we uncovered more than 286 bacterial species in the oropharynx of N. atra. In addition, the bacterial species identified using 16S Sanger sequencing accounted for only 2% of those identified through NGS of 16S metagenomics. The bacterial microbiota of the oropharynx of N. atra were modeled better using NGS of 16S metagenomics compared to microbial culture-based techniques. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri were also identified in the NGS of 16S metagenomics. Understanding the bacterial microbiota that are native to the oropharynx of N. atra, in addition to the bite wound, may have additional therapeutic implications regarding empiric antibiotic selection for managing N. atra bites.

DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

2018 ◽  
Vol 41 (3) ◽  
pp. 255-264 ◽  
Author(s):  
J. Abraham Pérez-Pérez ◽  
David Espinosa-Victoria ◽  
Hilda V. Silva-Rojas ◽  
Lucía López-Reyes
Keyword(s):  
Bacterial Diversity ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Brain Heart Infusion ◽  
Rrna Gene ◽  
Eisenia Foetida ◽  
Bacterial Isolates ◽  
Bacterial Microbiota ◽  
Decomposition Of Organic Matter ◽  
Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

scholarly journals Phenotypic and phylogenetic characterization of Lactobacillus species isolated from traditional Lighvan cheese

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Haleh Forouhandeh ◽  
Sepideh Zununi Vahed ◽  
Hossein Ahangari ◽  
Vahideh Tarhriz ◽  
Mohammad Saeid Hejazi
Keyword(s):  
16S Rrna ◽  
Random Amplified Polymorphic Dna ◽  
Bacterial Species ◽  
16S Rrna Sequencing ◽  
Lactobacillus Species ◽  
Culture Methods ◽  
Phylogenetic Characterization ◽  
Rrna Sequencing ◽  
Specific Culture ◽  
Lighvan Cheese

Abstract Lighvan cheese (Lighvan panir) is among the most famous traditional cheese in Iran for its desired aroma and flavor. Undoubtedly, the lactic acid bacteria especially the genus Lactobacillus are the critical factors in developing the aroma, flavor, and texture in Lighvan cheese. In this study, the Lactobacillus population of the main Lighvan cheese was investigated. The Lactobacillus of the main Lighvan cheese was isolated using specific culture methods according to previously published Guidelines. Then, the phylogenetic features were investigated and the phenotypic characteristics were examined using specific culture methods. Twenty-eight Gram-positive bacterial species were identified belonged to the genus Lactobacillus. According to the same sequences as each other, three groups (A, B, and C) of isolates were categorized with a high degree of similarity to L. fermentum (100%) and L. casei group (L. casei, L. paracasei, and L. rhamnosus) (99.0 to 100%). Random amplified polymorphic DNA (RAPD) fingerprint analysis manifested the presence of three clusters that were dominant in traditional Lighvan cheese. Cluster І was divided into 4 sub-clusters. By the result of carbohydrate fermentation pattern and 16S rRNA sequencing, isolates were identified as L. rhamnosus. The isolates in clusters II and III represented L. paracasei and L. fermentum, respectively as they were identified by 16S rRNA sequencing and fermented carbohydrate patterns. Our result indicated that the specific aroma and flavor of traditional Lighvan cheese can be related to its Lactobacillus population including L. fermentum, L. casei, L. paracasei, and L. rhamnosus. Graphical abstract

scholarly journals Bacterial Inhibition on Beauveria bassiana Contributes to Microbiota Stability in Delia antiqua

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangyuan Zhou ◽  
Yunxiao Gao ◽  
Mei Liu ◽  
Letian Xu ◽  
Xiaoqing Wu ◽  
...  
Keyword(s):  
Beauveria Bassiana ◽  
Mycelial Growth ◽  
Bacterial Species ◽  
Management Strategies ◽  
Underlying Mechanism ◽  
Conidial Germination ◽  
Delia Antiqua ◽  
Bacterial Microbiota ◽  
Fungal Microbiota ◽  
Microbial Environment

