What kind of analysis did you perform for beta diversity?

Of course, the microbiome will be different in your treatments. In addition, if differences cannot be found at the higher taxnomic level, then you can see difference at lower taxonomic levels.

It deppends.. which indexes are you comparing for alpha diversity?

Also, remember for beta diversity you have indexes than only consider presence/absence, abundance, or both..

Alpha diversity indices are most influenced by the abundance of local communities. When looking for beta diversities, the index you are using is crucial to understand if these abundances are taken into account or not. Bray-Curtis and Sorensen, for example, are based on the same equation. The only difference is the assumption of abundance-based (Bray-Curtis) or presence/absence (Sorensen). You can normalize alpha diversity matrices before running beta diversity tests by using Raupp-Crick correction, for example. It decreases the bias that different abundances would cause in beta diversity inferences. I would rather use beta Bray balanced.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

Thanks a lot for your insights. I actually used shannon index for alpha diversiity and bray-curtis distance for beta diversity.

It depends on what conclusion you are trying to make with your assumption. Bray-Curtis distance based beta diversity will be influenced primarily by your most abundant species. My interpretation would be that your dominant taxa/community are shared across your treatments, but the rank abundance curves are different. If you are primarily concerned about the dominant organisms in the gut microbiome, then no you cannot assume that the communities are different. On the other hand, since Shannon diversity index / entropy combines and therefor confounds evenness and richness characteristics, it's hard to say precisely what is differing about the alpha diversity and why. For example, are there fewer rare species in one treatment? or is the rank abundance curve less evenly distributed in one treatment? Either of these effects would qualify as being a "different" microbial community composition even though the dominant community members are likely shared across treatments. If you are concerned about the whole community, or pattern and process of assembly that takes into account the lower abundant organisms (or if you are primarily interested in the lower abundance organisms), then you do already have enough information to know the treatments are different, but you probably want to spend some time figuring out precisely what is different about them before proceeding with your analysis.