Next Generation Sequencing Has Changed The Landscape Of Microbial Ecology

PCR is the amplification of DNA by denaturing, annealing, and extension of a DNA template. Specific sequences can be amplified using single-stranded DNA that complements the target sequences known as primers. This process heats DNA until the strands separate, then primers bind to the target regions. DNA polymerase enzymes and single base nucleotides (dNTPs) are used to synthesize new strands of DNA to the target sequence. The end product will contain large quantities of the target sequence (Bean et al. 2015). The most notable in phylogenic studies is the 16S rRNA gene, because of it’s highly conserved primer-binding site and hyper variable regions that provide species-specific sequences within bacteria and archaea (Kolbert and Persin 1999). This gene is a component of the 30S small subunit of prokaryotic ribosome’s and serves as the primary site of protein synthesis. (Woese and Fox 1977). The 16S rRNA sequence can be amplified and matched to national databases provided by the National Center for Biotechnology Information (NCBI) using software termed Basic Local Alignment Search Tool (BLAST) to find regions of similarity between biological sequences for bacterial identification. Thus, providing a cost effective and timely method when compared to biochemical

In the 1990s, further research in comparative genomics of bacteria and archea showed that in prokaryotic genomes, a majority of genes were acquired

Special Event 1 will require you to watch a video from the Howard Hughes Medical Institute Holiday Lecture Series titled Microbe Hunters. The video is 1 hour in length. You may start and stop the video as you answer the following questions. When you have completed the questions please submit your answers via email to your instructor for Special Event 1 points.

The most represented classes were Acidobacteria and Alphaproteobacteria, which together comprised almost 30% of all bacterial amplicons, followed by the considerably lower representation of Deltaproteobacteria, DA052, and Sphingobacteria (Table 1S). Members of the dominant classes Actinobacteria, Alphaproteobacteria, and Sphingobacteria showed similar patterns between sample sites. However, Deltaproteobacteria had a higher relative abundance at RP in comparison with SB or HH1, and Elusimicrobia was in higher abundance at RP than at HH1. Levels of Nitrospirae and Spirochaetes were the highest at RP than in all other samples.

In room 303 we have been studying many poems from Doris Lessing. Doris was born in in Persia and now lives in Iran. She came from a large family of five. She shares her own experiences when she writes and that is what makes her unique. Her talent for writing came from a variety of her experiences. One poem she wrote called “No Witchcraft for sale” was very interesting. It had three important messages and those messages are the poisonous snake is dangerous, stay loyal, and amazing things can happen.

The gut microbiota is extremely diverse – consisting of over 1,000 identified unique species of bacteria. It is indeed difficult to wrap one’s head around it – despite bacteria being microscopically small, and having an undetectable mass, the bacteria of the gut in a human can weigh over 2 pounds! This incredibly diverse mass of bacteria is also mostly unique on an individual basis – over 70% of the bacteria per gut are unique to each person [1]. Thus, the gut microbiota of each individual can effectively function as a unique source of identity.

Bacteria have an intrinsic role to humans thriving commensally in and outside the body, despite their evolutionary and structural differences from us. Their prokaryotic classification gives insight to methods used in identification and observation. Researchers can pinpoint certain genes they know are vital across their phylogeny. An example of this would include autosomal genes, like those that encode for structural proteins used in translation. Particularly, the 16s rRNA gene is highly conserved across prokaryotic species, but unlike many conserved genes, it also includes small variable regions specific to each species. This makes the 16s gene useful as an identification signature for prokaryotes, and it is the most common genetic marker used today (Janda). This is not only due to its presence in nearly all prokaryotes, but because it has been genetically unchanged over time, for the most part. However a flaw to using the 16s rRNA gene is that it cannot be a definite identification

