Abstract

Research into the human microbiome has led to our realization that the human body is a hub of trillions of microorganisms and most of the microbes that inhabit our body supply a crucial environment that benefits the entire host-microbe system. Several milestone discoveries have been carried out to understand the role of their existence in and on the human surfaces. The indigenous microbiota of healthy humans has a specific phylogenetic and functional context. Perturbations in microbial communities lead to dysbiotic conditions that come out with the onset of several non-infectious polymicrobial diseases. Present findings of the implication of microbiota are encouraging and pave a way to understand the insights of human microbiota especially in human healthcare, where several antibiotics are being degraded by microorganisms by adapting several mechanisms to cope up with their deleterious effect. This review provides an overview into the human microbiome, various approaches to study the microbiome, its significance, associated challenges with the human health and further research needed to exploit the potential of the human microbiota.

Introduction

A human body harbors approximately one trillion of microorganisms in and on the surfaces, and their count shares the same number of cells as an average adult body [1]. Nobel laureate Joshua Lederberg introduced the term ‘Microbiome’ to understand the ecological community of inhabitant commensals, symbionts and pathobionts [2]. These indigenous microorganisms co-evolve and co-exist at different anatomical sites with distinct communities. Therefore, humans are now considered as ‘Superorganisms’, where microorganisms interact with the human cells and may impact their physiology, metabolism and immune responses in a harmonious relationship [3]. These commensal microorganisms include bacteria, fungi, viruses, and protozoa; which make the integral constituents of the microbiome; a well-established terminology dedicated for the total number of microorganisms, metagenomes and their interactions within a biological system. Bacteria comprise the major chunk of the microbiome and therefore designated as a new term ‘Bacteriome’ [4]. With the initiative of the National Institute of Health (NIH), the Human Microbiome Project (HMP) (www. hmpdacc.org/hmp) was founded in 2008 for exploring the inhabitant microorganisms of a human body; the 16S rRNA and shotgun sequencing revealed more than 14.23 terabytes of sequenced data, which is now publically available [5]. In this investigation, samples from various human body parts like skin, gut, urogenital tract, oral cavity and nasal passages were collected from three hundred individuals. Studies revealed that the intestinal microbiota contains the largest number of microorganisms followed by the oral cavity. Metagenomics of the Human Intestinal Tract (MetaHIT) (www.metahit.eu) and Human Oral Microbiome Database (HOMD) (www.homd. org) are another two established databases that deal with the human microbiome. The MetaHIT project was established to understand the effect of the gut inhabitant microorganisms on the health of humans. Specifically, it focuses on two disorders - IBD and obesity. The gut microbiota of a healthy individual chiefly harbors Bacteroides, Bifidobacterium, Enterococcus, Escherichia coli, Enterobacter, Staphylococcus, Lactobacillus, Clostridium and Salmonella [6].

The HOMD is founded by National Institute of Dental and Craniofacial Research during 2010 for maintaining the data of culturable and non-culturable microorganisms of the human’s oral cavity. Presently, HOMD comprises 700 prokaryotic species having 68% cultivable and 32% non-cultivable taxa [7].

