Food safety is an important part of the assessments that researchers conduct on herbicides. For your first question regarding herbicide residues, you might find it useful to look at a previous response on GMO Answers that addresses that question: http://gmoanswers.com/ask/if-roundup-safe-human-consumption-trace-amounts-food-then-it-safe-drink-it-if-not-where-line. Also, actual data on pesticide residues in the U.S. food supply are regularly collected by USDA Agricultural Marketing Service (AMS). The 2012 Annual Summary once again confirms that pesticide residues on foods are at levels below the tolerances established by the EPA and do not pose a safety concern. For more information, please visit the USDA AMS website.
Regarding your second question, the role of gut microbes in maintaining health is currently a hot topic in science and in the media. There is a lot of work being done in this area, and there is good evidence for a role of gut microbiota in some clinical diseases.
Recently, the German BfR, the scientific agency of the Federal Republic of Germany that is responsible for preparing expert reports and opinions on food, reported that it finalized a reevaluation of glyphosate, which stated, “A research project initiated by BfR and performed by the University of Veterinary Medicine in Hanover investigated the influence of a glyphosate containing herbicide on microbial metabolism and communities in ruminants. The results of this study are summarized in the draft suggesting that there is no negative impact on the microflora in the rumen. In particular, there was no indication that Clostridium bacteria might multiply under the influence of glyphosate.”
One critical factor in this study is that it uses a well-recognized technique that uses a mixed population of organisms under conditions designed to more closely simulate the complex matrix of feed and microbes than pure cultures grown in purified media. Previous studies have used pure cultures with purified media that don’t account for synergy in metabolism for mixed populations and may make them more susceptible to pH changes.