As complex organisms surviving in a world of molecular and physical challenges our long ancestry has meant we have evolved a remarkably complex system of defence and repair. Regular insults have played a major role in natural selection traits and diverse defence mechanisms have evolved to support our survival and reproduction in the face of substantive risk.
The result is our beautiful, intricate and complex immune system, in which we have developed two primary structural divisions, one that is encoded through our genes (germ line encoded: innate) and needs little or no education to be up and running and one that requires coercion, education and evolution (adaptive: cellular and humoral) to provide us with an exquisite and contextual set of defensive capabilities and enduring molecular memories.
So compellingly attractive to researchers was this second part of our immune armamentarium that for decade’s they focussed on it as the site of primary modification, with vaccines being the best understood outcome. Then in the early 1990s immunology’s ‘dirty little secret’, was exposed. The innate structures, that historical artefact of human survival began to take centre stage. The previously quiescent part of the emerging science of immunology began to stretch its proteins and expose its receptors and its intimate and essential relationship with our commensal as well as our transient pathobiontic and pathogenic bacteria, viruses, fungal agents, and parasitic organisms.
Charles Janeway was the first immunologist to explain that immune responses could not occur unless antigen-presenting cells were first activated, and that they were activated via pattern recognition receptors (PRRs) that recognised evolutionarily conserved molecules on infectious nonself organisms. In effect, he said that the immune system’s default state is off and that it can be turned on by bacteria.
Then Polly Matzinger proposed her ‘Danger Theory’ in which she suggested that we could also experience what is known now as sterile inflammation, an adverse or inappropriate response to damaged endogenous cellular material called alarmins, and that this would happen due to the patterns in our damaged tissues being bound to the same triggering receptors that we have used to initiate a self defence mechanism against pathogens.
These two significant shifts in thinking have underpinned many other uncoupling’s of the relationship we enjoy or tolerate between those cells that reside within and on us; essentially those that are not us, and those cells that are us and yet appear to be difficult to tolerate, that is our own cells and their contents can create inappropriate inflammation with disproportionate consequences.
My route to bring home these concepts into clinical practice is via the gastrointestinal tract which as we know is a passageway for dietary nutrients, microorganisms and xenobiotics. The gut is also home to viruses, bacteria, protozoa, and fungi, resulting in the formation of complex populations of microbes, collectively called the commensal microbiota, whose role in health management is becoming ever clearer. While the microbiota and their dietary metabolites maintain gut homeostasis, we also have to use an extensive range of innate and adaptive immune mechanisms to cope with them and our luminal environment. For the last 20 years or so, multiple bi-directional and interconnected instructive mechanisms between microbiota, luminal content, metabolites and mucosal immune systems have been uncovered, explored and dissected to ensure a better comprehension of their effects on human health, providing us with health generating opportunities.
Indeed, epithelial and immune cell-derived mucosal signals shape microbiota composition, while microbiota and their by-products primarily provided by the food selection consumed shape the mucosal immune system. Various genetic and environmental perturbations alter gut mucosal responses which impact on microbial ecology structures. On the other hand, changes in microbiota alter intestinal mucosal responses, gene expression and tolerance and open up a range of risks and benefits.
The relentless, continuous exposure of our intestinal mucosal surfaces to these triggers is reflected in the biological necessity for a multifaceted, integrated epithelial and immune cell-mediated regulatory system. Various specialised cells have evolved to be responsible for the barrier function of the intestinal surface (e.g., M cells, Paneth cells, goblet cells, and columnar epithelial cells) and these are strictly regulated through both positive and negative stimulation by the luminal microbiota and their available food stuffs through a range of secret and coded messages. Others work to maintain ecological diversity and eubiosis, generate appropriate defensive cells and translate environmental challenges through diplomatic cross talk to induce immunological tolerance and inflammation containment.
Secret Messages and Code Breakers:
This enormous repertoire of commensal microbes necessitates host “friend–foe” recognition based on general motifs rather than that of individual microbial species.
Innate immune cells possess germ-line encoded receptors that recognise conserved molecular entities associated with either microbes or host cell damage (Microbe Associated Molecular Patterns and Damage Associated Molecular Patterns, respectively). These pattern-recognition receptors (PRRs) are found both on the cell membrane and in specific intracellular compartments.
