Fourth Annual Microbiome Symposium November 9th, 2017

BRB II/III AuditoriumPhiladelphia, PA 19104

Table of Contents

Wireless Access Instructions................................................................................... 3

Agenda......................................................................................................................4

Speaker Biographies.................................................................................................5

Lecture Abstracts......................................................................................................7

Short Talk Abstracts.................................................................................................9

Poster Abstracts......................................................................................................13(Posters will be displayed during event reception)

Acknowledgements.................................................................................................26

Attendee List...........................................................................................................27

Wireless Access Instructions (AirPennNet-Guest)

Automatic configuration through AirPennNet-Help

AirPennNet-Help is a wireless network which delivers a wizard called Cloudpath to assist University of Pennsylvania students, faculty, staff, and guests with a PennKey to configure and connect their devices to AirPennNet. When in a campus wireless zone:

1. Connect to the wireless network: AirPennNet-Help.2. Open a web browser and navigate to: www.upenn.edu3. Follow the on-screen instructions to configure your device to connect to AirPennNet.

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E.R. Marookian Auditorium (Lecture Room 130) Hill Pavilion 380 South University Avenue Philadelphia, PA 19104

Auditorium BRB II/III 421 Curie Boulevard Philadelphia, PA 19104

* Fourth Annual Microbiome Symposium *Co-Organizers: Robert Baldassano MD; Daniel Beiting PhD; Frederic Bushman PhD; Gary Wu MD

Wednesday, November 8th, 2017 Venue: E.R. Marookian Auditorium (Lecture Room 130/Hill Pavilion)

6-7p

University Community & General Public Talk “I Contain Multitudes: The Microbes Within Us and a Grander View of Life” Ed Yong, MPhil; Science journalist, National Geographic contributor, and award winning author

Joan C. Hendricks, VMD/PhD Dean, School of Veterinary Medicine

Thursday, November 9th, 2017 Venue: BRB II/III Auditorium 7-8a Registration & Breakfast

8-8:15

Welcome & Opening Remarks David Piccoli, MD

Chief, Division of Gastroenterology, Hepatology & Nutrition Children’s Hospital of Philadelphia

Jonathan Epstein, MD Executive Vice Dean & CSO; Perelman School of Medicine

8:15-9

“Control of Pathogen Colonization by Host Immunity and the Microbiota in the Gut “ Gabriel Nunez, MD Paul de Kruif Endowed Professor, Inflammation & Immunology; Co-Director, Immunology & Host Response Program; Department of Pathology, University of Michigan

Introduction/Moderation: Gary Wu, MD

9:05-9:35

Short Talks • “Commensal microbes induce serum IgA responses that protect against polymicrobial sepsis”

Joel Wilmore, PhD • “Origins of the Anaerobic Gut Lumen: Microbes vs. Chemistry”

Elliot Friedman, PhD Introduction/Moderation: Gary Wu, MD

9:40-10:25 “Colon Cancer: Bugs, Community and Genes” Cynthia Sears, MD Professor of Medicine, Johns Hopkins University

Introduction/Moderation: Gary Wu, MD 10:25-10:45 Coffee Break

10:45-12:15

New Technologies • Microbiome Database – Daniel Beiting, PhD• ICU Specimen Biobanking – Ronald Collman, MD• High Throughput Screening & Microbial Metabolomics – Sara Cherry, PhD• Proteomics in the Microbiome – Benjamin Garcia, PhD• Oxford Nanopore – Lisa Mattei, PhD• Pipelines for Metagenomic Analysis – Kyle Bittinger, PhD

Introduction/Moderation: Frederic Bushman, PhD 12:15-1:15 Lunch

1:15-2:00 “Moms, Milk and Microbes: How to Build Healthy Babies” Grace Aldrovandi, MD/CM Chief of the Division of Pediatric Infectious Diseases, University of California, Los Angeles

Introduction/Moderation: Robert Baldassano, MD

2:05-2:40

Short Talks • “Population structure of the human gut microbiome across ethnically diverse sub-Saharan Africans”

Meagan Rubel, MPH, PhD Candidate• “Bacterial Contamination of Stethoscopes used in an Intensive Care Unit through 16S rRNA Gene Analysis”

Vincent Knecht, BS Introduction/Moderation: Robert Baldassano, MD

2:45-3:15 Coffee Break

3:20-4:05 “Diverse Mechanisms of Antagonism Among Abundant Gut Bacteroidales” Laurie Comstock, PhD Associate Microbiologist, Brigham and Women's Hospital; Associate Professor of Medicine, Harvard Medical School

Introduction/Moderation: Daniel Beiting, PhD

4:10-4:55 “Mechanisms of Bacterial Competition in the Inflamed Gut” Manuela Raffatellu, MD Professor, Department of Pediatrics, University of California, San Diego

Introduction/Moderation: Daniel Beiting, PhD

5:00-5:10 Closing Remarks Daniel Beiting, PhD

5:15-6:15 Reception & Posters

Speaker Biographies

Gabriel Nunez, MD Dr. Nuñez earned his M.D. degree from the University of Seville, Spain, in 1977. He received postdoctoral training in Immunology at the University of Texas Southwestern Medical Center, Dallas (1979–1984) and residency training in Anatomical Pathology at Washington University in St Louis (1985–1990). In 1987, he joined the laboratory of Stanley Korsmeyer at Washington University, where he studied the function of the anti-apoptotic protein BCL-2. In 1991, he joined the Department of Pathology at the University of Michigan in Ann Arbor as an Assistant Professor and was promoted to full Professor in 2001. He holds the Paul de Kruif Endowed Professorship in Academic Pathology. He is also the Co-Director of the Immunology and Host Response Program at the University of Michigan Comprehensive Cancer Center. His laboratory identified NOD1 and NOD2, the first members of the Nod-like receptor (NLR) family, a class of pattern-recognition receptors that mediate cytosolic sensing of microbial organisms. Dr. Nuñez and colleagues showed that genetic variation in a NLR family member, NOD2, is strongly associated with susceptibility to Crohn's disease. Currently, the Nuñez laboratory is interested in signaling pathways regulating innate immunity, the pathogenesis of inflammatory disease and the role of the microbiota in host defense and colitis. Dr. Nuñez is the author of more than 375 scientific publications. His research program is supported by grants from the National Institutes of Health.

Cynthia Sears, MD Cynthia L. Sears, M.D. received her medical degree from Thomas Jefferson Medical College followed by training in internal medicine at The New York Hospital in New York City. She trained in Infectious Diseases at the Memorial Sloan Kettering Cancer Institute and the University of Virginia where she was a member of the infectious diseases faculty until 1988. Subsequently, Dr. Sears joined the faculty at Johns Hopkins University School of Medicine. She is now the Microbiome Program Leader for the Bloomberg Kimmel Institute for Cancer Immunotherapy and the Director of the Johns Hopkins Germfree Murine Facility as well as Professor of Medicine, Oncology and Molecular Microbiology and Immunology in the Divisions of Infectious Diseases, Gastroenterology and Tumor Immunology, Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and the Bloomberg School of Public Health. She is an expert in foodborne and enteric infections and has studied the pathogenesis of enterotoxigenic Bacteroides fragilis (ETBF) both in the laboratory and in clinical settings over the past 25 years. For the last several years, the focus of the Sears laboratory has turned to determining how the microbiota and specific bacteria induce colon carcinogenesis. The Sears laboratory integrates studies in humans and mouse models, employing microbiology, bioinformatics and immunologic methods to achieve their goal. Dr. Sears served as an Associate Editor for Clinical Infectious Diseases from 2000-2016. She has been an active member of the Infectious Diseases Society of America (IDSA) for more than 20 years, serving the Society in numerous capacities. Since November, 2016, she is the Vice President of the IDSA Board of Directors.

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Grace Aldrovandi, MD/CM Dr. Grace Aldrovandi, MD, CM is the Professor and Division Chief of Pediatric-Infectious Diseases at UCLA. She attended McGill University in Montreal, Canada, where she obtained her B.A. in Political Science and BSc in Physiology. She also received her Medical Degree and completed her internship and residency at McGill University Facility of Medicine. She came to Los Angeles and trained as a fellow of Infectious Diseases at UCLA and later moved on to become a Professor of Pediatrics, Pathology, and Molecular Microbiology and Immunology at the Keck School of Medicine of USC where she extensively studied breastfeeding and HIV transmission at The Saiban Research Institute of CHLA. Her influential work showing that there was no net benefit to ceasing breastfeeding to prevent HIV transmission has changed World Health Organization guidelines. In 2004, she was awarded the Elizabeth Glaser Scientist Award for her work on breast milk transmission of HIV. In 2014, she was part of a national consortium awarded $21 million from the NIH National Institute of Allergy and Infectious Diseases for studies that advanced the prevention and treatment of HIV and its complications for infants, children, adolescents, and pregnant/postpartum women throughout the world. Dr. Aldrovandi is a world-class translational physician-scientist and has published over 100 peer-review publications and eight book chapters and has lectured internationally. She is currently a member of the American Academy of Pediatrics Committee on Pediatric AIDS and of the Brighton Collaboration Vaccine Safety Working Group. She has been the American Academy of Pediatrics representative on the National Association of County and City Health Officials and on the CDC’s Smallpox Guidelines Project. She has also chaired national and international studies on HIV pathogenesis within the International Maternal, Pediatric, and Adolescent AIDS Clinical Trials Network (IMPAACT) and the Adolescent Trial’s Network (ATN).

Laurie Comstock, PhD Laurie Comstock is an Associate Professor at Harvard Medical School with a primary appointment in Infectious Diseases at Brigham and Women’s Hospital. She obtained a Ph.D. from Wake Forest University Medical Center studying Borrelia burgdorferi. She performed her post-doctoral work at the Center for Vaccine Development at the University of Maryland Medical Center studying Vibrio cholerae. With a background in bacterial pathogenesis and genetics, she began a new research direction more than 20 years ago studying the Bacteroidales, the most abundant order of human gut bacteria. Her lab has made fundamental discoveries regarding the biology of these important gut bacteria. Her lab is currently engaged in studying the ecology of the mammalian gut microbiota, specifically studying how abundant bacterial members of this ecosystem interact with each other to promote or limit growth.

Manuela Raffatellu, MD Manuela Raffatellu is a Professor in the Department of Pediatrics at the University of California, San Diego School of Medicine. She received her M.D. at the University of Sassari, Italy, in 2000 and her M.S. in Clinical and Tropical Microbiology at the same institution in 2002. She joined the laboratory of Dr. Andreas Bäumler as a postdoctoral fellow in 2002, first at Texas A&M University and then at the University of California, Davis. She started her own lab at the University of California, Irvine in 2008, where she was promoted to Associate Professor with tenure in 2014. Her research focuses on many aspects of Salmonella interaction with the mucosal immune response and with the intestinal microbiota in the inflamed gut. Her recent efforts aim to design new strategies to reduce Salmonella intestinal colonization without affecting the microbiota composition. She is the recipient of several awards, including the IDSA ERF/NFID Astellas Young Investigator Award, the ICAAC Young Investigator Award from the American Society for Microbiology, and the Burroughs Wellcome Funds Investigator in the Pathogenesis of Infectious Disease Award.

