The human microbiome has been studied extensively. It can be compared to a separate “organ” which helps the whole organism function normally. However, we still know little about the microbiome as its structure may vary a lot depending on a number of factors.
The Department of Genetics at the University Medical Centre Groningen functions in one of the oldest universities in the Netherlands. The researchers aim at finding correlations between the person’s microbiome and his or her health. The scaled research was undertaken in collaboration with their colleagues from many scientific centers, including experts from Novosibirsk State University, when the scientists studied microbiomes of 1000+ people living as a consistent population in the northern Netherlands. Apart from the microbiome data itself, the team gathered a lot of additional information on the people’s diets, their illnesses and treatment, different medical parameters. The results of this research were published in the special issue of the journal Science devoted to Microbiome, on 29 April, 2016.
Studying gross sample of microbiomes, researchers usually sequence (read the nucleotide sequence of) one small sample of bacteria genomes. As a rule, it is analyzed with 16S rRNA gene sequencing, which provides a reconstruction of only the taxonomic structure of the population studied. It identifies which bacterial families and genera are represented in the microbiome and to what extent.
In this particular research, scholars used a more sophisticated method, mass parallel sequencing of the whole DNA pool in the sample. Due to this method, they both “increased the resolution” of the research by estimating the presence of species and genera as well as particular bacterial strains, and were able to characterize the functional structure of the microbiomes under study, which showed genes of particular metabolic processes and ontological groups present in particular samples.
The studies revealed that at least 60 categories of food and types of diet have a profound effect on the diversity of gut bacteria and the microbiome.
Foods like fruits, vegetables, coffee, tea, wine, yogurt and buttermilk can increase the diversity of bacteria in a person's intestines as they contain a greater variety of bacterial genera. Such a diversity can help ward off illness. On the other hand, the scientists found out, foods containing simple carbohydrates and high in calories appear to reduce bacterial diversity in the gut. These include high-fat whole milk and sugar-sweetened soda.
Apart from the diet, the microbiome is influenced by at least 19 types of medications such as PPI (acidity regulators), statins (cholesterol regulators), laxatives (treating constipation), antibiotics, the diabetes drug metformin, antacids, antistiffness factor, beta-blocking agents (for arrhythmia), beta-sympathomimetic agents (for treating asthmatic episodes), opiate-based pain management medications, antiplatelet drugs, oral contraceptives, ACE inhibitors, biophosphonates (for osteoporosis), calcium-based medications, SSRI anti-depressants and other anti-depressant drugs, folates (vitamin M), etc.
Negative effects of antibiotics and mediations decreasing stomach acidity seem to be obvious, but researchers also found the effect of antidepressant drugs and ACE inhibitors, which are used for cardiac decompensation and lowering blood pressure, on gut bacteria leading to the decrease of their diversity.
The structure of the human microbiome is known to depend on geography. Not without interest for the scholars were the possibilities to spread these findings to other population samples. The Groningen team compared their results with those of the Flemish Gut Flora Project group, who performed a similar analysis on samples taken from 5,000 volunteers in Belgium and published their results in the same issue of Science. The findings from the two groups overlapped about 80%, indicating that they are on the right track, the researchers said, which is a very high indicator in studying microbiomes. Both sets of researchers emphasized that their studies only help explain a fraction of gut bacteria variation.
