Progress in microbiome research in Iran

Abstract

Almost all animals on Earth, whether sedentary sponge, an insect, an elephant or humans, live in a co-evolutionary association with large communities of microbes.  The total microorganisms that reside in a particular tissue habitat are termed microbiota (or microflora) and their collective genomes in a microbiota are termed microbiome.  The immense size, diversity and rapid growth of microbial populations in various microbiomes provide an enormous opportunity for genetic exploration.

Microbial composition of microbiome is formed by host factors such as genetics and diet, probably early in life. Gut microbiota is able to influence host physiology, development, nutrition, and metabolism; control pathogens, and regulate immune responses in health and disease. It is estimated that human microbiome consists of about 40 to 100 trillion genes. Based on the 16S rRNA gene sequence data, all regions of the human gastrointestinal tract (GIT) contain nutrition-dependent diverse bacterial communities. Environmental factors such as antibiotics could disrupt gut-microbiome interactions, leading to acute or chronic disease in some individuals.  Although most current research is focused on bacterial composition, archaea, fungi, and viruses are also included in the host microbiome.

The gastrointestinal tract of healthy humans is colonized by populations of microorganisms ─ gut microbiota that contributes directly to digestion and nutrition by the fermentative degradation of various chemicals contained in foods, for example, polysaccharides in plant cell walls.  It is suggested that the combined metabolic activities of microbial and human genome represent a “superorganism”.

Advance in DNA sequencing technologies and bioinformatics is rapidly increasing our knowledge of the number, taxonomic diversity and functional contribution of the gut microbiome that depend on age, diet, medication and antibiotic usage. In addition, GIT microbes contribute to micronutrients and may potentially detoxify toxic substances.

Research interest to understand the nature and functional activity of microbial communities in non-human animals, particularly farm animals, has a long history. However, during the past decade, there has been a rapid growth of research activity on the human microbiome. In contrast to in situ animal studies, most current analyses of the diversity of human and animal model microbiota in the GI tract have been dominated by molecular analyses of fecal bacterial diversity, and it is assumed that it represents microbial composition throughout the GIT. Some animal studies reveal a localized bacterial functional preference for a specific GI region.

With the advancement in molecular technology of rRNA sequencing in identifying culture-independent microbes, there has been a rapid growth of research activity on human microbiome. Moreover, in 2007 the US NIH Microbiome Research Project was initiated with the aim of understanding the human microbial compositions and their genetics, as well as metabolic contribution to normal health and disease.  Establishment of other national and international microbiome research collaborations followed. During the past decade, there has been an extensive growth of publications related to human microbiome research. For example, a PubMed search on “human microbiome” in 2007 showed 526 entries, while a recent search produced 7618, a 15-fold growth in 10 years.

Early human microbiome research activity involved identifying microbial compositions of body regions and their role in normal physiology. Current interest includes studying the interactions between host and microbes in health and disease, with some emphasis on the nature of microbial composition during prenatal, neonatal and early life, when the host’s microbiome seems to get established. Although human microbiome projects and potential health benefits may get the most attention, other research projects such as animal, plant and environmental microbiomes are ongoing too. In addition, potential commercial application of microbiome research is also getting significant economic interest in the health industry; examples are microbial replacement for immunological disorders, type-2 diabetes, obesity, cardiovascular disease, and neurological disorders.  In addition, research is also ongoing for discovering and developing new applications of microbiome in pharmaceutical and industrial applications

An analysis of gut microbiota has revealed three predominant “enterotypes”, dominated by Bacteroides, Prevotella, and Ruminococcus. Although the basis for this enterotype clustering is unknown, it appears that long-term diet and nutrition play an important role. Thus, it is suggested that a long-term optimal diet is an easiest and simplest way to modulate healthy gut microbiota. Such findings would have practical importance for the development of health interventions that could promote beneficial bacteria and inhibit the growth of bacteria responsible for disease and inflammatory response.

The scientific literature has demonstrated that certain microbes of the gut microbiota act as probiotics that could provide beneficial effects for their host. Identifying nutritive food items that could be included in regular diets to promote the beneficial microbes is of interest to health practitioners and pharmaceutical industries. As mentioned above, the nutrient content of diet plays an important role in the maintenance of and modifying, the resident gut microbiota.

In this issue of the Journal, Alizadeh Sani et al, using an ex-vivo study, showed that Oryzatensin, a rice bioactive peptide, acts as antibacterial and negatively controls the growth of certain colonic bacteria such as Bifidobacteria. This study, in addition to other ongoing research projects as well as organizing mini-symposium on micorbime in Iran, shows that albeit being fragmented, there is active microbiome research in Iranian academic institutions. It is hoped that with the establishment of an Iranian National Microbiome Research Project researchers with common scientific interests will get together to study and benefit from microbiome potentials for improved health and wellbeing.