Les Dethlefsen, Sue Huse, Mitchell L. Sogin, David A. Relman
The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may...
Gene-expression patterns reveal underlying biological processes in Kawasaki disease (2007)
Popper, Stephen J, Shimizu, Chisato, Shike, Hiroko, Kanegaye, John T, Newburger, Jane W, Sundel, Robert P, ...
Abstract Background Kawasaki disease (KD) is an acute self-limited vasculitis and the leading cause of acquired heart disease in children in developed countries. No etiologic agent(s) has been...
Rubins, Kathleen H, Hensley, Lisa E, Wahl-Jensen, Victoria, Daddario DiCaprio, Kathleen M, Young, Howard A, Reed, Douglas S, ...
Abstract Background Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever. In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions, we...
Development of the Human Infant Intestinal Microbiota (2007)
Chana Palmer, Elisabeth M. Bik, Daniel B. DiGiulio, David A. Relman, Patrick O. Brown
Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human...
Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis (2007)
Gogol, Emily B, Cummings, Craig A, Burns, Ryan C, Relman, David A
Abstract Background Bordetella pertussis , the causative agent of whooping cough, is a highly clonal pathogen of the respiratory tract. Its lack of genetic diversity, relative to many bacterial...
Genomic features of Bordetella parapertussisclades with distinct host species specificity (2006)
Brinig, Mary M, Register, Karen B, Ackermann, Mark R, Relman, David A
Abstract Background The respiratory pathogen Bordetella parapertussis is a valuable model in which to study the complex phenotype of host specificity because of its unique two-species host range. One...
Dimitri A. Diavatopoulos, Craig A. Cummings, Leo M. Schouls, Mary M. Brinig, David A. Relman, Frits R. Mooi
Bordetella pertussis, B. bronchiseptica, B. parapertussishu, and B. parapertussisov are closely related respiratory pathogens that infect mammalian species. B. pertussis and B. parapertussishu are...
Cultivation of Tropheryma whipplei from cerebrospinal fluid (2003)
Maiwald, Matthias, Von Herbay, Axel, Fredricks, David N, Ouverney, Cleber C, Kosek, Jon C, Relman, David A
Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this...
Cultivation of Tropheryma whipplei from cerebrospinal fluid (2003)
Maiwald, Matthias, Von Herbay, Axel, Fredricks, David N, Ouverney, Cleber C, Kosek, Jon C, Relman, David A
Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this...
Cultivation of Tropheryma whipplei from cerebrospinal fluid (2003)
Maiwald, Matthias, Von Herbay, Axel, Fredricks, David N, Ouverney, Cleber C, Kosek, Jon C, Relman, David A
Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this...
Belcher, Christopher E., Drenkow, Jörg, Kehoe, Bettina, Gingeras, Thomas R., McNamara, Nancy, Lemjabbar, Hassan, ...
Bordetella pertussis, the causative agent of whooping cough, has many well-studied virulence factors and a characteristic clinical presentation. Despite this information, it is not clear how B....
Bacterial diversity within the human subgingival crevice
Kroes, Ian, Lepp, Paul W., Relman, David A.
Molecular, sequence-based environmental surveys of microorganisms have revealed a large degree of previously uncharacterized diversity. However, nearly all studies of the human endogenous bacterial...
Does Blood of Healthy Subjects Contain Bacterial Ribosomal DNA?
Nikkari, Simo, McLaughlin, Ian J., Bi, Wanli, Dodge, Deborah E., Relman, David A.
Real-time PCR methods with primers and a probe targeting conserved regions of the bacterial 16S ribosomal DNA (rDNA) revealed a larger amount of rDNA in blood specimens from healthy individuals than...
Maiwald, Matthias, Von Herbay, Axel, Lepp, Paul W., Relman, David A.
Whipple's disease is a systemic disorder associated with a cultivation-resistant, poorly characterized actinomycete, Tropheryma whippelii. We determined a nearly complete rRNA operon sequence of T....
