NOTE: Below is the abstract of a new study by scientists at Leipzig University which found that Roundup herbicide, based on the chemical glyphosate, negatively impacted the gastrointestinal bacteria of poultry in vitro. The researchers found that highly pathogenic bacteria resisted Roundup, whereas beneficial bacteria were moderately to highly susceptible to it. 

The study provides a scientific basis to farmer reports of increased gastrointestinal disease in animals fed GM Roundup Ready soy, which is tolerant to Roundup.

Here is an interesting video presentation by a Danish egg producer Claus Storgaard who found drastic improvements in the health and egg production of his hens after changing from GM to non-GM soy feed ("Changeover to non-GMO diet in egg production"):
 http://sustainablepulse.com/2012/12/15/monsanto-feels-pain-europe-roundup-herbicide-dangers/
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The effect of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro.

Shehata, A. A., W. Schrodl, et al. (2012). Curr Microbiol. Publ online 9 December.

 http://www.ncbi.nlm.nih.gov/pubmed/23224412

Abstract: The use of glyphosate modifies the environment which stresses the living microorganisms. The aim of the present study was to determine the real impact of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro. The presented results evidence that the highly pathogenic bacteria as Salmonella Entritidis, Salmonella Gallinarum, Salmonella Typhimurium, Clostridium perfringens and Clostridium botulinum are highly resistant to glyphosate. However, most of beneficial bacteria as Enterococcus faecalis, Enterococcus faecium, Bacillus badius, Bifidobacterium adolescentis and Lactobacillus spp. were found to be moderate to highly susceptible. Also Campylobacter spp. were found to be susceptible to glyphosate. A reduction of beneficial bacteria in the gastrointestinal tract microbiota by ingestion of glyphosate could disturb the normal gut bacterial community. Also, the toxicity of glyphosate to the most prevalent Enterococcus spp. could be a significant predisposing factor that is associated with the increase in C. botulinum-mediated diseases by suppressing the antagonistic effect of these bacteria on clostridia.