How To sequence the 16s gene affordably  MR DNA 16s sequencing

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.

 

 

 

 

 

Select item 27671629

 

14.

Proc Natl Acad Sci U S A. 2016 Sep 26. pii: 201609981. [Epub ahead of print]

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.

Smirnov A1, Förstner KU2, Holmqvist E1, Otto A3, Günster R1, Becher D3, Reinhardt R4, Vogel J5.

Author information

 

 

Abstract

The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA landscape of organisms with potentially new RNA biology that are emerging from microbiome and environmental studies requires the use of more functionally relevant criteria. One such criterion is the association of RNAs with functionally important cognate RNA-binding proteins. Here we analyze the full ensemble of cellular RNAs using gradient profiling by sequencing (Grad-seq) in the bacterial pathogen Salmonella enterica, partitioning its coding and noncoding transcripts based on their network of RNA-protein interactions. In addition to capturing established RNA classes based on their biochemical profiles, the Grad-seq approach enabled the discovery of an overlooked large collective of structured small RNAs that form stable complexes with the conserved protein ProQ. We show that ProQ is an abundant RNA-binding protein with a wide range of ligands and a global influence on Salmonella gene expression. Given its generic ability to chart a functional RNA landscape irrespective of transcript length and sequence diversity, Grad-seq promises to define functional RNA classes and major RNA-binding proteins in both model species and genetically intractable organisms.

KEYWORDS:

Hfq; ProQ; RNA–protein interaction; noncoding RNA; small RNA

PMID: 27671629 DOI: 10.1073/pnas.1609981113

[PubMed - as supplied by publisher] Free full text

Similar articles

 

Secondary Source ID

 

 

 

Select item 27671513

 

15.

Iran J Immunol. 2016 Sep;13(3):220-8. doi: IJIv13i3A7.

The Immunostimulatory Effect of Lactic Acid Bacteria in a Rat Model.

Karamese M1, Aydin H, Sengul E, Gelen V, Sevim C, Ustek D, Karakus E.

Author information

 

 

Abstract

BACKGROUND:

Probiotics are "live", beneficial microbes that provide important health benefits in their hosts. There is significant interest in the modulation and regulation of the immune function by probiotics.

OBJECTIVE:

To investigate the immunomodulatory effects of a probiotic mixture, including Lactobacillus and Bifidobacterium species, by detecting serum cytokine and immunoglobulin levels.

METHODS:

The rats were randomly divided into 4 groups. The first group was "Control group" and other 3 groups were probiotic application groups who received different doses of probiotics. The probiotic mixture included 12 probiotic bacteria, mostly Lactobacillus and Bifidobacterium strains. Probiotic mixture was administered to rats for 12 consecutive days. TNF-α, TGF-β, IL-1-β, IL-6, and IL-10 levels as well as serum IgG and IgA concentrations were detected in the sera after 12 days.

RESULTS:

Probiotics led to a decrease in the levels of TNF-α, IL-6 and TGF-β; however, they led to increase in the serum levels of IL-10, IgG and IgA. There were significant differences between control group and probiotic application groups (p<0.05).

CONCLUSION:

These data suggest that the commensal microbiota are important for stimulating both proinflammatory and regulatory responses in order to rapidly clear infections and minimize inflammation-associated tissue damage.

PMID: 27671513 DOI: IJIv13i3A7

[PubMed - in process]

Similar articles

 

Select item 27671352

 

16.

Microbiome. 2016 Sep 27;4(1):51.

The impact of sequence database choice on metaproteomic results in gut microbiota studies.

Tanca A1, Palomba A1, Fraumene C1, Pagnozzi D1, Manghina V2, Deligios M2, Muth T3,4, Rapp E3, Martens L5,6,7, Addis MF1, Uzzau S8,9.

Author information

 

 

Abstract

BACKGROUND:

Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification.

RESULTS:

Here, we present a systematic investigation of variables concerning database construction and annotation and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. In particular, the contribution of experimental metagenomic databases was revealed to be mandatory when dealing with mouse samples. Moreover, the use of a "merged" database, containing all metagenomic sequences from the population under study, was found to be generally preferable over the use of sample-matched databases. We also observed that taxonomic and functional results are strongly database-dependent, in particular when analyzing the mouse gut microbiota. As a striking example, the Firmicutes/Bacteroidetes ratio varied up to tenfold depending on the database used. Finally, assembling reads into longer contigs provided significant advantages in terms of functional annotation yields.

CONCLUSIONS:

This study contributes to identify host- and database-specific biases which need to be taken into account in a metaproteomic experiment, providing meaningful insights on how to design gut microbiota studies and to perform metaproteomic data analysis. In particular, the use of multiple databases and annotation tools has to be encouraged, even though this requires appropriate bioinformatic resources.

KEYWORDS:

Bioinformatics; Gut microbiota; Mass spectrometry; Metagenomics; Metaproteomics

PMID: 27671352 DOI: 10.1186/s40168-016-0196-8

[PubMed - as supplied by publisher] Free full text

Similar articles

 

 

Select item 27671222

 

17.