PRR superfamilies are broadly classified based upon structural homology and the requirement of different adaptor proteins that ensure their function and downstream signal transduction. The PRRs include members of the Toll-like receptors (TLRs), nucleotide-binding, and oligomerization domain containing receptors [NOD-like receptors (NLRs)], retinoic acid-inducible gene (RIG) I-like RNA helicases, C-type lectins, and AIM2 like receptors (ALRs).
Within the NOD-like receptor (NLR) family, there are several NLRP (NLR family, pyrin domain-containing) proteins that are involved in the formation of complex, inflammation driving inflammasomes. These multi-protein complexes are a key part of the network of cellular events required for secretion of the pro-inflammatory cytokines IL-1β and IL-18. Even if the discovery of the inflammasome is relatively recent, studies on the role of the NLRP3 inflammasome downstream effectors IL-1β and IL-18 already date back more than 20 years.
The NLRP3 inflammasome is the best-characterised and has recently been implicated in gut homeostasis and determining the severity of inflammation in inflammatory bowel disease (IBD) and inflammation-associated colorectal cancer as well as functional disorders of the gastrointestinal tract. This also led to the discovery that other NOD like receptors including NLRP6 and NLRP12 also contribute to the maintenance of intestinal homeostasis and modulation of the gut microbiota, which in turn influences the health of the intestine and distant organs.
In theory activation of the inflammasome in the epithelial layer of the intestine should be beneficial, as it would help to maintain homeostasis through sensing of commensal microbiota, bacterial clearance, and defensin synthesis. However, if the epithelial barrier is disrupted and becomes ‘leaky’, the microbiota gains access to the lamina propria and contacts cells of the immune system such as dendritic cells and macrophages. In such a case, inflammasome activation may well have a deleterious effect on mucosal inflammation and associated systemic consequences may materialise including inflammatory bowel disease (IBD), cancer, diabetes,, autoimmune disorders, atherosclerosis,, allergies, brain function, functional gut disorders and even obesity and non-alcoholic fatty liver disease.,
Undercover Organisms & Organelles
One of the most significant undercover operatives in the generation of mucosal immune tolerance, and its adverse loss of diplomacy – reflected as unresolving inflammation are the mitochondrial organelles found in abundance in most human tissues, and in great concentrations in the immune and constitutive tissues of the gut.,,,
Stimulation by DAMPS derived from stressed mitochondria and commensal bacteria, viral and fungal-derived microbe-associated molecular patterns (MAMPS) as well as pathogen induced reactive oxygen species (ROS) and associated PRR triggers from lipopolysaccharides and other pathogenic exudates provoke the assembly of inflammasomes, which are involved in maintaining the integrity of the intestinal epithelium, defensive clearance, bacterial eubiosis and immune maturation and tolerance.,
Mitochondria it appears retain enough of their proteobacterial DNA to be described as ‘dysbiotic’, once they become dysfunctional, through multiple mechanisms. It is the newly uncovered cross relationship between dysbiotic microbiota in the gut and dysbiotic mitochondria that represent one of the most exciting mechanisms for explaining multiple inflammation driven illnesses. Mitochondria, that are aged, swollen, leaky, releasing ROS molecules, soluble ATP, oxidised mitochondrial DNA and cardiolipin amongst others are now recognised as key triggers of inflammasome formation and innate immune activation.
To induce appropriate diplomacy and restore tolerance in the gut and other systemically related tissues needs these mechanisms to be taken into account. Fortunately once we understand that a holistic (an old but valid moniker) approach to restoration of multiple intersecting pathways is required, the role of monotherapeutic interventions are understood to be less relevant, and induction of change on multiple points using modest but aggregating processes has powerful and often surprising outcomes.
