DNA sequencing is one of the most important techniques in the field of molecular biology, according to which the order of nucleotides can be determined in a piece of DNA. There are several different methods for DNA sequencing. Today, with advances in the field Nanotechnology and bioinformatics, methods have developed to increase the speed and efficiency of DNA sequencing, which has made it possible to carry out large projects such as sequencing the human genome cheaper, more accurately and more quickly. Today, DNA sequencing is an integral part of modern science. This technique is used in various fields of microbiology, including tracking infectious diseases and studying the diversity of microbial communities. There are different ways to sequence DNA. But each of these techniques has its advantages and disadvantages. To get acquainted with these methods, This article is a review that analyzes the generations of sequencing from the past to the present that has been collected from articles, reputable book sites and articles.

Background: Sporadic colorectal cancer is the fourth most common cancer in Iran. The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is involved in the cellular defense against alkylating agents. Genetic alterations in the MGMT gene may impair the protein’s ability to remove alkyl groups from the O6-position of guanine, thereby raising the mutation rate and increasing the risk of sporadic colorectal cancer. Methods: We hypothesized that amino acid substitution polymorphisms in the MGMT gene may be associated with the genetic susceptibility to sporadic colorectal cancer. We assessed five non-synomymous polymorphisms (Pro58Ser, Leu84Phe, Arg128Gln, Ile143Val, and Gly160Arg) in the MGMT gene by PCR/Pyrosequencing. The population studied consisted of 200 sporadic colorectal cancer patients and 200 healthy individuals (blood donors), all of Iranian origin. Allele frequencies and genotypes were compared between the two groups. Odds ratios were calculated and the interactions among the polymorphisms, age and sex were examined. Result: There was a significant association between two amino acid substitution polymorphisms (Arg128Gln and Gly160Arg) of MGMT gene and sporadic colorectal cancer. Conclusion: we could show a significant association between the two polymorphisms and colorectal cancer. This might be a superior marker for colon cancer screening in the future.

This research investigated the factors influencing bioremediation (biopile) of arid soils contaminated by weathered hydrocarbons. Five soils were thoroughly characterised to determine total petroleum hydrocarbons (TPH), their physicochemical properties and microbial diversity. Identified biopile-limiting factors are to be elevated petroleum hydrocarbon concentrations, high electrical conductivity and the magnitude of the recalcitrant hydrocarbon fraction. To optimise the biopile parameters, microcosm study was conducted which showed significant TPH reduction in three of five soils (BP-1, BP-2 and BP-4) but not in other two (BP-3 and BP-5), where BP-3 had a very high hydrocarbon concentration (123,757 mg kg-1) and BP-5 had a high proportion of recalcitrant hydrocarbons (>70 % of C29). Highest TPH removal (68 %) occurred in soil BP-2 and the lowest (5 %) in soil BP-3 over 56 days. Surfactant (Triton) addition, nutrient amendment or the soil dilution did not improve TPH degradation in soils BP-3 and BP-5. Phylogenetic analysis conducted during the remediation process found that hydrocarbon concentration and hydrocarbon fraction exerted the main effect on bacterial abundance, diversity and assemblage composition. At lower concentrations ( ~1000-4000 mg kg-1), bacterial diversity and abundance increased significantly, whilst decreased in higher concentrations. Although high TPH content and detection of TPH degraders, TPH biodegradation is limited in soil (BP-5) due to the presence of less soluble hydrocarbon fraction which indicated low TPH bioavailability (~7 %). Biopile could be applied as a technology to remediate three soils (BP-1, BP-2 and BP-4) but further modification of the biopile treatments required for other two soils BP-3 and BP-5.

Baluchi sheep is the dominant fat-tail breed in Iran. We studied the microbial communities in the rumen of four Baluchi lambs fed a high concentrate conventional diet. Using DNA extracted from the rumen samples, we found the partial ribosomal rRNA of bacterial and archaeal were amplified by polymerase chain reaction (PCR). The amplicons were sequenced using 454 Titanium Pyrosequencing and the data analyzed using the QIIME software package. The results indicated that Prevotella, a member of thephylum Bacteroidetes, dominated and its relative abundance accounted for 70. 7 ± 2. 68 % of the bacteria. Firmicutes was the second most abundant phylum, and Selenomonas and unclassified Veillonellaceae and Lachnospiraceae were present at relative abundances of 2. 4 ± 0. 62, 2. 1 ± 0. 21 and 1. 9 ± 0. 58 %, respectively. Entodiniumwas the most abundant genus of protozoa, comprising 61. 6 ± 4. 52 % of the protozoal community, followed by Polyplastron and Isotricha with relative abundances of 18. 2 ± 2. 35 and 9. 7 ± 5. 62 %, respectively. More than half of the archaeal community (53. 3 ± 1. 87 %) was composed of members of the Methanobrevibacter gottschalkiiclade. The second and third most dominant archaea were members of the order Methanomassiliicoccales (28. 3 ± 5. 23 %) and Methanobrevibacter wolinii and relatives (8. 5 ± 4. 26 %). Based on this, rumen microbes of Baluchi lambs fed a total-mixed rations diet were similar to rumen microbes of ruminants fed similar diets in the other geographic regions around the world.

Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme regulating folate metabolism, which affects DNA methylation and synthesis. One of the most important polymorphisms identified in the MTHFR gene is C677T. MTHFR activity is lowered in individuals with 677TT genotype.Using Pyrosequencing, we analyzed the MTHFR genotypes in 118 colorectal cancer patients and 189 normal matched controls. Whereas the CC, CT and TT genotypes of MTHFR among the colorectal cancer patients were 51.7%, 28.0 % and 20.3% respectively, we were able to find 47.1% of 677CC, 27.0% of 677CT and 25.9% of 677TT in normal controls. An inverse association was observed between the risk of colorectal cancer and TT genotype with the odds ratios (OR) of 1, 0.94 and 0.71 for CC, CT, and TT genotypes, respectively. This association was similar in both sexes, but in patients with high levels of folate intake. Our study corroborates previous findings of an inverse association between MTHFR 677TT genotype and colorectal cancer, especially at high levels of folate.