Germs are not all bad

Germs are not all bad. Even H. Pylori that can cause peptic ulcers may be healthy for some.

It is starting to become generally accepted that germs are not all bad. Many people take pro-biotics to help restore healthy gut bacteria, fermented foods are all the rage, and there are even gastroenterologists that perform transplants of healthy gut bacteria. Research into our resident bacterial population or microbiome is suggesting a two-way relationship between many disease states and changes to the microbiome, for instance changes to gut bacteria types and populations may be associated with depression, but it is just as likely that the depression may change the bacteria as the bacteria lead to depression. But it’s taken a while to get here.

Ever since Louis Pasteur found that the wrong bacteria could spoil beer the focus of a lot of medicine has been to find a microbe responsible for a disease, and to destroy it or prevent it causing illness. This has been a brilliant strategy and pasteurisation, good hygiene, vaccination, and anti-biotics have saved millions of lives and increased life expectancy and quality. But an extrapolation of the knowledge that some microbes can cause disease into a belief that they all should be eradicated has given us such things as anti-bacterial liquid soaps containing parabens, compounds that are probably carcinogenic and could cause premature birth or lower birth rate. The focus on micro-organisms has sometimes lead to them being identified as a cause of a disease when they may only be correlative accompaniment to a disease state.

A particular case is Helicobacter Pylori. Australians Barry Marshall and Robert Warren were awarded a noble prize for isolating this bacterium and investigating its role in gastritis and peptic ulcer disease. (Oi Oi Oi.) This knowledge has changed peptic ulcer disease from a chronic, intractable condition to one that is easily treatable, and has improved the lives of many. But while the benefit of eradicating H. Pylori to treat peptic ulcers is clear, the benefit of doing so in other circumstances is controversial and complicated. It is certainly not obvious that eradicating H. Pylori always improves health outcomes. The outcome of eliminating H. Pylori to treat gastritis seems to differ according to which part of the stomach is colonised, which may even change with nationality;i infection with H. Pylori may reduce the incidence of reflux oesophagitis, and again this could be affected by racial characteristics;ii It could even be that H. Pylori infection prevents some diseases such as Barrett’s oesophagous and oesophageal cancer, and that this could be a stronger effect in some race groups.iii

Some have proposed that rather than being a cause of excessive stomach activity, H. Pylori is used by the body to regulate stomach acidity, as the bacterium actually neutralises acid.iv

We diagnose and treat people by asking them to describe how they feel. So we treat the stomach pain, heartburn and reflux that someone experiences without testing for bacteria. When patients come in and say that they have been diagnosed with gastritis from H. Pylori infection we ask the patient to tell us how that feels. They describe their pain, or reflux, or other symptoms and we treat to relieve these problems. We do target a cause of the problem, but it is a cause diagnosed in the Chinese medicine picture of the patient, not H. Pylori. Sometimes the way someone’s condition is described leads to medicinals being chosen that have been found to have anti-microbial properties, but that is not why they are chosen. And we will judge the success of a treatment on the entirely unscientific and non-empirical outcome of the patient feeling better and not having the ailments that they describe, rather than by testing for a bacterium. Sometimes without being targeted the bacterium it is subsequently found to be eradicated, and we could consider that in such people it may have been a part of the problem. Other people may recover from their ailment but still carry H. Pylori, in which case we could consider that the bacterium wasn’t the problem, and that it can go on preventing disease and regulating acidity. We think that this flexible approach allows us to cope with the complexity of biological systems with many unknown and unmeasurable variables, where the presence of a particular bacterium may sometimes cause one disease, sometimes protect against another, may be harmful in one person, and beneficial in someone else.

In fairness, there’s a good article here here by a microbiologist about our complex symbiosis with microorganisms:

i Nemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S, Mashiba H, Sasaki N, Taniyama K (2000). Changes in Helicobacter pylori-induced gastritis in the antrum and corpus during long-term acid-suppressive treatment in Japan
Aliment Pharmacol Ther. 2000 Oct;14(10):1345-52

ii Hassan Ashktorab , Omid Entezari, Mehdi Nouraie, Ehsan Dowlati, Wayne Frederick, Alfreda Woods, Edward Lee, Hassan Brim, Duane T. Smoot and 3 more (2012). Helicobacter pylori Protection Against Reflux Esophagitis
Digestive Diseases and Sciences November 2012, Volume 57, Issue 11, pp 2924-2928

iii Rubenstein JH, Inadomi JM, Scheiman J, Schoenfeld P, Appelman H, Zhang M, Metko V, Kao JY (2014). Association Between Helicobacter pylori and Barrett’s Esophagus,Erosive Esophagitis, and Gastroesophageal Reflux Symptoms
Clin Gastroenterol Hepatol. 2014 Feb;12(2):239-45

iv Keilberg D, Ottemann KM (2016). How Helicobacter pylori senses, targets and interacts with the gastric epithelium.
Environ Microbiol. 2016 Mar;18(3):791-806.