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Lecture Abstracts

“Control of Pathogen Colonization by Host Immunity and the Microbiota in the Gut”

Gabriel Nunez, MDThe mechanisms that allow enteric pathogens to colonize the intestine in the presence of the microbiota are unclear. Furthermore, how host immunity and the indigenous microbiota regulate pathogen colonization in the gut remain poorly understood. Our laboratory is using Citrobacter rodentium, a mouse pathogen that models human infections by enteropathogenic E. coli, to understand the mechanisms that regulate the colonization and clearance of the pathogen in the gut. These studies have revealed how the pathogen colonizes and replicates successfully early during infection and how host immunity and the indigenous microbiota cooperate to eradicate the pathogen in the later stage of the infection. These studies have also revealed that Clostridia species protect the host from colonization by C. rodentium and Salmonella enterica in the intestine. In addition, these studies have shown that the intestine of mice after birth lack protective Clostridia species providing an explanation to account for the enhanced susceptibility of mice and humans to enteric infection during the neonatal period.

“Colon Cancer: Bugs, Communities and Genes” Cynthia Sears, MD

The colonic microbiome is hypothesized to contribute to the induction and progression of colon cancer. While select bacterial species have been implicated in colon carcinogenesis, recent data also suggest that bacterial community organization and composition are carcinogenic. Studies of paired surgical CRC samples and normal colon mucosa as well as colon biopsies of healthy controls undergoing screening colonoscopy revealed that sporadic colon tumors located proximal to the hepatic flexure are characterized by invasive polymicrobial biofilms that extend to normal colon tissue far distant from the tumor. In contrast, colon mucosal biofilms occur less frequently in individuals with colon cancer distal to the hepatic flexure and in only about 15% of mucosal samples from healthy colonoscopy controls. This talk will present an update on the intersection of individual microbes, biofilms, host genetics and mechanisms of colon carcinogenesis. Together our studies support a model by which specific bacteria with their virulence genes as well as microbiota organization act with host immune responses and genetics to contribute to colon cancer pathogenesis.

“Moms, Milk and Microbes: How to Build Healthy Babies” Grace Aldrovandi, MD/CM

Microbial colonization of the infant gut is a complex process that is important for lifelong health. Breastfeeding has long been associated with distinct infant stool bacteria and protection against a variety of infectious and inflammatory disease. However, the mechanisms by which breastfeeding confers these benefits are poorly understood. In this talk, we will discuss the role of milk microbes in the establishment of the infant microbiome.

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“Diverse mechanisms of antagonism among abundant gut Bacteroidales” Laurie Comstock, PhD

Despite the large number of studies analyzing the gut microbiota, there are still relatively few mechanistic studies aimed at understanding basic biological properties of this ecosystem and its members. In recent years, our lab has been studying how predominant gut Bacteroidales members interact with each other in both beneficial and competitive/antagonistic relationships. These studies are essential to understanding how these bacteria become established in the mammalian intestine to form stable health-promoting communities. This seminar will highlight various types of secreted antimicrobial molecules produced by the gut Bacteroidales. We are beginning to understand the breadth of secreted antimicrobial molecules produced by the gut Bacteroidales, their targets and mechanisms of action in sensitive cells, and their importance in conferring a fitness benefit to these bacteria in the mammalian gut microbiota.

“Mechanisms of Bacterial Competition in the Inflamed Gut” Manuela Raffatellu, MD

Mucosal surfaces are often the first interface between the host, the commensal microbiota and pathogenic microorganisms. Among the most complex of these environments is the gut mucosa, where trillions of bacteria (the commensal microbiota) coexist with the host in a mutually beneficial equilibrium. Infection with enteric pathogens like Salmonella Typhimurium disrupts this equilibrium by causing intestinal inflammation, a response that suppresses the growth of the commensal microbiota and favors the growth of S. Typhimurium by several mechanisms. Infection with S. Typhimurium results in the upregulation of antimicrobial proteins that inhibit bacterial growth by limiting the availability of essential nutrients, including metal ions, in a process termed “nutritional immunity”. My lab studies the mechanisms by which S. Typhimurium evades nutritional immunity and acquires metal ions in the inflamed gut, allowing this pathogen to successfully compete with the microbiota for these essential nutrients.

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Short Talk Abstracts

“Commensal microbes induce serum IgA responses that protect against polymicrobial sepsis” Joel R. Wilmore, Brian Gaudette, Daniela Gomez Atria, and David Allman Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA

Serum IgA antibodies are readily detected in mice and people, yet the relationship between serum and mucosal IgA responses and the role of serum IgA antibodies in host protection remain uncertain. Often serum IgA is thought of as ‘natural’ antibody suggesting it is sourced from relatively non-specific T-independent B1 B cell responses and not a function of exposure to commensal microbes. We report that select commensal bacteria induce several facets of systemic IgA-mediated immunity. Exposing conventional mice to a unique microflora including several members of the Proteobacteria phylum elevated serum IgA levels, and led to the induction of large numbers of long-lived IgA-secreting bone marrow plasma cells. These IgA-secreting bone marrow plasma cells are characterized by high levels of somatic hypermutation and correlate with significantly increased numbers of IgA+ Peyer’s patch germinal center B cells. Furthermore, serum IgA induced after colonization with this unique microbiota bound to a restricted collection of bacterial taxa, and antigen-specific serum IgA antibodies were readily detected after intestinal colonization with the Proteobacteria member Helicobacter muridarum. Using the cecal ligation and puncture (CLP) model of polymicrobial sepsis we observed that mice with high concentrations of serum IgA are resistant to sepsis induced mortality. In contrast, CLP was lethal in mice containing low concentrations of serum IgA, an outcome that was reversed by transferring serum containing high concentrations of IgA. We conclude that commensal microbes overtly influence the serum IgA repertoire and provide constitutive protection against bacterial sepsis.

“Origins of the Anaerobic Gut Lumen: Microbes vs. Chemistry” Elliot S. Friedmana, Kyle Bittingerb, Tatiana V. Esipovac, Likai Houd,1, Lillian Chaua, Jack Jianga, Clementina Mesarose, Peder J. Lundc,f, Xue Liangg,2, Garret A. FitzGeraldg, Mark Goulianh, Daeyeon Leed, Benjamin A. Garciac,f, Ian A. Blaire, Sergei A. Vinogradovc,j,* Gary D. Wua*

a Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 b Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 c Department of Biochemistry and Biophysics, Perelman School of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 d Department of Chemical and Biomolecular Engineering, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 e Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104

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f Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 g Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 h Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 j Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, 19104

Background: The succession from aerobic and facultative anaerobic bacteria to obligate anaerobes in the infant gut microbiota, as well as the differences in the composition of the mucosally-adherent and the luminal gut microbiota, provide indirect evidence in humans that the gut microbiota consumes oxygen diffusing from intestinal tissue to maintain anaerobic conditions in the lumen of the gut. However, the distribution of oxygen between the host and its gut microbiota remain poorly characterized due to technical limitations. We investigated the role of the microbiota and fecal chemistry in establishing and maintaining anaerobic conditions in the lumen of the gut. Methods: The phosphorescence quenching method was used to quantify oxygen levels in both the intestinal tissue and the gut lumen of conventional and germ-free mice. In conventional mice, oxygen levels were correlated with the biomass and composition of both mucosally-adherent and luminal microbes along the length of the intestinal tract. In vitro experiments using the feces of conventional and germ-free mice were used to examine differences in oxygen depletion kinetics. Lipidomic and proteomic profiling was performed to identify oxygen-consuming chemical reactions. Results: The luminal oxygen levels along the length of the gut were found to be the same in both conventional and germ-free mice; these include high oxygen levels in the proximal small intestine and anaerobic conditions in the distal gut. In vitro oxygen measurements revealed that germ- free feces effectively consume oxygen, although at a rate significantly slower than feces from conventional mice. Lipidomic and proteomic analyses of germ-free feces from in vitro experiments showed significant oxidation of unsaturated phospholipids and moderate oxidation of proteins. In conventional mice, we show that the taxonomic composition of the gut microbiota adherent to the gut mucosa and in the lumen throughout the length of the gut paralleled levels of luminal oxygen determined by our empirical measurements. Consistent with the notion that the gut microbiota can consume oxygen, there was an increase in biomass of the gut microbiota in the distal gut corresponding to the decrease in luminal oxygen. Conclusions: The remarkable finding that germ-free feces can consume oxygen provides an explanation for observations in gnotobiotic mice where individual obligate anaerobes can effectively colonize the gut of germ-free mice and demonstrate fermentative metabolism. In total, these results demonstrate the dynamic oxygen interaction of the mammalian host with its gut microbiota. Both the microbiota and the chemistry of feces regulate luminal oxygen levels that, in turn, shape the distinctive compositions of the community in different regions of the gut.

aCurrent affiliation: School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China bCurrent affiliation: Merck Research Laboratory Cambridge Exploratory Science Center, Cambridge, Massachusetts

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“Population structure of the human gut microbiome across ethnically diverse sub-Saharan Africans” Meagan A. Rubel2,†, Matthew EB Hansen1,†, Aubrey G. Bailey3, Jaanki R. Dave1,5, Alessia Ranciaro1, Simon R. Thompson1,#, Michael Campbell1,^, William R. Beggs1, , Sununguko Wata Mpoloka6, George Mokone7, Maitseo M. M. Bolaane8, Thomas Nyambo9, Frederic D. Bushman3 & Sarah A. Tishkoff1,4

1. Department of Genetics, Perelman School of Medicine, University of Pennsylvania,Philadelphia, PA 19104

2. Department of Anthropology, School of Arts and Sciences, University of Pennsylvania,Philadelphia, PA 19104

3. Department of Microbiology, Perelman School of Medicine, University of Pennsylvania,Philadelphia, PA, 19104

4. Department of Biology, School of Arts and Sciences, University of Pennsylvania,Philadelphia, PA 19104

5. The Commonwealth Medical College, Scranton, PA 185096. Department of Biological Sciences, University of Botswana, Gaborone, Botswana7. Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone,

Botswana8. History Department, University of Botswana, Gaborone, Botswana9. Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es

Salaam, Tanzania

Global populations with different degrees of industrialization have shown marked differences in their gut microbial (GM) composition. Notably, “Westernized” microbiomes from individuals on processed diets largely derived from industrial agropastoralism show decreased diversity as compared to rural, non-industrialized groups practicing traditional forms of subsistence. Prior research has tended to focus on comparing individual populations from geographically disparate regions, which ignores the complex relationships with neighboring groups. Here, we report the GM bacterial compositions of seven ethnically diverse rural populations in Tanzania and Botswana (N=114) and one Western cohort from Philadelphia, U.S.A. (N=12), using 16S ribosomal sequence (16S rRNA V1-V2) classification. The seven African populations include two current or recent hunter-gatherer populations, three small-scale agropastoralist communities, and two current or recent pastoralists groups. A subset of Africans were genotyped on a 5M Omni SNP array, and this was used to test the relative impact of host genetic relatedness on compositional fitness. We find that GM diversity distances are strongly associated with host genetic similarity after controlling for geographic distance. Partitioning the bacterial abundance variation using linear mixed models indicates that several bacteria, most notably Ruminococcus, associate significantly with host relatedness. Some Botswanan Bantu agropastoralist GMs cluster close to U.S. samples, which could be the result of factors such as increased urbanization and industrialization. The mean bacterial diversity per host decreases from Tanzania to Botswana to the U.S., while the mean bacterial phylogenetic distances between individuals in the same population increases from Tanzania to Botswana to the U.S. Although the GMs of all populations have a similar rank order of most abundant bacteria, with Prevotellaceae and Ruminoccocceae as the two most abundant known taxonomic families, there is diversity in their relative abundances and in the presence/absence of lowly abundant bacteria. There is no clear

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signal of GM compositional "types" associated with subsistence lifestyle, and the evidence for unique single taxa that can distinguish pastoralism or hunter-gatherer life-style is marginal. Instead, we find evidence that the range of GM compositions is influenced by geographic region and host genetics.

