2021 Fall TUMI Pilot and Feasibility Grant Awardees Announced!
The TransUniversity Microbiome Initiative is excited to announce the third round of Awardees for the Fall 2021 (Round 3) TUMI Pilot and Feasibility Grants. TUMI assembled a panel of over twenty reviewers to assess and select our 8 finalists. Below you will find brief summaries of each of the eight funded projects. TUMI looks forward to supporting this research over the coming months, and we are unbelievably excited by the creative microbiome research proposed across grounds. Stay tuned for microbiome research updates from each of these investigators!!
The Microbiome of Long-Term Central Venous Catheters
Key Personnel: Dr. Julia Scialla, MD, MHS. (Associate Professor in the Department of Medicine, Division of Nephrology), Dr. Jennie Ma, PhD. Dr. (Professor of Biostatistics in the Department of Public Health Sciences)
Summary: A central venous catheter (CVC) is a plastic tube placed through the skin into a blood vessel that allows for administration of lifesaving therapies such as chemotherapy and hemodialysis (HD). However, CVCs are also potential sources of catastrophic blood stream infections. In 2019, acute care hospitals in the United States recorded over 18,000 central line associated bloodstream infections (CLABSI). Despite continual yearly improvement, this staggering number is associated with over 2,700 excess deaths and $865 million in increased hospital costs2. One particularly at-risk population is patients receiving HD through a CVC. In this population a CVC may be used over many months or years. Nationally, the mean rate of CLABSI in patients receiving HD through a CVC is 2.16 events per 100 patient months, corresponding to an approximate patient risk of 25% per year. This is a staggering risk that is associated with metastatic infections, hospitalization, and death.
Despite the tremendous burden of CLABSI in CVCs, there are no widely used methods for surveillance to prevent clinical infection. Prior studies using metagenomic sequencing have shown that clinically uninfected lines may demonstrate polymicrobial colonization in the biofilm, whereas clinically infected lines typically show one dominant taxa. In other small studies, high bacterial DNA burden is an accurate marker of clinical infections. Thus rising bacterial DNA burden or development of a dominant taxa may be novel markers for impending infection that can be harnessed to surveil CVC health. No previous work has attempted to describe longitudinal changes in the device microbiome. Thus far most studies have focused on short-term central lines and sampled lines after removal. Patients on HD require long-term vascular access and unnecessary removal can lead to life-threatening complications when sites for additional vascular access are exhausted. In this application we will establish critical preliminary data to assess the feasibility of using bacterial DNA burden and composition in the CVC biofilm to assess lines commonly used in patients treated with HD.
Intestinal microbiome of infants with biliary atresia: candidate biomarker and gateway to new therapies
Key Personnel: Sandra Oliphant and Tina Hashemi (study coordinators, UVA), Kyle Soltys MD (PI, Pittsburgh), Bart Rountree MD (PI, Bon Secours), Marc Tsou (PI, CHKD).
Summary: Biliary atresia (BA) is a biliary disease of young infants that, untreated, leads universally to cirrhosis and the need for liver transplantation. The cause may be infectious but remains unknown, and BA can be challenging to diagnose in timely fashion. Despite available treatment, most children require liver transplantation during childhood. Investigations of the pathogenesis of BA, and to develop better diagnostic tools and therapies, remain a critical need. Limited data suggests that the composition of the intestinal microbiome of infants with BA is distinctive versus infants with other forms of liver disease, and between those infants with BA who respond well to treatment versus those who do not. We propose to definitively characterize the intestinal microbiome in infants with biliary atresia. Our approach will constitute the first ever search for the signature of an infectious disease trigger in the gut, and may establish the intestinal microbiome as a diagnostic biomarker and/or prognostic indicator.
