16s Ribosomal Sequencing
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.
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.
Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies. Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline. The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism. The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.
Adebayo AS, Survayanshi M, Bhute S, Agunloye AM, Isokpehi RD, Anumudu CI, et al. (2017) The microbiome in urogenital schistosomiasis and induced bladder pathologies. PLoS Negl Trop Dis 11(8): e0005826. https://doi.org/10.1371/journal.pntd.0005826
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.
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:
NEW: Long read full 16s ~1400bp amplicon diversity average 5k reads per sample (minimum 20 samples) for $220/sample
LONG read ITS1-4 sequencing for fungi
long read 18s 1700bp spanning many variable regions (several options available)
long read custom assays from 600bp up to 8000bp (custom assay setup costs
range from $15-$20/barcode)
Prokaryotes today are divided into two domains, Archaea and Bacteria. These two domains are of particular interest in areas of research including:
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.