Two of the key points of intervention in the ART (Avoidance, Resistance and Tolerance)of diplomatic immunological restitution include the application of ‘food as medicine’, in which specific foods are selected to induce specific immunological cell generation via conversion through optimal eubiosis and gene transcription. They in turn transfer this value derived from the active metabolites (butyrate and propionate)to distant tissues, such as the lung and the reduction of asthma, inflammation management and metabolic conditions.,,, The other is the use of specific mitochondrial enhancers, to diminish the activation and release of mitochondrial inducing inflammasome triggers which can be applied to have induce local and system anti-inflammatory effects.,,,,
The barrier permeabilisation that exists in many dysbiotic gastrointestinal problems and permits the adverse generation of a family of effector immune T cells is also energetically managed and the role of mitochondria in the restoration and management of barrier quality is an exciting new therapeutic opportunity.
The synergistic benefits of these important strategies can be further enhanced through additional lifestyle interventions as well as selected therapeutics and pharmacologic’s, but ultimately the recognition that the great majority of non-communicable diseases need multiple points of intervention to reverse or manage complex and often overlapping problems, opens up the functional medicine model as a mechanism of data collection and analysis, with subsequent coordinated treatments as a therapeutically powerful ally in clinical care and every day decision making for the majority of patients.
 Janeway CA Jr. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harb Symp Quant Biol. 1989;54 Pt 1:1-13.
 Matzinger P. The danger model: a renewed sense of self. Science. 2002 Apr 12;296(5566):301-5
 Hansen JD, Vojtech LN, Laing KJ. Sensing disease and danger: a survey of vertebrate PRRs and their origins. Dev Comp Immunol (2011) 35:886–97.
 Kawai T, Akira S. Toll-like receptors and their crosstalk with other innate receptors in infection and immunity. Immunity (2011) 34:637–50.
 Yeretssian G. Effector functions of NLRs in the intestine: innate sensing, cell death, and disease. Immunol Res (2012) 54:25–36.
 Goubau D, Deddouche S, Reis E, Sousa C. Cytosolic sensing of viruses. Immunity (2013) 38:855–69.
 Hardison SE, Brown GD. C-type lectin receptors orchestrate antifungal immunity. Nat Immunol (2012) 13:817–22.
 Ratsimandresy RA, Dorfleutner A, Stehlik C. An update on PYRIN domain-containing pattern recognition receptors: from immunity to pathology. Front Immunol (2013) 4:440.
 Agostini L, Martinon F, Burns K, et al. NALP3 forms an IL-1beta-processing inflammasome with increased activity in Muckle–Wells autoinflammatory disorder. Immunity 2004; 20: 319–325.
 Zambetti LP, Mortellaro A. NLRPs, microbiota, and gut homeostasis: unravelling the connection. J Pathol. 2014 Aug;233(4):321-30.
 Lissner D, Siegmund B. The multifaceted role of the inflammasome in inflammatory bowel diseases. Scientific World Journal 2011; 11: 1536–1547.
 Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut (2006) 55:205–1110
 Saxena M, Yeretssian G. NOD-Like Receptors: Master Regulators of Inflammation and Cancer. Front Immunol. 2014 Jul 14;5: 327.
 Choi AJ, Ryter SW. Inflammasomes: molecular regulation and implications for metabolic and cognitive diseases. Mol Cells. 2014 Jun;37(6):441-8
 Robbins GR, Wen H, Ting JP. Inflammasomes and metabolic disorders: old genes in modern diseases. Mol Cell. 2014 Apr 24;54(2):297-308
 Martinon F, Aksentijevich I. New players driving inflammation in monogenic autoinflammatory diseases. Nat Rev Rheumatol. 2014 Sep 23.
 Matsuura E, Atzeni F, Sarzi-Puttini P, Turiel M, Lopez LR, Nurmohamed MT. Is atherosclerosis an autoimmune disease? BMC Med. 2014 Mar 18;12:47
 Spears LD, Razani B, Semenkovich CF. Interleukins and atherosclerosis: a dysfunctional family grows. Cell Metab. 2013 Nov 5;18(5):614-6.
 Krause K, Metz M, Makris M, Zuberbier T, Maurer M. The role of interleukin-1 in allergy-related disorders. Curr Opin Allergy Clin Immunol. 2012 Oct;12(5):477-84
 Singhal G, Jaehne EJ, Corrigan F, Toben C, Baune BT. Inflammasomes in neuroinflammation and changes in brain function: a focused review. Front Neurosci. 2014 Oct 7;8:315.