Abramson, Tzvia, Kedem, Hassya, Relman, David A.
Filamentous hemagglutinin (FHA) is a dominant cell surface-associated Bordetella pertussis adhesin. Recognition that this protein is secreted in significant amounts and that bacterial adhesins may...
Fredricks, David N., Relman, David A.
Molecular methods are increasingly used to identify microbes in clinical samples. A common technical problem with PCR is failed amplification due to the presence of PCR inhibitors. Initial attempts...
Cotter, Peggy A., Yuk, Ming H., Mattoo, Seema, Akerley, Brian J., Boschwitz, Jeff, Relman, David A., ...
Adherence to ciliated respiratory epithelial cells is considered a critical early step in Bordetella pathogenesis. For Bordetella pertussis, the etiologic agent of whooping cough, several factors...
Stereotyped and specific gene expression programs in human innate immune responses to bacteria
Boldrick, Jennifer C., Alizadeh, Ash A., Diehn, Maximilian, Dudoit, Sandrine, Liu, Chih Long, Belcher, Christopher E., ...
The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene...
Individuality and variation in gene expression patterns in human blood
Whitney, Adeline R., Diehn, Maximilian, Popper, Stephen J., Alizadeh, Ash A., Boldrick, Jennifer C., Relman, David A., ...
The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed...
Brinig, Mary M., Lepp, Paul W., Ouverney, Cleber C., Armitage, Gary C., Relman, David A.
Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival...
Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the Human Subgingival Crevice
Ouverney, Cleber C., Armitage, Gary C., Relman, David A.
Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis...
Bordetella pertussis Infection of Primary Human Monocytes Alters HLA-DR Expression
Shumilla, Jennifer A., Lacaille, Vashti, Hornell, Tara M. C., Huang, Jennifer, Narasimhan, Supraja, Relman, David A., ...
Bordetella pertussis is the causative agent of whooping cough, a potentially lethal respiratory disease in children. In immunocompetent individuals, B. pertussis infection elicits an effective...
Methanogenic Archaea and human periodontal disease
Lepp, Paul W., Brinig, Mary M., Ouverney, Cleber C., Palm, Katherine, Armitage, Gary C., Relman, David A.
Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of...
Rubins, Kathleen H., Hensley, Lisa E., Jahrling, Peter B., Whitney, Adeline R., Geisbert, Thomas W., Huggins, John W., ...
Smallpox has played an unparalleled role in human history and remains a significant potential threat to public health. Despite the historical significance of this disease, we know little about the...
Jahrling, Peter B., Hensley, Lisa E., Martinez, Mark J., LeDuc, James W., Rubins, Kathleen H., Relman, David A., ...
Smallpox virus (variola) poses a significant threat as an agent of bioterrorism. To mitigate this risk, antiviral drugs and an improved vaccine are urgently needed. Satisfactory demonstration of...
Diavatopoulos, Dimitri A, Cummings, Craig A, Schouls, Leo M, Brinig, Mary M, Relman, David A, Mooi, Frits R
Bordetella pertussis, B. bronchiseptica, B. parapertussishu, and B. parapertussisov are closely related respiratory pathogens that infect mammalian species. B. pertussis and B. parapertussishu are...
Rapid quantitative profiling of complex microbial populations
Palmer, Chana, Bik, Elisabeth M., Eisen, Michael B., Eckburg, Paul B., Sana, Theodore R., Wolber, Paul K., ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
Diversity of the Human Intestinal Microbial Flora
Eckburg, Paul B., Bik, Elisabeth M., Bernstein, Charles N., Purdom, Elizabeth, Dethlefsen, Les, Sargent, Michael, ...
The human endogenous intestinal microflora is an essential “organ” in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features...
Brinig, Mary M., Cummings, Craig A., Sanden, Gary N., Stefanelli, Paola, Lawrence, Andrew, Relman, David A.
