Analysis of the intestinal microbiota at the heart of probiotic research and development

To celebrate the World Microbiome Day, we are offering an article explaining how the analysis of the intestinal microbiome is essential in the context of research to develop effective and targeted probiotic formulas to support your health as well as for specific health conditions.

Let’s untangle microbiome, microbiota, microbes, and microorganisms

The expression “gut microbiota” refers to the community of microorganisms (mainly bacteria, but also yeasts, microscopic fungi, and viruses) living in our intestines. When we are talking about the microbiome, we are referring to these microbes in a way that also includes the effect of their genes and their metabolism on the host. The microbiota begins to develop in the baby’s intestines from birth, and could possibly even start during our time in our mother’s uterus according to some studies. In infants, the microbiota includes only a few types of bacteria and gradually evolves into an ever increasing diverse community of microbes starting with the incorporation of a solid diet. Then, from childhood until adulthood, the microbiota usually becomes more stable in composition, before starting to lose some microbial diversity with agingi. In an adult weighing around 70 kilos, the intestinal microbiota can contain up to 100 trillion microorganisms (i.e. 100,000,000,000!) and alone can weigh around 200 gramsii.

Several factors influence the composition of the gut microbiota throughout life, either positively, such as healthy diet and physical activity, or negatively, such as chronic disease, poor diet, or the use of antibiotics. Changes in the proportion of beneficial and pathogenic microorganisms (called dysbiosis) are often reversible. As the adult microbiota tends to be stable – it is said to be resilient – the return to normal after a challenge causing a temporary imbalance, such as after taking antibiotics, can be accelerated by certain probiotic supplements and thereby prevent or reduce the duration of occasional diarrhea associated with antibiotic intakeiii.

Why is the microbiome of interest for scientists?

For several years, scientists have been studying the intestinal microbiome, trying to understand the associations between the presence or absence of certain bacteria, or the loss of diversity of the microbiota and health status (intestinal, emotional, and mental). It is now known that a state of dysbiosis is observed in several diseases. In contrast, the role of each of the bacterial types present remains to be established: these bacteria are alive and can consume or release molecules in the intestine which can influence other neighboring bacteria as well as our intestinal or immune cells. Because the number of bacteria in the gut is so large (trillions!), genomic analysis techniques must be used to differentiate between the different types of bacteria present in a sample of the microbiome (usually a fecal sample is used as a representative specimen of the bacteria present in the colon). These analysis techniques must be sophisticated because there are 150 to 200 times more genes in the microbiome of an adult than in the whole genome of our actual human cells.

Fortunately, we can identify the different bacteria contained in a fecal sample by quantifying the bacterial 16S ribosomal RNA gene, which is present in all bacteria. While this gene is part of the general cellular machinery producing proteins from messenger RNA that is common to all bacteria, each bacterial species can be distinguished from each other based on the presence of species-specific variable regions within the 16S gene.

Preclinical and clinical research at RIMaP

At the Rosell® Institute for Microbiome and Probiotics (RIMaP), one of Lallemand Health Solutions’ research centers, we have implemented high-throughput sequencing methods using the MiSeq system (Illumina). By systematically sequencing the 16S genes contained in the fecal samples obtained from clinical trials participants, we hope to better understand the role of the microbiome (as well as the role of probiotics!) on health.

Briefly, fecal samples are diluted, and bacterial DNA is extracted. Then, the DNA is subjected to amplification to proportionally increase the level of each sequence of the 16S genes (with general primers associated with regions conserved in all bacterial species) to facilitate the reading of the sequences by the MiSeq. The sequences are compiled and analyzed using bioinformatics tools to identify changes in microbiome composition after taking the probiotic compared to the baseline composition (before taking the probiotic). During bioinformatics analysis, the genetic information of specific 16S regions (the variable regions) is compared with public databases to identify the bacterial species present within a fecal sample and is quantified to measure the relative proportions of each.

However, in order to obtain information about the metabolic functions of a given microbiome, it is necessary to identify all the bacterial genes contained in a fecal sample; this technique is called metagenomic sequencing. Our team is currently working to implement metagenomic sequencing in our laboratories. Moreover, with scientific advances in -omics techniques (genomics, proteomics, metabolomics), it will become possible to understand not only the interactions between the different bacterial species, between them and with their host (us!), but we will likely be able to identify individuals who could respond better to one probiotic over another in a personalized manner based on their health status, diet, and microbiome composition.

A recent clinical study conducted by Lallemand Health Solutions (in the process of publication) suggests that our probiotic strain B. longum R0175 could persist longer in the stool of some individuals after stopping the supplement (about 15 days compared to about 5 days for others), depending on the speed of their intestinal transit and the composition of their microbiome. Will this ‘microbial signature’ which seems to favor a slightly longer persistence of R0175 be associated with an improvement in the beneficial effects of the strain in a future study? More details will follow on this, stay tuned!

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i Gut microbiota for health. (Tout sur notre microbiote intestinal). Récupéré sur Gut microbiota for health:
ii Sender R, F. S. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 14(8): e1002533.,
iii Nutrition Insight. (2016). Lallemand Flagship Probiotic Formula Lacidofil Reduces Duration of Antibiotic-Associated Diarrhea. Récupéré sur Nutrition Insight: