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 Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute

nachricht Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>