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16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

Environ Sci Pollut Res Int. 2016 Jul;23(13):13245-54. doi: 10.1007/s11356-016-6474-y. Epub 2016 Mar 29.

Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.

Yausheva Е1, Sizova Е2,3, Lebedev S2,3, Skalny A2, Miroshnikov S3, Plotnikov A4, Khlopko Y4, Gogoleva N5, Cherkasov S4.

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Abstract

The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina). Regarding the gut microflora of worms in the control group, high diversity of microorganisms (303 OTUs) was noted. Most of those belong to the taxa Firmicutes (51.9 % of the total high-quality united reads), Proteobacteria (24.1 % of the total), and Actinobacteria (13.3 % of the total), which were represented by numerous species of gen. Clostridium (C. saccharobutylicum, C. saccharoperbutylacetonicum, C. beijerinckii), gen. Pseudomonas (P. hydrogenovora, P. aeruginosa, and P. putida), gen. Bacillus (B. megaterium, B. silvestris), gen. Cellulomonas (B. megaterium, B. silvestris), and other numerically smaller genera. Adding of zinc nanoparticles to the substrate decreased the diversity of bacteria (78 OTUs) as well as percentage of bacteria belonging to the taxon Firmicutes (-41.6 %) and increased the proportion of Proteobacteria due to growth in abundance of gen. Verminephrobacter (+46 %) and gen. Ochrobactrum (+19.5 %).

KEYWORDS:

16S metagenome; Eisenia fetida; High-throughput sequencing; Microcrystalline cellulose; Microflora; Nanoparticles; Taxa; Zinc

PMID: 27023811 DOI: 10.1007/s11356-016-6474-y

[PubMed - in process]

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5.

Helicobacter. 2016 Mar 18. doi: 10.1111/hel.12306. [Epub ahead of print]

Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment.

Oh B1, Kim JW2, Kim BS3.

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Abstract

BACKGROUND:

Probiotic supplementation is utilized to alleviate the side effects associated with antibiotic therapy for Helicobacter pylori infection. Several studies have described the effects of administration of probiotics on the gut microbiota during antibiotic therapy. However, most of these studies have focused on specific bacteria, thereby providing limited information on the functional roles of the altered microbiota. Therefore, we examined the impact of probiotic supplementation on the structure and functional dynamics of the gut microbiota during H. pylori eradication, using whole-metagenomic sequence analysis.

METHODS:

Subjects were divided into two groups: the antibiotics group, which received only antibiotics, and the probiotics group, which received antibiotics with probiotic supplementation. The structural and functional profiles of gut microbiota was analyzed using metagenomic DNA extracted from the feces during treatment by Illumina MiSeq system.

RESULTS:

The overall alterations in microbiota, as revealed by whole metagenome sequencing, were similar with results from our previous 16S rRNA gene-based analysis. The proportional shift in functional gene families was greater in the antibiotics group than in the probiotics group. In particular, the proportion of genes related to selenocompound metabolism was reduced in the probiotics group, whereas genes associated with the metabolism of nucleotide sugars were increased.

CONCLUSION:

The functional alterations of gut microbiota may link to the reduction in intestinal irritation and maintenance of bacterial diversity observed following probiotic supplementation with antibiotic therapy. The potential beneficial roles of altered gut microbiota following probiotic supplementation are expected a reduction in side effects such as intestinal irritation and antibiotics resistance.

© 2016 John Wiley & Sons Ltd.

KEYWORDS:

Whole metagenome sequence; functional profile; gut microbiota; probiotics

PMID: 26991862 DOI: 10.1111/hel.12306

[PubMed - as supplied by publisher]

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6.

Genom Data. 2016 Jan 16;7:222-5. doi: 10.1016/j.gdata.2016.01.011. eCollection 2016.

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach.

Singh A1, Subudhi E1, Sahoo RK1, Gaur M1.

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Abstract

Deulajhari hot spring is located in the Angul district of Odisha. The significance of this hot spring is the presence of the hot spring cluster adjacent to the cold spring which attracts the attention of microbiologists to understand the role of physio-chemical factors of these springs on bacterial community structure. Next-generation sequencing technology helps us to depict the pioneering microflora of any ecological niche based on metagenomic approach. Our study represents the first Illumina based metagenomic study of Deulajhari hot spring DH1, and DH2 of the cluster with temperature 65 °C to 55 °C respectively establishing a difference of 10 °C. Comprehensive study of microbiota of these two hot springs was done using the metagenomic sequencing of 16S rRNA of V3-V4 region extracting metagenomic DNA from the two hot spring sediments. Sequencing community DNA reported about 28 phyla in spring DH1 of which the majority were Chloroflexi (22.98%), Proteobacteria (15.51%), Acidobacteria (14.51%), Chlorobi (9.52%), Nitrospirae (8.54%), and Armatimonadetes (7.07%), at the existing physiochemical conditions like; temperature 65 °C, pH 8.06, electro conductivity 0.020 dSm(- 1), and total organic carbon (TOC) 3.76%. About 40 phyla were detected in cluster DH2 at the existing physiochemical parameters like temperature 55 °C, pH 8.10, electro conductivity 0.019 dSm(- 1), and total organic carbon (TOC) 0.58% predominated with Chloroflexi (41.98%), Proteobacteria (10.74%), Nitrospirae (10.01%), Chlorobi (8.73%), Acidobacteria (6.73%) and Planctomycetes (3.73%). Approximately 68 class, 107 order, 171 genus and 184 species were reported in cluster DH1 but 102 class, 180 order, 375 genus and 411 species in cluster DH2. The comparative metagenomics study of the Deulajhari hot spring clusters DH1, and DH2 depicts the differential profile of the microbiota. Metagenome sequences of these two hot spring clusters are deposited to the SRA database and are available in NCBI with accession no. SRX1459734 for DH1 and SRX1459735 for DH2.