“Bacterial Contamination of Stethoscopes used in an Intensive Care Unit through 16S rRNA Gene Analysis” Vincent R. Knecht, Hari Shankar, Aurea Simon-Soro, Erik L. Clarke, Brendan J. Kelly, John E. McGinniss, Ize Imai, Ayannah S. Fitzgerald, Kyle Bittinger, Frederic D. Bushman, Ronald G. Collman

Departments of Medicine, Microbiology and Pediatrics, University of Pennsylvania School of Medicine

Background. Hospital acquired infections (HAI) increase patient morbidity and mortality, and are a burden on the health care system. Some HAIs may result from transmission of pathogens between patients. One potential vector of transmission may be stethoscopes carried by practitioners and used on multiple patients. Previous studies of stethoscope contamination in the hospital setting have been limited to culture based techniques, and show varying levels of contamination with potential pathogens. We wished to comprehensively define the bacterial communities on stethoscopes in an intensive care unit (ICU), a particularly important location for HAIs. Methods. We swabbed the diaphragm surface of three sets of stethoscopes: (a) Personal stethoscopes carried by physicians (n=20); (b) Disposable stethoscopes for single-patient use that were kept in individual patients’ rooms (n=20); (c) Disposable single-patient stethoscopes that were clean (newly-unboxed) prior to use (n=10). Environmental controls included the saline and swab used for stethoscope sampling, and PCR reagents. DNA was extracted from stethoscope samples and environmental controls, and subjected to bacterial 16S rRNA gene V1V2 sequencing, as well as estimate of bacterial content based on 16S amplicon quantification following PCR. An addition set of physician stethoscopes (n=10) were sampled before and after cleaning with a hydrogen peroxide wipe (which is a common practice among physicians to “decontaminate” stethoscopes between patients). Results. Physician stethoscopes had the highest level of bacterial contamination, followed by Patient Room stethoscopes, while Clean stethoscopes were indistinguishable from environmental background. Physician stethoscopes also showed the highest richness of bacterial taxa. Community analysis by weighted UniFrac showed Physician and Patient Room stethoscopes were indistinguishable, and significantly different from Clean stethoscopes and environmental controls (which were themselves indistinguishable from each other). Stethoscope communities were dominate by taxa typical of skin (Propionibacterium, Corynebacterium, Staphylococcus), oral (Prevotella, Actinomyces, Porphomonas), and gut (Bacteroides) origin. Among nosocomial pathogens that can be identified to the species level with this primer set (S. aureus, E. fecalis & faecium, S. maltophilia), detection was common and often exceeded 1% relative abundance. Cleaning of Physician stethoscopes resulted in a significant reduction in bacterial contamination, although 16S levels were reduced to that of Clean stethoscopes in only half of those cleaned. Conclusions. Stethoscopes used in an ICU are significantly contaminated with bacterial DNA. Contaminating bacteria are mainly normal skin, oral and gut flora, but also frequently include bacteria associated with HAIs. Standard cleaning practices reduce the overall level of bacterial contamination, although only half of the time reaches the level of background. Physician stethoscopes may be a vector for patient-patient transfer of relevant bacteria within an ICU.

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Poster Abstracts

1. “Transfer of Anelloviridae Populations between Graft and Host duringLung Transplantation”Arwa Abbas1, Jacque C. Young1, Erik L. Clarke1, Joshua M. Diamond1, Ize Imai1, Andrew R. Haas1, Edward Cantu1, David J. Lederer2, Keith Meyer3, Rita K. Milewski1, Kim M. Olthoff1, Abraham Shaked1, Jason D. Christie1, Frederic D. Bushman1*, Ronald G. Collman1*

1. University of Pennsylvania Perelman School of Medicine2. Columbia University College of Physicians and Surgeons3. University of Wisconsin School of Medicine and Public Health

*Corresponding authors

Lung transplantation is the only long-term option for end-stage lung diseases but median survival for lung transplant recipients remains low. Certain respiratory tract microorganisms are known to influence lung transplantation outcomes. Solid organ transplantation and the accompanying immunosuppression disrupt host–virus interactions, which can result in reactivation of latent viruses, virus transfer from donor to recipient, and de novo infections. However, colonization and infection are typically identified using targeted clinical assays for specific viruses, leaving the behavior of full viral populations–the “virome”–understudied. We interrogated the virome in bronchoalveolar lavage and serum in the peri-transplant period in 46 lung donor-recipient pairs, and longitudinally during the first 6-16 months post-transplant in 13 pairs. Shotgun metagenomic sequencing revealed a community of DNA viruses from groups known to replicate in animal cells and bacteria. Anelloviridae, a family of non-enveloped single-stranded DNA viruses, dominated donor and recipient lung and blood viromes and perioperative dynamics of these viruses in the lung were associated with primary graft dysfunction. We then developed methods to track temporal dynamics of these viruses and observed transfer of Anelloviridae lineages from the donor organ to recipient in 4/7 subjects where transfer from the donor could be queried, and transfer of lineages from the recipient into the allograft in 6/10 cases that could be queried. The longitudinal behavior of Anelloviridae populations was complex–some lineages persisted, others disappeared, and new lineages appeared within a lung transplant recipient. Thus, metagenomic analysis revealed that whole viral populations can move between graft and host in both directions, showing that organ transplantation is associated with implantation of both the allograft and commensal viral communities.

2. “Regulation of Keratinocyte Gene Expression by the Skin Microbiome”Casey Bartow-McKenney1*, Jackie Meisel1, Joseph Horwinski1, Elizabeth Grice1

1Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA *Corresponding author; casb@upenn.edu

The skin microbiome represents a milieu of microorganismal communities adapted to their host in both composition and physiological potential, demonstrating a coevolutionary relationship that inhabits one of the largest human organs. However, cutaneous host-microbiome relationships of

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the skin remain poorly characterized, including the extent to which the microbiota modulate host genetic control. Our preliminary data from murine whole skin (dermis + epidermis) demonstrated that 2,820 genes were differentially expressed (DE) between germ-free (GF) and conventionally raised (CR) mice. Because epidermal keratinocytes are the predominant cells in contact with skin microbiota, here we explore the epidermal-specific host response to microbial colonization by utilizing RNA-seq on keratinocytes isolated from GF, CR, and conventionalized (CV) mice, a model for acute colonization. Our preliminary analyses found the expression profiles of GF and CR mice to be most distinct, with over 6,000 DE genes, thus recapitulating our previous findings. Additionally, genes that were DE between all three colonization states exhibit a pattern whereby average expression in CV mice falls significantly between the average expression levels of GF and CR mice, demonstrating a microbial-induced shift in CV keratinocyte transcription after colonization. Moreover, CR mice were enriched in DE genes with ontology attributes such as cellular adhesion and epidermal development. Upon further inspection, CR mice exhibited an overall significant increase in expression of genes necessary for the construction, formation, and subsequent degradation of corneodesomes, the main adhesive junction between keratinocytes that strengthens the epidermis until programmed proteolysis occurs, resulting in desquamation. These findings suggest a physiological response by the murine epidermis to the microbiome whereby keratinocytes differentially regulate processes necessary for the maintenance of effective barrier function and epidermal homeostasis. A further understanding of this host-microbiome relationship may aid in identifying etiological causes and putative amelioration of skin disorders such as psoriasis and atopic dermatitis, which have been previously associated with shifts in the composition of the skin microbiome.

3. “Microbial lineages in sarcoidosis: A metagenomic analysis tailored for lowmicrobial content samples” Erik L. Clarke1, Abigail P. Lauder1, Casey E. Hofstaedter6, Young Hwang1, Ayannah S. Fitzgerald2, Ize Imai2, Wojciech Biernat5, Bartłomiej Rękawiecki4, Hanna Majewska5, Anna Dubaniewicz4, Leslie A. Litzky3, Michael D. Feldman3, Kyle Bittinger6, Milton D. Rossman2, Karen C. Patterson2, Frederic D. Bushman1, and Ronald G. Collman2

Departments of 1 Microbiology, 2 Medicine, and 3 Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA Departments of 4 Pulmonology and 5 Pathomorphology and Neuropathology, Medical University of Gdansk, Poland 6 Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, PA

Rationale: The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers. Objective: We sought to identify bacterial, fungal or viral lineages in specimens from sarcoidosis patients enriched relative to controls using metagenomic DNA sequencing. Since DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination. Methods: We analyzed specimens from sarcoidosis subjects (n=93), non-sarcoidosis control subjects (n=72) and various environmental controls (n=150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, bronchoalveolar lavage (BAL), Kveim reagent, and fresh granulomatous spleen from a

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sarcoidosis patient. All specimens were analyzed by bacterial 16S and fungal ITS rRNA gene sequencing. In addition, BAL was analyzed by shotgun sequencing of fractions enriched for viral particles, and Kveim and spleen were subjected to whole-genome shotgun sequencing. Measurements and Main Results: In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared to non-sarcoidosis tissues; in the other tissue set, we detected enrichment of several bacterial lineages in sarcoidosis, but not Cladosporiaceae. BAL showed limited enrichment of Aspergillus fungi. Several microbial lineages were detected in Kveim and spleen, including Cladosporium. No microbial lineage was enriched in more than one sample type after correction for multiple comparisons.Conclusions: Metagenomic sequencing revealed enrichment of microbes in single types of sarcoidosis samples, but limited concordance across sample types. Statistical analysis accounting for environmental contamination was essential to avoiding false positives.