Non-Invasive 4D Imaging of Living Host-Microbiome Interfaces
Key Personnel: Eric Donarski (Graduate Student)
Summary: The human gut microbiome consists of vast bacterial communities containing both beneficial commensal bacteria as well as pathogenic strains. Some of these bacteria form cohesive communities called biofilms that provide protection from mechanical and chemical factors, including turbulence due to fluid flow, host secreted antimicrobial compounds, as well as antibiotics. In vitro studies on bacterial biofilms have established that the procession from individual cell actions to coordinated communal behavior forms a social phenotype wherein spatial structure of the microbial community is a key determinant for higher-order function. However, the individual cell behaviors and the resulting social phenotypes of bacterial communities near living human epithelial interfaces remain largely unknown.
Current live-cell microscopy approaches for imaging host-microbiome interfaces have limited spatial and temporal resolution and often fail to recapitulate the physiological conditions experienced by bacteria in the human gut. Recent advances in tissue culture technology have begun to address the latter issue. For example, microfluidic organ-on-chip devices (tissue chips) enable physiologically relevant reconstitution of host epithelia, endothelia, and epithelia-bacteria co-cultures under precisely controllable physical and chemical conditions. When grown in tissue chips, human intestinal organoid-derived tissue cultures faithfully reproduce intestinal tissue physiology, including polarized epithelia with villi-like structures, strong barrier function, mucus production, and brush border digestive enzyme activity. Currently available tissue chips are however incompatible with recent light sheet fluorescence microscopy platforms. This incompatibility precludes non-invasive high-resolution live-cell imaging of bacterial cell behaviors at these faithfully reconstituted host-microbiome interfaces. The goal of the proposed work is to develop dual-channel microfluidic devices that provide the same physiological conditions as tissue chips, but additionally provide unobstructed optical access for non-invasive, high-resolution, 3D time-lapse imaging by lattice light-sheet microscopy.
Microbial composition of semen affects expression of PtdSer on sperm and therefore affects fertility
Key Personnel: Dylan Hutchison, MD (Research Resident), Claudia M. Rival, PhD (Research Scientist), Ryan P. Smith, MD (Associate Professor), and Jeffrey J. Lysiak, PhD (Associate Professor) Department of Urology, University of Virginia.
Summary: Every year approximately 7 million couples seek infertility treatment in the United States, and half of these cases will be attributable to the male. In fact, the cause of infertility in 40% of these men will be unknown. There has been very little advancement in male infertility evaluation over the last several decades. The standard evaluation consists of a conventional semen analysis which relies only on morphology, numbers, and motility to assess a male’s fertility. Potential causes of male factor infertility include urogenital tract infections; yet, to date there are few studies on the seminal microbiome. Results of these limited studies suggest that the seminal microbiome does have an impact on male fertility and semen parameters; however, the specific molecular mechanisms by how it may impact male fertility are lacking. This project aims to understand how the seminal microbiome might influence the expression of a molecule on the sperm surface that is essential for fertilization. Results from these studies will provide insight into the urogenital microbiome, its possible impact on sperm function, and explore potential treatable aspects of male infertility.
Archaea in human health and disease
Key Personnel: Emily Byrd (Graduate Student)
Summary: The resident microbiota play positive and negative roles in human health; therefore, manipulation of the microbiota may be an effective means to bolster health. In order to do this, mechanistic understanding of host-microbiota interplay is required. Although an increasing number of studies present functional information concerning roles of discrete microbes, the overwhelming majority of data on the microbiota are correlation-based. This is especially true concerning methanogens, the methane- producing members of the Archaea. Methanogens play a key role in the degradation and availability of metabolites and are considered keystone species in diverse, non-human environments. It has been hypothesized that methanogens play a similar role in the human gastrointestinal (GI) tract and may influence human health, positively or negatively. This seems likely as methanogens are the predominant Archaea in the GI tract and are present in nearly 100% of the world’s population. However, to date, there have been virtually no causative or functional studies on the contributions of methanogens to health or disease. Here, we will examine the potential for methanogens to modulate host and bacterial gene expression and metabolism.
