The average diet (excluding the consumed residues of glyphosate) is probably far worse via the "gut flora" influence than a healthier diet with average glyphosate residues, though this is just a guess.

Coca-cola sells a product which causes immense harm directly (diabetes) and indirectly (raising cost healthcare insurance), though this is probably disputed. Gut flora might actually have a big role to play in our inability to act against what harms us, even though we may intellectually understand what harms us.

What is good for the gut is good for the body. What is bad for the gut is bad for the body. But what is good for the gut?

What is good for the mind is good for the body. What is bad for the mind is bad for the body.
But what is good for the mind?

Somewhere and everywhere we end up making trade-offs. What is good for the mind is bad for the body. Oh well... But if it is bad for the body, is it not also bad for the mind?

If there were an evil empire it would be Monsanto. They are audaciously corrupt paying off scientists and ignoring EU parliamentary hearings.

Their product has been linked to cancer by one expert WHO panel.

Forget Monsanto.

So the philosophical/ethical question is, whether or not harming an organism which lives within the human being, in a beneficial symbiotic relationship, constitute harming the human body. — Metaphysician Undercover

You're use of the term "beneficial" makes moot the preliminary paragraph. If the poison I give you sickens you, it is immoral to give it, regardless of whether it damages your gut flora, your kidneys, or whether it just irritates your throat. If it benefits you, it's not.

Ecologies are all connected from the bottom to the top. It's all enormously complicated.

Gut flora is an ecological system. Humans and agriculture are a part of many different ecological systems. Harming one part of ecological systems can harm other parts whose connection is not obvious.

Roundup (glyphosate) isn't known to harm monarch butterflies. I haven't read anything to that effect. But glyphosate kills many grasses and broad-leaf plants, one of which is the collection of milkweeds. Mono cropping and the widespread use of glyphosate has greatly reduced the number of milkweed plants that are found in and around fields.

Populations of Monarch butterflies have been greatly reduced because the one plant that their larvae feed on -- the milkweed -- have been largely killed off. Similarly, many different kinds of bees -- including the European honey bee -- need a variety of wild flowers to feed on. They can't survive just on orange blossoms. Again, glyphosate has eliminated many of the species that produce wild blossoms.

Glyphosate has more general effects than the Neonicotinoids, developed by Bayer, which kills off many insects (including bees, butterflies, and most other things that fly, creep, or crawl). Neonicotinoids are nerve poisons.

Most of our fruits and vegetables depend on pollinators. No pollinators, no fruits and vegetables. Unless you want to spend your days with a small brush moving pollen from blossom to blossom, doing the work that bees gladly do, don't spray nerve gas on your peach trees.

Are you on Monsanto's payola?

Report by Wiley 5/17/17

An analysis of data in Illinois has found a link between higher county-level use of an herbicide called glyphosate and reduced abundance of adult monarch butterflies, especially in areas with concentrated agriculture.

Good thing Bayer is purchasing them, no bugs will remain. Or perhaps not...

Are you on Monsanto's payola?

Report by Wiley 5/17/17
An analysis of data in Illinois has found a link between higher county-level use of an herbicide called glyphosate and reduced abundance of adult monarch butterflies, especially in areas with concentrated agriculture. — Cavacava

As I explained:

Populations of Monarch butterflies have been greatly reduced because the one plant that their larvae feed on -- the milkweed -- have been largely killed off. — Bitter Crank

Roundup is used on crops because the crops are GMO-immune to the herbicide. ("glyphosate inhibits a key enzyme found only in plants and bacteria – EPSP synthase".) Milkweed, and most other weeds are not -- and they die off rather quickly (except for the weeds that are developing natural immunity to Roundup -- but milkweed isn't one of those plants).

The monarchs aren't being poisoned, they're being starved out of existence, at least as far as glyphosate (Roundup) is concerned.

Adult monarch butterflies don't eat plants -- they don't have mouth-parts for chewing. The adults are nectar feeders. They lay eggs on the milkweed plants, and when the eggs hatch, the larvae (caterpillars) chew up the plant. When they have eaten enough, they spin a cocoon and emerge as adults after maturing in the chrysalis. Monarchs caterpillars are dependent on ONE plant -- the various variety of milkweeds. They don't and they won't eat other plants. No milkweeds, no monarchs. Got that?

If adult monarchs are being killed, it is most likely not from herbicides. Much more likely adult monarchs would be killed by pesticides, which are used against insects (insects--broadly speaking). The usual chemical in pesticides is some sort of nerve-toxic agent that kills the animal. That's what the neonicotinoids do. Neonicotinoids are related to nicotine, which in concentration is quite toxic to animals.

Nicotine of course comes from tobacco. Tobacco is part of the nightshade family that includes tobacco, tomatoes, potatoes, ground cherries, peppers, eggplant, chinese lanterns, and petunias.

Roundup has been listed by the State of California as a carcinogen.

Generally speaking, I don't approve of heavy use of any herbicide, pesticide, or fertilizer.

That's a totally disgusting video.

You're use of the term "beneficial" makes moot the preliminary paragraph. If the poison I give you sickens you, it is immoral to give it, regardless of whether it damages your gut flora, your kidneys, or whether it just irritates your throat. If it benefits you, it's not. — Hanover

I don't see your point. It is not immoral to quit doing something which is beneficial to someone else. Consider that it is beneficial for me if my neighbour picks up my groceries at the store, and brings them to my house. It is not immoral for my neighbour to quit doing this.