4. “Profiling Complex Population Genomes with Highly Accurate SingleMolecule Reads: Cow Rumen Microbiomes” Cheryl Heiner1, Itai Sharon2, Steve Oh1, Alvaro G. Hernandez3, Itzhak Mizrahi4 and Richard Hall1

1PacBio, Menlo Park, CA; 2Tei-Hai College, Upper Galilee, and MIGAL Galilee Research Institute, Israel; 3University of Illinois at Urbana-Champaign; 4Ben-Gurion University of the Negev, Israel

Determining compositions and functional capabilities of complex populations is often challenging, especially for sequencing technologies with short reads that do not uniquely identify organisms or genes. Long-read sequencing improves the resolution of these mixed communities, but adoption for this application has been limited due to concerns about throughput, cost and accuracy. The recently introduced PacBio Sequel System generates hundreds of thousands of long and highly accurate single-molecule reads per SMRT Cell. We investigated how the Sequel system might increase understanding of metagenomic communities. In the past, focus was largely on taxonomic classification with 16S rRNA sequencing. Recent expansion to WGS sequencing enables functional profiling as well, with the ultimate goal of complete genome assemblies. Here we compare the complex microbiomes in 5 cow rumen samples, for which Illumina WGS sequence data was also available. To maximize the PacBio single molecule sequence accuracy, libraries of 2 to 3 kb were generated, allowing many polymerase passes per molecule. The resulting reads were filtered at predicted single-molecule accuracy levels up to 99.99%. Community compositions of the 5 samples were compared with Illumina WGS assemblies from the same set of samples, indicating rare organisms were often missed with Illumina. Assembly from PacBio CCS reads yielded a contig >100 kb in length with 6x coverage. Mapping of Illumina reads to the 101 kb contig verified the PacBio assembly and contig sequence. These results illustrate ways in which long accurate reads may benefit analysis of complex communities.

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5. “Analysis of the Association between Pediatric Respiratory TractMicrobiome and Asthma Exacerbation and Severity” Mingzhou Fu MPH, Melinda Mary Pettigrew PhD

Yale University School of Public Health

Introduction: Although recent studies have found that the lower respiratory tract microbiome was different in asthmatics compared to non-asthmatics in adults, the microbiome of asthmatics between asthma exacerbation and non-exacerbation has not been well investigated. Objectives: The primary objective of the study was to investigate the change of microbial abundance and diversity in the lower and upper respiratory tracts of asthmatics associated with asthma exacerbation. Methods: This was a cross sectional study where asthmatic children from 5-18 years old were recruited at the emergency department at LeBonheur Children’s Hospital, Memphis, TN. Recruited children were further grouped by asthma exacerbation level and asthma severity level. Induced sputum samples and nasopharyngeal swabs were collected to analyze the microbiome in the two sites with Illumina based sequencing. The primary outcome to measure was the microbial abundance and diversity in the two sites with or without current asthma exacerbation. The secondary outcome to measure was the microbial abundance and diversity in the two sites with various levels of asthma severity. The additional outcome to measure was the specific microbial taxa in the two sites associated with an increased or decreased risk of asthma exacerbation or severity. Results: 51 children from 5-10 years old were recruited. The relative abundance of 9 taxa (e.g. Moraxella) were significantly higher in nasopharyngeal samples, and the relative abundance of 26 taxa (e.g. Streptococcus) were significantly higher in induced sputum samples. No significant difference in abundance and diversity was found with various asthma exacerbation and severity levels in both of the two sites. No specific taxon was significantly associated with an increased or a decreased risk of asthma exacerbation or severity. Conclusion: No significant change of microbial abundance and diversity in the two sites was associated with asthma exacerbation or severity. No specific taxon in the two sites was associated with an increased or a decreased risk of asthma exacerbation or severity. Larger, comparative studies need to be performed to discover subtle difference.

6. “Early Life Stress is Associated with Altered Adult Gut Microbiome inHumans” Liisa Hantsoo, Brendan McGeehan, Stephanie Criniti, Ceylan Tanes, Michal Elovitz, Charlene Compher, Gary Wu, C. Neill Epperson

Background: Early life stress (ELS) programs a dysregulated stress response, including inflammatory and hypothalamic pituitary adrenal (HPA) response, that persists into adulthood. In rodents, ELS produces an altered adult gut microbiome, particularly ratio of Firmicutes to Bacteroidetes, accompanied by greater stimulated proinflammatory cytokine response. In human adults, ELS history is associated with an exaggerated proinflammatory cytokine response to acute stress. However, it is unknown in humans whether 1) ELS is associated with altered gut microbiota and 2) whether exaggerated inflammatory response to acute stress is associated with altered gut microbiota. This study assessed whether 1) ELS and 2) inflammatory or HPA response to acute stress are associated with gut microbiome composition. Methods: Female participants were recruited from a study examining stress, inflammation and pregnancy

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outcomes. Women underwent a twenty-minute laboratory stressor (Trier Social Stress Test; TSST) at 21-34 weeks gestation; serum cytokines (interleukin(IL)-6, tumor necrosis factor-α (TNFα), interferon-γ (IFNγ)) and cortisol were collected pre-stressor (T-5) and post-stressor (T+30, T+65, T+140); area under the curve (AUC) was calculated to represent response over time. Participants completed the Adverse Childhood Experiences (ACE) questionnaire to indicate exposure to ELS; ACE scores 0-1 were considered low ACE, >=2 high ACE. Stool was sampled at 20-26 weeks gestation; 16S sequencing was performed, purified products were analyzed using Illumina MiSeq. Alpha diversity was measured in bacterial richness (number of operational taxonomic units; OTUs) at 10,000 read depth, and Shannon index. Beta diversity was measured with weighted and unweighted UniFrac distances. Differential abundance was assessed in taxa with >1% mean abundance across samples; multiple tests were corrected with the Benjamini-Hochberg method, and false discovery rate (fdr) < 0.05 were considered significant. Permutation Multivariate Analysis of Variance (PERMANOVA) tested associations of microbiome composition with cytokines, cortisol, and ACE. Results: n = 48 women provided gut microbiome and ACE data; a subset of n = 17 completed the TSST. 1) Regarding ACE, there were no differences between high/low ACE groups for richness (p=0.82), Shannon index (p=0.58), nor UniFrac distances (p’s>0.05). High ACE participants had higher relative abundance of Bacteroides (fdr=0.004), Ruminococcaceae (fdr=0.03), Faecalibacterium (fdr=0.007), Dialister (fdr=0.02), Enterobacteriaceae (fdr=0.01), and lower relative abundance of Eubacterium (fdr=0.004), and Phascolarctobacterium (fdr=0.002) versus low ACE. 2) Regarding inflammatory response to acute stress, there were no associations between cytokineAUCs and richness (p’s>0.05), nor Shannon index (p’s>0.05). There was a significant association between cortisol AUC and unweighted UniFrac distance (p=0.041). Cortisol AUC was positively associated with differential abundance of Ruminococcaceae (fdr<0.0001), Prevotella (fdr<0.0001), Ruminococcus (fdr=0.04), and negatively with Bacteroides (fdr=0.006), Megasphaera (fdr=0.0001), and Eubacterium (fdr=0.028). Conclusions: A novel finding in humans, exposure to multiple ACEs was associated with differential abundance of several gut taxa, consistent with rodent models indicating ELS produces lasting impact on gut microbiota. While cytokine response to acute stress was not associated with gut microbiome composition, cortisol response was associated with differential abundance of several taxa, suggesting different gut microbial compositions may associate with altered reactivity to acute stress.

7. “Investigation of the presence of Mycobacterium avium subsp.paratuberculosis in children with Crohn disease using quantitative DNA sequence-based approaches” Casey E. Hofstaedter1, Máire A. Conrad1, Ana M. Misic2, Marie-Eve Fecteau2, Judith Kelsen1, Kyle Bittinger1, Daniel P. Beiting2, Dipti Pitta2, Raymond W. Sweeney2, Robert Baldassano1

1The Children’s Hospital of Philadelphia, Philadelphia, PA, 2School of Veterinary Medicine at The University of Pennsylvania, Philadelphia, PA

Background and Aim: Mycobacterium avium subsp. paratuberculosis (MAP) has been suspected to play a role in Crohn disease (CD) pathogenesis. Prior studies of MAP detection in dairy cows have been more extensively investigated, successfully detecting the organisms by culture and PCR. These studies have shown the organism to be the causative agent in Johne’s disease, an enteritis in ruminants that is histopathologically similar to CD. We aim to use

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techniques which successfully detect MAP in cow feces and apply them to human feces and intestinal biopsy samples of patients with CD and healthy controls to see if MAP infection is correlated with active disease in children with CD. Methods: Using feces and intestinal biopsy samples from known MAP-positive and negative calves, we performed several Mycobacterium-specific DNA extraction methods, aimed at lysing the thick and complex mycobacterial cell wall. To identify the presence of MAP in these samples, we used quantitative PCR and DNA-sequencing methods, both targeted and metagenomic. We applied these methods to samples from pediatric patients with CD and healthy controls. The intestinal samples were taken from eight patients, newly diagnosed with ileocolonic, granuloma-positive CD. Two samples were taken from each patient: one from the terminal ileum, and the other from either the cecum, left colon, or rectum. For half of the patients, tissue samples were obtained during endoscopy, and the other half were obtained during surgical resection. Five out of the eight patients were treatment naïve at the time of sample collection. The other three received antibiotics leading up to sample collection. Results: We correctly identified the presence of MAP in intestinal biopsies from infected dairy calves using quantitative PCR, which aligned with culturing data from these biopsies. In our small subset of samples, we were unable to detect the presence of MAP in humans by any of these techniques. Conclusion: While other groups have been able to identify the presence of this organism as being enriched in patients with CD compared to controls, we have not been able to see this enrichment in our patient population. The successful detection of MAP from intestinal biopsies in calves demonstrates that we can use these techniques to quantitatively identify the number of organisms in intestinal biopsies, without the use of culture-based methods. Here, we have confirmed the difficulty in detecting this organism in humans. Future work is ongoing to improve the sensitivity of our techniques and increase the number of patient samples tested for MAP presence, as only a small subcohort of CD patients may be affect by this organism.

