The importance of the human oral microbiome

A Spanish project which seeks to understand how dietary habits and hygiene influence the human oral microbiome and investigates the consequences for health was presented at the FAPESP/EU-LIFE Symposium.

By Karina Toledo  |  Agência FAPESP – Understanding how dietary habits and hygiene influence the human oral microbiome and investigating their consequences for health are the goals of a Spanish research project entitled Saca La Lengua (“Stick Out Your Tongue”). The project is coordinated by the Center for Genomic Regulation (CRG) in Barcelona.

Preliminary results were presented by CRG researcher Julia Ponomarenko on June 7 during the FAPESP/EU-LIFE Symposium on Cancer Genomics, Inflammation & Immunity, a three-day event held at FAPESP’s headquarters to foster collaboration between scientists in São Paulo State and Europe.

“We collected saliva samples from 1,502 children aged 15-16 in 25 Spanish cities. We thought it would be fun for them to spit into a test tube,” Ponomarenko said in an interview with Agência FAPESP.

The researchers extracted and sequenced the DNA contained in the samples. To facilitate the identification of microorganisms in the children’s saliva, they targeted the gene encoding 16S rRNA, which is found in all species of bacteria, with minor variations.

“Our method of analysis allowed us to construct a profile of the bacteria present in the mouth of each child,” Ponomarenko said. “We reached the genus level, but it proved impossible to deepen the analysis enough to identify all the species.”

The most abundant genera in the samples analyzed were Streptococcus, Prevotella, Haemophilus, Neisseria, Veillonella, Rothia, Porphyromonas, Actinomyces, Fusobacterium and Gemella.

“Bacteria of the genus Streptococcus were found in 100% of the samples and were the most abundant group, at 68%,” Ponomarenko said.

The researchers then searched for correlations among these data and the children’s responses to a questionnaire about eating habits, hygiene and other aspects of their lifestyle, such as their pets and type of dwelling.

“For example, we were able to identify the bacteria that tend to be present in the mouths of children who consume sweet drinks, energy drinks or savory snacks,” Ponomarenko said. “Now we’re going to start analyzing the information in greater depth and find more correlations. In the future, we can expand the sample to study a specific aspect, such as the consumption of colas, and determine the effects of this habit.”

The Brazilians who presented on the first day of the symposium included Emmanuel Dias Neto, a researcher at A.C. Camargo Cancer Center and principal investigator of the Thematic Project “Epidemiology and genomics of gastric adenocarcinomas in Brazil”, supported by FAPESP.

“This is a very aggressive tumor, the second most lethal in the world,” Dias Neto said. “In Brazil, there are some 20,000 new cases per year, and the disease causes 15,000 annual deaths.”

The project will be conducted on three different fronts, he added. In the epidemiological study, some 2,000 volunteers will be interviewed. The aim is to investigate the use of medication, dietary habits, food additives, tobacco, alcohol, and other factors that may influence the tumor’s development.

“We’ll have two control groups – one comprising people with no complaints of gastric problems and the other in which people have something wrong with their stomach but haven’t been diagnosed with cancer. A third group will consist of patients diagnosed with cancer of different types and at different stages. We also plan to obtain blood and tumor samples,” Dias Neto said.

The material collected will be used in the second module of the project, focusing on molecular biology and genomics. Stomach bacteria will be analyzed, and a study will be performed to find out whether the bacteria are linked to the development of more or less aggressive tumors. Tumors of familial origin will also be investigated in search of molecular markers to assist in cancer diagnosis, prognosis and treatment.

The patients’ response to neoadjuvant (pre-surgical) chemotherapy will also be studied. “Today, the standard protocol is to treat the patient for a period and only then operate,” Dias Neto said. “In many cases, however, we observe during surgery that the treatment has had no effect. The patient wasted time, money and health by waiting. If we can find a way to identify who will benefit from neoadjuvant chemotherapy before we begin, we’ll have made important progress.”

Also in the field of cancer research, Wilbert Zwart of The Netherlands Cancer Institute presented data from studies designed to investigate how female hormone receptors (cellular proteins activated by estrogen or progesterone) bind to DNA and influence the proliferation of breast tumors.

“About 75% of breast tumors are positive for estrogen receptors, meaning the cancer cells contain these proteins,” Zwart said. “So potentially they’re treatable with drugs that inhibit the action of estrogen receptors, such as tamoxifen.”

Many patients are cured by hormone therapy, he went on, but some relapse later in life. “This relapse usually takes the form of metastasis. That’s something we want to avoid at all costs,” he said.

According to Zwart, research has shown that these receptors’ DNA binding patterns can reveal the behavior of tumor cells and the response to therapy. “So what we do is look at the different DNA binding patterns and compare them with the tumor’s behavior in the patient to see whether it’s resistant to therapy or not,” he said. “We often find there is indeed a difference. Our goal is to translate these differences into predictive tools that will be useful to guide decisions regarding treatment.”

The seminar program also featured presentations on research to prevent and treat such diseases as leishmaniasis, Chagas, diabetes, leukemia, xeroderma pigmentosum (an inherited genetic mutation that causes a condition characterized by an extreme sensitivity to ultraviolet light and a high risk of skin cancer) and glioma (brain cancer), among other life science-related fields.

Building bridges

To stimulate collaboration between the scientific community in São Paulo State and EU-LIFE’s more than 7,000 researchers, a cooperation agreement was signed during the opening session of the symposium by FAPESP Vice President Eduardo Moacyr Krieger and EU-LIFE Chair Geert Van Minnebruggen.

Established in 2014, EU-LIFE is an alliance of 13 top life science research centers located in as many western European countries. “We aim to promote best practice in research and collaboration, not just among the members of our community but also with foreign groups who work in the same field. We interact with the European Commission and the governments of the countries represented on behalf of these institutions to help them obtain funding,” said EU-LIFE Coordinator Marta Agostinho.

The partnership with FAPESP, according to Agostinho, arose from a confluence of objectives. Krieger agreed: “Both institutions have similar missions,” he said. “They both aim to promote excellence and international collaboration.

FAPESP Scientific Director Carlos Henrique de Brito Cruz recalled during his presentation that negotiations resulting in the cooperation agreement began approximately a year earlier during FAPESP Week Barcelona in Spain. Brito Cruz then presented an overview of science and technology in São Paulo State.

Minnebruggen, who delivered a presentation on the scope of EU-LIFE’s activities, highlighted the importance of connecting research in several disciplines to more effectively address such challenges as food production and sustainability, healthy aging, and neurological disorders.

“It’s really very important to find solutions to diseases like Alzheimer’s,” Minnebruggen said. “Thousands of people are diagnosed with such disorders every day.“