Biol. Rev. (2018), 93, pp. 1518–1557. 1518 doi: 10.1111/brv.12407 No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases Douglas B. Kell1,2,3,∗ and Etheresia Pretorius3 1School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, Lancs M1 7DN, U.K. 2The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, Lancs M1 7DN, U.K. 3Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Matieland, 7602, South Africa ABSTRACT Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer’s, Parkinson’s), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially ‘external’ causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment. Key words: amyloid, inflammation, iron dysregulation, blood clotting, LPS, amplification. CONTENTS I. Introduction ..............................................................................................1519 II. State –2a: infection, dysbiosis and atopobiosis ...........................................................1520 (1) The gut as the main source of the blood microbiome ................................................1520 (2) Periodontitis and the oral cavity as another major source of blood microbes .........................1522 (3) Urinary tract infections (UTIs) .......................................................................1522 III. Step –1: a dormant blood and tissue microbiome ........................................................1522 (1) Microbial dormancy in laboratory cultures ...........................................................1523 (2) Detection of dormant bacteria ........................................................................1523 (3) Molecular Koch’s postulates ..........................................................................1523 IV. Step –2b external stresses, and a possible role for vitamin d .............................................1524 (1) Evidence that a low 25(OH)D3 level is an effect rather than a cause of inflammation ................1524 (2) Vitamin D and iron metabolism mediated by hepcidin ...............................................1526 V. Step 0: iron dysregulation caused by externally induced stresses .........................................1527 VI. Step 1: iron dysregulation leading to cell death ...........................................................1528 * Address for correspondence (Tel: +44 161 3064492; E-mail: [email protected]). Biological Reviews 93 (2018) 1518–1557 © 2018 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Iron Dysregulation and Dormant Microbes 1519 VII. Step 2: microbial reactivation and virulence via free ‘iron’ ...............................................1528 VIII. Step 3: iron dysregulation and disease ....................................................................1529 IX. Step 4: microbes can produce and shed inflammagens such as LPS and LTA ...........................1529 (1) LPS as the inflammagen par excellence .................................................................1530 (2) LTA shedding from Gram-positive bacteria ..........................................................1531 X. Step 5: induction by lps and lta of inflammatory cytokines ...............................................1531 XI. Step 6: induction of fibrin amyloid formation by ‘iron’, LPS and LTA ...................................1532 (1) Co-amyloid formation by fibrin(ogen) and other amyloids ...........................................1535 XII. Step 7: direct induction of cell death by LPS .............................................................1536 XIII. Step 8: inflammation induces coagulopathies and these contribute to disease ............................1536 XIV. Step 9: induction of cytokine production by amyloid formation and vice versa ............................1537 XV. Step 10: direct causation of disease by inflammation? ....................................................1538 XVI. Step 11: cell death (hence disease) caused by amyloids ...................................................1538 XVII. How general do we consider these mechanisms to be for various diseases? ...............................1538 XVIII. Conclusions ..............................................................................................1538 XIX. Acknowledgements .......................................................................................1539 XX. References ................................................................................................1539 ‘The great enemy of truth is very often not the lie – deliberate, contrived (abnormalities in the blood system, including its clotting and dishonest – but the myth – persistent, persuasive and unrealistic. properties). Many of these diseases also share other properties Too often we hold fast to the clich´es of our forebears. We subject all such as an increase in ‘insoluble’ forms of normally soluble facts to a prefabricated set of interpretations. We enjoy the comfort proteins and of microparticulate material. Although they of opinion without the discomfort of thought’. John F. Kennedy, are progressive diseases, their progress is far from uniform, Commencement Address, Yale University, June 11 1962 and they are often accompanied by fluctuating changes in physiological states (such as ‘flares’ in rheumatoid arthritis). ‘These germs - these bacilli - are transparent bodies. Like glass. Like However, these ‘hallmarks’ are effectively physiological water. To make them visible you must stain them. Well, my dear biomarkers; they are responses to one or more initial Paddy, do what you will, some of them won’t stain; they won’t take external stimuli, and they can and do serve as mediators cochineal, they won’t take any methylene blue, they won’t take gentian for (later) manifestations of overt disease. Since effects do violet, they won’t take any colouring matter. Consequently, though we not happen without causes, however, the question then know as scientific men that they exist, we cannot see them’. Sir Ralph arises as to the identity of these external stimuli. In some Bloomfield-Bonington. The Doctor’s Dilemma. George Bernard Shaw, 1906. cases (especially atherosclerosis and metabolic syndrome) there is evidence for a significant dietary component. However, based on a now considerable and wide-ranging literature, we here bring together evidence that: (i)the I. INTRODUCTION main external stimuli are microorganisms; (ii)incontrast to what happens in conventional infectious diseases they do A very large number of chronic, degenerative diseases not proliferate unchecked, but commonly enter dormant are accompanied by inflammation. Many of these diseases states that make them invisible to classical microbiology; are extremely common in the modern ‘developed’ world, and (iii) they can be reactivated from these dormant states and include vascular (e.g. atherosclerosis, type 2 diabetes, by the presence of ‘free’ iron (a necessary nutrient that in metabolic syndrome, pre-eclampsia, stroke), autoimmune unliganded form is normally at low levels in the host). This [e.g. rheumatoid arthritis (RA), multiple sclerosis], reactivation releases highly potent inflammagens such as and neurodegenerative (e.g. Alzheimer’s, Parkinson’s, lipopolysaccharide (LPS) from Gram-negative organisms Amyotrophic lateral sclerosis) diseases. On the face of it and lipoteichoic acid (LTA) from Gram-positives. Various these diseases are quite different from each other, but sequelae, including coagulopathies, amyloid formation and in fact they share a great many hallmarks [and often cell death follow from this, and thus we argue that this comorbidities (see e.g. Agustí & Faner, 2012; Altamura & general explanation – that we refer to here as the Iron Muckenthaler, 2009; Figueira