8. “Application of Shotgun Metagenomics to Study Multi-Kingdom MicrobialCommunities of Chronic Non-Healing Wounds and Their Association With Clinical Outcomes” Lindsay Kalan1, Michael Loesche1, Sue Gardner2, and Elizabeth Grice1

1Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA 2University Of Iowa, College of Nursing, Iowa City, IA, USA

Wound healing requires the execution of highly coordinated and sequential events. Increased microbial bioburden can stall this process in the inflammatory stage resulting in chronic delayed healing, even in the absence of overt infection. Our previous work using bacterial and fungal ribosomal RNA gene profiling defined the multikingdom, polymicrobial communities residing in chronic wounds and their dynamics during healing and complication. However, the functional determinants of pathogenesis such as virulence and biofilm formation factors, and their association with chronic wound outcomes have not been defined. We employed metagenomic shotgun sequencing of chronic wound microbiota to track strain level dynamics of pathogenic microbiota while enabling metabolic and functional reconstruction of microbial communities. Diabetic foot ulcers (DFU; n=100) were sampled every 2 weeks until wound closure, amputation, or the end of the study (26 weeks). Distinct strains of Staphylococcus aureus

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differentiated fast versus slow healing wounds, while Streptococcus spp. and virulence factors targeting host immune responses were enriched in unhealed wounds. Pathogenic fungal species and the bacterial anaerobes Veillonella spp., Porphyromonas somarae, and Prevotella spp., distinctly resided in highly necrotic tissue. Gene ontology analysis revealed genes related to spore formation were significantly enriched in unhealed wounds (P<0.001). Further, in wounds not healed after 12 wks, pfam domains in the metallopeptidase clan CL0126 were found in significantly higher abundance (P<0.00001). Finally, genes conferring resistance to five classes of antibiotics and the topical antibiotic polymyxin were widespread in this cohort, regardless of clinical outcome. This study provides new clinical and functional insight towards microbial community dynamics in DFU, suggesting microbial strain level variation is a better predictor of outcomes and the wound microenvironment drives community structure.

9. “Molecular analysis of the endobronchial stent microbial biofilm”John E. McGinniss1, Ize Imai1, Melanie Brown1, Laura Frye1, Andrew R. Haas1, Anthony R. Lanfranco1, Vincent R. Knecht1, Fredric D. Bushman2, Ronald G. Collman1,2

1Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania School of Medicine 2Department of Microbiology, University of Pennsylvania School of Medicine

Background: Endobronchial stents are increasingly used to treat lower airway compromise in various lung diseases. Placement of synthetic material in a biological site in contiguity with a non-sterile compartment typically results in microbial colonization and biofilm formation. Such biofilms are known to contribute to inflammation and infection in biliary stenting, urinary stenting, intravenous catheters and other biomaterials applications. Endobronchial stents may also physically disrupt airway mucociliary clearance. Despite the widespread use of airway stenting, there has been little investigation of endobronchial stent biofilms, and no molecular characterization with deep sequencing. Methods: We performed culture-independent analysis of the luminal biofilm of 46 lower airway stents that were removed from 20 patients with lung transplantation-associated airway compromise (N=19) or benign airway stenosis (n=1). Swabs of the inner stent surface were subject to bacterial 16S rRNA gene sequencing on the Illumina platform. Results: Corynebacterium species were the most common bacterial taxa found in biofilm communities, identified in most stent samples. Community analysis revealed three main types of stent biofilm. One community type was dominated by Corynebacteria and frequently contained few other taxa. A second stent type was dominated by Staphylococcus species. The third community was more diverse and characterized by Pseudomonas spp., Prevotella spp., and Streptococcal spp. Stent biofilm composition was not associated with stent material (bare metal; covered metal; silicone); transplant versus malignant indication for stenting; nor with underlying lung disease in the transplant group. Longitudinal analysis of 10 subjects with serial placement of multiple stents revealed frequent transitions between biofilm types. Conclusions: Several discrete biofilm types can form in the endobronchial stent niche, which are independent of disease or stent material. Corynebacteria appear to have a major role in endobronchial stent microbial biofilms. These data will enable further studies on the establishment of stent biofilms, and the relationship of biofilm composition to inflammation and granulation tissue formation, pulmonary infection, anastomotic healing, stent patency and other outcomes of lower airway stenting.

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10. “Commensal microbiota contributes to Interferon responsiveness inmyeloid progenitor cells” Danielle Minichino, Dr. Lehn Weaver, Dr. Edward Behrens

During inflammation, hematopoiesis can be altered to produce more effector cells, such as myeloid cells, that perpetuate and amplify secondary immune responses. The mechanisms regulating hematopoiesis during inflammation remain elusive and understanding them are required for the development of novel therapeutics for uncontrolled inflammatory diseases. To date, we have demonstrated that depletion of intestinal microbiota using broad spectrum antibiotic treatment protects mice from inflammatory induced myelopoiesis in two different chronic inflammatory disease models. The current study investigates the cell intrinsic mechanisms in myeloid progenitors that are affected by antibiotic treatment. Myeloid precursors from an antibiotic treated mouse continue to have reduced myelopoietic capacity even when placed in vitro culture systems supplemented with supportive cytokines for one week. Genome–wide transcriptome analysis of myeloid progenitors highlights a hypo- responsiveness to interferon signaling. We then further confirmed this by testing interferon responses in vitro by determining interferon gamma induction of surface Sca-1. We show that precursor cells from antibiotic treated mice have impaired Sca-1 responses. Current research continues to delineate the exact mechanism by which the interferon gamma signal pathway is diminished in precursors from antibiotic treated mice, and its connection to the myelopoietic program.

11. “Nasal Microbiota in Patients with Granulomatosis with PolyangiitisCompared to Healthy Controls” Rennie L. Rhee, Antoine Sreih, Catherine E. Najem, Peter C. Grayson, Chunyu Zhao, Kyle Bittinger, Ronald G. Collman, Peter A. Merkel

Background: Granulomatosis with polyangiitis (GPA; formerly Wegener’s) is a multi-organ systemic vasculitis characterized by granulomatous inflammation and frequent relapses. Upper respiratory involvement, particularly rhinosinusitis, occurs in up to 90% of patients with GPA and is often the first manifestation of disease. Prior studies have suggested a potential link between nasal microbes, in particular Staphylococcus aureus, and GPA but these studies relied on culture-dependent methods. This study comprehensively examined the entire community of nasal microbiota in patients with GPA compared to healthy controls using deep sequencing methods. Methods: The nasal microbiota of 60 patients with GPA and 41 healthy controls was sampled using nasal swabs of the middle meatus and analyzed by sequencing of the bacterial 16S rRNA gene (V1-V2 region). The abundance profiles of the 11 most abundant bacterial taxa were compared using the Wilcoxon rank sum test, correcting for false discovery rate (FDR). Additional comparative analyses within the GPA cohort were performed by: i) ANCA type (PR3 vs MPO) which is a laboratory marker that identifies clinically and genetically distinct subgroups of GPA; ii) presence or absence of sinonasal damage (a marker of disease severity) determined by the Vasculitis Damage Index (VDI); and iii) disease activity (active vs remission). The effects of antibiotics and immunosuppressive therapies (both current and within the past 6 months) were evaluated using generalized linear models. Results: Corynebacterium, Propionibacterium, and Staphylococcus featured as prominent bacterial taxa in the nasal swab samples, consistent with previous reports. After clustering the sequence reads into operational taxonomic units, we identified two abundant groups of Staphylococcus in the data: one closely related to S. aureus

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and the other similar to S. epidermis. The S. epidermis cluster and Propionibacterium were decreased in abundance in GPA vs controls (Figure 1). In multivariate analyses, patients with GPA receiving non-glucocorticoid immunosuppressive therapy had a higher abundance of Propionibacterium independent of other medications and disease activity (p = 0.01) that was similar to the abundance seen in healthy controls (Figure 2). Among patients with GPA, there was a lower abundance of the S. aureus cluster in i) subjects with PR3- vs MPO-ANCA; and ii) subjects with vs. those without sinonasal damage (Figure 3). In multivariate analyses, ANCA type remained significantly associated with abundance of S. aureus independent of medications, sinonasal damage, and disease activity (p = 0.01). Conclusions: Nasal microbial communities differ between patients with GPA and controls as well as between clinically-distinct subsets of GPA. Interestingly, a lower abundance of Propionibacterium was found in patients with GPA, particularly among those off immunosuppressive therapies, raising the possibility that immunosuppressive therapies may help restore “beneficial” microbes which are present in healthy patients. These data support the theory that microbes are involved in the disease process of GPA.

Figure 1: Differential abundance of Propionibacterium (left) and Bacillales (right) between patients with granulomatosis with polyangiitis (GPA) and controls. Compared to healthy controls, patients with GPA had a lower abundance of Propionibacterium, primarily composed of P. acnes (FDR p-value = 0.04), and Bacillales, primarily composed of Staphylococcus epidermidis (FDR p-value = 0.04).

Figure 2: Relative abundance of Propionibacterium acnes by use of non-glucocorticoid immunosuppressive therapies in GPA compared to controls. Patients with GPA who were not receiving non-glucocorticoid immunosuppressive therapies had a significantly lower abundance of P. acnes compared to controls (FDR p-value < 0.01) while GPA patients on immunosuppressives were more similar to controls (FDR p-value > 0.05).

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Figure 3: Differential abundance of Staphylococcus between subgroups of granulomatosis with polyangiitis (GPA). (Left) Patients with GPA who had sinonasal damage (a marker of disease severity) had a lower abundance of Staphylococcus compared to patients without sinonasal damage (p = 0.04). (Right) Differences were also seen by ANCA type (a laboratory marker that identifies clinically and genetically distinct subsets of GPA). There was a lower abundance of Staphylococcus among patients with PR3-ANCA compared to MPO-ANCA (p = 0.04).

12. “Evolution of an Aberrant Facultative-Dominant Oral MicrobiomeFollowing Lung Transplantation” Aurea Simon-Soro1, Michael B. Sohn3, Kyle Bittinger2, Ize Imai1, Vincent R. Knecht1, Melanie Brown1, Aubrey Bailey2, Erik Clarke2, Edward Cantu1, Joshua M. Diamond1, Jason D. Christie1, Frederic D. Bushman2, Ronald G. Collman1.

