While one can assume it is theoretically possible based on some of the landmark papers published in the past few years, my hunch is that we are yet to do the baseline characterization of the different microbiome profiles in different animal species. I am willing to wager that the profiles will be much more complicated in farm animals than in humans and lab animals. Taking dairy as an example, one would expect the profile to change based on geographical location (humidity, temperature, wild animals, feed type, vectors, microbial load in air, water, feed and soil...etc.), biosecurity, management (crowdedness, duration of allowed nursing before calves removal to milk replacer, type of replacer...etc.) diet formulation (especially the influence on digestive system's pH; grain vs roughage). While I would love to see this examined (one of my colleagues is interested in biofilms and we discussed this same issue you are asking about), you maybe up to something big if you are thinking of going there. Hope to see you do :-) May the force be with you. 

Abdorrahman Alghamdi. Thanks for your response. I am thinking more about comparing herds within a local area rather than across large geographic locations and feed types. And I don't think it would need to be overly specific on a first-try basis. Maybe the first try would be to do a low-density profile on 20-30 herds in an area and see if there are differences and if these are related to overall herd health (SSC, mortality, respiratory, uterine infections, etc). Just thinking at this point.

Hi Jack, a qualitative mapping of bacterial population is of poor interest in my opinion. But a quantitative one (by pyro-sequencing) is very expensive but seems necessary to monitor bacterial populations equilibrium at least at the animal level. Thus, It seems difficult to study a large population for the moment. A first approach we have recently made about mammary gland microbiome in some animals of our own experimental farm was already very long to do and analyze but encouraging. It seems possible to characterize animals with actual infection or greater risk of infection to safer animals. For an interflock analysis, You will need a very enormous work to have sufficient analysis to evaluate and differentiate intra and inter flock variability. There i now a national french meta-programm at the INRA level (managed by the microbiological department of research) who try to use this approach as well for mammary and uterine diseases but for the moment at a very limited scale. Best regards

Pierre Guy Marnet,  Thank you for your response. This is very helpful. Just thinking ahead for a presentation I will be making a few months from now.

I have no paper published to help you on this new programm but you have just an abstract of the first work done we me in my RG profile but unfortunately it is in French! But You can take a look of the numerous new paper about microbiome of ewe mammary gland by example. Best  regards

Can't say much about cattle, but our experience in lab-reared flocks of chickens is not only the microbiome variable between members, but more variable within an individual throughout the intestinal tract so I suspect an measure of gut health is some way off and as Pierre says it may be quantity of specific components that matter.