Eggshell microbiota is similar to gut microbiota of adult hens. The eggshell microbiota do not survive egg cleaning and subsequent incubation. In commercial production, eggshell microbiota is not transferred to chickens and microbiota of one-week-old chicks is completely different. For more details, see HERE.
Slightly different material is that represented by eggshell waste when hatching is completed. Microbiota of this material is the first to what just hatched chicks are exposed. This microbiota is different from the microbiota originally deposited on the eggshells and is also different from caecal microbiota of one-week-old chicks. The eggshell remains commonly comprise representatives of phylum Proteobacteria and genera like Pseudomonas or Acinetobacter. Alternative composition is that dominated by Bacteroidetes and represented by Chryseobacterium. Acinetobacter but not Pseudomonas is present together with Chryseobacterium. Last common profile of microbiota in eggshell remains is characteristic by dominance of Firmicutes represented by Clostridium disporicum. C. disporicum is usually accompanied by Enterococcus and E. coli. Besides ubiquitously distributed E. coli, C. disporicum is the only environmental microbiota member which is present also in the chickens as a part of their skin and respiratory tract microbiota.