A mouse model for studying gastrointestinal microbial ecology

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2005.Includes bibliographical references (p. 131-133).The mammalian gastrointestinal (GI) tract harbors a complex microbial ecosystem with hundreds of bacterial species at total levels as high as 10¹¹⁻¹² cells/g tissue. These bacteria play an important role in the health of the host as well as in causing disease, but studies on the roles of the GI microflora are hindered by the lack of a suitable model system. This thesis characterizes and uses a defined flora mouse model to study interactions between exogenous bacteria and the GI microflora. The first part of the thesis characterizes a defined flora mouse model consisting of immunodeficient C.B-17 SCID mice colonized with the eight bacterial strains of the altered Schaedler flora (ASF). Specific and sensitive molecular methods were developed to accurately estimate the levels of different ASF strains. Distribution of specific ASF strains along the GI tract was dependent on the oxygen tolerance of the strains. Fecal levels of different strains, which are typically used as a model for colonic bacteria, were different from colonic levels, although all colonic strains were present in feces. ASF strains were persistent in the mouse GI tract even in the face of long-term exposure to other bacteria. The second part of the thesis evaluates the presence of different ASF strains in inbred and outbred mouse models from different vendors to establish the potential for widespread use of these strains as representatives of the mouse GI microflora. Seven of the eight strains were persistent in both inbred and outbred mice from all vendors studied. This indicates the potential for the ASF strains to be used as a model system even in mouse models that do not harbor a defined flora.(cont.) The third part of the thesis explores ecological interactions following infection by an intestinal pathogen, Citrobacter rodentium, in defined flora C.B-17 SCID mice. Bulk levels of the pathogen and the ASF strains in different regions of the large intestine and their spatial localization across the luminal-mucosal cross-section were assessed. C. rodentium exhibited accelerated dynamics, and infection was followed by increases in levels of specific ASF strains and in total bacterial levels in infected mice as compared to control mice. Different ASF strains were observed to have specific spatial niches that did not vary between infected and control mice. These results suggest that the role of the microflora in preventing colonization of pathogens is a complex process that potentially involves more than one bacterial species.by Ramahi Bhushan Sarma-Rupavtarm.Ph.D

Molecular techniques for the study of Helicobacter sp. interaction with host microflora in the mouse model

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2000.Includes bibliographical references (leaves 68-76).by Ramahi Sarma-Rupavtarm.S.M

Genotypic diversity within a natural coastal bacterioplankton population

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science 307 (2005): 1311-1313, doi:10.1126/science.1106028.The genomic diversity and relative importance of unique genotypes within natural bacterial populations has remained largely unknown. Here, we analyze the diversity and annual dynamics of a group of coastal bacterioplankton (>99% 16S rRNA identity to Vibrio splendidus). We show that this group consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average <1 cell/ml). Overall, the genomes show extensive allelic diversity and size variation. Individual genotypes rarely recurred in samples and allelic distribution did not show spatial or temporal substructure. Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral.This work was supported by grants from the Department of Energy Genomes to Life program and the National Science Foundation. Sequences have been submitted to Genbank under accession numbers AY836800-AY837464