1
Structural and Dynamics of Healthy Adult's Microbiota

Mahdi Hussein Abdelrazig

Professor of Hematology, Omdurman Ahlia University, Sudan

1.1 Introduction

Microbiota are the range of microorganisms that may be commensal, symbiotic, or patho?genic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses [1-3], and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

The term microbiome describes either the collective genomes of the microbes that reside in an ecological niche or within the microbes themselves [4-6]. The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont [7, 8]. The presence of microbiota in human and other metazoan guts has been critical for understanding the co-evolution between metazoans and bacteria [9, 10]. Microbiota play key roles in the intestinal immune and metabolic responses via their fermentation product (short-chain fatty acid), acetate [11]. All plants and animals, from simple life forms to humans, live in close association with microbial organisms [12]. Several advances have driven the perception of microbiomes, including:

• the ability to perform genomic and gene expression analyses of both single cells and entire microbial communities in the disciplines of metagenomics and metatranscriptom?ics [13];
• databases accessible to researchers across multiple disciplines [13]; and
• methods of mathematical analysis suitable for complex datasets [13].

Biologists have come to appreciate that microbes make up an important part of an organism's phenotype, far beyond the occasional symbiotic case study [13]. Commensalism, a concept developed by Pierre-Joseph van Beneden (1809-1894), a Belgian professor at the University of Louvain during the nineteenth century [14], is central to the microbiome, where microbiota colonize a host in a non-harmful coexistence. The relationship with their host is called mutualistic when organisms perform tasks that are known to be useful for the host [15, 16], and parasitic when disadvantageous to the host. Other authors define a situation as mutualistic where both benefit and commensal where the unaffected host benefits the symbiont [17]. A nutrient exchange may be bidirectional or unidirectional, may be context dependent, and may occur in diverse ways [17]. Microbiota that are expected to be present, and that under normal circumstances do not cause disease, are deemed normal flora or normal microbiota [15]; normal flora may not only be harmless, but may be protective of the host [18]. The human microbiota includes bacteria, fungi, archaea, and viruses. Micro-animals, which live on the human body, are excluded. The human microbiome refers to their collective genomes [15].

Humans are colonized by many microorganisms; the traditional estimate was that humans live with ten times more non-human cells than human cells; more recent estimates have lowered this to 3:1 and even to about 1:1 [19, 20]. In fact, these are so small that there are around 100 trillion microbiota on the human body [21]. The Human Microbiome Project sequenced the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina [15]. The Project reached a milestone in 2012 when it published initial results [22]. Organisms evolve within ecosystems so that the change of one organism affects the change of others. The holog?enome theory of evolution proposes that an object of natural selection is not the individual organism, but the organism together with its associated organisms, including its microbial communities; coral reefs. The hologenome theory originated in studies on coral reefs [23]. Coral reefs are the largest structures created by living organisms, and contain abundant and highly complex microbial communities. Their innate immune systems do not produce antibodies, and they should seemingly not be able to respond to new challenges except over evolutionary time scales. The puzzle of how corals managed to acquire resistance to a specific pathogen led to a 2007 proposal that a dynamic relationship exists between corals and their symbiotic microbial communities. It is thought that by altering its composition, the holobiont can adapt to changing environmental conditions far more rapidly than by genetic mutation and selection alone. Extrapolating this hypothesis to other organisms, including higher plants and animals, led to the proposal of the hologenome theory of evolution [23]. As of 2007, the hologenome theory was still being debated [24]. A major criticism has been the claim that V. shiloi was misidentified as the causative agent of coral bleaching, and that its presence in bleached O. patagonica was simply that of opportunistic colonization [25]. If this were true, the basic observation leading to the theory would be invalid. The theory has gained significant popularity as a way of explaining rapid changes in adaptation that cannot otherwise be explained by traditional mechanisms of natural selection. Within the hologenome theory, the holobiont has not only become the principal unit of natural selection, but the result of other step of integration that it is also observed at the cell (symbiogenesis, endosymbiosis) and genomic levels [7].

Microbial therapeutics, including fecal microbiota transplants (FMTs), bacterial consortia, and probiotics are increasingly being tested in patients with Clostridium difficile (C. diff) infections and other gastrointestinal (GI) disorders [25] including inflammatory bowel disease (IBD), and more recently, non-GI indications such as autism [25, 26] and cancer. In parallel to microbial therapeutics, microbial signatures are being evaluated as a novel class of biomarkers, applied for stratification of efficacy and safety in clinical trials across multiple indications [28]. This rapid increase in microbial therapeutics and biomarkers notably demands a rigorous reevaluation of the factors influencing an individual's personal gut microbiome over time. Such understanding is essential for optimizing clinical trials with any microbial component. For example, without a complete understanding of the factors influencing the gut microbiome in health and disease, we cannot determine whether the optimal FMT should be sourced from a patient who previously responded to a therapy or a healthy donor who is matched for age and sex. In this text, we present a comprehensive assessment of the gut microbiome of 946 well-defined healthy French donors from the Milieu Interieur (MI) Consortium, with 1359 shotgun metagenomic samples. Designed to study the genetic and environmental factors underlying immunological variance between individuals, the MI Consortium comprises 500 women and 500 men evenly stratified across five decades of life, from 20 to 69 years of age, for whom extensive metadata, including demographic variables, serological measures, dietary information, and systemic immune profiles are available and easily accessible [28]. Integrating these data with those from cancer patients, we demonstrate clear evidence for altered microbial communities in cancer patients across multiple non-GI indications. To build on the findings of several landmark microbiome studies [29], many of which relied on an older reference library for taxonomic classification of microbial sequence reads [30], we leveraged an expanded set of reference genomes with a novel taxonomy that corrects many misclassifications in public databases to discover new biological insights, particularly around age and sex [31]. An independent dataset was used for replication of many of the findings [32]. Study of short-term longitudinal samplings from half the donors found that individuals are more similar to themselves over time compared with others [33]. However, the degree of stability between individuals was quite variable and was influenced by lifestyle factors as well as baseline composition. Overall, the aims of the study are threefold. First, we introduce a new microbiome analysis approach that uses an expanded set of reference genomes with a novel taxonomy to discover new, statistically robust insights into host/bacteria biology that will enable personalized medicine approaches for microbial therapeutics and biomarkers. Second, we provide the rich metadata and 1000-plus deep shotgun metagenomic samples described here as a resource on which future microbiome studies can test and build new computational tools, as well as be compared against disease cohorts. Finally, while demonstrating the utility of this resource as a control population, we define global shifts in the gut microbiomes of patients with non-GI tumors compared with healthy donors normalised based on relative evolutionary divergence [31]. The impact of this procedure was particularly prominent for species of the genus Clostridium, which were split into 121 unique genera spanning 29 families...