Given the multiple roles of associated microbiota in improving animal host fitness in a microbial environment, increasing numbers of researchers have focused on how the associated microbiota keeps stable under complex environmental factors, especially some biological ones. Recent studies show that associated microbiota interacts with pathogenic microbes. However, whether and how the interaction would influence microbiota stability is limitedly investigated. Based on the interaction among Delia antiqua, its associated microbiota, and one pathogen Beauveria bassiana, the associated microbiota's response to the pathogen was determined in this study. Besides, the underlying mechanism for the response was also preliminarily investigated. Results showed that B. bassiana neither infect D. antiqua larvae nor did it colonize inside the associated microbiota, and both the bacterial and fungal microbiota kept stable during the interaction. Further experiments showed that bacterial microbiota almost completely inhibited conidial germination and mycelial growth of B. bassiana during its invasion, while fungal microbiota did not inhibit conidial germination and mycelial growth of B. bassiana. According to the above results, individual dominant bacterial species were isolated, and their inhibition on conidial germination and mycelial growth of B. bassiana was reconfirmed. Thus, these results indicated that bacterial instead of fungal microbiota blocked B. bassiana conidia and stabilized the associated microbiota of D. antiqua larvae during B. bassiana invasion. The findings deepened the understanding of the role of associated microbiota–pathogen microbe interaction in maintaining microbiota stability. They may also contribute to the development of novel biological control agents and pest management strategies.

scholarly journals The functional ClpXP protease of Chlamydia trachomatis requires distinct clpP genes from separate genetic loci

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefan Pan ◽  
Imran T. Malik ◽  
Dhana Thomy ◽  
Beate Henrichfreise ◽  
Peter Sass
Keyword(s):  
Chlamydia Trachomatis ◽  
Bacterial Species ◽  
Human Pathogens ◽  
Bacterial Physiology ◽  
Sexually Transmitted ◽  
Clp Proteases ◽  
Obligate Intracellular Pathogen ◽  
Antibacterial Target ◽  
Insight Into

Abstract Clp proteases play a central role in bacterial physiology and, for some bacterial species, are even essential for survival. Also due to their conservation among bacteria including important human pathogens, Clp proteases have recently attracted considerable attention as antibiotic targets. Here, we functionally reconstituted and characterized the ClpXP protease of Chlamydia trachomatis (ctClpXP), an obligate intracellular pathogen and the causative agent of widespread sexually transmitted diseases in humans. Our in vitro data show that ctClpXP is formed by a hetero-tetradecameric proteolytic core, composed of two distinct homologs of ClpP (ctClpP1 and ctClpP2), that associates with the unfoldase ctClpX via ctClpP2 for regulated protein degradation. Antibiotics of the ADEP class interfere with protease functions by both preventing the interaction of ctClpX with ctClpP1P2 and activating the otherwise dormant proteolytic core for unregulated proteolysis. Thus, our results reveal molecular insight into ctClpXP function, validating this protease as an antibacterial target.

scholarly journals High Resolution Melt Assays to Detect and Identify Vibrio parahaemolyticus, Bacillus cereus, Escherichia coli, and Clostridioides difficile Bacteria

2020 ◽  
Vol 8 (4) ◽  
pp. 561
Author(s):  
Allison C. Bender ◽  
Jessica A. Faulkner ◽  
Katherine Tulimieri ◽  
Thomas H. Boise ◽  
Kelly M. Elkins
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Bacillus Cereus ◽  
Vibrio Parahaemolyticus ◽  
Bacterial Species ◽  
Human Pathogens ◽  
High Resolution Melt ◽  
E Coli ◽  
Clostridioides Difficile ◽  
Sensitivity Specificity

Over one hundred bacterial species have been determined to comprise the human microbiota in a healthy individual. Bacteria including Escherichia coli, Bacillus cereus, Clostridioides difficile, and Vibrio parahaemolyticus are found inside of the human body and B. cereus and E. coli are also found on the skin. These bacteria can act as human pathogens upon ingestion of contaminated food or water, if they enter an open wound, or antibiotics, and environment or stress can alter the microbiome. In this study, we present new polymerase chain reaction (PCR) high-resolution melt (HRM) assays to detect and identify the above microorganisms. Amplified DNA from C. difficile, E. coli, B. cereus, and V. parahaemolyticus melted at 80.37 ± 0.45 °C, 82.15 ± 0.37 °C, 84.43 ± 0.50 °C, and 86.74 ± 0.65 °C, respectively. A triplex PCR assay was developed to simultaneously detect and identify E. coli, B. cereus, and V. parahaemolyticus, and cultured microorganisms were successfully amplified, detected, and identified. The assays demonstrated sensitivity, specificity, reproducibility, and robustness in testing.

