The science/balance of probiotics and prebiotics, whether naturally occurring in food or supplemented, is controversial at best, and the studies that have suggested improvement in ALS that did not pan out are legion. There have also been documented harms in some probiotic regimens, and there are some clear contraindications such as those with artificial heart valves/grafts/other implants.
It is certainly not true that any drug that has GI side effects (a list of thousands) is harming the microbiome, or that we can characterize today whether any supplement has the ability to affect any aspect of microbiome that could actually affect the natural history (progression) of ALS.
As always, most people here would recommend that, well or healthy, any supplements or rx taken have some clear rationale behind them, because metabolizing any rx or supplement taxes the body, and we know that ALS affects the metabolism. We would also recommend that these substances be started one at a time and that any necessary labs such as liver function tests for those on riluzole be diligently completed.
The effort required to breathe, swallow, move, speak, digest -- whatever the PALS can still do -- can be compromised by virtually any regimen at any time. I agree with the dietician that good food [I would include liquids in that] is the foundation of anything safe that you try. That is also why many of us strongly oppose the use of traditional corn syrup-based tube formulae and recommend real food blends and/or "close to nature" tube feeds such as Whole Story. Starving the body of nutrition is tied with lack of needed respiratory support as the quickest way to lose function prematurely, and poor nutrition only accelerates respiratory decline.