KEYWORDS:

16S rRNA; Deulajhari; Metagenomics; Next-generation sequencing

PMID: 26981412 PMCID: PMC4778664 DOI: 10.1016/j.gdata.2016.01.011

[PubMed] Free PMC Article

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7.

Genom Data. 2016 Jan 7;7:187-8. doi: 10.1016/j.gdata.2016.01.004. eCollection 2016.

Profiling of microbial community of Odisha hot spring based on metagenomic sequencing.

Singh A1, Subudhi E1.

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Abstract

Deulajhari hot spring has diverse temperature and pH range varying from 43 °C to 65 °C and 7.83 to 8.10 respectively. Dense foliage around Deulajhari hot spring contributes to the high total organic carbon content (TOC). In our experiment we took sediment samples from the two Deulajhari hot springs (S1 and S2) out of the cluster having temperature of 43 °C and 55 °C and pH of 7.83 and 7.14 respectively. Sediment samples were analysed using 16S rRNA of V3-V4 region by amplicon metagenome sequencing. Over 34 phyla were detected in cluster S1 and 32 phyla in cluster S2 at the existing physiochemical parameters temperature 43 °C, pH 7.83, electroconductivity 0.019 dSm(- 1), and total organic carbon (TOC) 3.80% for S1 and temperature 55 °C, pH 7.14, electroconductivity 0.019 dSm(- 1), and total organic carbon (TOC) 0.97% for S2. Existence of a vast number of unresolved sequences 179 out of 292 in S1 and 186 out of 314 in S2 at the genus level emphasizes the significance of our study. Metagenome sequence information for the both clusters S1 and S2 of Deulajhari is available at NCBI, SRA database with accession number SRX1459732 and SRX1459733 respectively. Direct link to the deposited data: www.ncbi.nlm.nih.gov/sra/SRX1459732 www.ncbi.nlm.nih.gov/sra/SRX1459733.

KEYWORDS:

16S rRNA; Deulajhari; Illumina platform; Metagenome; TOC

PMID: 26981405 PMCID: PMC4778635 DOI: 10.1016/j.gdata.2016.01.004

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8.

Genom Data. 2015 Dec 28;7:127-8. doi: 10.1016/j.gdata.2015.12.019. eCollection 2016.

Cultivation-independent comprehensive investigations on bacterial communities in serofluid dish, a traditional Chinese fermented food.

Chen P1, Wu Z1, Zhao Y2, Wei Y2, Xu R1, Yan L3, Li H1.

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Abstract

Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture, is made from vegetables by fermentation. In this study, bacterial community of the fermented serofluid dish was assessed by Illumina amplicon sequencing. The metagenome comprised of 49,589 average raw reads with an average 11,497,917 bp and G + C content is 52.46%. This is the first report on V4 hyper-variable region of the 16S rRNA metagenome sequence employing Illumina platform to profile the microbial community of this little known fermented food from Gansu Province, China. The metagenome sequence can be accessed at NCBI, SRA database accession no. SRP065370.

KEYWORDS:

16S rRNA; Cultivation-independent; Jiangshui; Microbial diversity; Serofluid dish

PMID: 26981386 PMCID: PMC4778640 DOI: 10.1016/j.gdata.2015.12.019

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40.

Mol Ecol. 2014 Sep;23(18):4498-510. doi: 10.1111/mec.12885. Epub 2014 Sep 8.

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions.

Bragina A1, Oberauner-Wappis L, Zachow C, Halwachs B, Thallinger GG, Müller H, Berg G.

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Abstract

Sphagnum-dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem and strongly contribute to global biosphere functioning. Sphagnum is colonized by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation. An interenvironmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic lifestyle under poikilohydric and ombrotrophic conditions. To realise a plasticity-stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair and self-controlling mechanisms. Multiple microbe-microbe and plant-microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR-dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio-resource for environmental biotechnology - with respect to novel enzymes or stress-protecting bacteria.

TRIAL REGISTRATION:

ClinicalTrials.gov .

© 2014 John Wiley & Sons Ltd.

KEYWORDS:

FISH-CLSM; Sphagnum moss; bog ecosystem; illumina-based metagenomics; plant microbiome

PMID: 25113243 DOI: 10.1111/mec.12885

[PubMed - indexed for MEDLINE]

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Microbiome. 2015 Oct 27;3:50. doi: 10.1186/s40168-015-0116-3.

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities.

Checinska A1, Probst AJ2, Vaishampayan P1, White JR3, Kumar D4, Stepanov VG4, Fox GE4, Nilsson HR5, Pierson DL6, Perry J7, Venkateswaran K8.

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Abstract

BACKGROUND:

The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment.

RESULTS:

Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site.

CONCLUSIONS:

The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.

PMID: 26502721 PMCID: PMC4624184 DOI: 10.1186/s40168-015-0116-3

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16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

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