scholarly journals Technologies for the Selection, Culture and Metabolic Profiling of Unique Rhizosphere Microorganisms for Natural Product Discovery

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1955 ◽  
Author(s):  
Saliya Gurusinghe ◽  
Tabin L. Brooks ◽  
Russell A. Barrow ◽  
Xiaocheng Zhu ◽  
Agasthya Thotagamuwa ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Metabolic Profiling ◽  
Plant Growth Promoting Rhizobacteria ◽  
Microbial Culture ◽  
Culture Methods ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Molecular Features ◽  
Successful Recovery ◽  
Plant Growth Promoting

Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel “rhizochip” prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.

scholarly journals Adhesion of Streptococcus mutans to Different Types of Brackets

2007 ◽  
Vol 77 (6) ◽  
pp. 1090-1095 ◽  
Author(s):  
William Papaioannou ◽  
Sotiria Gizani ◽  
Maria Nassika ◽  
Efterpi Kontou ◽  
Melachrini Nakou
Keyword(s):  
Stainless Steel ◽  
Streptococcus Mutans ◽  
Bacterial Species ◽  
Culture Technique ◽  
Orthodontic Brackets ◽  
Clinical Strain ◽  
Microbial Culture ◽  
Salivary Pellicle ◽  
Different Types ◽  
The Difference

Abstract Objective: To examine the difference in the adhesion of Streptococcus mutans to three different types of orthodontic brackets and the effect of the presence of an early salivary pellicle and Streptococcus sanguis on adhesion. Materials and Methods: Three adhesion experiments were performed using stainless steel, ceramic, and plastic orthodontic brackets. In the first experiment a clinical strain of S mutans adhered to the three different types of brackets (n = 6 for each). For the second, the brackets were treated with saliva before adhesion of S mutans (n = 6 per type of bracket). Finally, the third experiment concerned saliva coated brackets (n = 6 per type of bracket), but before S mutans, S sanguis bacteria were allowed to adhere. The bacteria were always allowed to adhere for 90 minutes in all the experiments. Adhesion was quantitated by a microbial culture technique by treating the brackets with adhering bacteria with trypsin and enumerating the total viable counts of bacteria recovered after cultivation. Results: There were consistently no differences in the adherence to stainless steel, ceramic, or plastic brackets. The presence of an early salivary pellicle and S sanguis reduced the number of adhering S mutans to all three types of brackets. Conclusions: Adhesion of bacteria to orthodontic brackets depends on several factors. The presence of a salivary pellicle and other bacterial species seem to have a significant effect on the adhesion of S mutans, reducing their numbers and further limiting any differences between types of brackets.

scholarly journals Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species

2010 ◽  
Vol 76 (23) ◽  
pp. 7881-7884 ◽  
Author(s):  
Shana Topp ◽  
Colleen M. K. Reynoso ◽  
Jessica C. Seeliger ◽  
Ian S. Goldlust ◽  
Shawn K. Desai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Species ◽  
Human Pathogens ◽  
Expression Systems ◽  
Genetic Studies ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Control Gene Expression ◽  
Diverse Species ◽  
Wide Range

ABSTRACT We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria.

scholarly journals Multidrug Pump Inhibitors Uncover Remarkable Activity of Plant Antimicrobials

2002 ◽  
Vol 46 (10) ◽  
pp. 3133-3141 ◽  
Author(s):  
George Tegos ◽  
Frank R. Stermitz ◽  
Olga Lomovskaya ◽  
Kim Lewis
Keyword(s):  
Broad Spectrum ◽  
Plant Pathogens ◽  
Bacterial Species ◽  
Permeability Barrier ◽  
Gram Negative Bacteria ◽  
Human Pathogens ◽  
Gram Negative ◽  
Low Level ◽  
Broad Spectrum Antibiotics ◽  
Level Of Activity

