Journal of Gastroenterology and Hepatology Research Online Submissions: http://www.ghrnet.org/index./joghr/ Journal of GHR 2013 December 21 2(12): 885-896 doi:10.6051/j.issn.2224-3992.2013.02.371 ISSN 2224-3992 (print) ISSN 2224-6509 (online) EDITORIAL Metagenomic Study of Human Gastrointestinal Tracts in Health and Diseases Firouz Abbasian, Tayyebeh Saberbaghi Firouz Abbasian, Tayyebeh Saberbaghi, Department of Micro- tracts. Metagenomics is an approach in which whole genome biology, Science and Research campus, Islamic Azad University, contents of a community of (micro) organisms in a niche of interest Tehran, Iran is investigated in order to detect its microbial diversity and also Correspondence to: Firouz Abbasian, Department of Microbiolo- to study special trait(s) of the habitat[1,2]. This technique employs gy, Science and Research campus, Islamic Azad University, Tehran, the hyper-variable sections of special marker genes, especially Iran. the 16S ribosomal RNA (rRNA), to identify microbial diversity. Email: [email protected] Also, this technique is able to detect the functional ability of Telephone:+98-911-136-3088 existing microorganisms in an environment based on the identified Received: September 16, 2013 Revised: September 28, 2013 genes[3]. The metagenomic approach can be used for any natural Accepted: October 2, 2013 environment where microbial genomic sources are available. Published online: December 21, 2013 The Human Microbiome Project is an international study of the microbial communities associated with different parts of our body[4]. ABSTRACT Most of the existing information regarding the microbial diversity of human body and their role in different physiological functions Metagenomics is a new emerged technology used to investigate the of the gastrointestinal tract are based on in vitro or culture based microbial diversity in an environment and to study their function in studies. However, the new approaches have opened new windows a given environment. The Human Microbiome Project is a global for understanding these relationships between human cells and project to research diversity of microbial communities associated microbial strains. with human body and to investigate their effects on physiology of The gastrointestinal tract consists of different parts, including organs. These studies also are interested to link between the existence mouth, esophagus, stomach, small intestine, colon and rectum. of a microbial population and several inflammatory, physiological, These tracts function as digestive and absorptive organ for our metabolic and psychological disorders. Based on metagenomic body and at the same time are known as a major exocrine and studies, this paper aims to review the newest information regarding [5,6] endocrine hormone producer and an important immune organs . microbial diversity of the intestinal tracts and their physiologic and/or Based on the conventional culture-based approaches, a few pathologic influences on human body. hundred microorganisms has been detected at different parts of gastrointestinal tracts and the population of obligate anaerobic © 2013 ACT. All rights reserved. bacteria, specially Bacteroidetes, are one thousands time more than the population of facultative organisms. However, based Key words: Metagenomics; Biodiversity; Intestinal flora; Mal- on culture-independent approaches 1,012 cells lives in 1g stool, nutrition; Physiological disorders; Psychological disorders consisting of over 13,000 microbial species that most of them belonged to the Firmicutes and Bacteroidetes (respectively, 75% Abbasian F, Saberbaghi T. Metagenomic Study of Human Gastroin- [7,8] and 16%) . This number in some papers is suggested more than testinal Tracts in Health and Diseases. Journal of Gastroenterology 1,800 genera and 15,000 to 36,000 species, varying based on the and Hepatology Research 2013; 2(12): 885-896 Available from: [9] bacterial classification system . Only 20% of these microorganisms URL: http://www.ghrnet.org/index.php/joghr/article/view/546 [7] are detectable by conventional culture-based methods . Although the diversity may differ in each individual person or society, the INTRODUCTION ecological niche of the microbial combination is similar[10]. In this Employment of new emerged detecting technologies, referred to paper, diversity and function of normal flora of the gastrointestinal as metagenomics, has changed our view of microbial diversity tracts is reviewed based on the newest information obtained from in different habitats, including the micro-flora of gastrointestinal culture independent technologies. 