Understanding Microbiome Data: A Primer for Clinicians

Abstract

The human gut contains 10¹⁴ bacteria and many other micro-organisms such as Archaea, viruses and fungi. This gut microbiota has co-evolved with host determinants through symbiotic and co-dependent relationships. Bacteria, which represent 10 times the number of human cells, form the most depicted part of this black box owing to new tools. Re-evaluating the gut microbiota showed how this entity participates in gut physiology and beyond this in human health. Studying and handling this real ‘hidden organ' remains a challenge for clinicians. In this review, we aimed to bring information about gut microbiota, its structure, its roles and the way to capture and measure it. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to 4 major phyla. Besides its biodiversity, the major characteristics of gut microbiota are stability over time and resilience after perturbation. In pathological situations, dysbiosis (i.e. imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum and an increase in Gammaproteobacteria. Beyond depicting gut microbial composition, metagenomics allows the description of the combined genomes of the microorganisms present in the gut, giving access to their potential functions. In fact, each individual overall microbial metagenome outnumbers the size of human genome by a factor of 150. Besides a functional core in which there is redundancy for mandatory functions assuring the robustness of the ecosystem, human gut contains an important diversity and high number of non-redundant bacterial genes. Clinical data, treatment and all the factors able to influence microbiome should enter integrated big data sets to put in light pathways of interplay within the supra organism composed of gut microbiome and host. A better understanding of dynamics within human gut microbiota and microbes-host interaction will allow new insight into gut pathophysiology especially regarding resilience mechanisms and dysbiosis onset and maintenance. This will lead to description of biomarkers of diseases, development of new probiotics/prebiotics and new therapies.

Bacteroides fragilis Lipopolysaccharide and Inflammatory Signaling in Alzheimer’s Disease

“…Homo sapiens and their complex microbiome, consisting chiefly of bacteria with microbial eukaryotes, archaea, fungi, protozoa, viruses, and other microorganisms making up the balance, together compromise the entire metaorganism whose symbiotic associations and host interactions are critical to human health and disease ( Hugon et al, 2015 ; Seksik and Landman, 2015 ; Youssef et al, 2015 ). There are approximately 52 recognized divisions of bacteria, however, humans, have co-evolved with – 2 dominant phyla: Bacteroidetes [about 20% of all gastrointestinal (GI) tract bacteria] and Firmicutes (about 80%); with Actinobacteria (about 3%), Proteobacteria (~1%), and Verrucomicrobia (~0.1%) making up significantly smaller fractions.…”

Gut–Liver Axis Derangement in Non-Alcoholic Fatty Liver Disease

“…The GM is enriched in several genes important for glycan and aminoacid metabolism, xenobiotic metabolism, methanogenesis, and biosynthesis of vitamins [ 16 ]. This may explain why GM contributes to host nutrition, bone mineral density, modulation of the immune system, xenobiotics metabolism, intestinal cell development and proliferation, and protection against pathogens [ 17 ].…”

Biodiversity, Physical Health and Climate Change: A Synthesis of Recent Evidence

“…In considering the role of biodiversity on human health it is useful to start by recognising the human body as an ecosystem, with both internal and external microbiota, something that has been termed the human core microbiome (Karkman et al 2017). The human gut alone contains some 1,014 bacterial strains and species as well as other micro-organisms and viruses, the mix of which is unique to each individual and which changes during the life course (Odamaki et al 2016;Seksik and Landman 2015). The concept of the exposome has been developed to recognize the role of factors shown in Fig.…”