1 Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 2 Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 3 Department of Statistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

The oral microbiome is a central driver of oral health, and its changes can also contribute to lung infections, which are important in lung transplant recipients. The goal is to understand oral microbial dynamics after lung transplantation, and relationship to clinical and outcome measures. Oropharyngeal wash samples (OW) were collected from healthy subjects (n=14) and pre-transplant subjects (n=22), and longitudinal samples were collected from individuals undergoing lung transplantation (n=33) at 6 weeks, 3 months and 6 months post-transplant. Oral microbiome was characterized by high- throughput sequencing of bacterial 16S rRNA gene, and OW pH was measured. Clinical data were analyzed to understand whether clinical parameters are related to a particular structure of the oral microbiome. We identified three broads OW ecotypes based on imputed bacterial respiratory patterns and linked to measured pH: facultative bacterial respiration dominant and acidic pH (orotype 1); predominant anaerobic bacteria and neutral pH (orotype 2); or dominant aerobic bacteria and basic pH (orotype 3). Healthy subjects OW were distributed in a gradient through the distribution of ecotypes. Compared to healthy individuals, pre-transplant subjects had decreased richness and diversity; loss of anaerobic and increased facultative bacteria; and a marked shift towards orotype 1 and absence of orotype 3. Post- transplant subjects at six weeks had richness and diversity that were closer to although still lower than normal, and a near-normal distribution among oral ecotypes. This pattern was sustained at 3 months post-transplant. By 6 months after transplant, however, OW bacterial richness and diversity was

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significantly reduced, and the oral communities resembled the orotype 1-dominated profile of pre- transplant subjects. Oral ecotypes did not correlate with the negative outcomes of primary graft dysfunction, acute rejection, chronic allograft dysfunction, or death. Thus, pre-transplant patients have markedly abnormal oral microbial communities. Following transplantation, oral communities more closely resemble those of healthy people for the first three months, but later on, evolve to resemble pre-transplant aberrant communities. The development of abnormal oral microbiomes may contribute to oral complications that impact quality of life in subjects following lung transplantation. Further studies will determine whether oral communities are related to infectious complications in these subjects.

13. “Exploring microbiomic variability in the context of the humanchronobiome” Carsten Skarke1,2,5, Nicholas Lahens1,&, Seth Rhoades1,&, Amy Campbell1, Kyle Bittinger3, Aubrey Bailey3, Christian Hoffmann3, Randal S. Olson4, Lihong Chen1, Guangrui Yang1, Thomas S. Price1, Jason H. Moore4,5, Frederic D. Bushman3,5, Casey S. Greene1,5, Gregory R. Grant5,6, Aalim M. Weljie1,5 & Garret A. FitzGerald1,2,5

1 Department of Systems Pharmacology and Translational Therapeutics, 2 Department of Medicine, 3 Department of Microbiology, 4 Institute for Biomedical Informatics, 5 Institute for Translational Medicine and Therapeutics (ITMAT), 6 Department of Genetics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA & These co-authors contributed equally.

Physiological function, disease expression and drug effects vary by time-of-day. Clock disruption in mice results in cardio-metabolic, immunological and neurological dysfunction; circadian misalignment using forced desynchrony increases cardiovascular risk factors in humans. Here we integrated data from remote sensors, physiological and multi-omics analyses to assess the feasibility of detecting time dependent signals - the chronobiome – despite the “noise” attributable to the behavioral differences of free-living human volunteers. The majority (62%) of sensor readouts showed time-specific variability including the expected variation in blood pressure, heart rate, and cortisol. While variance in the multi-omics is dominated by inter-individual differences, temporal patterns are evident in the metabolome (5.4% in plasma, 5.6% in saliva) and in several genera of the oral microbiome. This demonstrates, despite a small sample size and limited sampling, the feasibility of characterizing at scale the human chronobiome “in the wild”. Such reference data at scale are a prerequisite to detect and mechanistically interpret discordant data derived from patients with temporal patterns of disease expression, to develop time-specific therapeutic strategies and to refine existing treatments.

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14. “Bacterial amyloid curli acts as a carrier for DNA to elicit an autoimmuneresponse via TLR2 and TLR9” Tursi SA1, Lee EY2, Medeiros NJ1, Lee MH1, Nicastro LK1, Buttaro B1, Gallucci S1, Wilson RP1, Wong GCL2,3, Tükel Ç1.

1Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America. 2Department of Bioengineering, California Nano Systems Institute, University of California, Los Angeles, California, United States of America. 3Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, California, United States of America.

Bacterial biofilms are associated with numerous human infections. The predominant protein expressed in enteric biofilms is the amyloid curli, which forms highly immunogenic complexes with DNA. Infection with curli-expressing bacteria or systemic exposure to purified curli-DNA complexes triggers autoimmunity via the generation of type I interferons (IFNs) and anti-double-stranded DNA antibodies. Here, we show that DNA complexed with amyloid curli powerfully stimulates Toll-like receptor 9 (TLR9) through a two-step mechanism. First, the cross beta-sheet structure of curli is bound by cell-surface Toll-like receptor 2 (TLR2), enabling internalization of the complex into endosomes. After internalization, the curli-DNA immune complex binds strongly to endosomal TLR9, inducing production of type I IFNs. Analysis of wild-type and TLR2-deficient macrophages showed that TLR2 is the major receptor that drives the internalization of curli-DNA complexes. Suppression of TLR2 internalization via endocytosis inhibitors led to a significant decrease in Ifnβ expression. Confocal microscopy analysis confirmed that the TLR2-bound curli was required for shuttling of DNA to endosomal TLR9. Structural analysis using small-angle X-ray scattering revealed that incorporation of DNA into curli fibrils resulted in the formation of ordered curli-DNA immune complexes. Curli organizes parallel, double-stranded DNA rods at an inter-DNA spacing that matches up well with the steric size of TLR9. We also found that production of anti-double-stranded DNA autoantibodies in response to curli-DNA was attenuated in TLR2- and TLR9-deficient mice and in mice deficient in both TLR2 and TLR9 compared to wild-type mice, suggesting that both innate immune receptors are critical for shaping the autoimmune adaptive immune response. We also detected significantly lower levels of interferon-stimulated gene expression in response to purified curli-DNA in TLR2 and TLR9 deficient mice compared to wild-type mice, confirming that TLR2 and TLR9 are required for the induction of type I IFNs. Finally, we showed that curli-DNA complexes, but not cellulose, were responsible elicitation of the immune responses to bacterial biofilms. This study defines the series of events that lead to the severe pro-autoimmune effects of amyloid-expressing bacteria and suggest a mechanism by which amyloid curli acts as a carrier to break immune tolerance to DNA, leading to the activation of TLR9, production of type I IFNs, and subsequent production of autoantibodies.

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15. “HmmUFOtu: An HMM and Phylogenetic Placement based Ultra-Fasttaxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies” Authors: Qi Zheng1,*, Casey Bartow-McKenney2, Jacquelyn Meisel2 and Elizabeth A. Grice1,2,*

1. Department of Dermatology, Perelman School of Medicine, University of Pennsylvania2. Genomics and Computational Biology Program, Department of Dermatology, University

of Pennsylvania* Corresponding authors

Over the last decade, joint advances in next-generation sequencing technology and bioinformatics pipelines have dramatically improved our understanding of host-associated and environmental microbiota. Standard microbiome community analysis typically involves amplicon sequencing of the prokaryotic 16S rRNA gene. These sequences are then clustered into operational taxonomic units (OTUs) for downstream diversity analyses, but also to reduce computational burden and allow for rapid analysis of datasets. Taxonomy is then assigned to all reads of an OTU, based on the assignment of a representative read. Although straightforward in principle, present methods often rely on heuristics while constructing (or “picking”) OTUs to avoid computationally expensive algorithms, and ignore the prior knowledge of microbial phylogeny to further reduce the computational complexity. Here, we present HmmUFOtu, a novel tool for processing 16S rRNA sequences that addresses major limitations of current OTU picking and taxonomy assignment methods. HmmUFOtu relies on rapid per-read phylogenetic placement, followed by OTU picking and taxonomic assignment based on the phylogeny of known taxa. By benchmarking on simulated, mock community, and real datasets, we show that HmmUFOtu achieves high assignment accuracy, sensitivity, specificity and precision, even at species-level resolution. Compared to standard pipelines, HmmUFOtu more accurately recapitulates community diversity and composition. HmmUFOtu can perform taxonomic assignment in a species-resolution reference tree with ~ 200,000 nodes for 1 million 16S sequencing reads within 8 hours on a modest Linux workstation with 16 processors and 32 GB RAM. HmmUFOtu is written in C++98 and freely available at https://github.com/Grice-Lab/HmmUFOtu/.

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Acknowledgements The PennCHOP Microbiome Program The Penn Vet Center for Host Microbial Interactions The Joint Penn-CHOP Center for Digestive Liver & Pancreatic Medicine The Center for Molecular Studies in Digestive & Liver Diseases Symposium Planning Committee Robert Baldassano, MD Daniel Beiting, MD Frederic Bushman, PhD Gary Wu, MD

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Last Name First Name Title Institution or Company EmailAbbas Arwa PhD Candidate University of Pennsylvania arwaa@pennmedicine.upenn.eduAbrams Julian MD, MS Columbia University Medical Center ja660@cumc.columbia.eduAbt Michael PhD University of Pennsylvania michael.abt@pennmedicine.upenn.eduAggarwala Varun Postdoctorate Researcher University of Pennsylvania varunaggarwala01@gmail.comAlavi Abass Prof University of Pennsylvania abass.alavi@uphs.upenn.eduAlbenberg Lindsey DO University of Pennsylvania albenbergl@email.chop.eduAldrovandi Grace MD/CM/VISITING SPEAKER University of California, Los Angeles galdrovandi@mednet.ucla.eduAnderson Sean PhD University of Pennsylvania seanth@pennmedicine.upenn.eduAnton Farrington Lauren PhD University of Pennsylvania lanton@pennmedicine.upenn.eduAudrain-McGovern Janet PhD UPENN SOM Audrain@pennmedicine.upenn.eduBaldassano Bob MD Children's Hospital of Philadelphia baldassano@email.chop.eduBarekat Kayla Graduate Student University of Pennsylvania kbarekat@pennmedicine.upenn.eduBartow-McKenney Casey Graduate Student University of Pennsylvania casb@upenn.eduBass Antonia PhD Student University of Pennsylvania antoniab@pennmedicine.upenn.eduBeiting Dan PhD University of Pennsylvania danielbeiting@gmail.comBenitez Alain Clinical Research Program

ManagerChildren's Hospital of Philadelphia beniteza@email.chop.edu

Bhat Archana Programmer/Analyst Drexel Univerity asb352@drexel.eduBittinger Kyle PhD Children's Hospital of Philadelphia bittingerk@email.chop.eduBjanes Elisabet PhD Candidate University of Pennsylvania elisabetbjanes@gmail.comBobokalonov Jamshed PhD USDA Jamshed.Bobokalonov@ARS.USDA.GOVBongers Gerold PhD Janssen gbongers@its.jnj.comBradley Charles VMD, DACVP University of Pennsylvania, SVM cbradle2@vet.upenn.eduBreton Jessica MD Children's Hospital of Phildelphia bretonj@email.chop.eduBrown Amy PhD University of Pennsylvania aegreen@pennmedicine.upenn.eduBrown Melanie Research Project Manager University of Pennsylvania melab@mail.med.upenn.eduBushman Rick PhD University of Pennsylvania bushman@pennmedicine.upenn.eduCampbell Amy Graduate Student UPenn, Genomics and Computational

