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Do you use certified organic vegetables? Maybe that is part of the problem.
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Organic vegetables are grown in manure, which can be very high in nitrogen AND bacteria. Veggies should always be washed before feeding them to anything... even bugs.
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I am 100% sure the problems I have had in previous seasons was a direct result of the way I supplemented my geckos.
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I have a very strong hunch that is what's going on with some of my problems, too. More than half of my losses this year are directly connected with a double power failure and 30% of my breeding stock being new, but there is definitely something else going on with the rest. I do not inbreed, so that's not the problem with my geckos... and I have been extremely careful in choosing my new breeder stock from reputable breeders and NOT gecko mills.
Last year, I switched from my normal regimen of RepCal calcium w/VitD and Herptivite to the T-Rex Sandfire Leopard Gecko Dust, and had ZERO fertile eggs for over 2 months until I switched back! This year is the first year I have used Vionate in my gutload, and I strongly suspect that is what's going on. It is the only thing I have done differently from previous years. The next time I change products/regimens, I am going to use a 'control' group and NOT switch all of my colonies at once!