Why does gut dysbiosis always involve Enterobacteriaceae?

Several studies by Maes et al. have implicated Enterobacteriaceae in CFS. Specifically there are elevated antibody responses to the LPS of commensal Enterobacteriaceae which correlates immune markers and abdominal symptoms ^1,2. This suggests Enterobacteriaceae or their components (LPS) have translocated from the gut into the body (i.e. leaky gut) and stimulated an immune response. This post compiles some factors found to influence Enterobacteriaceae growth and translocation in other diseases, which may also be of some relevance in ME/CFS.

Enterobacteriaceae and disease

Enterobacteriaceae are a large family of gram-negative facultative bacteria, which belong to the class Gammaproteobacteria and phylum Proteobacteria. The Enterobacteriaceae family contains gut symbionts but also many familiar pathogens (e.g. Klebsiella, E. coli, Salmonella, Citrobacter, Enterobacter, etc). Proteobacteria and Enterobacteriaceae are normally present in the gut at relatively low levels, and exist in close proximity to the mucosa, since as facultative bacteria they can tolerate oxygen diffusing from the epithelium ³. However they are amongst the most frequently overgrown gut bacteria in many conditions, including gut infections, IBD, IBS, constipation, celiac disease, AIDS, SIRS, obesity, Parkinson’s disease and major depression.

Enterobacteriaceae promote disease via immune activation; largely because they are a major source of potent inflammatory PAMPs such as lipopolysaccharide (LPS) ⁴. For instance in the gut Enterobacteriaceae/LPS can increase inflammatory tone ⁵, slow intestinal motility ⁶, exacerbate NSAID-induced intestinal injury ⁷, increase intestinal permeability in celiac disease ⁸, promote intestinal hypersensitivity in IBS ⁹ and exacerbate inflammation in IBD, amongst other things. Translocation of LPS into blood is associated with systemic immune activation, neuroinflammation ¹⁰, insulin resistance ¹¹, etc.

So elevated levels of Enterobacteriaceae is bad! But how does it occur in the first place? Below are some mechanisms which could be important.

Dietary factors

Diets high in sugar, fat and protein, but low in plants and indigestible carbohydrate (e.g. western or weight-loss diets), favour the growth of Proteobacteria and Enterobacteriaceae ^12,13. This could be for several reasons. Diets high in protein promote a putrefactive microbial metabolism which generates harmful metabolites ¹⁴, while diets high in indigestible carbohydrate (resistant starch and fibre) promote a saccharolytic metabolism which generates beneficial short-chain fatty acids (SCFAs) ¹². SCFAs acidify the colon and inhibit Enterobacteriaceae ¹². Diets high in fat, saturated fat and omega-6 promote Enterobacteriaceae growth and LPS translocation, while omega-3 does the opposite ^15–18. The beneficial effects of omega-3 on the gut microbiota are due to regulation of intestinal alkaline phosphatase (IAP) ¹⁸.

Low stomach acid

Suppression of gastric acid secretion by proton pump inhibitor (PPI) administration was found to induce jejunum dysbiosis, consisting of an overgrowth of aerobic bacteria and Enterobacteriaceae, and a decrease in Bifidobacteria ⁷. Many other studies have found an association between PPI use and small intestinal bacterial overgrowth (SIBO) in humans ¹⁹ (note that Enterobacteriaceae can be hydrogen-producers ²⁰). This may involve several mechanisms: gastric acid can inhibit the growth of many bacteria, promote protein digestion and trigger other intestinal secretions/processes.

Immunodeficiencies

The gut barrier regulates levels of mucosal bacteria by releasing antimicrobial peptides and IgA ^21,22. Innate immune functions are impaired in inflammatory bowel disease (IBD), especially Crohn’s disease, which allows for increased growth of bacteria such as invasive E. coli  ^23,24. Also genetic variations which impair function of the NOD2 gene (encodes an intracellular immune receptor) is associated with increased abundance of Enterobacteriaceae in IBD ²⁵. In both HIV/AIDS and ICL there is major disruption of the intestinal immune system, resulting in barrier disruption and translocation of LPS ^26,27.

Inflammation & oxidative stress

Gut inflammation has been shown to induce blooms in Proteobacteria and Enterobacteriaceae. This is due to the increased formation of oxidation products (e.g. nitrate) which can serve as electron acceptors in the anaerobic respiration of some facultative bacteria ^28,29. In fact nitrate reductase activity is most prevalent in the genomes of Enterobacteriaceae ³⁰. Moreover some Enterobacteriaceae pathogens (e.g. Salmonella) may actually induce inflammation as part of an evolutionary survival strategy ²⁹. Notably antibiotic treatment can induce low-grade gut inflammation which enhances the growth of Enterobacteriaceae ^28–30. Inflammation can also increase intestinal permeability and may therefore allow bacterial translocation, perhaps especially in the ileum ³¹.

References

1.         Maes, M. et al. Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome. J. Affect. Disord. 136, 909–17 (2012).

2.         Maes, M., Leunis, J.-C., Geffard, M. & Berk, M. Evidence for the existence of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) with and without abdominal discomfort (irritable bowel) syndrome. Neuro Endocrinol. Lett. 35, 445–453 (2014).

