Thank you for your warm compliments! Made my day, you did! I might steal that first sentence for a testimonial on my website! With your permission, of course.
I'd like to answer your questions and respond to your comments. First, if you'd like to know more about my background, check out my website: https://www.biology4everyone.com/about/
That will give you a good bit of info! Bottom line: yes, I have a Ph.D. in cell and molecular biology and am now semi-retired. Over the years, I spent a lot of time educating myself about how to communicate complex science in plain language for everyone to understand.
Point 1. I was merely quoting the authors. They are the ones that talked about reinfecting to maintain persistence. Some of the bacteria in our gut do that by producing spores that remain in the gut and "germinate" to replace the lost population. So it is a kind of reinfection. And yes, they are commensal organisms.
Point 2. As to the desirable gut microbes, did you happen to look at my previous article: How to Increase The Good Guys in Your Gut? It may not be what you're looking for as it doesn't list all the species but it touches on that topic.
Lastly, I have decided to focus on microbiomes for a while. I like the topic and it's a way of following the advice of another writer who recommended that writers like myself should be beekeepers, not zookeepers. I was being a zookeeper, as you'll see if you look at other articles I've written. I will still stray from a one-lane path now and again but for now, I think microbiomes are my bees! :)
I look forward to hearing more of your comments and ideas for directions I might pursue.