Functional Analysis of an Enteric Neuron-on- a-Chip in the Presence of Intestinal Microbial Metabolites
Key Personnel: Arabinda Mandal (Research Scientist)
Summary: Intestinal failure is a devastating and potentially life-threatening condition that afflicts hundreds of thousands of people. There are several etiologies and all of them can exacerbated by intestinal dysmotility. The complex physiology of intestinal motility and function is only partially understood, but there is a growing appreciation that the intestinal microbiota play an important role in enteric neuron development and neuron-potentiated intestinal motility and pathophysiology. This study utilizes an innovative organ on chip technology to identify potential pathways of communication between the gut bacteria and intestinal neurons.
Characterizing the role of the aggregative adherence fimbriae of enteroaggregative Escherichia coli in adherence and interactions with mucin
PI: James Nataro, M.D., Ph.D., M.B.A.
Key Personnel: Laura Gonyar (Research Scientist)
Summary: Enteroaggregative Escherichia coli (EAEC) is a common cause of diarrhea in both developed and developing countries. EAEC infection, even asymptomatic, is associated with linear growth faltering in children in developing countries, and the mechanism of this association is not known. Growth faltering is a significant, understudied public health concern, contributing to life-long deficits in growth, cognitive abilities, and socioeconomic potential. Better elucidation of the interactions between EAEC and the human gastrointestinal mucosa is needed to understand the role of EAEC infection in the etiology of growth faltering. The aggregative adherence fimbriae (AAF) expressed by EAEC mediate physical attachment to the gastrointestinal mucosa, as demonstrated in human tissue culture cells and human tissue explant models, and also promote IL-8 secretion and immune cell migration in tissue culture models. A role for AAF in infection of animal models is not proven and animal models do not fully recapitulate EAEC disease, which emphasizes the need for human-derived model systems to fully understand the role of AAF in EAEC infection.
Human colonoids are derived from human colon biopsies and represent a novel model system for studying enteric pathogenesis. Human colonoids recapitulate many aspects of normal intestinal physiology, allowing for more complete modeling of the human gastrointestinal mucosa than traditional cell culture methods. Importantly, differentiated colonoids produce a layer comprising the secreted mucin MUC2. This mucus layer is an important barrier that pathogens must traverse to colonize the surface of the epithelium, and these interactions are not well understood using existing model systems. We previously identified that AAF/II, produced by EAEC strain 042, determines the abundance and location of EAEC adherence within the mucus layer during infection of colonoids seeded as 2D monolayers on Transwell supports. Culture of colonoids in the recently developed Emulate Gut-on-a-Chip system results in the formation of a taller, more complex mucus layer than culture on Transwell supports, representing a significant advancement in modeling the gastrointestinal mucosa. We propose to characterize the role of AAF in adherence and interactions with mucins in the novel Gut-on-a-Chip model system.
A Young Mouse Microbiome Protects Aged Mice from C. difficile Infection
PI: Jae Shin, Ph.D.
Key Personnel: Deiziane Viana da Silva Costa (Research Scientist), Caroline Whitt (Medical Student), Sophia Goldbeck (Undergraduate Student)
Summary: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated infections and is thought to be the reason behind diarrheal diseases being the only infectious cause of death to increase in the United States between 2000 and 2014. More importantly, the elderly population is disproportionately affected by CDI, both in numbers and in deaths. Although many factors put older patients at risk for worse outcome with CDI, advance age by itself comes up as an important factor leading to more severe outcomes even when controlling for various comorbidities. Our lab has been leading the research on the effect of aging on CDI outcome using an aged mouse model of CDI. We have shown that the aged mice had higher mortality compared to young mice, which was mediated by a difference in host response rather than a difference in infection burden. We also demonstrated that fecal microbiota transplant (FMT) from young mice conferred protection from death by CDI in aged mice but FMT from age mice did not transfer the susceptible phenotype to young mice. From our microbiome analysis, the members of the Bacteroidetes phylum seem to be associated with the protective effects of the young mouse microbiome and the diversity of the microbiome in the aged did not change with FMT. This project aims to show the protection that a young mouse microbiome confers on aged mice against CDI is caused by specific bacteria that affect the bile acid metabolism in the gut, which leads to a change in host immune response.