a few of the assays offered by MR DNA lab http://www.mrdnalab.com

VISIT MR DNA at http://www.mrdnalab.com

16s rRNA Sequencing Primer List
Updated Earth Microbiome Project (EMP) 16s v4
515F	GTGYCAGCMGCCGCGGTAA
806R	GGACTACNVGGGTWTCTAAT
Original Earth Microbiome Project (EMP) 16s v4
515F	GTGCCAGCMGCCGCGGTAA
806R	GGACTACHVGGGTWTCTAAT
Other Common 16s rRNA Primers
515F	GTGYCAGCMGCCGCGGTAA
926R	CCGYCAATTYMTTTRAGTTT
909R	CCCCGYCAATTCMTTTRAGT
archaea 349F	GYGCASCAGKCGMGAAW
A344F	AYGGGGYGCASCAGGSG
archaea 806R	GGACTACVSGGGTATCTAAT
arch21F	TTCCGGTTGATCCYGCCGGA
arch519R	TTACCGCGGCGGCTG
arch1059R	GCCATGCACCWCCTCT
arc344F	ACGGGGYGCAGCAGGCGCGA
arch915R	GTGCTCCCCCGCCAATTCCT
27F	AGRGTTTGATCMTGGCTCAG
519Rmod	GTNTTACNGCGGCKGCTG
519Rmodbio	GWATTACCGCGGCKGCTG
1492R	GGGTTACCTTGTTACGACTT
338R	AGTGCTGCCTCCCGTAGGAGT
28F	GAGTTTGATCNTGGCTCAG
519R	GTNTTACNGCGGCKGCTG
341F	CCTACGGGNGGCWGCAG
785R	GACTACHVGGGTATCTAATCC
805R	GACTACNVGGGTATCTAATCC
799F	ACCMGGATTAGATACCCKG
1193R	CRTCCMCACCTTCCTC
a799wF	AMCVGGATTAGATACCCBG
new1193R	ACGTCATCCCCACCTTCC
16com1F	CAGCAGCCGCGGTAATAC
16com2R	CCGTCAATTCCTTTGAGTTT
926F	AAACTYAAAKGAATTGACGG
1394R	ACGGGCGGTGTGTRC
Tx9F	GGATTAGAWACCCBGGTAGTC
1391R	GACGGGCRGTGWGTRCA
1100F	YAACGAGCGCAACCC
1492R	GGGTTACCTTGTTACGACTT
rambacV3F	CCTACGGGAGGCAGCAG
rambacV4R	GGACTACHVGGGTWTCTAAT
104F	GGCGVACGGGTGAGTAA
530R	CCGCNGCNGCTGGCAC
530F	GTGCCAGCMGCNGCGG
bac926R	CCGTCAATTYYTTTRAGTTT
1100R	GGGTTNCGNTCGTTR

18s rRNA Sequencing Primer List
EukV4F	CCAGCASCYGCGGTAATTCC
EukV4R	ACTTTCGTTCTTGATYRA
ionesV4R	ACTTTCGTTCTTGA
zigEukV4R	ACTTTCGTTCTTGATYRATGA
euk1391F	GTACACACCGCCCGTC
EukB-Rev	TGATCCTTCTGCAGGTTCACCTAC
Euk7F	AACCTGGTTGATCCTGCCAGT
Euk570R	GCTATTGGAGCTGGAATTAC
uni18sF	AGGGCAAKYCTGGTGCCAGC
uni18sR	GRCGGTATCTRATCGYCTT
nem18sF	CGATCAGATACCGCCCTAG
nem18sR	TACAAAGGGCAGGGACGTAAT
paraOxyF	GCYGCGGTAATWCCAGCTCT
paraoxyR	TGCNCTTCCGTCAATTYCTT
1080F	GGGRAACTTACCAGGTCC
1578R	GTGATRWGRTTTACTTRT
SSU316F	GCTTTCGWTGGTAGTGTATT
758R	CAACTGTCTCTATKAAYCG
AML1	ATCAACTTTCGATGGTAGGATAGA
AML2	GAACCCAAACACTTTGGTTTCC
wanda	CAGCCGCGGTAATTCCAGCT
960F	GGCTTAATTTGACTCAACRCG
1200R	GGGCATCACAGACCTG
1560F	TGGTGCATGGCCGTTCTTAGT
2035R	CATCTAAGGGCATCACAGACC
Euk60F	GAAACTGCGAATGGCTCATT
Euk515R	ACCAGACTTGCCCTCC
Euk516F	GGAGGGCAAGTCTGGT
Euk1055R	CGGCCATGCACCACC
eukss18F	CACCAGGTTGATTCTGCC
eukss530R	GTGCCAGCMGCCGCGG
Euk528F	CCGCGGTAATTCCAGCTC
EukR18R	CGTTATCGGAATTAACCAGAC
SSUF04	GCTTGTAAAGATTAAGCC
SSUR22	GCCTGCTGCCTTCCTTGGA