 Shanahan F. The colonic microbiota in health and disease. Curr Opin Gastroenterol. 2013 Jan;29(1):49-54
 Duseja A, Chawla YK. Obesity and NAFLD: the role of bacteria and microbiota. Clin Liver Dis. 2014 Feb;18(1):59-71
 Bieghs V, Trautwein C. The innate immune response during liver inflammation and metabolic disease. Trends Immunol. 2013 Sep;34(9):446-52.
 Harijith A, Ebenezer DL, Natarajan V. Reactive oxygen species at the crossroads of inflammasome and inflammation. Front Physiol. 2014 Sep 29;5:352.
 Cauwels A, Rogge E, Vandendriessche B, Shiva S, Brouckaert P. Extracellular ATP drives systemic inflammation, tissue damage and mortality. Cell Death Dis. 2014 Mar 6;5:
 O’Neill LA. Cardiolipin and the Nlrp3 inflammasome. Cell Metab. 2013 Nov 5;18(5):610-2.
 Zhou R, Yazdi AS, Menu P, Tschopp J. A role for mitochondria in NLRP3 inflammasome activation. Nature. 2011 Jan 13;469(7329):221-5.
 Tschopp J. Mitochondria: Sovereign of inflammation? Eur J Immunol. 2011 May;41(5):1196-202
 Bird L. Innate immunity: Linking mitochondria and microbes to inflammasomes. Nat Rev Immunol. 2012 Mar 9;12(4):229.
 Shimada, K. et al. Oxidized mitochondrial DNA activates the NLRP3 inflammasome during apoptosis. Immunity 16 Feb 2012
 Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ.Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014 Feb;20(2):159-66.
 Huffnagle GB. Increase in dietary fiber dampens allergic responses in the lung. Nat Med. 2014 Feb;20(2):120-1
 Lin HV, Frassetto A, Kowalik EJ Jr, Nawrocki AR, Lu MM, Kosinski JR, Hubert JA, Szeto D, Yao X, Forrest G, Marsh DJ. Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS One. 2012;7(4)
 den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013 Sep;54(9):2325-40.
 Dashdorj A, Jyothi KR, Lim S, Jo A, Nguyen MN, Ha J, Yoon KS, Kim HJ, Park JH, Murphy MP, Kim SS.Mitochondria-targeted antioxidant MitoQ ameliorates experimental mouse colitis by suppressing NLRP3 inflammasome-mediated inflammatory cytokines. BMC Med. 2013 Aug 6;11:178.
 Mao P, Manczak M, Shirendeb UP, Reddy PH. MitoQ, a mitochondria-targeted antioxidant, delays disease progression and alleviates pathogenesis in an experimental autoimmune encephalomyelitis mouse model of multiple sclerosis. Biochim Biophys Acta. 2013 Dec;1832(12):2322-31
 Fink BD, Herlein JA, Guo DF, Kulkarni C, Weidemann BJ, Yu L, Grobe JL, Rahmouni K, Kerns RJ, Sivitz WI. A mitochondrial-targeted coenzyme q analog prevents weight gain and ameliorates hepatic dysfunction in high-fat-fed mice. J Pharmacol Exp Ther. 2014 Dec;351(3):699-708.
 Semple BD. Early preservation of mitochondrial bioenergetics supports both structural and functional recovery after neurotrauma. Exp Neurol. 2014 Nov;261:291-7
 Nicolson GL, Ash ME. Lipid Replacement Therapy: a natural medicine approach to replacing damaged lipids in cellular membranes and organelles and restoring function. Biochim Biophys Acta. 2014 Jun;1838(6):1657-79.
 Wang A, Keita ÅV, Phan V, McKay CM, Schoultz I, Lee J, Murphy MP, Fernando M, Ronaghan N, Balce D, Yates R, Dicay M, Beck PL, MacNaughton WK, Söderholm JD, McKay DM. Targeting mitochondria-derived reactive oxygen species to reduce epithelial barrier dysfunction and colitis. Am J Pathol. 2014 Sep;184(9):2516-27.