The cell wall of mycobacteria consists of an outer membrane, analogous to that of Gram-negative bacteria, attached to the peptidoglycan (PG) via a connecting polysaccharide arabinogalactan (AG). Although the primary structure of these components is fairly well deciphered, issues such as the coverage of the PG layer by covalently attached mycolates in the outer membrane and the spatial details of the mycolic acid attachment to the arabinan have remained unknown. It is also not understood how these components work together to lead to the classical acid-fast staining of mycobacteria. Because the majority of Mycobacterium tuberculosis bacteria in established experimental animal infections are acid-fast negative, clearly cell wall changes are occurring. To address both the spatial properties of mycobacterial cell walls and to begin to study the differences between bacteria grown in animals and cultures, the cell walls of Mycobacterium leprae grown in armadillos was characterized and compared with that of M. tuberculosis grown in culture. Most fundamentally, it was determined that the cell wall of M. leprae contained significantly more mycolic acids attached to PG than that of in vitro grown M. tuberculosis (mycolate:PG ratios of 21:10 versus 16:10, respectively). In keeping with this difference, more arabinogalactan (AG) molecules, linking the mycolic acids to PG, were found. Differences in the structures of the AG were also found; the AG of M. leprae is smaller than that of M. tuberculosis, although the same basic structural motifs are retained.The hallmark of mycobacteria is their cell wall consisting of a peptidoglycan layer attached to a mycolic acid containing outer membrane via the polysaccharide arabinogalactan. Profound and fundamental questions remain about this architecture, including how division occurs and how molecules, both nutrients and drugs, enter the cell. Although its impermeability is stressed (1), anomalies exist such as the susceptibility of in vitro grown Mycobacterium tuberculosis to lysozyme at concentrations between 0.1 and 3 mg/ml.2 Also, the acid fastness of in vivo bacteria varies, in a manner dependent upon their growth state (2). Considered together, these phenomena point to the need to understand the cell wall physical spatial organization and how the cell wall changes during in vivo growth.Mycobacterium leprae cannot be cultured in vitro and is propagated in nine-banded armadillos (Dasypus novemcinctus) (3). In this animal, as in the mouse foot pad model and human lepromatous leprosy, the bacteria grow logarithmically but with a very slow generation time of 12-14 days (4). Although there is a robust humoral response to M. leprae in armadillo, it would appear that the immune system does little to slow the growth of the bacteria and that the slow growth rate is an intrinsic property of the highly attenuated M. leprae, marked by less than 50% genomic coding capacity (5). This is in contrast to M. tuberculosis that presents an initial doubling time in animal models of about 2.4 days (5) u...