Microbes are bacteria, archaea and eukaryotes. The earth was formed 4.6 million years ago. And a few million years later, by 3.5 billion years ago, earth was already inhabited by a diversity of organisms. The earliest organism is Prokaryotes and within the next billion years, two distinct groups of prokaryotes called bacteria and archaea diverged. Eukaryotes cell evolved from a prokaryotes community, a host cell containing even smaller prokaryotes .The microbial world accounted for all known life forms for nearly 50 to 90% of Earth's history. We are still researching microbial organisms today in marine environment, extreme environments. A microbial observatory is an NSF-funded project dedicated to the discovery and characterization of novel microorganisms and microbial communities of diverse

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Often scientists work with bacteria that do not come in a labeled test tube— for example, bacterial samples taken from infected human tissue or from the soil—and the scientist must then identify the unknown microorganism in order to understand what behavior to expect from the organism, for example, a certain type of infection or antibiotic resistance. However, because of the relatively few forms of bacteria compared to animals and because of the lack of bacterial fossil records due to their asexually reproductive nature, the taxonomy used to classify animals cannot be applied to bacteria (Brown 275). In order to classify unknown bacteria, a variety of physiological and metabolic tests are available to narrow a sample down from the fathomless number of possibilities into a more manageable range. Once these tests have been performed, the researcher can consult Bergey’s Manual of Determinative Bacteriology, a systematically arranged and continually updated collection of all known bacteria based on their structure, metabolism, and other attributes.

Composition and/or function changing in gut microbiota has been associated with a number of chronic disease such as colon cancer, colitis, irritated bowel syndrome, diabetes, obesity and atherosclerosis (1-5). Akkermansia muciniphila is a gram negative, strictly anaerobic, oval-shaped bacteria (6). Characteristics of this bacteria are obligate chemo-organotroph, non-motile, ability to growth on gastric mucin, sensitive to ampicillin, and able to use mucin as carbon, nitrogen and energy source (6). C+G content of DNA is 47.6 mol% (6). Phylogenetic tree based on 16srRNA gene demonstrated that Akkermansia is associated to the genera Verrucomicrobium and Prosthecobacter (6). This bacteria is a new genus that belongs to the division Verrucomicrobia

The researchers used shot-gun sequencing which is a technique that uses smaller fragments of deoxyribonucleic acid (DNA) sequences that are reassembled into one sequence by looking for regions of overlap. All of the 3.6M reads, were first trimmed for 99% accuracy for all known organisms then characterized with Sequence-based

Environmental microbes are microorganisms that are capable of adapting and occupying a wide range of environmental conditions. Their biodiversity is well represented within the three major domains of life and can even extend into the ambiguous realm of viruses. As their categorical name indicates, environmental microbes can be found distributed throughout distinct ecological niches and based on their specific biological interactions within each ecosystem microbes can confer beneficial, adverse or neutral consequence to other surrounding life forms. In this experiment, we are interested in analyzing the air samples within the MIC 104 laboratory in order to determine the abundance of airborne species. Based on the biological restrictions imposed by the laboratories relative aseptic

This is the introduction and presents the problem the paper addresses. Now a team from the Max-Planck-Institute (MPI) for Terrestrial Microbiology in Marburg, Germany, by tapping the DNA synthesis expertise of the U.S. Department of Energy Joint Genome Institute (DOE JGI), has reverse engineered a biosynthetic pathway for more effective carbon fixation. This novel pathway is based on a new CO2-fixing enzyme that is nearly 20 times faster than the most prevalent enzyme in nature responsible for capturing CO2 in plants by using sunlight as energy. The study was published in the November 18, 2016 issue of Science. "We had seen how efforts to directly assemble synthetic pathways for CO2-fixation in a living organism did not succeed so far," said Tobias Erb of MPI, who led the study. "So we took a radically different, reductionist approach by assembling synthetic principal components in a bottom-up fashion in a test tube "The team started with several theoretical CO2-fixation routes that could result in continuous carbon cycling. But they didn 't stop there. "We did not restrict our design efforts to known enzymes, but considered all reactions that seemed biochemically feasible," Erb said. Unlike DNA sequencing, where the language of life is read from the genome of an organism, DNA synthesis entails first the identification of a particular genetic element -- such as an enzyme for fixing carbon from the atmosphere -- and writing and expressing that code in a new system.

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