Bordetella pertussis, an obligate human pathogen and the agent of whooping cough, is a clonal species, despite the dynamic selection pressures imposed by host immunity and vaccine usage. Because the...
Molecular analysis of the bacterial microbiota in the human stomach
Bik, Elisabeth M., Eckburg, Paul B., Gill, Steven R., Nelson, Karen E., Purdom, Elizabeth A., Francois, Fritz, ...
The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain largely unknown. We characterized bacterial diversity within the human gastric...
Belcher, Christopher E., Drenkow, Jörg, Kehoe, Bettina, Gingeras, Thomas R., McNamara, Nancy, Lemjabbar, Hassan, ...
Bordetella pertussis, the causative agent of whooping cough, has many well-studied virulence factors and a characteristic clinical presentation. Despite this information, it is not clear how B....
Bacterial diversity within the human subgingival crevice
Kroes, Ian, Lepp, Paul W., Relman, David A.
Molecular, sequence-based environmental surveys of microorganisms have revealed a large degree of previously uncharacterized diversity. However, nearly all studies of the human endogenous bacterial...
Does Blood of Healthy Subjects Contain Bacterial Ribosomal DNA?
Nikkari, Simo, McLaughlin, Ian J., Bi, Wanli, Dodge, Deborah E., Relman, David A.
Real-time PCR methods with primers and a probe targeting conserved regions of the bacterial 16S ribosomal DNA (rDNA) revealed a larger amount of rDNA in blood specimens from healthy individuals than...
Maiwald, Matthias, Von Herbay, Axel, Lepp, Paul W., Relman, David A.
Whipple's disease is a systemic disorder associated with a cultivation-resistant, poorly characterized actinomycete, Tropheryma whippelii. We determined a nearly complete rRNA operon sequence of T....
Abramson, Tzvia, Kedem, Hassya, Relman, David A.
Filamentous hemagglutinin (FHA) is a dominant cell surface-associated Bordetella pertussis adhesin. Recognition that this protein is secreted in significant amounts and that bacterial adhesins may...
Fredricks, David N., Relman, David A.
Molecular methods are increasingly used to identify microbes in clinical samples. A common technical problem with PCR is failed amplification due to the presence of PCR inhibitors. Initial attempts...
Cotter, Peggy A., Yuk, Ming H., Mattoo, Seema, Akerley, Brian J., Boschwitz, Jeff, Relman, David A., ...
Adherence to ciliated respiratory epithelial cells is considered a critical early step in Bordetella pathogenesis. For Bordetella pertussis, the etiologic agent of whooping cough, several factors...
Stereotyped and specific gene expression programs in human innate immune responses to bacteria
Boldrick, Jennifer C., Alizadeh, Ash A., Diehn, Maximilian, Dudoit, Sandrine, Liu, Chih Long, Belcher, Christopher E., ...
The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene...
Individuality and variation in gene expression patterns in human blood
Whitney, Adeline R., Diehn, Maximilian, Popper, Stephen J., Alizadeh, Ash A., Boldrick, Jennifer C., Relman, David A., ...
The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed...
Brinig, Mary M., Lepp, Paul W., Ouverney, Cleber C., Armitage, Gary C., Relman, David A.
Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival...
Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the Human Subgingival Crevice
Ouverney, Cleber C., Armitage, Gary C., Relman, David A.
Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis...
Bordetella pertussis Infection of Primary Human Monocytes Alters HLA-DR Expression
Shumilla, Jennifer A., Lacaille, Vashti, Hornell, Tara M. C., Huang, Jennifer, Narasimhan, Supraja, Relman, David A., ...
Bordetella pertussis is the causative agent of whooping cough, a potentially lethal respiratory disease in children. In immunocompetent individuals, B. pertussis infection elicits an effective...
Methanogenic Archaea and human periodontal disease
Lepp, Paul W., Brinig, Mary M., Ouverney, Cleber C., Palm, Katherine, Armitage, Gary C., Relman, David A.
Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of...
