Over the past several decades, research has redefined the interactions between gut microbes and vertebrates, now recognizing that the intestinal microbiome and its mammalian host have shared co-evolutionary metabolic interactions that span millennia. Studies from the Human Microbiome Project (HMP) have estimated that humans possess ten times more bacterial cells than there are human cells. In the gastrointestinal (GI) tract, the bacterial cohort contributes approximately 3.3 million non-redundant microbial genes, far exceeding that of the human input [1]. This genetic diversity is likely to provide the necessary cues through host-microbial interactions for the development of regulated signals that promote immunological tolerance, metabolic regulation, and stability, and other factors that may then help control local and extra-intestinal end-organ (e.g., renal, hepatic) physiology. The intestinal mucosa is the largest and most dynamic immunological environment of the body. Often the first point of pathogen or antigen exposure, many microbes use it as a point of entry into the rest of the body. The gut immune system therefore needs to be prepared to respond to insults either from pathogens or other molecular triggers while at the same time not responding to other presumably innocuous environmental antigens, food particles, and commensal bacteria and their respective metabolites. Misdirected immune responses to antigens thought harmless are thought by some to be the underlying cause of food allergies and debilitating conditions such as inflammatory bowel diseases with their unregulated and overcompensated, pro-inflammatory sequelae [2]. As a consequence, dysbiosis of the GI tract describes alteration of bacterial populations thought to increase the risk of developing gut barrier dysfunction with consequent increased permeability, also referred to as a ‘‘leaky gut,’’ with consequent translocation of bacteria, bacterial endotoxins, or environmental antigens across the gut wall. While the immune system is thought to be involved, mechanistic data that link immune function disruption to adverse end-organ physiological functions, which are present for the kidney, are mostly missing for the gut. The supposition that the GI tract bacterial cohort could indirectly and adversely influence the physiological function of an end-organ such as the liver or kidney, by contributing pro-inflammatory activity in the gut mucosa, is a novel concept with biological plausibility [2, 3]. Uremic toxins (e.g., glycation end products, p-cresyl sulfate, indoxyl sulfate) can produce pro-inflammatory responses, including leukocyte stimulation and endothelial dysfunction, which can promote GI tract dysbiosis [3–5]. Therefore, it is highly probable that the 100 trillion bacteria in the GI tract could negatively and positively influence the nutritive, metabolic, physiological, and importantly immunological functions of the host [2]. The diversity of commensal bacteria in the GI tract can, in turn, account for the varied macrophage responses that have been encountered in the intestines [6]. Macrophages, in their eradication of pathogenic microbes so as to maintain homeostasis, are an essential component of innate immunity. The activated phenotype exists in macrophages that present antigens to T lymphocytes in order to initiate an appropriate immune response after recognition of microbial proteins [7]. In addition to serving as antigen-presenting cells, activated macrophages & Luis Vitetta luis.vitetta@sydney.edu.au; luis_vitetta@medlab.co