The gut connection
I've been reading many things about MS these last few years and looking back on all this, at least to me it seems that there's some connection to the digestive system. I'll refer to other sources as much as I can, but these are mostly my own thoughts on all this. Since I have no medical background, that's all they are: thoughts. Don't consider any of this as advice.
The most obvious link to the gut is undoubtedly the many diets that seem to exist for MS. There's the Swank diet that warns about using too many fatty acids, and warns about using the wrong kinds of fatty acids. There's the Wahls diet that tries to make your mitochondria (the energy plants of your cells) as healthy as possible. There are several anecdotes out there about about people improving as a result of a change in diet, the best known is probably the story about Roger MacDougall.
Of course all this does not offer any proof about a connection with MS, but at least many people seem to believe you can influence the disease by your eating habits. You are what you eat, I guess.
On the helminthic therapy page you could read about the use of parasitic worms to try to improve one's immune system, something that falls within the 'old friends' hypothesis. As you can read in  however, apart from a possibly direct interaction with the immune system, helminths also seem to have an effect on the composition of the bacteria around them. So perhaps a part of the effect that they seem to cause is actually caused by the bacteria, by the microbiome that now has a different composition.
The microbiome of MS patients
I couldn't really find all that much about the microbiome of MS patients, the only thing I could find is an article  from 1991 in which the bacteria in the stool from MS patients are compared to the bacteria from healthy people. Although the test was done for a relatively small group of people, it seemed to indicate that members from a certain bacteria species, from the Bifidobacteria type, were reduced or even absent when compared to the control group. To be even more specific, the deficiency was in members from subtypes of the Bifidobacterium Adolescentis species.
Equally interesting as disgusting, FMT stands for Fecal Microbiota Transplant. In case you're wondering 'is this what I think it is?', yes: it's transferring the stool from one person to another. At the same time, one hopes that during this procedure the microbial composition of the gut from one person, is transferred to the other.
Before you decide to leave this page and go to a nicer one about fluffy kittens, you may find it interesting to know that this procedure has a very high success rate (say 85% or perhaps more, see ) for treating C.diff infections. C.diff stands for Clostridium difficile, and is a bacterium that causes much diarrhea and suffering, and can even lead to death. Furthermore, it's notoriously difficult to treat with antibiotics, which sometimes even make things worse by removing some of the few helpful bacteria you have left. Given the simplicity of the procedure and the high success rate, one can only wonder why this is usually only used as a last resort. Is it the yuck-factor?
Anyway, a Dr Bodory of the Center of Digestive Diseases documented a number of cases in which he treated people with MS with FMTs. Those people were there for digestive problems, not to get their MS treated in any way. Nevertheless, in  he describes how these people seemed to improve (MS-wise) after the procedure. This is certainly one of the most direct links between the microbiome and MS.
Of course, even if there's a connection between gut bacteria and MS, it's very difficult to say what that connection exactly is. Is there not enough of one species, too much of another? Much still needs to be learned, and a lot of research is directed towards unraveling this mysterious ecosystem within. It was only recently (2011) discovered that the microbiome of people can be subdivided into three categories, three so-called enterotypes .
One type that we have already encountered before, is the species Bifidobacterium. Apparently, these bifidobacteria are related to the permeability of the gut. If one has enough bifidobacteria, this improves the gut barrier and helps prevent toxic substances leaking from your gut into your bloodstream .
Say you'd want to improve the amount of bifidobacteria in your gut, how would you do that? Well, there are undoubtedly many probiotic supplements you can buy that contain one or more subspecies. I haven't encountered any supplement yet that contains Bifidobacterium Adolescentis though. Remember that this was the species that proved deficient in people with MS. You can stimulate the occurrence of these bacteria by making sure you eat foods that contain a substance called 'inulin' (NOT insulin, mind the spelling!). Onions, garlic and leek contain this in reasonable amounts and chicory root and jerusalem artichoke contain it in particularly high amounts. Apparently researchers found out that our early ancestors consumed about 135 grammes of inulin daily. They would certainly have had plenty of bifidobacteria.
That inulin indeed stimulates bifidobacteria can be found in . In that article, researchers found that it definitely stimulated Bifidobacterium adolescentis and also Faecalibacterium prausnitzii. Unrelated to MS, it is interesting that in  an inverse relationship was found between Inflammatory Bowel Disease (IDB) and Faecalibacterium prausnitzii, meaning that people with IDB tended to have less of those bacteria.
These are just things that I found interesting and seem to suggest a link between what goes on in the gut and Multiple Sclerosis. I can't really draw any conclusion based on all this, but even though I didn't like them when growing up, it seems that onions aren't my enemy after all.
-  http://www.bbc.co.uk/news/health-20341418
-  http://www.ncbi.nlm.nih.gov/pubmed/1755926
-  http://www.sciencedaily.com/releases/2011/10/111031114945.htm
-  http://www.cdd.com.au/pdf/publications/...
-  http://www.nytimes.com/2011/04/21/science/21gut.html?_r=0
-  http://humanfoodproject.com/can-a-high-fat-paleo-diet-cause-obesity-and-diabetes/
-  http://www.ncbi.nlm.nih.gov/pubmed/18590586
-  http://www.ncbi.nlm.nih.gov/pubmed/22357539