885 © 2013 ACT. All rights reserved. Amornyotin S et al. Metagenomic Study of Gastrointestinal Tracts For instance, hard palate, keratinized gingiva and buccal mucosa are THE NORMAL FLORA OF INTESTINAL TRACT occupied with Firmicutes (mostly Streptococcus sp. and Gemella AT BIRTH sp.) followed by Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria in a diminishing order[25]. Also, throat, tonsils, While intestinal tract is sterile at the birth, it may be contaminated [11] tongue and saliva are inhabited mostly by Firmicutes, especially through birth . Although based on researches in 1990s, mode of Streptococcus sp., Veillonella sp. and Lachnospiraceae (Oribacterium delivery (normal vaginal birth or caesarean section) had no significant [12,13] sp. and Catonella sp.) followed by Bacteroidetes (Prevotella sp.), effect(s) on the normal flora of the neonatal intestinal tracts , Neisseria sp., Fusobacteria (Fusobacterium sp. and Leptotrichia nowadays researchers believe in an entirely different way. In normal sp.), Actinobacteria (Actinomyces sp.) and TM7 in a diminishing vaginal delivery, the neonate is affected by both mother’s vaginal and order. However, the abundance of Firmicutes in the plaques formed intestinal flora, and the neonate’s gut is colonized predominantly by E. [14-16] on both supra-and sub-gingival habitats is decreased but the number coli, Enterococci, Bifidobacterium, Lactobacillus and Prevotella . of Actinobacteria shows a significant increase[25]. In addition to the However, since the neonates delivered via caesarean mode are not strains found in the throat and tongue, these last habitat are occupied exposed to the mother’s vaginal/intestinal flora, their intestinal by Rothia sp., Corynebacterium sp., Porphyromonas sp. and microbial composition is similar to the microbial flora of skin, Capnocytophaga sp[25]. The pathogenic microorganisms involved in consisting of a lower microbial diversity in which Staphylococcus is [14,15] oral and systemic infections like Treponema sp., Aggregatibacter sp., a dominant population . Megasphaera sp., S. pyogenes, S. pneumoniae, H. influenzae and N. In a culture based research, it has been shown that the mode of meningitidis are also found in those area in low abundance[25]. feeding has fundamental effects on the normal flora of the intestine at the first days of birth[17]. Approximately 24 hours after a normal birth, the intestinal tract acquire some microorganisms originated ESOPHAGUS from mother’s vagina or her intestinal tracts through delivery or The esophagus is a unique part of gastrointestinal tracts since [18] taking milk . Regardless of mode of feeding, the intestine is foods are not deposing in the tract. Based on the culture dependent occupied mostly by E. coli, also some other enterobacteriaceae methods using the samples given from luminal washes of the tract, [12] and gram-positive cocci by the end of first week . Microarray most researches showed a sterile environment where sometimes based investigations showed that the microbial population of is contaminated by the transit microorganisms originating from intestine is formed after one week, but the flora will not reach to its upstairs or downstairs organs[26] like Herpesvirus, Cryptococcus sp. [18] equilibrium by the end of infancy . These flora constitutes mainly and Candida sp[28-31]. However, based on 16SrRNA pyrosequencing, of Bifidobacterium sp., E. coli, Enterococcus sp., Streptococcus sp., esophagus is occupied by a stable flora consisting of same series of Staphylococcus sp., Actinomyces sp., Clostridium sp. and Bacteroides microorganisms as the oral cavity and nasal swab and roughly 140 [19, 20] sp . It has been shown that roughly 6 day after birth the intestinal species from six phylum of the microorganisms Firmicutes (mostly tracts of breastfed and bottle-fed infants were dominantly colonized by Streptococcus sp. and Veillonellance), Bacteroides (mostly Prevotella Bifidobacteria and enterobacteriaceae, respectively. These conditions sp.), Actinobacteria, Proteobacteria, Fusobacteria, and TM7[27-29]. continued by the end of one month when Bifidobacteria were the The habitat is dominantly occupied by Streptococci (78% of the dominant bacteria in both groups. In this age, however, the number of microbial population)[27]. The composition of esophageal flora change Bifidobacteria in the stool of bottle-fed infants was 1/10 in comparison in different physiologic and pathologic conditions, such as gastro- [17] to breast-fed infants . In a study performed based on 16S rRNA esophageal reflux disease (GERD) and Barrett’s esophagus. In these amplification, Bifidobacterium sp. was dominant member of the fecal pathologic and inflammatory conditions, the tract is more hospitable samples taken from infants below four month old, and the number of for anaerobic and microaerophilic bacteria. For instance, it has this bacteria raised from