Sequencing the microbiome with MR DNA

How To sequence the 16s and ITS fungal gene affordably  MR DNA 16s sequencing microbiome and metagenome low prices

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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Select item 27092122

 

21.

Front Microbiol. 2016 Apr 5;7:462. doi: 10.3389/fmicb.2016.00462. eCollection 2016.

Carrageenan Gum and Adherent Invasive Escherichia coli in a Piglet Model of Inflammatory Bowel Disease: Impact on Intestinal Mucosa-associated Microbiota.

Munyaka PM1, Sepehri S2, Ghia JE3, Khafipour E4.

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Abstract

Inflammatory bowel diseases (IBD) including Crohn's disease (CD), and ulcerative colitis (UC), are chronic conditions characterized by chronic intestinal inflammation. Adherent invasive Escherichia coli (AIEC) pathotype has been increasingly implicated in the etiopathogenesis of IBD. In a 21-day study, we investigated the effects of AIEC strain UM146 inoculation on microbiota profile of the ileal, cecal, ascending and descending colon in a pig model of experimental colitis. Carrageenan gum (CG) was used to induce colitis in weaner piglets whereas AIEC strain UM146 previously isolated from a CD patient was included to investigate a cause or consequence effect in IBD. Treatments were: (1) control; (2) CG; (3) AIEC strain UM146; and (4) CG+UM146. Pigs in groups 2 and 4 received 1% CG in drinking water from day 1 of the study while pigs in groups 3 and 4 were inoculated with UM146 on day 8. Following euthanization on day 21, tissue mucosal scrapings were collected and used for DNA extraction. The V4 region of bacterial 16S rRNA gene was then subjected to Illumina sequencing. Microbial diversity, composition, and the predicted functional metagenome were determined in addition to short chain fatty acids profiles in the digesta and inflammatory cytokines in the intestinal tissue. CG-induced colitis decreased bacterial species richness and shifted community composition. At the phylum level, an increase in Proteobacteria and Deferribacteres and a decrease in Firmicutes, Actinobacteria, and Bacteroidetes were observed in CG and CGUM146 compared to control and UM146. The metabolic capacity of the microbiome was also altered in CG and CGUM146 compared to UM146 and control in the colon. We demonstrated that CG resulted in bacterial dysbiosis and shifted community composition similar to what has been previously observed in IBD patients. However, AIEC strain UM146 alone did not cause any clear changes compared to CG or control in our experimental IBD pig model.

KEYWORDS:

16S rRNA gene sequencing; Crohn's disease; adherent invasive Escherichia coli; carrageenan gum; microbiome; pigs; ulcerative colitis

PMID: 27092122 PMCID: PMC4820460 DOI: 10.3389/fmicb.2016.00462

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Select item 27072196

 

22.

Sci Rep. 2016 Apr 13;6:24340. doi: 10.1038/srep24340.

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels.

Liu H1, Guo X2, Gooneratne R3, Lai R1, Zeng C1, Zhan F1, Wang W1,4.

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Abstract

Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.

PMID: 27072196 PMCID: PMC4829839 DOI: 10.1038/srep24340

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Select item 27057545

 

23.

Biomed Res Int. 2016;2016:6598307. doi: 10.1155/2016/6598307. Epub 2016 Feb 14.

Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.

Wang Y1, Li R2, Zhou Y3, Ling Z4, Guo X3, Xie L5, Liu L1.

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Abstract

BACKGROUND:

Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty.

RESULTS:

Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF) to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods.

CONCLUSIONS:

We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

PMID: 27057545 PMCID: PMC4769744 DOI: 10.1155/2016/6598307

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Select item 27055030

 

24.

PLoS One. 2016 Apr 7;11(4):e0153215. doi: 10.1371/journal.pone.0153215. eCollection 2016.

Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica).

Barbosa A1, Balagué V2, Valera F3, Martínez A4, Benzal J3, Motas M5, Diaz JI6, Mira A7, Pedrós-Alió C2.