Biologyacampbe@pennmedicine.upenn.edu

Chang Vivian BA Children's Hospital of Phildelphia changv@email.chop.eduChau Lillian Technical Director University of Pennsylvania chaul@upenn.eduChen Qijun PhD School of Medicine qijun@upenn.eduChen Jian MS Drexel cjcobalt@icloud.comChen Dongning PhD student GI dongning@seas.upenn.eduCherry Sara PhD University of Pennsylvania cherrys@pennmedicine.upenn.eduChoi Yongwon PhD University of Pennsylvania ychoi3@pennmedicine.upenn.eduClarke Erik BSc University of Pennsylvania ecl@pennmedicine.upenn.eduCollins Michiyah Undergraduate Freshman University of Pennsylvania michiyah@sas.upenn.eduCollman Ron MD Perelman School of Medicine collmanr@pennmedicine.upenn.eduCompher Charlene Professor of Nutrition Science Penn Nursing compherc@upenn.eduComstock Laurie PhD/VISITING SPEAKER Harvard Medical School lcomstock@rics.bwh.harvard.eduConrad Mary Sr. Scientist Axial Biotherapeutics mary@axialbiotherapeutics.comConrad Maire MD Children's Hospital of Philadelphia conradm@email.chop.eduCribas Emily Graduate Student University of Pennsylvania ecribas@PennMedicine.upenn.eduCriniti Stephanie M.S. University of Pennsylvania scriniti@pennmedicine.upenn.eduCrissey Mary Ann Research Specialist University of Pennsylvania mascris@pennmedicine.upenn.eduCruz Elisa PhD University of Pennsylvania ecru@pennmedicine.upenn.eduDavis Amy MD/PhD Student University of Pennsylvania davisamy@pennmedicine.upenn.eduDevoto Marcella PhD The Children's Hospital of Philadelphia devoto@chop.edu

Diamond Mark MD, PhD University of Pennsylvania mark.diamond@uphs.upenn.eduDoerner Jess PhD University of Pennsylvania doerns126@gmail.comDokras Anuja MD/PhD University of Pennsylvania adokras@obgyn.upenn.eduDoms Robert MD/PhD University of Pennsylvania DomsR@email.chop.eduDoto Aoife PhD University of Pennsylvania rochea@pennmedicine.upenn.eduDOUGLAS STEVEN MD Children's Hospital of Philadelphia-

PSOMdouglas@email.chop.edu

Douglas Steven Professor of Pediatrics Children's Hospital of Philadelphia douglas@email.chop.eduDrigo Danielle I-Gram Study Coordinator Children's Hospital of Philadelphia drigod@email.chop.eduDuda John MD Philadelphia VA Medical Center john.duda@va.govDuncan Turner - PacBio tduncan@pacificbiosciences.comEarl Joshua MS Drexel University College of Medicine jpe39@drexelmed.eduEhrlich Rachel MS Drexel rle36@drexel.eduEigen David Managing Member P5 Health Ventures david@p5hv.comElgarten Caitlin MD Children's Hospital of Philadelphia elgartenc@email.chop.eduElhanafi Sherif MD University of Pennsylvania Sherif.elhanafi@uphs.upenn.eduElovitz Michal MD University of Pennsylvania melovitz@obgyn.upenn.eduEpstein Jonathan MD University of Pennsylvania epsteinj@mail.med.upenn.edu

Attendees

27

Last Name First Name Title Institution or Company EmailErlichman Jessi MPH Children's Hospital of Philadelphia erlichman@email.chop.eduEwing Rachel Editor, Penn Medicine Magazine Penn Medicine rachel.ewing@uphs.upenn.edu

Fecteau Marie-Eve DVM School of Veterinary Medicine mfecteau@vet.upenn.eduFirrman Jenni Molecular Biologist USDA jenni.firrman@ars.usda.govFitzgerald Ayannah Research Nurse Coordinator University of Pennsylvania ayannah@pennmedicine.upenn.eduFlowers Laurice PhD University of Penn Dermatology

Departmentflowersl@pennmedicine.upenn.edu

Ford Eileen MS, RDN Children's Hospital of Philadelphia forde@email.chop.eduFrankel Jeffrey Veterinary Student (V21) University of Pennsylvania, School of

Veterinary MedicineJSFrank@vet.upenn.edu

Friedman Elliot Senior Research Investigator; Technical Director, Microbial Culture and Metabolomics Core

University of Pennsylvania elliotf@mail.med.upenn.edu

Fu Mingzhou MPH Yale University mingzhou.fu@yale.eduFUJITA RYO - Mitsubishi Tanabe Pharma Corporation Fujita.Ryo@mh.mt-pharma.co.jp

Galgano Alissa - Children's Hospital of Philadelphia galganoa@email.chop.eduGerber Jeff MD/PhD Children's Hospital of Philadelphia gerberj@email.chop.eduGhura Shivesh PhD University of Pennsylvania sghura@penn.eduGiger Urs Dr. PennVet giger@vet.upenn.eduGilmour Susan PhD Lankenau Institute for Medical Research Gilmours@mlhs.org

Gonzalez Lavinia PhD Student University of Pennsylvania golavi@pennmedicine.upenn.eduGonzalez Michael PhD Children's Hospital of Philadelphia gonzalezm2@email.chop.eduGoulian Mark Professor, Department of Biology University of Pennsylvania Goulian@sas.upenn.edu

Graves Dana DDS Penn Dental School dtgraves@upenn.eduGrice Elizabeth Assistant Professor, Dermatology University of Pennsylvania, Perelman

School of Medicineegrice@upenn.edu

Griesman Trevor Graduate Student UPenn microbiology griesman@pennmedicine.upenn.eduGu Christopher MPH UPenn chgu@pennmedicine.upenn.eduHalim Farid Dr Biology mohd@sas.upenn.eduHamel Steven - University of Pennsylvania hamels@seas.upenn.eduHantsoo Liisa PhD University of Pennsylvania, Perelman

School of MedicineLiisaHa2@pennmedicine.upenn.edu

Harb Ali PennChildren's Hospital of Philadelphia Microbiome Program (CCEB)

Ali.Harb@pennmedicine.upenn.edu

Harris-Foster Jasmine IGRAM Clinical Research Assistant

Children's Hospital of Philadelphia harrisfosj@email.chop.edu

Hatterschide Joshua Graduate Student University of Pennsylvania Jhatt@pennmedicine.upenn.eduHenrickson Sarah MD/PhD Children's Hospital of Philadelphia

Allergy Immunologyhenricksons@email.chop.edu

Hickey Jessica I-Gram Clinical Research Assistant

Children's Hospital of Philadelphia Hickeyjm@chop.email.edu

Himmelstein Daniel Open Sourcerer University of Pennsylvania daniel.himmelstein@gmail.comHofstaedter Casey E. BS Children's Hospital of Philadelphia hofstaedtc@email.chop.eduHogan Karen PhD UPenn Dept of Biology hogank@sas.upenn.eduHolt G MBBS - ghol7955@med.usyd.edu.auHornby Pamela PhD AGAF Janssen R&D LLC phornby@its.jnj.comHorton Daniel Assistant Professor of Pediatrics

and EpidemiologyRutgers University daniel.horton@rutgers.edu

Hoton Daniel MD, MSCE Rutgers University daniel.horton@rutgers.eduHunter Chris PhD Penn Vet chunter@vet.upenn.eduHwang Young PhD University of Pennsylvania yhwang@pennmedicine.upenn.eduImai Ize MS University of Pennsylvania imaii@pennmedicine.upenn.eduJamikeshova Albina Student Drexel University aj548@drexel.eduJennis Matt PhD Janssen mjennis1@its.jnj.comJu Linyang Mt Dept of Biology, UPenn lyju@sas.upenn.eduKalan Lindsay PhD University of Pennsylvania lkalan@pennmedicine.upenn.eduKatz Joshua PhD The Dow Chemical Company jskatz@dow.comKeating Brendan D.Phil UPenn bkeating@mail.med.upenn.eduKelly Brendan MD University of Pennsylvania PSOM brendank@mail.med.upenn.eduKelsen Judith MD The Children's Hospital of Philadelphia kelsen@email.chop.edu

28

Last Name First Name Title Institution or Company EmailKhan Amna MD, FACE University of Pennsylvania and

Philadelphia VAMCamna.khan@uphs.upenn.edu

Khan Sarah Student University of Pennsylvania skhan100@sas.upenn.eduKhawar Myra Student Rutgers Unviersity myrakhawar@gmail.comKing Leslie PhD Penn Vet lbking@upenn.eduKnecht Vincent Research Specialist University of Pennsylvania School of

Medicineknecht@pennmedicine.upenn.edu

Kong Jenny PhD Children's Hospital of Philadelphia kongj3@email.chop.eduKreeger Karen Science Writer Penn Medicine Communications karen.kreeger@uphs.upenn.eduLai HuiChuan Visiting Scholar, PhD, RD Children's Hospital of Philadelphia laih2@email.chop.eduLeiby Jacob Technician University of Pennsylvania jleiby@pennmedicine.upenn.eduLevinson Arnold MD Perelman School of Medcine frog@upenn.eduLewis James Professor of Medicine University of Pennsylvania lewisjd@upenn.eduLewis Felicia Medical Epidemiologist Centers for Disease Control and

Preventionfelicia.lewis@phila.gov

Li Hongzhe PhD University of Pennsylvania hongzhe@pennmedicine.upenn.eduLiang Guanxiang PhD Children's Hospital of Philadelphia liangg1@email.chop.eduLiu Changchun PhD University of Pennsylvania lchangc@seas.upenn.eduLiu Xin PhD upenn merryliuxin@gmail.comLiu Xiaobin PhD upenn xiaobin@pennmedicine.upenn.eduLiu LinShu PhD Linshu.liu@ars.usda.gov Linshu.liu@ars.usda.govLopez Haber Cynthia Doña University of Pennsylvania cynlopez@pennmedicine.upenn.eduLubin Jean-Bernard PhD Children's Hospital of Philadelphia lubinj@email.chop.eduLund Peder Post-Doc University of Pennsylvania pederl@pennmedicine.upenn.eduMacRae-Crerar Aurora Dr. (Lecturer of Critical Writing,

Penn)University of Pennsylvania aurorama@sas.penn.edu

Mahalak Karley PhD USDA karley.mahalak@ars.usda.govMantegazza Adriana PhD Children's Hospital of Philadelphia mantegazza@email.chop.eduMarks Mickey Professor Children's Hospital of Philadelphia marksm@pennmedicine.upenn.eduMarquez de Prado Blanca PhD Children's Hospital of Philadelphia marquezdeb@email.chop.eduMarquis Katie Grad Student Penn kmarquis@pennmedicine.upenn.eduMartin Viviane Director, PCI-PSOM Licensing