Colorectal Dis. 2016 Sep 27. doi: 10.1111/codi.13534. [Epub ahead of print]

A collaborative study of the current concepts and challenges for treatment of anastomotic leakage in colorectal surgery.

Vallance A1,2, Wexner S3, Berho M4, Cahill R5, Coleman M6, Haboubi N7, Heald RJ8, Kennedy RH9, Moran B8, Mortensen N2, Motson RW10, Novell R11, O'Connell PR5, Ris F12, Rockall T13, Senapati A14, Windsor A15, Jayne DG16.

Author information

 

 

Abstract

The reduction of the incidence, detection, and treatment of anastomotic leakage (AL) continues to challenge the colorectal surgical community. AL is not consistently defined and reported in clinical studies, its occurrence is variably reported and its impact on long-term morbidity and healthcare resources has received relatively little attention. Controversy continues about the best strategies to reduce the risk. Diagnostic tests lack sensitivity and specificity, resulting in delayed diagnosis and increased morbidity. Intraoperative fluorescence angiography has recently been introduced as a means of real-time assessment of anastomotic perfusion with preliminary evidence suggesting that it may reduce the rate of AL. In addition, concepts are emerging about the role of the rectal mucosal microbiome in AL and the possible role of new prophylactic therapies. In January 2016 a meeting of expert colorectal surgeons and pathologists was held in London, UK to identify the ongoing controversies surrounding AL in colorectal surgery. The outcome of the meeting is presented in the form of research challenges that need to be addressed. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

PMID: 27671222 DOI: 10.1111/codi.13534

[PubMed - as supplied by publisher]

Similar articles

 

 

Select item 27671074

 

18.

Antimicrob Agents Chemother. 2016 Sep 26. pii: AAC.01289-16. [Epub ahead of print]

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults.

Burnham CA1, Hogan PG2, Wallace MA2, Deych E2, Shannon W2, Warren DK2, Fritz SA3.

Author information

 

 

Abstract

Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial community, richness, and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n=8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach water baths) and ICU patients (n=7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before, and again after, decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the community-dwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus significantly decreased over time (P=0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to the enrollment sampling (from enrollment to final sampling, P=0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota.

Copyright © 2016, American Society for Microbiology. All Rights Reserved.

PMID: 27671074 DOI: 10.1128/AAC.01289-16

[PubMed - as supplied by publisher]

Similar articles

 

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.

Select item 27670882

 

19.

Sci Rep. 2016 Sep 27;6:33965. doi: 10.1038/srep33965.

Probiotic legacy effects on gut microbial assembly in tilapia larvae.

Giatsis C1, Sipkema D2, Ramiro-Garcia J2,3,4, Bacanu GM2, Abernathy J5, Verreth J1, Smidt H2, Verdegem M1.

Author information

 

 

Abstract

The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.

PMID: 27670882 DOI: 10.1038/srep33965

[PubMed - as supplied by publisher] Free full text

Similar articles

 

 

Select item 27670644

 

20.

Mol Nutr Food Res. 2016 Sep 27. doi: 10.1002/mnfr.201600552. [Epub ahead of print]

Reduction in cardiometabolic risk factors by a multifunctional diet is mediated via several branches of metabolism as evidenced by non-targeted metabolite profiling approach.

Tovar J1, de Mello VD2, Nilsson A3, Johansson M3, Paananen J2, Lehtonen M4, Hanhineva K2, Björck I3.

Author information

 

 

Abstract

SCOPE:

MFD, a diet based on multiple functional concepts and ingredients with antiinflammatory activity, was previously shown to improve different cardiometabolic risk-associated markers in healthy subjects. Here, we assessed the impact of MFD on plasma metabolome and explored associations of the differential metabolites with clinical parameters, searching for metabolic determinants related to the effects of MFD.

METHODS AND RESULTS:

Forty-four overweight healthy volunteers completed a randomized crossover intervention comparing MFD with a control diet devoid of the active components of MFD. Fasting plasma samples were analyzed with non-targeted metabolite profiling at baseline and at the end (4 wk) of each diet period by liquid chromatography coupled to quadrupole-time of flight-MS system, revealing a vast impact of MFD on metabolic homeostasis. Main metabolite classes affected included acylcarnitines, furan fatty acids, phospholipids (plasmalogens, phosphatidylcholines, phosphatidylethanolamines), and various low-molecular weight products from the bioactivity of gut microbiota. Circulating levels of several of these metabolites correlated with changes in clinical blood lipid biomarkers.

CONCLUSIONS:

The metabolomics approach revealed that consumption of MFD affected different areas of metabolism, highlighting the impact of a healthy diet on plasma metabolome. This seems linked to reduced cardiometabolic risk and provides mechanistic insight into the effects of MFD. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

KEYWORDS:

Cardiometabolic diseases; Dietary prevention; Functional foods; Metabolic syndrome; Plasma metabolomics

PMID: 27670644 DOI: 10.1002/mnfr.201600552

[PubMed - as supplied by publisher]

Similar articles

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.

 

Insert your HTML here.
Ask About Our Affordable Metagenome Sequencing Program. Only $500!!