Rubins, Kathleen H., Hensley, Lisa E., Jahrling, Peter B., Whitney, Adeline R., Geisbert, Thomas W., Huggins, John W., ...
Smallpox has played an unparalleled role in human history and remains a significant potential threat to public health. Despite the historical significance of this disease, we know little about the...
Jahrling, Peter B., Hensley, Lisa E., Martinez, Mark J., LeDuc, James W., Rubins, Kathleen H., Relman, David A., ...
Smallpox virus (variola) poses a significant threat as an agent of bioterrorism. To mitigate this risk, antiviral drugs and an improved vaccine are urgently needed. Satisfactory demonstration of...
Diavatopoulos, Dimitri A, Cummings, Craig A, Schouls, Leo M, Brinig, Mary M, Relman, David A, Mooi, Frits R
Bordetella pertussis, B. bronchiseptica, B. parapertussishu, and B. parapertussisov are closely related respiratory pathogens that infect mammalian species. B. pertussis and B. parapertussishu are...
Rapid quantitative profiling of complex microbial populations
Palmer, Chana, Bik, Elisabeth M., Eisen, Michael B., Eckburg, Paul B., Sana, Theodore R., Wolber, Paul K., ...
Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and...
Molecular analysis of the bacterial microbiota in the human stomach
Bik, Elisabeth M., Eckburg, Paul B., Gill, Steven R., Nelson, Karen E., Purdom, Elizabeth A., Francois, Fritz, ...
The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain largely unknown. We characterized bacterial diversity within the human gastric...
Brinig, Mary M., Cummings, Craig A., Sanden, Gary N., Stefanelli, Paola, Lawrence, Andrew, Relman, David A.
Bordetella pertussis, an obligate human pathogen and the agent of whooping cough, is a clonal species, despite the dynamic selection pressures imposed by host immunity and vaccine usage. Because the...
Nakamura, Mari M., Liew, Sin-Yee, Cummings, Craig A., Brinig, Mary M., Dieterich, Christine, Relman, David A.
To survive in a host environment, microbial pathogens must sense local conditions, including nutrient availability, and adjust their growth state and virulence functions accordingly. No comprehensive...
Genomic features of Bordetella parapertussis clades with distinct host species specificity
Brinig, Mary M, Register, Karen B, Ackermann, Mark R, Relman, David A
Genomic analysis of human and ovine Bordetella parapertussis strains reveals differences distinguishing the host-restricted subgroups.
Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
Gogol, Emily B, Cummings, Craig A, Burns, Ryan C, Relman, David A
Development of the Human Infant Intestinal Microbiota
Palmer, Chana, Bik, Elisabeth M, DiGiulio, Daniel B, Relman, David A, Brown, Patrick O
Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human...
Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Lösekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, ...
We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial...
Gene-expression patterns reveal underlying biological processes in Kawasaki disease
Popper, Stephen J, Shimizu, Chisato, Shike, Hiroko, Kanegaye, John T, Newburger, Jane W, Sundel, Robert P, ...
Analysis of patterns of gene expression in peripheral blood from children with Kawasaki disease revealed dynamic and variable gene expression programs involving neutrophil activation and apoptosis.
Lawley, Trevor D., Bouley, Donna M., Hoy, Yana E., Gerke, Christine, Relman, David A., Monack, Denise M.
Transmission is an essential stage of a pathogen's life cycle and remains poorly understood. We describe here a model in which persistently infected 129X1/SvJ mice provide a natural model of...
Rubins, Kathleen H, Hensley, Lisa E, Wahl-Jensen, Victoria, Daddario DiCaprio, Kathleen M, Young, Howard A, Reed, Douglas S, ...
Primate blood cells were analysed for changes in global gene expression patterns at several time points following infection with Ebola virus, providing insights into potential mechanisms of viral...
Rubins, Kathleen H., Hensley, Lisa E., Bell, George W., Wang, Chunlin, Lefkowitz, Elliot J., Brown, Patrick O., ...