Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

The largest ever catalog of bacteria in the human body contain over 150 thousands genomes

12.03.2019

A large number of previously uncharacterized bacteria living in and on humans was discovered and analyzed by scientists at the University of Trento, Italy. This computational metagenomic study appeared in "Cell"

Dr. Segata explains: «We genetically characterized and catalogued a large number of bacteria and archaea that are part of the human microbiome, but remained so far unexplored, uncharacterized, and undescribed.


The image below represents the 'human microbiome tree of life' which includes the thousands of new species that were discovered in this work. It is thus a representation of the total diversity of the human microbiome across human populations, age, conditions, and body sites that is described in the article. The image was generated by an open source software written by the authors and the image can be freely used.

Credit: ©University of Trento

We also observed that many of these microbes tend to be only rarely identified in Westernized populations, most probably as a indirect consequence of the complex industrialization processes».

Similarly to other living organisms, microbes evolve and are under selection pressure as the environment, including diet and lifestyle, changes. In some cases, human-associated microbes that can be crucial for our health are at risk of extinction.

The research team investigated some of these cases. The presented study integrates genomics, microbiology, and big data and engaged several researchers at the CIBIO Department of the University of Trento as well as students of the masters program in Quantitative and Computational Biology at the same institute.

The study also involved partners at Harvard University (US) that were responsible for the microbiome sampling of a Malagasy population, and at Otago University (New Zealand), National Research Council in Spain (Valencia), and University of Warwick (UK).

Nicola Segata focuses his research on the human microbiome. He explains: «It's the collection of bacteria, archaea, viruses, fungi, and parasites that populate human body sites such as the gut, the mouth, the skin, and the urogenital tract.

The human microbiome is in symbiosis with our own cells and plays a key role for our health, for example, in the metabolism of dietary compounds, in regulating the so-called gut-brain-axis, in protecting us from pathogenic agents, and in modulating our immune system. It has also been recently shown that the microbiome is involved in the etiology of some cancers and in the success of anti-tumoral immunotherapy approaches».

The approach of his team in studying the human microbiome is called "computational metagenomics": they study the microbiome by analyzing its genetic information. From a drop of saliva, a skin swab, or a gram of stool they extract the total DNA of the microbes in the sample, and they subject the DNA to high-throughput sequencing. The resulting huge amount of genetic data is analyzed with specialized software to reconstruct the genomes of the microbes present in the microbiome.

Dr. Segata details some aspects of the new study: «Our findings are the result of a multidisciplinary team at CIBIO comprising microbiologists, statisticians, and computer scientists that identified a total of almost 5,000 microbial species recapitulating over 154,000 newly reconstructed genomes describing the human microbiome across ages, body sites, lifestyles, and diseases.

Each of us is colonized by several hundreds of these species. But a large fraction of them (77%) were previously unknown. Many of these species are relatively rare, but some are very prevalent in human populations worldwide, and their discovery is the starting point for testing their potential role in autoimmune, gastrointestinal, and oncologic diseases.

To obtain these results, we analyzed an extremely large dataset of publicly available and newly obtained microbiome samples spanning geography, population lifestyles, and age. Overall, we considered 9,428 human microbiome samples that have been studied using DNA sequencing technology called metagenomics».

A collaborator on the study, Dr. Curtis Huttenhower of the Harvard T.H. Chan School of Public Health, commented that, "Very large-scale studies of the human microbiome have begun to be particularly important for understanding population health. A surprising finding about the microbiome has been how personalized it is, though, and the level of detail necessary to understand its influence on each individual's health.

Techniques such as those developed in this study have the ability to identify new microbes unique to each person, and the genes and molecules unique to those microbes, that can in turn carry out immune signaling or modify dietary processes in the gut.

The fact that we found such striking differences around the world during this work also calls out the microbiome's relevance to global health - for example, in explaining some of the differences in response to vaccines that might be attributable to microbial rather than human genetic diversity."

On the discovery and analysis of one of these bacteria, Segata continues: «The most common previously unknown candidate species, that we called "Cibiobacter qucibialis", is the seventh most prevalent human-associated microbe in the worldwide population. We studied it by reconstructing more than 1,800 genomes. We think this species could be of particular relevance for further understanding the functions of the human microbiome».