3.         Albenberg, L. et al. Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota in Humans and Mice. Gastroenterology (2014). doi:10.1053/j.gastro.2014.07.020

4.         Hakansson, A. & Molin, G. Gut Microbiota and Inflammation. Nutrients 3, 637–682 (2011).

5.         Rodes, L. et al. Effect of probiotics Lactobacillus and Bifidobacterium on gut-derived lipopolysaccharides and inflammatory cytokines: an in vitro study using a human colonic microbiota model. J. Microbiol. Biotechnol. 23, 518–26 (2013).

6.         Pasqualetti, V. et al. Antioxidant activity of inulin and its role in the prevention of human colonic muscle cell impairment induced by lipopolysaccharide mucosal exposure. PLoS One 9, e98031 (2014).

7.         Wallace, J. L. et al. Proton pump inhibitors exacerbate NSAID-induced small intestinal injury by inducing dysbiosis. Gastroenterology 141, 1314–22, 1322.e1–5 (2011).

8.         Cinova, J. et al. Role of intestinal bacteria in gliadin-induced changes in intestinal mucosa: study in germ-free rats. PLoS One 6, e16169 (2011).

9.         Crouzet, L. et al. The hypersensitivity to colonic distension of IBS patients can be transferred to rats through their fecal microbiota. Neurogastroenterol. Motil. 25, (2013).

10.       Gárate, I. et al. Stress-induced neuroinflammation: role of the Toll-like receptor-4 pathway. Biol. Psychiatry 73, 32–43 (2013).

11.       Fei, N. & Zhao, L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J. 7, 880–4 (2013).

12.       Simpson, H. L. & Campbell, B. J. Review article: dietary fibre-microbiota interactions. Aliment. Pharmacol. Ther. 42, 158–179 (2015).

13.       Brown, K., DeCoffe, D., Molcan, E. & Gibson, D. L. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 4, 1095–119 (2012).

14.       Windey, K., De Preter, V. & Verbeke, K. Relevance of protein fermentation to gut health. Mol. Nutr. Food Res. 56, 184–96 (2012).

15.       Kim, K.-A., Gu, W., Lee, I.-A., Joh, E.-H. & Kim, D.-H. High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One 7, e47713 (2012).

16.       Ghosh, S. et al. Fish oil attenuates omega-6 polyunsaturated fatty acid-induced dysbiosis and infectious colitis but impairs LPS dephosphorylation activity causing sepsis. PLoS One 8, e55468 (2013).

17.       Mani, V., Hollis, J. H. & Gabler, N. K. Dietary oil composition differentially modulates intestinal endotoxin transport and postprandial endotoxemia. Nutr. Metab. (Lond). 10, 6 (2013).

18.       Kaliannan, K., Wang, B., Li, X.-Y., Kim, K.-J. & Kang, J. X. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci. Rep. 5, 11276 (2015).

19.       Fujimori, S. What are the effects of proton pump inhibitors on the small intestine? World J. Gastroenterol. 21, 6817–9 (2015).

20.       Bures, J. et al. Small intestinal bacterial overgrowth syndrome. World J. Gastroenterol. 16, 2978–90 (2010).

21.       Wang, G. Human antimicrobial peptides and proteins. Pharmaceuticals (Basel). 7, 545–94 (2014).

22.       Kubinak, J. L. et al. MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health. Cell Host Microbe 17, 153–163 (2015).

23.       Gersemann, M., Wehkamp, J. & Stange, E. F. Innate immune dysfunction in inflammatory bowel disease. J. Intern. Med. 271, 421–8 (2012).

24.       Glocker, E. & Grimbacher, B. Inflammatory bowel disease: is it a primary immunodeficiency? Cell. Mol. Life Sci. 69, 41–8 (2012).

25.       Knights, D. et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 6, 107 (2014).

26.       Lee, P. I. et al. Evidence for translocation of microbial products in patients with idiopathic CD4 lymphocytopenia. J. Infect. Dis. 199, 1664–70 (2009).

27.       Klatt, N. R., Funderburg, N. T. & Brenchley, J. M. Microbial translocation, immune activation, and HIV disease. Trends Microbiol. 21, 6–13 (2013).

28.       Winter, S. E. & Bäumler, A. J. Why related bacterial species bloom simultaneously in the gut: Principles underlying the ‘like will to like’ concept. Cell. Microbiol. 16, 179–184 (2014).

29.       Winter, S. E., Lopez, C. a & Bäumler, A. J. The dynamics of gut-associated microbial communities during inflammation. EMBO Rep. 14, 319–27 (2013).

30.       Winter, S. E. & Bäumler, A. J. Dysbiosis in the inflamed intestine: chance favors the prepared microbe. Gut Microbes 5, 71–3 (2014).

31.       Yue, C., Ma, B., Zhao, Y., Li, Q. & Li, J. Lipopolysaccharide-induced bacterial translocation is intestine site-specific and associates with intestinal mucosal inflammation. Inflammation 35, 1880–8 (2012).