ITS Sequencing Primer List
ITS1F	CTTGGTCATTTAGAGGAAGTAA
ITS2R	GCTGCGTTCTTCATCGATGC
ITS4R	TCCTCCGCTTATTGATATGC
ITS3F	GCATCGATGAAGAACGCAGC
ITS3kyo2F	GATGAAGAACGYAGYRAA
ITS5F	GGAAGTAAAAGTCGTAACAAGG
ITS7	GTGARTCATCGAATCTTTG
ITS9	GAACGCAGCRAANNGYGA
ITS6pyth	GAAGGTGAAGTCGTAACAAGG
ITS7Rpyth	AGCGTTCTTCATCGATGTGC
gITS7F	GTGARTCATCGARTCTTTG
ITS4ngsR	TTCCTSCGCTTATTGATATGC
ramITS1ooF	CGGAAGGATCATTACCAC
ramITS58ooR	AGCCTAGACATCCACTGCTG
ENDONTSF	AAGGTCTCCGTAGGTGAAC
ENDONTSR	GTATCCCTACCTGATCCGAG
its58funFbar1	AACTTTYRRCAAYGGATCWCT
its4funR	AGCCTCCGCTTATTGATATGCTTAART
symbiITS1	GAATTGCAGAACTCCGTG
symbiITS2	GGATCCATATGCTTAAGTTCAGCGGGT
traceITS1ooF	GGAAGGATCATTACCACAC

 

 

Why Should I Choose the 16s Sequencing Service?

 

Prokaryotes today are divided into two domains, Archaea and Bacteria. These two domains are of particular interest in areas of research including:

 

• Soil Ecology
• Gastroenterology
• Medical microbiology
• Food Science
• etc.

 

The initial objective of the many studies within these fields among others is often the same; identify which microbes are present, or more importantly, which are absent. The 16s rRNA gene is an excellent sequencing target in order to complete such studies. There are nine hypervariable regions found in the 16s rRNA gene, and each of these regions is flanked by a highly conserved region. Our in-house 16s rRNA sequencing primer pairs are specifically designed to target these flanking conserved regions thereby allowing us at MR DNA to perform PCR amplification and DNA sequencing of your submitted microbial samples. Of the nine hypervariable regions found in the 16s rRNA gene, some regions may be better suited to complete certain phylogenetic studies over others. Feel free to consult our experts at MR DNA is order to determine which 16s rRNA primer pair is best suited to meet your sequencing needs.

 

The already cost effective method of 16s rRNA sequencing continues to reduce in cost as sequencing technology continues to advance. By utilizing the technology made available by next-generation sequencing platforms, we are able to generate the necessary data required to complete these 16s rRNA phylogenetic studies in a much more time efficient and cost-effective manner. For more information concerning our 16s rRNA sequencing capabilities, feel free to Contact us.

 

 

 

What is 16s rRNA Sequencing?

 

16s rRNA sequencing has become one of the leading methods for phylogenetic studies. The popularization of 16s sequencing methods has been due in large part to the wide availability of PCR and Next-generation sequencing facilities, such as MRDNA. But what is 16s rRNA sequencing? And why should you choose 16s sequencing methods over other DNA sequencing methods?

 

16s rRNA sequencing refers to sequencing the 16s rRNA gene that codes for the small subunit (SSU) of the ribosome found in prokaryotes such as Bacteria and Archaea. There are several factors that make the 16s rRNA gene the perfect target to complete your taxonomy or phylogeny studies.

 

• Because the 16s gene codes for the SSU of the prokaryotic ribosome, researchers can rely on the fact that the their target gene will be present in every cell.
• The 16s gene contains both highly conserved regions as well as hypervariable regions.
  • The presence of the highly conserved regions allow researchers to design primer pairs that will accurately and reliably amplify the 16s hypervariable region of their choice.
  • The presence of the hypervariable regions affords researchers the ability to differentiate between closely related genera or species detected in their samples.
• The overall size of the 16s rRNA gene is relatively short. ~1500bp. While sequencing the entire 16s gene is difficult due to read length restrictions of many NGS platforms, sequencing one or more hypervariable regions is relatively quick and affordable.
  • Two of our most requested assays for 16s rRNA sequencing are 27F-519R (V1-V3 region) and 515F-806R (V4 region).
  • For questions regarding pricing feel free to contact us or visit our 16 ribosomal sequencing page.

