The use of molecular techniques to characterize the microbial communities in contaminated soil and water

2008 ◽  
Vol 34 (2) ◽  
pp. 265-276 ◽  
Author(s):  
Seidu Malik ◽  
Michael Beer ◽  
Mallavarapu Megharaj ◽  
Ravi Naidu
Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.


Author(s):  
Anjali Verma ◽  
◽  
Mamta Kumari ◽  
Namita Dhusia ◽  
Nandkishor More

2019 ◽  
Vol 17 (3) ◽  
Author(s):  
E J GUTIÉRREZ-ALCÁNTARA ◽  
D TIRADO-TORRES ◽  
G VÁZQUEZ-RODRÍGUEZ ◽  
E DELGADILLO-RUÍZ ◽  
M SALAZAR-HERNÁNDEZ ◽  
...  

2021 ◽  
pp. 128131
Author(s):  
Muhammad Azeem ◽  
Sabry M. Shaheen ◽  
Amjad Ali ◽  
Parimala G.S.A. Jeyasundar ◽  
Abdul Latif ◽  
...  

2011 ◽  
Vol 91 (2) ◽  
pp. 193-211 ◽  
Author(s):  
T. A. McAllister ◽  
K. A. Beauchemin ◽  
A. Y. Alazzeh ◽  
J. Baah ◽  
R. M. Teather ◽  
...  

McAllister, T. A., Beauchemin, K. A., Alazzeh, A. Y., Baah, J., Teather, R. M. and Stanford, K. 2011. Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle. Can. J. Anim. Sci. 91: 193–211. Direct-fed microbials (DFM) have been employed in ruminant production for over 30 yr. Originally, DFM were used primarily in young ruminants to accelerate establishment of the intestinal microflora involved in feed digestion and to promote gut health. Further advancements led to more sophisticated mixtures of DFM that are targeted at improving fiber digestion and preventing ruminal acidosis in mature cattle. Through these outcomes on fiber digestion/rumen health, second-generation DFM have also resulted in improvements in milk yield, growth and feed efficiency of cattle, but results have been inconsistent. More recently, there has been an emphasis on the development of DFM that exhibit activity in cattle against potentially zoonotic pathogens such as Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus. Regulatory requirements have limited the microbial species within DFM products to organisms that are generally recognized as safe, such as lactic acid-producing bacteria (e.g., Lactobacillus and Enterococcus spp.), fungi (e.g., Aspergillus oryzae), or yeast (e.g., Saccharomyces cerevisiae). Direct-fed microbials of rumen origin, involving lactate-utilizing species (e.g., Megasphaera elsdenii, Selenomonas ruminantium, Propionibacterium spp.) and plant cell wall-degrading isolates of Butyrivibrio fibrisolvens have also been explored, but have not been commercially used. Development of DFM that are efficacious over a wide range of ruminant production systems remains challenging because[0] comprehensive knowledge of microbial ecology is lacking. Few studies have employed molecular techniques to study in detail the interaction of DFM with native microbial communities or the ruminant host. Advancements in the metagenomics of microbial communities and the genomics of microbial–host interactions may enable DFM to be formulated to improve production and promote health, responses that are presently often achieved through the use of antimicrobials in cattle.


2018 ◽  
Vol 29 (4) ◽  
pp. 311-312 ◽  
Author(s):  
Yiu Fai Tsang ◽  
Yong Sik Ok ◽  
Ajit K. Sarmah ◽  
Bin Cao ◽  
Ming Hung Wong

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