The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of host-bacterial interactions, but relatively few comprehensive studies have been reported. We have used the rhesus macaque model to investigate forces shaping GI bacterial communities. We used DNA bar coding and pyrosequencing to characterize 141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial samples, allowing quantitative analysis of community composition in health and disease. Microbial communities of macaques were distinct from those of mice and humans in both abundance and types of taxa present. The macaque communities differed among samples from intestinal mucosa, colonic contents, and stool, paralleling studies of humans. Communities also differed among animals, over time within individual animals, and between males and females. To investigate changes associated with disease, samples of colonic contents taken at necropsy were compared between healthy animals and animals with colitis and undergoing antibiotic therapy. Communities from diseased and healthy animals also differed significantly in composition. This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale screening of the human gut microbiome.

R us se ll -L od ri gue, C hr is to ph er Monjure,

Chronic enterocolitis is the leading cause of morbidity in colonies of captive rhesus macaques (Macaca mulatta). This study's aim was to identify the common enteric pathogens frequently associated with chronic enterocolitis in normal, immunocompetent rhesus monkeys and to elucidate the influence of this clinical syndrome on the host immune system. We analyzed the fecal specimens from 100 rhesus macaques with or without clinical symptoms of chronic diarrhea. Retrospective analysis revealed an increased incidence of Campylobacter spp. (Campylobacter coli and Campylobacter jejuni), Shigella flexneri, Yersinia enterocolitica, adenovirus, and Strongyloides fulleborni in samples collected from animals with chronic diarrhea (P < 0.05). The presence of additional enteric pathogens, such as Escherichia coli, carrying the eaeA intimin or Stx2c Shiga toxin virulence genes, Balantidium coli, Giardia lamblia, Enterocytozoon bieneusi, and Trichuris trichiura was found in all animals regardless of whether diarrhea was present. In addition, the upregulation of interleukin-1␣ (IL-1␣), IL-3, and tumor necrosis factor alpha cytokine genes, accompanied by an increased presence of activated (CD4 ؉ CD69 ؉ ) T lymphocytes was found in gut-associated lymphoid tissues collected from animals with chronic enterocolitis and diarrhea in comparison with clinically healthy controls (P < 0.05). These data indicate that chronic enterocolitis and diarrhea are associated, in part, with a variety of enteric pathogens and highlight the importance of defining the microbiological status of nonhuman primates used for infectious disease studies. The data also suggest that chronic colitis in rhesus macaques may have potential as a model of inflammatory bowel disease in humans.

HIV-1 entry requires the cell surface expression of CD4 and either the CCR5 or CXCR4 coreceptors on host cells. Individuals homozygous for the ccr5Δ32 polymorphism do not express CCR5 and are protected from infection by CCR5-tropic (R5) virus strains. As an approach to inactivating CCR5, we introduced CCR5-specific zinc-finger nucleases into human CD4+ T cells prior to adoptive transfer, but the need to protect cells from virus strains that use CXCR4 (X4) in place of or in addition to CCR5 (R5X4) remains. Here we describe engineering a pair of zinc finger nucleases that, when introduced into human T cells, efficiently disrupt cxcr4 by cleavage and error-prone non-homologous DNA end-joining. The resulting cells proliferated normally and were resistant to infection by X4-tropic HIV-1 strains. CXCR4 could also be inactivated in ccr5Δ32 CD4+ T cells, and we show that such cells were resistant to all strains of HIV-1 tested. Loss of CXCR4 also provided protection from X4 HIV-1 in a humanized mouse model, though this protection was lost over time due to the emergence of R5-tropic viral mutants. These data suggest that CXCR4-specific ZFNs may prove useful in establishing resistance to CXCR4-tropic HIV for autologous transplant in HIV-infected individuals.

Little is known about the immune distribution and localization of antigen-specific T cells in mucosal interfaces of tissues/organs during infection of humans. In this study, we made use of a macaque model ofAccumulating evidence suggests that human ␥␦ T cells belong to nonclassical T cells that contribute to both innate and adaptive immune responses. Resident ␥␦ T cells within epithelia make up a portion of intraepithelial lymphocytes and may play a role in innate immunity against microbial invasions, immune surveillance of malignances, and even skin repair after damage (1, 16). Peripheral ␥␦ T cells circulating in the blood and lymphoid tissues appear to behave as both innate and adaptive immune cells (1, 5, 9, 16). Circulating V␥2V␦2 T cells exist only in primates and, in humans, constitute 60 to 95% of total blood ␥␦ T cells. Recent studies suggest that circulating V␥2V␦2 T cells in primates can recognize phosphoantigens from some bacteria, such as Mycobacterium tuberculosis, and possess both innate and adaptive immune features (1, 5, 9, 16). The finding that "unprimed" V␥2V␦2 T cells can recognize and react to wide ranges of nonpeptide ligands with the capability of "naïve" production of cytokines has been interpreted as a pattern recognition-like feature of innate immune cells.On the other hand, the capacity of V␥2V␦2 T cells to undergo major clonal expansion in primary infection and to mount rapid recall expansion upon reinfection has been proposed as an adaptive (memory-type) immune response of these ␥␦ T cells (5). Consistent with these memory-type responses is the demonstration of memory phenotypes of V␥2V␦2 T cells in the blood of humans (7).Tuberculosis (TB) is the second leading cause of death worldwide, killing about 1.8 million persons annually. While human CD4 T cells play a crucial role in immune protection against M. tuberculosis infection, other T-cell populations, including V␥2V␦2 T cells, are poorly characterized regarding their roles in immunity to TB. We recently demonstrated that Mycobacterium bovis BCG-vaccinated monkeys can mount memory-type immune responses of V␥2V␦2 T cells in the pulmonary compartment following M. tuberculosis infection by aerosol and that the rapid recall responses of these ␥␦ T cells coincide with protection against acutely fatal TB in juvenile rhesus monkeys (19). Nevertheless, immune responses of V␥2V␦2 T cells in patients with chronic TB appear to be suppressed (for a review, see reference 4). It has been debated whether the depression of the V␥2V␦2 T-cell response in TB is caused by the infection or allows the infection to progress (4). Further studies are needed to elucidate the biology and effector function of V␥2V␦2 T cells in M. tuberculosis infection.