 

 

Often times, researchers will have some confusion regarding the differences between 16s metagenomic sequencing methods and shotgun metagenomic sequencing methods. In short, shotgun metagenome sequencing is aptly named due to the fact that the goal of this DNA sequencing method is to sequence all genes from all organisms in a given sample. Whereas in the case of 16s metagenome sequencing, the goal is to sequence the 16s rRNA gene specifically.

 

Related Research

 

Periodontitis is caused by dysbiotic subgingival bacterial communities that may lead to increased bacterial invasion into gingival tissues. Although shifts in community structures associated with transition from health to periodontitis have been well characterized, the nature of bacteria present within the gingival tissue of periodontal lesions is not known. To characterize microbiota within tissues of periodontal lesions and compare them with plaque microbiota, gingival tissues and subgingival plaques were obtained from 7 patients with chronic periodontitis. A sequencing analysis of the 16S rRNA gene revealed that species richness and diversity were not significantly different between the 2 groups. However, intersubject variability of intratissue communities was smaller than that of plaque communities. In addition, when compared with the plaque communities, intratissue communities were characterized by decreased abundance of Firmicutes and increased abundance of Fusobacteria and Chloroflexi. In particular, Fusobacterium nucleatum and Porphyromonas gingivalis were highly enriched within the tissue, composing 15% to 40% of the total bacteria. Furthermore, biofilms, as visualized by alcian blue staining and atomic force microscopy, were observed within the tissue where the degradation of connective tissue fibers was prominent. In conclusion, very complex bacterial communities exist in the form of biofilms within the gingival tissue of periodontal lesions, which potentially serve as a reservoir for persistent infection. This novel finding may prompt new research on therapeutic strategies to treat periodontitis.

 

Baek K, Ji S, Choi Y. Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions. J Dent Res. 2017;:22034517732754.

 

 

 

In The News

Microbial genome sequencing is helping to improve our understanding of human health, disease, and microbial evolution. The human body contains trillions of cells with a variety of microbes that play a critical role in human health and disease, but the area of mechanism remains a mystery. Microbes are not only present in the human body; they are everywhere e.g. human or animal guts, homes, plants, oceans, and soil. Microbial research has gone under-appreciated for a long time, but with the help of next-generation sequencing (NGS), scientists are now investigating this vast microbial world. Multiple studies have been published in the last 5-10 years examining the microbial communities that exist inside our bodies and how these microbiomes can be influenced by the environment. The microbiome of the human gut can be rapidly and accurately cataloged by shotgun metagenomic sequencing via the Illumina NovaSeq 6000 System. Fecal samples, which have an abundant amount of microbes present (making it ideal to extract microbial DNA for genome sequencing), are a great candidate to help determine what is happening in the human GI tract. With NGS systems like the Illumina NovaSeq 6000, the scientific community is now able to generate gigabytes of data per sample. Many researchers today are excited about the value of microbiome sequencing and a number of clinicians believe it will become a routine part of health care, much like a blood draw.

But don’t limit microbiome sequencing to doctor’s offices and research laboratories. Direct-to-consumer tests are taking advantage of microbiome sequencing as well. One-time users are able to get an accurate snapshot of their gut health, and for the more avid citizen scientist, there are also time-series sampling options so that one can follow changes in their gut microbiome over time. So, whether the goal is to track the effect of a new diet or the efficacy of your favorite probiotic, or maybe you’re just curious…the microbial genomic data generated by microbiome sequencing can help us all to better understand our body and health, and track changes in the gut over time. NGS is continually helping us to understand the genetic blueprints of organisms within communities and obtain genome sequences from more complex environments like the human gut. Services like these were at one time too expensive for some laboratories and consumers, but with high-throughput sequencers like the Illumina NovaSeq, a comprehensive view of complex microbial environments is now available to everyone for a fraction of the cost.

1. Makki K, Deehan EC, Walter J, et al. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018; 23:705—715.

2. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017; 8:172—184.

3. De Vadder F, Grasset E, Mannerås Holm L, et al. Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks. Proc Natl Acad Sci U S A. 2018; 115:6458—6463.

4. Cheung SG, Goldenthal AR, Uhlemann AC, et al. Systematic Review of Gut Microbiota and Major Depression. Front in Psychiatry. 2019; 10:34.

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…or something like this:

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Here’s a list of SEO-optimized keywords for MR DNA’s microbiome services:

1. Microbiome sequencing
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These keywords can help improve the visibility of MR DNA’s microbiome sequencing services online.

Here is a detailed list of microbiome research primers, including sequences where available, grouped by their target regions.

