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Gram staining and simple staining techniques may or may not reveal the presence of endospores in a bacterial sample. Since confirming the presence or absence of the endospores establishes the identification pathway to pursue, methods for visualizing the endospores and the free spores in a sample were developed. Relatively few species of bacteria produce endospores, so a positive result from endopore staining methods is an important clue in bacterial identification. In a clinical setting, identification of pathogens includes describing the shape and position of the endospores present. During microscopic examinations, the endospore stain can yield this information. While staining is probably the most common approach, laboratories that use phase-contrast microscopy can obtain the same information without the staining step.

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