Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Big data processing enables worldwide bacterial analysis

06.10.2016

Sequencing data from biological samples such as the skin, intestinal tissues, or soil and water are usually archived in public databases. This allows researchers from all over the globe to access them. However, this has led to the creation of extremely large quantities of data. To be able to explore all these data, new evaluation methods are necessary. Scientists at the Technical University of Munich (TUM) have developed a bioinformatics tool which allows to search all bacterial sequences in databases in just a few mouse clicks and find similarities or check whether a particular sequence exists.

Microbial communities are essential components of ecosystems around the world. They play a key role in key biological functions, ranging from carbon to nitrogen cycles in the environment to the regulation of immune and metabolic processes in animals and humans. That is why many scientists are currently investigatin microbial communities in great detail.


The Sequence Read Archive, a public database for deposition of sequences, currently stores over 100,000 gene sequence datasets which previously could not be evaluated in their whole. (Photo: Fotolia/ Dreaming Andy)

Sequencing for microbiological DNA analysis

The Sanger sequencing method developed in 1975 used to be the gold standard to decipher the DNA code for 30 years. Recently, next generation sequencing technologies, or NGS as they are called, have led to a new revolution: With minimal personnel requirements, current devices can, within 24 hours, generate as much data as a hundred runs of the very first DNA sequencing method.

... more about:
»DNA »DNA sequencing »data processing »rRNA »sequence

Today, the sequencing analysis of bacterial 16S rRNA genes is the most frequently used identification method for bacteria. The 16S rRNA genes are seen as ideal molecular markers for reconstructing the degree of relationship between organisms, as their sequence of nucleotides (the building blocks of DNA) has been relatively conserved throughout evolution and can be used to infer phylogenetic relationships between microorganisms. The acronym rRNA stands for ribosomal ribonucleic acid.

The Sequence Read Archive (SRA), a public database for deposition of sequences, currently stores over 100,000 such 16S rRNA gene sequence datasets. This is because the new technical procedures for DNA sequencing have caused the volume and complexity of genome research data over the past few years to grow exponentially. The SRA is home to datasets which previously could not be evaluated in their whole.

"Over all these years, a tremendous amount of sequences from human environments such as the intestine or skin, but also from soils or the ocean has been accumulated", explains Dr. Thomas Clavel from the Institute for Food and Health (ZIEL) at the TU Munich. "We have now created a tool which allows these databases to be searched in a relatively short amount of time in order to study the diversity and habitats of bacteria", says Clavel — "with this tool, a scientists can conduct a query within a few hours in order to find out in which type of samples the bacterium he is interested in can be found — for example a pathogen from a hospital. This was not possible before." The new platform is called Integrated Microbial Next Generation Sequencing (IMNGS) and can be accessed via the main website www.imngs.org.

A detailed description of how IMGS functions using the intestinal bacterium Acetatifactor muris has been published in the current online issue of "Scientific Reports". Registered users can carry out queries filtered by the origin of the bacterial data, or also download entire sequences.

Such bioinformatics approach may soon become indispensable in routine daily clinical diagnostics. However, one critical aspect is that many members of complex microbial communities remain to be described. "Improving the quality of sequence datasets by collecting new reference sequences is a great challenge ahead", says Clavel — "moreover, the quality of datasets is not yet good enough: the description of individual samples in databases is incomplete, and hence the comparison possibilities using IMNGS are currently still limited."

However, Clavel imagines that a collaboration with clinics could be a catalyst for progress, provided the database is filled more meticulously. "If we had very well-maintained databases, we could use innovative tools such as IMNGS to possibly help diagnosis of chronic illnesses more rapidly", says Clavel.

Publication:
Ilias Lagkouvardos, Divya Joseph, Martin Kapfhammer, Sabahattin Giritli, Matthias Horn, Dirk Haller and Thomas Clavel: IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies, Scientific Reports 2016. DOI: 10.1038/srep33721.
http://www.nature.com/articles/srep33721

Contact: 
Dr. habil. Thomas Clavel
Technical University of Munich
ZIEL – Institute for Food and Health
Core Facility NGS/Microbiome
Phone: +49 81 61 71 55 34
Mail: thomas.clavel@tum.de

Weitere Informationen:

http://go.tum.de/864790

Dr. Ulrich Marsch | Technische Universität München
Further information:
https://www.tum.de/en/about-tum/news/press-releases/short/article/33432/

Further reports about: DNA DNA sequencing data processing rRNA sequence

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>