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February 10th-11th 2016 | San Diego, California, USA
Welcome to the Human Microbiome Congress 2016
Examining function in the human microbiome.
Part of Kisaco Research’s global conference portfolio
Draft Programme
*This agenda is subject to change*
Conference Day One: Wednesday February 10th, 2016
08:30
Registration for Conference and Exhibition Hall Opens for All Attendees
09:00
Chairperson’s Opening of Conference
Part 1: Characterising the normal/healthy human microbiome.
09:10
Exploring the Role of the Microbiome in Disease
Dr. Weinstock will discuss how the complex microbial communities that make up the human
microbiome are highly-integrated with the human body and can change with different health states
and may well cause such changes. The task of finding such causal relationships requires good sample
sets as well as many analysis approaches. Possible causal mechanisms could operate at the ensemble
level, or be due to changes in single organisms, or in multiple organisms. A number of such examples
will be presented.
George Weinstock, The Jackson Laboratory
9:35
Functionality of the Vaginal Microbiome in Reproductive Health
Progress has been made in recent years to characterize the vaginal microbiome composition in women
of reproductive age. Recent studies have further identified a shift in microbiome composition during
pregnancy towards a community with lower diversity, in which lactobacilli are enriched and anaerobic
organisms associated with bacterial vaginosis are excluded. Bacterial vaginosis, a dysbiosis of vaginal
flora, impacts approximately one in three women at any given time and is associated with pregnancy
complications including preterm birth occurring before 37 weeks gestation. Ascending infection of
bacterial species originating in the vagina has emerged as a mechanism estimated to contribute to 4050% of preterm births. This presentation will address what has been learned so far, and where future
investigations might take us.
10:00
Jennifer Fettweis, Virginia Commonwealth University
Interrogation and Characterization of Bacterial Proteins of the Human Gut Microbiome:
Our goal is to expand on the pioneering metagenomic sequencing and metabolomic methodologies
with the development and application of new chemical biology tools, mass spectrometry
metaproteomic methods, and bioinformatic search algorithms as techniques to identify and
quantitate gut bacterial proteins. We present a modified functional metaproteomics approach that
employs activity-based probes (ABPs) to directly measure, characterize, and quantitate gut microbial
proteins and their enzymatic functions. Biotin-containing small molecule ABPs are added to
microbiome samples to covalently label and isolate individual protein families from the complex gut
microbial proteome in a rapid and throughput manner.
Presented by:
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February 10th-11th 2016 | San Diego, California, USA
We target the identification of secreted and surfaceexpressed hydrolases, proteases, and
glycosidases, as these enzymes are at the microbiome interface and are likely key players in the
crosstalk between the host and bacteria. All ABP-labeled proteins are subjected to high performance
reverse phase liquid chromatography coupled with tandem mass spectrometry for protein
identification. Ultimately, our goal is to elucidate the normal distribution of gut bacterial proteins
among individuals (if one exists), identify which protein functionalities are essential for human
homeostasis, and determine what proteins and interactions with the host are altered or
compromised in dysbiosis.
The results from our work will facilitate the discovery of chemical and biological tools to probe the
roles that key enteric bacterial enzymes play in human health and microbiome-related diseases.
Importantly, our new methods and materials will provide a foundation for further development of
metaproteomic approaches to target a variety of key protein functionalities within human
microbiomes.
10:25
Dennis Wolan, The Scripps Research Institute.
Morning Networking Break: Coffee, Tea & Refreshments in the Exhibition Hall
11:00
Searching beyond the lamppost: new protein families dominate in newly explored environments
Adaptation of the human gut microbiome to its unique environment is typically described in terms of
the relative composition and diversity of microbial species. An alternative (and complementary)
perspective can provided by analyzing the relative distribution of protein families in metagenomic
datasets. While it was noticed in literature (Yooseph, 2007; Qin, 2010) that microorganisms living in
these newly studied envirnoments contain many novel, uncharacterized proteins and that these
proteins form families, such families were never defined nor submitted to public domain databases
(Finn, 2014).
We performed analysis of protein families distributions in the MetaHIT, currently the largest single
dataset for the human gut microbiome. We found about 300 highly overrepresented protein families,
with top 100 similarly overrepresented in all human metagenomics sets. Interestingly, most of them
are uncharacterized (Goodacre, 2013) and moreover, most were defined only recently. Similar analysis
performed even few years ago would artificially downplay the uniqueness of the human gut
microbiome, as distribution of well characterized protein families is similar to that in well studied
bacterial species. By large scale structure determination and distant homology analysis we assigned
putative functions to most of the overrepresented protein families (Figure 1). We show that protein
families overrepresented in the the gut microbiome are related to secretion, motility and chemotaxis,
also that surprisingly large percentage of them are extracellular. We compare those to the set of
overrepresented protein families in the the ocean micobiome, which contains more families with
functions linked to cell wall and outer membrane structure and biogenesis. These differences can be
rationalized by the need for very efficient nutrient intake mechanisms in the ocean due to the relative
shortage of nutrients while, in the human gut, the relative abundance of nutrients, high density of
microorganisms and presence of the host immune system require more proteins for protein-protein
and protein-carbohydrate interactions.
Full characterization of large sets of proteins, such as derived from metagenomic sequencing projects
require better libraries of protein families, which would correctly represent the wide variety of novel
proteins found in the newly characterized environments. Significant number of protein families in the
Presented by:
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For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
latest Pfam release provide such representation, allowing us to identify dominant protein families in
human gut and ocean environments.
