Marc Sze

University of Michigan | U-M · Department of Microbiology and Immunology

Background: Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial population...

Unlabelled: Two recent studies have reanalyzed previously published data and found that when data sets were analyzed independently, there was limited support for the widely accepted hypothesis that changes in the microbiome are associated with obesity. This hypothesis was reconsidered by increasing the number of data sets and pooling the results a...

Introduction Previous reports have shown that the gastrointestinal (GI) bacterial microbiota can have profound effects on the lungs, which has been described as the “gut-lung axis”. However, whether a “lung-gut” axis exists wherein acute lung inflammation perturbs the gut and blood microbiota is unknown. Methods Adult C57/Bl6 mice were exposed to...

Background Low biomass in the bacterial lung tissue microbiome utilizes quantitative PCR (qPCR) 16S bacterial assays at their limit of detection. New technology like droplet digital PCR (ddPCR) could allow for higher sensitivity and accuracy of quantification. These attributes are needed if specific bacteria within the bacterial lung tissue microbi...

Based on surface brushings and bronchoalveolar lavage fluid, Hilty and coworkers demonstrated microbiomes in the human lung characteristic of asthma and chronic obstructive pulmonary disease (COPD), which have now been confirmed by others. To extend these findings to human lung tissue samples. DNA from lung tissue samples was obtained from nonsmoke...

Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflamma...

PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent...

Chronic obstructive pulmonary disease (COPD), asthma, and cystic fibrosis (CF) are obstructive lung diseases with distinct pathophysiologies and clinical phenotypes. In this review article we highlight recent advances in our understanding of relationships between clinical phenotypes, host inflammatory response, and lung microbiota in these diseases...

Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria which produce SCFAs by fermenti...

PCR amplification of 16S rRNA genes is a critical, yet under appreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represe...

Background: Persons living with human immunodeficiency virus (PLWH) face an increased burden of chronic obstructive pulmonary disease (COPD). Repeated pulmonary infections, antibiotic exposures, and immunosuppression may contribute to an altered small airway epithelium (SAE) microbiome. Methods: SAE cells were collected from 28 PLWH and 48 HIV-...

An increasing body of literature suggests that both individual and collections of bacteria are associated with the progression of colorectal cancer. As the number of studies investigating these associations increases and the number of subjects in each study increases, a meta-analysis to identify the associations that are the most predictive of dise...

An increasing body of literature suggests that both individual and collections of bacteria are associated with the progression of colorectal cancer. As the number of studies investigating these associations increases and the number of subjects in each study increases, a meta-analysis to identify the associations that are the most predictive of dise...

The introduction of microCT has made it possible to show that the terminal bronchioles are narrowed and destroyed before the onset of emphysematous destruction in COPD. This report extends those observations to the cellular and molecular level in the centrilobular phenotype of emphysematous destruction in lungs donated by persons with very severe C...

Background Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations...

Background Helicobacter pylori (HP) infection is associated with reduced lung function and systemic inflammation in chronic obstructive pulmonary disease (COPD) patients. Azithromycin (AZ) is active against HP and reduces the risk of COPD exacerbation. We determined whether HP infection status modifies the effects of AZ in COPD patients. Methods P...

Rationale: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. Gene expression profiling across multiple regions of the same lung identified genes significantly related to emphysema. Objective: To determine whether the lung and epithelial expression of 127 emphysema-related genes is also related to lung fu...

Background Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome...

Meta-analysis of the RR of obesity based on evenness (A), richness (B), or the relative abundances of Bacteroidetes (C) and Firmicutes (D). Download

Power (A) and sample size (B) simulations for B/F ratio for differentiating between nonobese and obese for effect sizes of 1, 5, 10, and 15%. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Power (A) and sample size (B) simulations for RR of obesity based on Shannon diversity. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Power (A) and sample size (B) simulations for the relative abundance of Bacteroidetes for differentiating between nonobese and obese for effect sizes of 1, 5, 10, and 15%. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Individual and combined comparisons of obese and nonobese groups based on evenness (A), richness (B), or the relative abundances of Bacteroidetes (C) and Firmicutes (D). Download

Overall accuracy with which each study predicted nonobese and obese individuals based on that study’s random forest machine learning model applied to each of the other studies when trained by using the relative abundance of each phylum, class, order, family, or genus. The cross-validated AUC values for the training model are provided for each study...

Power (A) and sample size (B) simulations for richness for differentiating between nonobese and obese for effect sizes of 1, 5, 10, and 15%. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Power (A) and sample size (B) simulations for evenness for differentiating between nonobese and obese for effect sizes of 1, 5, 10, and 15%. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Funnel plots depicting the general lack of bias in the selection of data sets included in the analysis. Download

Power (A) and sample size (B) simulations for the relative abundance of Firmicutes for differentiating between nonobese and obese for effect sizes of 1, 5, 10, and 15%. Power calculations use the sampling distribution from the original studies, and the sample size estimations assume the same amount of sampling from each treatment group. Download

Two recent studies have re-analyzed published data and found that when datasets are analyzed independently there was limited support for the widely accepted hypothesis that changes in the microbiome are associated with obesity. This hypothesis was reconsidered by increasing the number of datasets and pooling the results across the individual datase...

Chronic systemic infections such as those with Helicobacter pylori (H. pylori) may contribute to the evolution and progression of chronic obstructive pulmonary disease (COPD). Using data from the Lung Health Study (LHS), we determined the relationship of H. pylori infection with the severity and progression of COPD. Using an immunoassay, we measure...

The relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (COPD). This report examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression. A culture-independent pyrosequen...

Objectives The present study assesses the relationship between contents of GD1 (glycerol dehydratase)-positive Lactobacillus, presence of Lactobacillus and the inflammatory response measured in host lung tissue in mild to moderate chronic obstructive pulmonary disease (COPD). We hypothesise that there will be a loss of GD1 producing Lactobacillus w...

Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the...

Rationale: The progression of chronic obstructive pulmonary disease (COPD) has been associated with infiltration of peripheral lung tissue by inflammatory immune cells that form tertiary lymphoid organs. These observations have documented the presence of an adaptive immune response without indentifying the antigens that drive it (Hogg JC, et al., N...

Background: Viral respiratory tract infections are implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). In lung tissue specimens from patients with stable, mild COPD and from control smokers without airflow obstruction, we determined the prevalence and load of nucleic acid from common respiratory viruses and concomitant...

Inflammatory lung disease is the major cause of morbidity and mortality in cystic fibrosis (CF); understanding what produces dysregulated innate immune responses in CF cells will be pivotal in guiding the development of novel anti-inflammatory therapies. To elucidate the molecular mechanisms that mediate exaggerated inflammation in CF following TLR...