The human microbiome in disease and pathology

Abstract

This narrative review seeks to examine the relationships between bacterial microbiomes and infectious disease. This is achieved by detailing how different human host microbiomes develop and function, from the earliest infant acquisitions of maternal and environmental species through to the full development of microbiomes by adulthood. Communication between bacterial species or communities of species within and outside of the microbiome is a factor in both maintenance of homeostasis and management of threats from the external environment. Dysbiosis of this homeostasis is key to understanding the development of disease states. Several microbiomes and the microbiota within are used as prime examples of how changes in species composition, particularly at the phylum level, leads to such diverse conditions as inflammatory bowel disease (IBD), type 2 diabetes, psoriasis, Parkinson’s disease, reflux oesophagitis and others. The review examines spatial relationships between microbiomes to understand how dysbiosis in the gut microbiome in particular can influence diseases in distant host sites via routes such as the gut–lung, gut–skin and gut–brain axes. Microbiome interaction with host processes such as adaptive immunity is increasingly identified as critical to developing the capacity of the immune system to react to pathogens. Dysbiosis of essential bacteria involved in modification of host substrates such as bile acid components can result in development of Crohn’s disease, small intestine bacterial overgrowth, hepatic cancer and obesity. Interactions between microbiomes in distantly located sites are being increasingly being identified, resulting in a ‘whole of body’ effect by the combined host microbiome.

Association Between Inflammatory Bowel Disease and Both Psoriasis and Psoriatic Arthritis

“…Some GWASs confirmed previously known shared risk loci and identified a number of non–human leukocyte antigen susceptibility loci common to psoriasis and CD . Gut dysbiosis, a state of microbial imbalance, is frequently observed in both IBD and psoriasis . It is well known that diseases of the gastrointestinal tract are often associated with skin manifestations, and the gut microbiome appears to be involved in the pathophysiology of many inflammatory diseases .…”

Effects of Chronic Bifidobacteria Administration in Adult Male Rats on Plasma Metabolites: A Preliminary Metabolomic Study

“…Great and important progress has been made in the last decade in terms of characterizing the bidirectional connection between the function of the central and enteric nervous systems, including the gastrointestinal tract. Through the use of different and elegant approaches, a series of preclinical studies have elucidated and described the crucial role of the gut microbiota in brain function through the well-known gut-brain axis [30,31]. In addition, there is strong evidence of the tight correlation between the peripheral dysregulation of gut microbiota and different brain disorders in humans [32], stimulating a growing interest in the involvement of metabolic compounds that may support gut composition and its activity through diet.…”

Nanopore sequencing technology and its applications

“…In a healthy physiological state, certain types and quantities of microorganisms live on the human body surface and body cavity. Imbalances in microbiota are linked to the development of various diseases 284,285 . While short‐read 16S rRNA sequencing has commonly been used to analyze microbial populations in humans, full‐length 16S rRNA sequencing using nanopore sequencing technology is an effective and low‐cost alternative 286,287 .…”