GroupUniversity of Pennsylvania martinv@upenn.edu

Mathur Vinayak PhD Georgetown University vm449@georgetown.eduMatsuda Rina Graduate Student University of Pennsylvania rmatsuda@pennmedicine.upenn.eduMattei Lisa none Children's Hospital of Philadelphia matteil@email.chop.eduMaxwell Betsy MD Children's Hospital of Philadelphia maxwelle@email.chop.eduMcCourt Richard - Academy of Natural Sciences of Drexel rmm45@drexel.edu

McGeehan Brendan MS Statistics University of Pennsylvania brenmc@pennmedicine.upenn.eduMcGinniss John MD UPenn Pulmonary and Critical Care john.mcginniss@uphs.upenn.eduMeng Wenzhao PhD University of Pennsylvania wmeng@pennmedicine.upenn.eduMiller Amanda Graduate Student Lewis Katz School of Medicine Temple

Universitytug25971@temple.edu

Minichino Danielle PhD Student University of Pennsylvania edani@mail.med.upenn.eduMitchell Matt PhD Drexel University mwmitchell@drexel.eduMitchell Jonathan PhD Children's Hospital of Philadelphia mitchellj2@email.chop.eduMoustafa Ahmed PhD ARC, Children's Hospital of

Philadelphiamoustafaam@email.chop.edu

Najem Catherine MD University of Pennsylvania catherine.najem@uphs.upenn.eduNakagawa Hiroshi MD, PhD Penn GI Division nakagawh@pennmedicine.upenn.eduNaseer Nawar Graduate Student University of Pennsylvania naseernawar@gmail.comNi Josephine MD University of Pennsylvania josieni@gmail.comNicastro Lauren Graduate Student Lewis Katz School of Medicine Temple

Universitytug03848@temple.edu

Novais Fernanda Research Associate University of Pennsylvania novais@upenn.eduNunez Gabriel MD, VISITING SPEAKER University of Michigan tamaraku@med.umich.eduOdnokoz Olena PhD University of Pennsylvania odnokoz@upenn.eduOgawa Sayaka BS University of Pennsylvania saogawa@pennmedicine.upenn.eduPaschos Georgios PhD UPENN gpaschos@pennmedicine.upenn.eduPattekar Ajinkya MD University of Pennsylvania ajinkyap@pennmedicine.upenn.eduPearson-Leary Jiah Post Doctoral Fellow Children's Hospital of Philadelphia pearsonlearyj@email.chop.eduPeterson Lance PhD Perelman School of Medicine Lancep@pennmedicine.upenn.eduPiccoli David MD Children's Hospital of Philadelphia piccoli@email.chop.eduPIERINI STEFANO PhD University of Pennsylvania stefanopierini@live.itPlanet Paul MD/PhD Children's Hospital of Philadelphia

UPennPlanetp@email.chop.edu

Plantz Kristen Ms. Children's Hospital of Philadelphia plantzk@email.chop.edu

29

Last Name First Name Title Institution or Company EmailPohlschroder Mechthild PhD UPenn pohlschr@sas.upenn.eduPoirier Kendra Clinical Research Assistant Children's Hospital of Philadelphia poirierk@email.chop.eduPoirier Kendra Clinical Research Children's Hospital of Philadelphia Keniapoirier@gmail.comPollock Tzvi Student University of Pennsylvania tpollock@pennmedicine.upenn.eduPourshariati Kate - Penn Museum katepour@upenn.eduPovelones Michael PhD PennVet mpove@vet.upenn.eduRaffatellu Manuela MD, VISITING SPEAKER University of California, Irvine manuelar@ucsd.eduRecober Ana MD Children's Hospital of Philadelphia recobera@email.chop.eduReynolds Jim MD University of Pennsylvania james.reynolds@uphs.upenn.eduRhee Rennie MD, MS University of Pennsylvania rennie.rhee@uphs.upenn.eduRicciotti Emanuela PhD University of Pennsylvania emanuela@pennmedicine.upenn.eduRoggiani Manuela PhD University of Pennsylvania roggiani@sas.upenn.eduRomasko Edward Scientist Children's Hospital of Philadelphia romaskoe@email.chop.eduRoos David PhD Univ Pennsylvania droos@sas.upenn.eduRosen Gail PhD Drexel University empr3ss@gmail.comRossi Heather Research Associate Children's Hospital of Philadelphia rossih@email.chop.eduRoy Paladhi Unmesha CRC Penn uroy@pennmedicine.upenn.eduRuan Catherine Student University of Pennsylvania cruan@wharton.upenn.eduRubel Meagan MPH University of Pennsylvania rubel@sas.upenn.eduRusso Nick Researcher HUP russon@pennmedicine.upenn.eduRyan Chanelle - Children's Hospital of Philadelphia ryanc3@email.chop.eduRyan Hannah CRNP Penn Medicine hannah.ryan@uphs.upenn.eduSaiman Yedidya MD/PhD University of Pennsylvania yedidya.saiman@uphs.upenn.eduSamuels Amanda - Veterinary School of Medicine samuelsa@vet.upenn.eduSanseviero Emilio PhD The Wistar institute esanseviero@wistar.orgSarwar Prioty - Biological Graduate Studies priotyf@pennmedicine.upenn.eduSchifferli Dieter DVM/PhD UPENN dmschiff@vet.upenn.eduScott Phil PhD Penn Vet PSCOTT@UPENN.EDUSears Cynthia MD, VISITING SPEAKER Johns Hopkins University csears@jhmi.eduSeeholzer Steven PhD Children's Hospital of Philadelphia seeholzer@email.chop.eduSengupta Shaon MD, FAAP University of Pennsylvania SenguptaS@email.chop.eduSharova Anna MPH Children's Hospital of Philadelphia

CPCEsharovaa@email.chop.edu

Shen David MD/PhD University of Pennsylvania David.tingchin.shen@gmail.comShenker Bruce PhD Penn Dental shenker@upenn.eduSherman John Research Associate Zymo Research jsherman@zymoresearch.comSherrill-Mix Scott PhD University of Pennsylvania shescott@upenn.eduSherwood Byron PhD Department of Biology - University of

Pennsylvaniabyrons@sas.upenn.edu

Sierra Jeannette PhD University of Pennsylvania luzjeasi@pennmedicine.upenn.eduSilverman Michael MD/PhD University of Pennsylvania silvermam1@email.chop.eduSimon-Soro Aurea DDS, PhD Microbiology. Perelman School of

Medicine. University of Pennsylvaniasimon.aurea@gmail.com

Skarke Carsten MD UPenn cskarke@pennmedicine.upenn.eduSmith Sarah PhD University of Pennsylvania sarahsa@pennmedicine.upenn.eduSocarras Kayla Kayla M. Socarras, M.S. Drexel University kms586@drexel.eduSong Jinzhao PhD SEAS songjinz@seas.upenn.eduSpindler Lori - University of Pennsylvania spindler@sas.upenn.eduSpitsin Sergei PhD Children's Hospital of Philadelphia spitsins@email.chop.eduSt. Geme III Joseph MD Children's Hospital of Philadelphia StGemeIIIJ@email.chop.eduStrange Cassidy Researcher University of Pennsylvania cstrange@pennmedicine.upenn.eduTanes Ceylan Bioinformatics Scientist Children's Hospital of Philadelphia tanesc@email.chop.eduTang Soon PhD University of Pennsylvania tangsoon@mail.med.upenn.eduTeles Flavia DDS, MS, DMSc School of Dental Medicine fteles@upenn.eduTerry Natalie M.D., PhD The Children's Hospital of Philadelphia terryn@email.chop.edu

Theken Katie PharmD,PhD University of Pennsylvania ktheken@pennmedicine.upenn.eduThomas Sunil Ph.D Lankenau Institute for Medical Research thomass-02@mlhs.org

Thomas-Gahring Audrey Chemist USDA-ARS audrey.thomas@ars.usda.govTomov Vesselin MD/PhD University of Pennsylvania tomovv@pennmedicine.upenn.eduTran Tam Graduate Student Penn - Biology Dept tamt@sas.upenn.eduTukel Cagla PhD Lewis Katz School of Medicine Temple

Universityctukel@temple.edu

Tursi Sarah Graduate Student Lewis Katz School of Medicine Temple University

tuf21076@temple.edu

Tuteja Sony PharmD University of Pennsylvania sonyt@pennmedicine.upenn.eduTwyman Christina MD University of Pennsylvania christina.twyman@uphs.upenn.edu

30

Last Name First Name Title Institution or Company EmailVan den Abbeele Pieter Contract Research and

Technology DirectorProDigest Pieter.VandenAbbeele@prodigest.eu

Wang Hong PhD University of Pennsylvania olittleviolinist@gmail.comWang Shuai PhD Vet School of Upenn wshuai@upenn.eduWang Minqian Graduate student Rutgers University mw539@scarletmail.rutgers.eduWang Zhuoyang Student University of Pennsylvania wangzy@sas.upenn.eduWeaver Lehn MD/PhD Children's Hospital of Philadelphia weaverl1@email.chop.eduWeiss West -- The Children's Hospital of Philadelphia

Research InstituteWeissW@email.chop.edu

Wherry John PhD University of Pennsylvania wherry@pennmedicine.upenn.eduWilmore Joel PhD University of Pennsylvania jwilmore@pennmedicine.upenn.eduWohl Rae MSW, LSW Children's Hospital of Philadelphia wohlr@email.chop.eduWoloszynek Stephen MD/PhD Candidate Drexel University stephenwoloszynek@gmail.comWong Kyoung Jae Research Assistant Prof University of Pennsylvania wonk@upenn.eduWong Andrea Research Technician University of Pennsylvania andwong@vet.upenn.eduWorthen Scott Professor Children's Hospital of Philadelphia worthen@email.chop.eduWu Vincent BS University of Pennsylvania wuv@pennmedicine.upenn.eduWu Gary MD University of Pennsylvania gdwu@pennmedicine.upenn.eduWynosky-Dolfi Meghan PhD University of Pennsylvania wynosky@vet.upenn.eduYang Xue-Jun MD Mount Sinai School of Medicine MY006@YAHOO.COMYong Ed MPhil Visiting Speaker edyong209@gmail.comZemel Babette Professor of Pediatrics Children's Hospital of

Philadelphia/UPENNzemel@email.chop.edu

Zhang Zhe PhD Children's Hospital of Philadelphia zhangz@email.chop.eduZhang Qian MD/PhD Upenn qian2@mail.med.upenn.eduZhang Lin Associate Professor Penn linzhang@pennmedicine.upenn.eduZhao Zhengqiao PhD Candidate Drexel University zz374@drexel.eduZhao Chunyu Bioinformatics Scientist Children's Hospital of Philadelphia zhaoc1@email.chop.eduZhao Zhengqiao PhD Candidate Drexel University zz374@drexel.eduZheng Qi PhD University of Pennsylvania zhengqi@pennmedicine.upenn.eduZhu Jay PhD University of Pennsylvania junzhu@pennmedicine.upenn.edu

31