Approaches to Studying The Microbiome

Analyzing the microbial diversity of a niche is a big challenge, as the sample contains billions of microorganisms. Traditional microbiological methods are not adequate to access the entire microbial community of a niche due to the improper synchronization of several physiological and chemical parameters involved in cultivating them [8]. With the best of microbiologist’s efforts, only 0.1-1% of microorganisms can be cultivated in laboratory conditions [9,10]. Therefore, an alternate technology, metagenomics has been developed, which has nothing to do with the nourishment of microbes, rather it directly deals with the cloning of community DNA followed by their sequence and functional based analysis [11,12]. This non-traditional methodology starts with the extraction of good quality, non-sheared and high molecular weight DNA. Various phylogenetic molecular markers like bacterial/archaealspecific 16S rDNA and fungal-specific inter transcribed spacer (ITS) regions, that can be used for identifying the respective microbial diversity [13]. With the advent of next-generation sequencers, it is now possible to generate massive quantity of sequenced data from several samples simultaneously. Roche is the pioneer in the next generation sequencing (NGS) which is based on the principle of pyrosequencing and provides approximately 400-700 bp reads [14]. In the past five years, more efficient sequencing platforms viz., Illumina’s Hiseq and Miseq, ThermoFisher’s Iontorrent, and Oxford Technologies’ Nanopore were emerged that replaced the Roche technology [15]. NGS based platforms sequence only small stretches of 16S rDNA regions like V_1-3 (464 bp), V_3-4 (344 bp), V_4-6 (474 bp) and V_7-9 (348 bp) to amplify the hypervariable regions [16,17]. Human DNA contamination is a big challenge for studying the various pathways using shotgun based sequencing because it adds unnecessary sequenced data, however amplicon based sequencing does not demand for human DNA free metagenome and works well with various sets of primers [18]. For example, NGS based ribotyping is an excellent tool to characterize the microbial profiling to understand the microbial ecology of a niche using amplicon based sequencing [18,19]. Several modified methods have been reported where prior removal and selective eukaryotic cell lysis have been employed for reducing human DNA contamination [20]. NEBNext^® Microbiome DNA Enrichment Kit (New England Biolabs, England), takes advantage of methylated DNA for its selective entrapment, leaving non-methylated bacterial DNA [21].

Massive sequencing of microbiome-based studies produces an enormous amount of data. Bacterial identification relies on 16S rRNA database like Greengenes, SILVA, and RDP, while functional identity is determined by MG-RAST, Pfam, TIGRfam, KEGG, SEED, CAGE and EBI databases. Several online tools are used for metagenome assembly and Gene calling and microbial diversity analysis (Table 1). Additionally, MEGAN, MG-RAST, and CAMERA can be used for comparative metagenomics (Table 1).

Alignment tools
SILVA aligner	Provides aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences	https://www.arb-silva.de/
Key DNA Tools	Utilizes short DNA stretches of 15 bp generated from reference core database	http://keydnatools.com/
Metagenome assembly
Velvet	Algorithms for de-novo short reads assembly	https://www.ebi.ac.uk/~zerbino/velvet/
Metasim	Sequencing stimulator use to generate collection of synthetic reads and compare predictions	https://ab.inf.uni-tuebingen.de/
Euler	RepeatGluer algorithm to find all the sub-repeats in a genomic sequence	http://nbcr.sdsc.edu/euler/
Ray-Meta	For parallel genome assembly and parallel sequencing	http://denovoassembler.sourceforge.net/
Gene Calling
Metag Gene Mark	Provides accesses to gene prediction in metagenomes and gene prediction program	exon.gatech.edu/meta_gmhmmp.cgi
Glimmer-mg	Gene prediction in metagenomic sequences augmented by phylogenetic classification and clustering	http://www.cbcb.umd.edu/software/ glimmer-mg/
Meta Gene Annotator	Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in unknown genomes	metagene.cb.k.u-tokyo.ac.jp/
Orphelia	ORF finding tool for predicting the protein coding genes in metagenomic sequences	orphelia.gobics.de/
Metagene	Diagnosis of inborn errors of metabolism	www.metagene.de/
Microbial diversity analysis
MLST	Characterization of the unambiguous isolates of bacteria and other organisms using nucleotide approaches	www.mlst.net/
MOTHUR	Analyzes 16S rRNA gene sequences in metagenome	https://www.mothur.org/
EstimateS	Computes a wide range of species richness estimators for sample-based abundance and incidence	http://viceroy.eeb.uconn.edu/estimates/
QIIME	An open-source bioinformatics tool for performing microbiome analysis from raw metagenomes	http://qiime.org/
PHACCS	A  dedicated  tool  for  estimating  the  structure  and  diversity  of  uncultured  viral communities	https://phaccs.soft112.com/
Comparative metagenomics
MEGAN	Algorithms for functional analysis	ab.inf.uni-tuebingen.de/software/megan/
MG-RAST	SEED-based environment that allows users to upload metagenomes for automated analyses	https://metagenomics.anl.gov/

Table 1: Online tools for microbial diversity analysis.