ABSTRACT Plant antimicrobials are not used as systemic antibiotics at present. The main reason for this is their low level of activity, especially against gram-negative bacteria. The reported MIC is often in the range of 100 to 1,000 μg/ml, orders of magnitude higher than those of common broad-spectrum antibiotics from bacteria or fungi. Major plant pathogens belong to the gram-negative bacteria, which makes the low level of activity of plant antimicrobials against this group of microorganisms puzzling. Gram-negative bacteria have an effective permeability barrier, comprised of the outer membrane, which restricts the penetration of amphipathic compounds, and multidrug resistance pumps (MDRs), which extrude toxins across this barrier. It is possible that the apparent ineffectiveness of plant antimicrobials is largely due to the permeability barrier. We tested this hypothesis in the present study by applying a combination of MDR mutants and MDR inhibitors. A panel of plant antimicrobials was tested by using a set of bacteria representing the main groups of plant pathogens. The human pathogens Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica serovar Typhimurium were also tested. The results show that the activities of the majority of plant antimicrobials were considerably greater against the gram-positive bacteria Staphylococcus aureus and Bacillus megaterium and that disabling of the MDRs in gram-negative species leads to a striking increase in antimicrobial activity. Thus, the activity of rhein, the principal antimicrobial from rhubarb, was potentiated 100- to 2,000-fold (depending on the bacterial species) by disabling the MDRs. Comparable potentiation of activity was observed with plumbagin, resveratrol, gossypol, coumestrol, and berberine. Direct measurement of the uptake of berberine, a model plant antimicrobial, confirmed that disabling of the MDRs strongly increases the level of penetration of berberine into the cells of gram-negative bacteria. These results suggest that plants might have developed means of delivering their antimicrobials into bacterial cells. These findings also suggest that plant antimicrobials might be developed into effective, broad-spectrum antibiotics in combination with inhibitors of MDRs.

Microbial Antagonists of Foodborne Pathogens on Fresh, Minimally Processed Vegetables

2002 ◽  
Vol 65 (12) ◽  
pp. 1909-1915 ◽  
Author(s):  
KAREN M. SCHUENZEL ◽  
MARK A. HARRISON
Keyword(s):  
Foodborne Pathogens ◽  
Inhibitory Activity ◽  
Bacterial Species ◽  
Microbiological Analysis ◽  
Microbial Composition ◽  
Minimally Processed ◽  
Naturally Occurring ◽  
Bacterial Microbiota ◽  
Bacterial Enumeration ◽  
Minimally Processed Vegetables

On many types of raw or minimally processed foods, the bacterial microbiota is often composed of mixed species. The activities of one bacterial species may influence the growth and activities of others that are present. The objective of this project was to evaluate the microbial composition of fresh and minimally processed vegetables to determine if naturally occurring bacteria on produce are competitive with or antagonistic to potentially encountered pathogens. Naturally occurring bacteria were obtained from ready-to-eat salad vegetables on four occasions to allow for seasonal variation. Minimally processed vegetables were sampled at various stages in their processing from raw vegetables to packaged products. Some portions were analyzed microbiologically within 24 h, while other portions were stored refrigerated and analyzed after 72 h. Microbiological analysis was conducted for bacterial enumeration and to obtain isolates. An agar spot method was used to screen isolates for antimicrobial activity against Staphylococcus aureus ATCC 27664, Escherichia coli O157:H7 E009, Listeria monocytogenes LCDC 81–861, and Salmonella Montevideo. Of the 1,180 isolates screened for inhibitory activity, 37 (3.22%) were found to have various degrees of inhibitory activity against at least one test pathogen. Many isolates showed inhibitory activity against all four pathogens. The isolates with the most extensive inhibition were removed from finished lettuce piece shreds. Of the 37 inhibitory isolates, 34 (91.9%) were gram negative. All isolates with inhibitory activity are able to multiply at both 4 and 10°C.

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