And a final highlight on the observed differences among human populations: «We specifically focused on non-Westernized populations that do not have access to high-fat diet, common drugs including antibiotics, and do not live in highly sanitized environments. Many novel microbes discovered in non-Westernized populations across continents tend to be almost undetectable in Westernized populations.

Our work thus enabled the study of such microbial species that could potentially be linked in the future with the increasing incidence of autoimmune diseases, allergies, and complex syndromes in the Westernized populations. It will thus be crucial to isolate, cultivate, and maintain these species that could be hypothetically reintroduced in Westernized populations with novel intervention strategies».

Media Contact

SALETTI ALESSANDRA
alessandra.saletti@unitn.it
0039-461-281-131

http://www.unitn.it 

Saletti Alessandra | EurekAlert!
Further information:
https://www.sciencedirect.com/science/article/pii/S0092867419300017?via%3Dihub
http://dx.doi.org/10.1016/j.cell.2019.01.001

More articles from Life Sciences:

nachricht Molecular 'clutch' puts infection-fighting cells into gear
22.07.2019 | National Centre for Biological Sciences

nachricht Living Components
22.07.2019 | Albert-Ludwigs-Universität Freiburg im Breisgau

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: MOF@SAW: Nanoquakes and molecular sponges for weighing and separating tiny masses

Augsburg chemists and physicists report how they have succeeded in the extremely difficult separation of hydrogen and deuterium in a gas mixture.

Thanks to the Surface Acoustic Wave (SAW) technology developed here and already widely used, the University of Augsburg is internationally recognized as the...

Im Focus: Better thermal conductivity by adjusting the arrangement of atoms

Adjusting the thermal conductivity of materials is one of the challenges nanoscience is currently facing. Together with colleagues from the Netherlands and Spain, researchers from the University of Basel have shown that the atomic vibrations that determine heat generation in nanowires can be controlled through the arrangement of atoms alone. The scientists will publish the results shortly in the journal Nano Letters.

In the electronics and computer industry, components are becoming ever smaller and more powerful. However, there are problems with the heat generation. It is...

Im Focus: First-ever visualizations of electrical gating effects on electronic structure

Scientists have visualised the electronic structure in a microelectronic device for the first time, opening up opportunities for finely-tuned high performance electronic devices.

Physicists from the University of Warwick and the University of Washington have developed a technique to measure the energy and momentum of electrons in...

Im Focus: Megakaryocytes act as „bouncers“ restraining cell migration in the bone marrow

Scientists at the University Würzburg and University Hospital of Würzburg found that megakaryocytes act as “bouncers” and thus modulate bone marrow niche properties and cell migration dynamics. The study was published in July in the Journal “Haematologica”.

Hematopoiesis is the process of forming blood cells, which occurs predominantly in the bone marrow. The bone marrow produces all types of blood cells: red...

Im Focus: Artificial neural network resolves puzzles from condensed matter physics: Which is the perfect quantum theory?

For some phenomena in quantum many-body physics several competing theories exist. But which of them describes a quantum phenomenon best? A team of researchers from the Technical University of Munich (TUM) and Harvard University in the United States has now successfully deployed artificial neural networks for image analysis of quantum systems.

Is that a dog or a cat? Such a classification is a prime example of machine learning: artificial neural networks can be trained to analyze images by looking...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

2nd International Conference on UV LED Technologies & Applications – ICULTA 2020 | Call for Abstracts

24.06.2019 | Event News

SEMANTiCS 2019 brings together industry leaders and data scientists in Karlsruhe

29.04.2019 | Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

 
Latest News

Toward molecular computers: First measurement of single-molecule heat transfer

22.07.2019 | Information Technology

First impressions go a long way in the immune system

22.07.2019 | Health and Medicine

New Record: PLQE of 70.3% in lead-free halide double perovskites

22.07.2019 | Power and Electrical Engineering

VideoLinks
Science & Research
Overview of more VideoLinks >>>