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Deep Baltic Sea Sediments Reveal the Microbial Community Composition Change Using Metagenomes
Deep Baltic Sea Sediments Reveal the Microbial Community Composition Change Using Metagenomes
It’s reported that metagenomes are used in analyzing the deep Baltic Sea sediment to figure out how the composition of buried microbial communities are related to the present environmental conditions. Sediment samples were collected from deep see floor, and the sediments vary in age, organic carbon content which can reveal the change in Baltic sea environment from the last ice age to Holocene Sample sediment was transferred to DNA extraction using the FastDNA SPIN Kit; and then the research further analyzed the DNA sequence using the MiSeq. By comparing the DNA sequences of Holocene marine with glacial’ water’s, it’s found that the genes encoding the Wood-Ljungdahl pathway are more abundant in ice-age sediment. Therefore, it shows that the changing sediment conditions have influenced the deep Baltic sediment microbial communities. I think the use of computer science tools are significant to the research, with the help of the computer science MiSeq, can help scholars find and compare the DNA sequences as soon as possible. ~Yanyan Chen
Helicobacter pylori
Salmonella typhi
Bacterial infections risks Gallbladder and Cholelithiosis
Bacterial infections risks Gallbladder and Cholelithiosis
It was found that Helicobacter and Salmonella typhi infections causes Gallbladder Cancer. However, other bacterial infections were lead to GBC or CL . BLAST , RDP classifier and greenGenes were the programs used to study the Gallbladder bile. BLAST is a tool that helps to compare and align the DNA sequence from the sample. The bile sample showed that there were no helicobacter or Salmonella typhi, but other bacterias were present. The predominant species in Bolivian GBC patients was Fusobacterium sp., but those in Chilean GBC patients were E. coli and Enterobacter sp..
http://journal.waocp.org/article_59593_1937103ddda3a56e2b33699617694db7.pdf
Sajath
Watermelon Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits
Watermelon Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits
The watermelon fruit is rich in water (90%), sugar, fiber, vitamins, amino acids, minerals and carotenoids, especially lycopene, flavonoids, and triterpenoids. The purpose of this study is to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. Red and Yellow watermelons were used from different countries. The computer science behind the study is QIIME quality control process . The tags were further compared with the reference database (Gold database) by using the UCHIME algorithm. A great sharing of genes was surprisingly observed in yellow and red cultivars, so despite being different cultivars, environmental conditions facilitate the development of relatively similar microbial composition in both types. The most interesting part of the the article is the abundance of 16s genes that is found in the watermelons.
https://www.frontiersin.org/articles/10.3389/fpls.2018.00004/full
Eugenia Kellyann Beache
Rapid Community DNA Sequencing
Rapid Community DNA Sequencing
In the age of technology and the constant threat of human exposure to diseases it is essential that we as a society can be able to identify bacteria rapidly as indicated in the article, "A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions ." It can be crucial for hospitals to identify unknown illnesses within a couple of hours of seeing a patient. Right now many of unknown illnesses if there is an outbreak or severe problem targeting a group the specimens are sent to the CDC. The MinION serves as the only potable real time device for DNA and RNA sequencing at an accuracy of 70"s %, that is pretty good for a 2 hour window as an identifier.
Current available sequencing takes days or weeks to complete its task whereas the MinION, produces nucleotide sequence data sequentially, enabling real-time metagenomic analysis. Also, MinION has advantages such as simple sample preparation, portability, quick turnaround, maneuverability, and relative inexpensiveness.
https://www.biorxiv.org/content/early/2017/01/20/101865.full.pdf+html
Charlene
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