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Abstract

The gastrointestinal tract microbiota is known to play very important roles in the well being of animals. It is a complex community composed by hundreds of microbial species interacting closely among them and with their host, that is, a microbial ecosystem. The development of high throughput sequencing techniques allows studying the diversity of such communities in a realistic way and considerable work has been carried out in mammals and some birds such as chickens. Wild birds have received less attention and in particular, in the case of penguins, only a few individuals of five species have been examined with molecular techniques. We collected cloacal samples from Chinstrap penguins in the Vapour Col rookery in Deception Island, Antarctica, and carried out pyrosequencing of the V1-V3 region of the 16S rDNA in samples from 53 individuals, 27 adults and 26 chicks. This provided the first description of the Chinstrap penguin gastrointestinal tract microbiota and the most extensive in any penguin species. Firmicutes, Bacteoridetes, Proteobacteria, Fusobacteria, Actinobacteria, and Tenericutes were the main components. There were large differences between chicks and adults. The former had more Firmicutes and the latter more Bacteroidetes and Proteobacteria. In addition, adults had richer and more diverse bacterial communities than chicks. These differences were also observed between parents and their offspring. On the other hand, nests explained differences in bacterial communities only among chicks. We suggest that environmental factors have a higher importance than genetic factors in the microbiota composition of chicks. The results also showed surprisingly large differences in community composition with other Antarctic penguins including the congeneric Adélie and Gentoo penguins.

PMID: 27055030 PMCID: PMC4824521 DOI: 10.1371/journal.pone.0153215

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Select item 27052710

 

25.

Food Microbiol. 2016 Aug;57:116-27. doi: 10.1016/j.fm.2016.02.004. Epub 2016 Feb 18.

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota.

Escobar-Zepeda A1, Sanchez-Flores A2, Quirasco Baruch M3.

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Abstract

Cotija cheese is a Mexican handcrafted product made from raw cow milk whose ripening process occurs spontaneously and, presumably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. In this work, we studied the dominance and richness of the bacteria in the Cotija cheese microbiome, as well as their metabolic potential by high-throughput sequencing. By the analysis of 16S ribosomal sequences, it was found that this metagenome is composed mainly of three dominant genera: Lactobacillus, Leuconostoc and Weissella, and more than 500 of non-dominant genera grouped in 31 phyla of both bacteria and archaea. The analysis of single-copy marker genes reported a similar result for dominant genera, although with greater resolution that reached the species level. Pathogenic bacteria such as Salmonella, Listeria monocytogenes, Brucella or Mycobacterium were not found. The Cotija cheese microbiome has the metabolic capacity for the synthesis of a wide range of flavor compounds, mainly involved with the metabolism of branched chain amino acids and free fatty acids. Genes associated with bacteriocin production and immunity were also found. Arguably, this is one of the most diverse metagenomes among the microbial communities related to fermented products.

Copyright © 2016 Elsevier Ltd. All rights reserved.

KEYWORDS:

Bacteriocins; Fermented food metagenomics; High-throughput sequencing; Lactic acid bacteria; Raw-milk ripened cheese

PMID: 27052710 DOI: 10.1016/j.fm.2016.02.004

[PubMed - in process]

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Select item 27048805

 

26.

MBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.

Hemme CL1, Green SJ2, Rishishwar L3, Prakash O4, Pettenato A5, Chakraborty R5, Deutschbauer AM6, Van Nostrand JD7, Wu L7, He Z7, Jordan IK8, Hazen TC9, Arkin AP10, Kostka JE3, Zhou J11.

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Abstract

Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

IMPORTANCE:

Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

Copyright © 2016 Hemme et al.

PMID: 27048805 PMCID: PMC4817265 DOI: 10.1128/mBio.02234-15

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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.

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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

 

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.

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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

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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.

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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]

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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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