16s Ribosomal Sequencing

Sequencing Services

 

MR DNA specializes in any type of amplicon sequencing.

 

From 16s, 18s, ITS, functional genes to any type of custom primer amplicon assay.

We have an extensive inhouse assay (primer) collection for 16s sequencing, 18s sequencing,  ITS sequencing, functional genes such as nirS, nifH, dsr,  pufM, nosZ, HMC,  and many more.  if you have a custom assay we inexpensively set it up for you.

 

NEW:  near full length diversity 16s, 18s and ITS sequencing ..  yes a 1400bp 16s sequencing approach for microbiome studies is now available at MR DNA,  we also have long 1700bp 18s sequencing and full length ITS1-4 sequencing .. long reads = better taxonomic differentiation right?

 

Amplicon Sequencing Prices.

Sequencing Platform Read Length/Assay Length Pricing
Ion Torrent PGM 300bp 515F bacterial + archaeal or ITS1-2 fungal diversity For nominal 15-20,000 reads/assay: $60/assay (any size project)
Ion S5 XL 400-500bp bacterial, archaeal, or ITS fungal diversity assays Same Pricing as Ion Torrent PGM
Ion S5 XL >500bp bacterial, archaeal, or ITS fungal diversity assays Same Pricing as Illumina MiSeq
Illumina MiSeq 2x300 PE 20,000 sequence diversity assays starting at:
$60 /assay (>300 assays)
$65/assay (150-300 assays)
$70/assay (100-150 assays)
$75/assay (50-100 assays)
$80/assay (1-50 assays)
For projects < 10 samples a $100 library fee is added
PacBio Sequel Full Length 16s sequencing Average 5,000 seqeunces per sample: $220/assay (Minimum 20 Samples)

 

 

 

 

MR DNA has all the major sequencing platforms and we have a large selection of amplicon sequencing programs ..  Everything can be customized to the needs of the customer, only limited by the capabilities of the sequencing technologies.

 

Any amplicons (bTEFAP® services) such as 16s, 18s, ITS, functional or custom assays.. if you have an amplicon with custom primers we can help sequence it.

 

Illumina miseq and hiseq amplicons

examples for any of our hundreds of inhouse assays

***2x300bp PE illumina 20,000 sequence diversity assays

$80/assay 1-50 assays (note: for projects < 10 assays per library, a $100 library fee is added),

$75 for 50-100 assays,

$70 for 100-150 assays,

$65 for 150-300,

$60 for > 300 assays.

additional discounts for very large projects also

 

PGM (ion torrent) amplicons

***300bp 515F bacterial + archaeal or ITS1-2 fungal diversity PGM assays with nominal 15-20,000 reads/assay for $60/assay (any size project)

 

PAC BIO SEQUEL:

Sequel long read amplicon sequencing for 16s, 18s, ITS and custom amplicons

MR DNA now accepts any size project (projects with < 10 samples do have a $100 indexing fee and a $20/sample additional PCR replication fee.)

 

Low average coverage ( < 500 sequences average per sample)  for $50/sample

Medium coverage (average 5000 sequences per sample)  for $150/sample

High coverage  10K average sequences scale for $260/sample

Custom scales can have as much data per sample as desired in multiples of 10K with price linearly increased.

 

custom assays from 700bp - 3000bp or larger of course have a barcoding that is typically $15/barcode

 

 

 

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.

MRDNA 16s Sequencing Primers

 

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.

 

 

Sequencing Platform Read Length/Assay Length Pricing
Ion Torrent PGM 300bp 515F bacterial + archaeal or ITS1-2 fungal diversity For nominal 15-20,000 reads/assay: $60/assay (any size project)
Ion S5 XL 400-500bp bacterial, archaeal, or ITS fungal diversity assays Same Pricing as Ion Torrent PGM
Ion S5 XL >500bp bacterial, archaeal, or ITS fungal diversity assays Same Pricing as Illumina MiSeq
Illumina MiSeq 2x300 PE 20,000 sequence diversity assays starting at:
$60 /assay (>300 assays)
$65/assay (150-300 assays)
$70/assay (100-150 assays)
$75/assay (50-100 assays)
$80/assay (1-50 assays)
For projects < 10 samples a $100 library fee is added
PacBio Sequel Full Length 16s sequencing Average 5,000 seqeunces per sample: $220/assay (Minimum 20 Samples)
MRDNA Bacteria Sequencing Contact Number
MRDNA 16s Sequencing Contact Info

 

 

 

 

MR DNA has all the major sequencing platforms and we have a large selection of amplicon sequencing programs ..  Everything can be customized to the needs of the customer, only limited by the capabilities of the sequencing technologies.

 

Any amplicons (bTEFAP® services) such as 16s, 18s, ITS, functional or custom assays.. if you have an amplicon with custom primers we can help sequence it.

 

Illumina miseq and hiseq amplicons

examples for any of our hundreds of inhouse assays

***2x300bp PE illumina 20,000 sequence diversity assays

$80/assay 1-50 assays (note: for projects < 10 assays per library, a $100 library fee is added),

$75 for 50-100 assays,

$70 for 100-150 assays,

$65 for 150-300,

$60 for > 300 assays.

additional discounts for very large projects also

 

PGM (ion torrent) amplicons

***300bp 515F bacterial + archaeal or ITS1-2 fungal diversity PGM assays with nominal 15-20,000 reads/assay for $60/assay (any size project)

 

PAC BIO SEQUEL:

Sequel long read amplicon sequencing for 16s, 18s, ITS and custom amplicons

MR DNA now accepts any size project (projects with < 10 samples do have a $100 indexing fee and a $20/sample additional PCR replication fee.)

 

Low average coverage ( < 500 sequences average per sample)  for $50/sample

Medium coverage (average 5000 sequences per sample)  for $150/sample

High coverage  10K average sequences scale for $260/sample

Custom scales can have as much data per sample as desired in multiples of 10K with price linearly increased.

 

custom assays from 700bp - 3000bp or larger of course have a barcoding that is typically $15/barcode

 

 

 

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.

MRDNA 16s Sequencing Primers

 

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.

 

 

 

MRDNA 16s Sequencing Primers