Dr. Huber’s assertions have been addressed previously, and I’d refer you to this response (http://gmoanswers.com/ask/i-dont-understand-how-you-can-say-gmo-food-safe-when-farmers-are-spraying-glyphosate-their-crops) on GMO Answers, by Marian Bleeke, as well as this blog post (http://thefanningmill.com/2014/01/10/deconstructing-don-huber-a-tale-of-two-talks/), written by organic farmer Rob Wallbridge.
Regarding your question, it is true that glyphosate is a chelator and that it has some antimicrobial properties. However, it is important when looking at an effect of any compound to understand the whole story. For instance, red blood cells bind oxygen. That’s an indisputable fact. So to say that blood prevents muscle cells of the body from gaining access to oxygen would be obviously faulty logic and would be based on looking at only half of the story. To extend the analogy, oxygen is also a potent antimicrobial compound for many good anaerobic gut organisms. That doesn’t mean that small amounts of oxygen in the gut will kill all of the organisms in the gut. Obviously, just the label “antimicrobial” is not very informative without more information.
In the glyphosate example that you cite, it appears that there is also a jump in logic that looks at only half of the story. In 2012, Dr. Stephen Duke et al. wrote a comprehensive review of glyphosate in which they explain that there are many natural chelators in soil, and that they are beneficial for facilitating transport of minerals into plants: http://pubs.acs.org/doi/abs/10.1021/jf302436u?prevSearch=%5BTitle%3A+glyphosate%5D+and+%5BContrib%3A+duke%5D&searchHistoryKey=. Moreover, to suggest that glyphosate as an antimicrobial preferentially affects good bacteria implies that all “good” and “bad” microbes can be defined by their metabolism, and there is no basis for this conclusion.
In risk assessment, hazard and exposure (dose) need to be considered for each organism. In 2013, the German BfR did a reevaluation of glyphosate, and, based on accusations about glyphosate affecting animal gut microbes, it commissioned a study to look at effects of glyphosate in an artificial rumen microbial system. As we’ve discussed previously on this site, ruminants rely on the microbes (bacteria, fungi, protozoa) in the rumen to predigest their feed before any other digestion occurs in the lower parts of their gastrointestinal tract. The BfR concluded that “no adverse effects on animal health are to be anticipated.” Likewise, animals have been fed glyphosate in long-term studies, and histological examination of gut tissues has not revealed any pathologies like you describe. Furthermore, these in vitro results are consistent with what has been observed with billions of animals fed diets containing ingredients derived from biotech crops.
Dr. Van Eenennaam published in 2013 that “large numbers of livestock in many countries have been consuming GE feed for over a decade. For example, in 2011 alone approximately 9 billion broiler chickens, weighing over 22.5 billion kg liveweight were produced in the United States. During that year 30 million tonnes of corn and 13.6 million tonnes of soy were used as broiler and breeder poultry feed of which 88% and 94%, respectively, was likely from GE crops. Production parameters, mortality and condemnation rates for the more than 105 billion broilers that have been processed in the US since 2000 are shown in Figure 2. In 2000 approximately 25% of corn and 50% of soy grown in the US was GE and hence poultry diets have likely contained an ever increasing proportion of GE feed from 2000 to 2011. This very large field data set does not reveal overt health problems associated with the consumption of GE feed, but rather shows a continuation of industry trends that were observed prior to the introduction of GE crops (Figure 2).” This link will allow you to see the figure and read the paper: http://www.jasbsci.com/content/4/1/37.