Significance of The Microbiome

The significance of the human microbiome got an attention when the fecal microbiota of healthy individual was utilized for treating recurrent infection of Clostridium difficile [22,23]. Since then, several studies have been carried out to understand the role of the human microbiome in human health. These unseen lodgers communicate well by replenishing the normal microbiota to overcome the deleterious effects of the pathogens [23]. However, side-effects and associated challenges with microbiome therapy can not be ignored and needs multiple clinical trials to establish it as a therapeutic [24]. Several investigations have proven the significant influence of inhabitant microorganisms on human physiology, metabolism and immune responses [4]. Recent discoveries have proven the role of gut microbiota in digestion, fat storage, food habits, angiogenesis and obesity [2,25,26]. Each healthy individual exhibits a unique microbiota which can be categorized into invariant and variant microbiota. Invariant microbiome constitutes the core microbiome, which rarely varies with the external factors, while the variant one significantly changes [27]. Moreover, one body harbors multiple core microbiomes depending on their habitats like oral, gut, skin and vaginal core microbiomes [28-31]. A healthy microbiome provides a baseline for maintaining a balance between the microbe associated metabolism and human health. Perturbations in healthy microflora cause dysbiotic conditions, where uninvited microorganisms encroach the space of normal inhabitants and significantly disrupt the normal communications [32]. Several investigations have been carried out to understand the role of altered microbial profile in diseased conditions like diabetes [33,34], bacteremia [35], endocarditis [36], cancer [37] and preterm births [38]. In an interesting report, gut dysbiosis has been reported for the altered spectra of microbial enzymes that influence the post-translational modification of the proteins involved in autoimmune diseases [38,39].

More recently the viral metagenome (virome) has been studied in different environments. This work is technically more challenging because there is no reference point equivalent to the ubiquitous 16S rRNA genes found in prokaryotes. Nevertheless, different viromes are being characterized to identify the pathogens and bacteriophages present. Interesting results are already emerging, with over 50% of the DNA or RNA sequences [40]. Ultimately, it is expected that new insights into the virus-host interactions will become possible. For example, knowledge of viral ecology could be used for monitoring emerging infections or assessing water quality [41]. Fungi constitute the another interesting microorganisms of the human microbiome, where Candida, Saccharomyces, Aspergillus, Fusarium and Penicillium, share the major chunk of the human mycobiome [42].

Additionally, viruses and fungi also constitute the significant chunk of microbiome and their existence could be utilized for detecting several infectious diseases [41].

Conclusion

With the understanding that replenishment of disturbed microbiota with a healthy one can be used for treating a disease, several apex companies like EpiBiome (www.epibiome.com), Enterome Biosciences (www.enterome.fr), Vedanta Biosciences (www.vedantabio.com) and Kallyope (www.kallyope.com) jumped into the commercialization of human-associated microbiota for their use in therapeutics and diagnostics. Microbiome therapy could be an alternate of antibiotics, when several mechanisms have been adapted by microorganisms to cope up with these antimicrobials [43]. There are global efforts to characterize the human microbiome through large-scale international initiatives, including the US-NIH based HMP, the European Commission’s Metagenomics of MetaHIT and the Canadian Microbiome Initiative (CMI). However, while our understanding of the phylogenetic and functional context of the human microbiome is rapidly increasing, it is still based on very few cohorts, resulting in underestimated variations due to parts of the world being understudied and under-represented in the data. At present, the majority of microbiome based studies focus on bacteriome analysis, where significant virome and mycobiome are less explored that can unlock the new horizons in host-microbe interaction based research to fully exploit the potential of the human microbiome.

Acknowledgement

KV and DV are thankful to the Principal, Gargi college, University of Delhi for her continuous encouragement of the work presented here.

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Article Information

Article Type: MINI REVIEW

Citation: Verma D, Vasdev K (2018) Understanding The Potential of The Human Microbiome. J Sys Biol Res 1(1): dx.doi.org/10.16966/ jsbr.103

Copyright: © 2018 Verma D, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication history: 

Received date: 18 Jan, 2018

Accepted date: 06 Mar, 2018

Published date: 12 Mar, 2018