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16S rRNA Primers (Bacteria & Archaea)

1. 27F: AGAGTTTGATCMTGGCTCAG / 1492R: GGTTACCTTGTTACGACTT
2. 8F: AGAGTTTGATCCTGGCTCAG / 534R: ATTACCGCGGCTGCTGG
3. 515F: GTGCCAGCMGCCGCGGTAA / 806R: GGACTACHVGGGTWTCTAAT
4. 341F: CCTACGGGNGGCWGCAG / 805R: GACTACHVGGGTATCTAATCC
5. 338F: ACTCCTACGGGAGGCAGCAG / 907R: CCGTCAATTCMTTTRAGTTT
6. 27F: AGAGTTTGATCMTGGCTCAG / 534R: ATTACCGCGGCTGCTGG
7. 515F: GTGCCAGCMGCCGCGGTAA / 926R: CCGTCAATTCMTTTRAGTTT
8. 63F: CAGGCCTAACACATGCAAGTC / 1387R: GGGCGGWGTGTACAAGGC
9. 519F: CAGCMGCCGCGGTAA / 785R: TTACTCCTGGGCTTGCT
10. 799F: AACMGGATTAGATACCCKG / 1193R: ACGTCATCCCCACCTTCC

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ITS Primers (Fungi)

11. ITS1: TCCGTAGGTGAACCTGCGG / ITS2: GCTGCGTTCTTCATCGATGC
12. ITS1F: CTTGGTCATTTAGAGGAAGTAA / ITS2: GCTGCGTTCTTCATCGATGC
13. ITS1F: CTTGGTCATTTAGAGGAAGTAA / ITS4: TCCTCCGCTTATTGATATGC
14. ITS3: GCATCGATGAAGAACGCAGC / ITS4: TCCTCCGCTTATTGATATGC
15. ITS1F: CTTGGTCATTTAGAGGAAGTAA / ITS4B: CAGGAGACTTGTACACGGTCCAG
16. ITS2: GCTGCGTTCTTCATCGATGC / ITS3: GCATCGATGAAGAACGCAGC
17. ITS5: GGAAGTAAAAGTCGTAACAAGG / ITS4: TCCTCCGCTTATTGATATGC
18. ITS1: TCCGTAGGTGAACCTGCGG / ITS4: TCCTCCGCTTATTGATATGC
19. ITS1F: CTTGGTCATTTAGAGGAAGTAA / ITS5: GGAAGTAAAAGTCGTAACAAGG
20. ITS1F: CTTGGTCATTTAGAGGAAGTAA / ITS2-KYO1: TAGAGGAAGTAAAAGTCGTAA

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Archaea-Specific Primers

21. 21F: TTCCGGTTGATCCYGCCGGA / 958R: YCCGGCGTTGAMTCCAATT
22. 344F: ACGGGGYGCAGCAGGCGCGA / 915R: GTGCTCCCCCGCCAATTCCT
23. 524F-Arch: TGYCAGCCGCCGCGGTAAHACCVGC / 958R-Arch: YCCGGCGTTGAMTCCAATT
24. 571F: GCCAGCAGCCGCGGTAA / 915R: GTGCTCCCCCGCCAATTCCT
25. 349F: GYGCASCAGKCGMGAAW / 806R: GGACTACNSGGGTMTCTAAT
26. 517F: GCYTAAAGSRNCCGTAGC / 958R: YCCGGCGTTGAMTCCAATT
27. 519F: CAGCMGCCGCGGTAA / 806R: GGACTACNSGGGTMTCTAAT
28. 340F: CCTACGGGGGCGCAG / 1000R: GGGCATCGTTTACGGG
29. 524F: TGYCAGCCGCCGCGGTAAHACCVGC / 958R: YCCGGCGTTGAMTCCAATT
30. 344F: ACGGGGYGCAGCAGGCGCGA / 915R: GTGCTCCCCCGCCAATTCCT

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Functional Genes

31. nirS: CCTAYTGGCCGCCRCART / nirK: GCCTCGATCAGRTTRTGGTT
32. amoA: GGGGTTTCTACTGGTGGT / amoA-R: CCCCTCKGSAAAGCCTTCTTC
33. dsrA: ACSCACTGGAAGCACG / dsrB: GTGGMRCCGTGCAKRTTGG
34. mcrA: GGTGGTGTMGGATTCACACARTAYGCWACAGC / mcrA-R: TCCAGGAACTACGAGTTTTWTCWTASWAACCA
35. pmoA: AAYTGGGGCATCCTTCC / pmoA-R: GAACGTCCTTACCGT
36. nifH: TGYGAYCCNAARGCNGA / nifH-R: ADSAWYCCAACATYTTCCAC
37. hzo: GGNTGYTAYACNGCNGGNTAYCC / hzo-R: TAYTTNGCNGGYTGYTGRTGNACCCA
38. soxB: TAAYTGGCAGGGATGCTT / soxB-R: TGNCCYTCRTGRCARTGGCAT

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This list incorporates a variety of primer sets, suitable for bacterial, archaeal, fungal, and functional gene studies. Let me know if you need additional details or further expansion!