Adam Godzik, Sanford Burnham Prebys Medical Discovery Institute
11:25
Structure and Function of the Cystic Fibrosis Lung Microbiome
Cystic Fibrosis (CF) is a genetic disease that results in buildup of thick mucus in the lung that becomes
infected with opportunistic pathogens, most famously, Pseudomonas aeruginosa. Molecular methods
have revealed that CF lungs are infected with a more diverse microbial community than is appreciated
by clinicians, highlighting the need for a more comprehensive understanding of CF microbial ecology.
Our group has been studying the physiology and dynamics of the CF microbial community focusing on
CF exacerbations, which are events of CF disease characterized by an increase in symptom severity.
Omics methods such as metagenomics, transcriptomics, and metabolomics have led to a new
understanding of how the core physiology of CF bacteria governs community dynamics and,
potentially, their involvement in exacerbations. With a variety of methods we have observed that as an
exacerbation develops the CF microbial community is actively fermenting. This fermentation is done by
lesser-known CF pathogens, the anaerobes. Antibiotic treatment wipes out this fermentative
community, explaining treatment efficacy. Co-occurrence networking of 16S rDNA microbiome and
metagenomic data identified the existence of two functional communities in the CF lung. These were a
community of classic CF pathogens (ie. P. aeruginosa) utilizing respiration and consuming amino acids,
and a fermentative community, comprised of mostly oral anaerobes. These two different communities
have contrasting effects on the pH of the lung environment. The fermentative community lowers the
lung pH and the respiratory community raises it. Our findings have led to a new hypothesis about how
the CF microbial community is governed by its own physiology and exists in stable and disturbed
states, much like those in classical ecology. This study demonstrates how the core metabolism of a
microbial community governs its structure and dynamics.
Robert A. Quinn, UCSD
11:50
Complex carbohydrate degradation by human gut bacteria during health and disease
The trillions of symbiotic microorganisms in the human gut expand our digestive physiology by
providing an armament of polysaccharide-degrading enzymes that are absent in the human genome.
Dietary polysaccharides, mixed with endogenous mucosal secretions, present a diverse menu of
complex carbohydrates that our gut symbionts have adapted strategies to sense, triage and degrade.
Understanding which species consume each nutrient, how abilities vary among taxa and what the
molecular mechanisms involved are, represent central problems in defining the relationship between
diet, microbiota and health.
We are taking microbiological, genomic, genetic and biochemical approaches to address these
problems. Our results have revealed that members of the phylum Bacteroidetes are major
contributors to carbohydrate digestion and rely on expression of discrete gene clusters that each
encodes the requisite proteins to catabolize a particular polysaccharide. Expression of each gene
cluster is activated by a locally encoded transcription factor that participates in carbohydrate sensing
and metabolism until its supply is exhausted. In the context of a single bacterium, many dozen
individual gene clusters may simultaneously be triggered to respond to available nutrients. Yet, in
experimental conditions in which such complex nutrient environments are modeled, there is an
ordered progression of carbohydrate utilization that is reminiscent of catabolite repression.
Presented by:
For Sponsorship Opportunities, email [email protected]
For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
Of central focus in our studies is the interplay between dietary fiber polysaccharides and mucosal
glycans. Some bacteria possess mechanisms to suppress utilization of mucosal glycans when dietary
alternatives are present, while others exhibit opposite behavior. Our results reveal that sensing and
triaging of glycans is a complex process that varies among species, underscoring the idea that these
phenomena are likely to be hidden drivers of microbiota community dynamics and may dictate which
microorganisms commit to various niches in a constantly changing nutritional environment.
Eric C. Martens, University of Michigan
12:15
Networking Lunch
13:45
Armpit Microbiome: Why should we care?
Microbes that live on our skin, in particular in our armpits, affect us on a daily basis and provide one of
the main reasons for bathing daily and using fragrances including underarm products. Body odor, on
humans and other animals, affects interactions with others, informs selection of a mate and predisposes
animals to mosquito bites, significant vectors of disease (Verhulst, 2011). Through an examination of the
primate armpit microbiome including humans, chimpanzees, gorillas, baboons and rhesus macaques,
we assessed the relative abundance and diversity of armpit microbes. Human armpits not only have the
lowest number of OTUs but also the lowest diversity among tested primates, leading to a microbiome
that is structurally unique from other primates.
To further investigate the effect of our unique skin microbiome on odor and attractiveness, we
conducted a citizen science project to combine odor assessment with 16S rRNA sequencing to determine
bacterial composition and its potential correlation with odor. In our study we collected volatile organic
compounds (mVOCs), presumably produced by bacterial metabolism of apocrine gland secretions, in
addition to worn T-shirts from our participants. With the T-shirts (worn nightly by participants who had
gone two days or more days without underarm product), we conducted a “Speed Smelling” event where
participants smelled T-shirts and rated the overall smell, odor intensity and attractiveness. Analysis of
these complementary datasets will allow for correlations between odor and the microbes living on skin,
and will allow us to draw larger conclusions about odor and mate selection.
Sarah Council, North Carolina Central University
14:10
A member of the microbiota modulates host metabolism to increase intestinal permeability and
disease
The commensal microbiota has important impacts on host physiology and health that are only
beginning to be elucidated. Most current studies, however, have focused only on the bacterial
microbiota despite the presence of fungal, archaeal and viral members. The presence of antiSaccharomyces cerevisiae (ASCA) antibodies has long been a prognostic tool for Crohn’s disease (CD)
and suggests that fungal members of the microbiota contribute to the course of disease severity.
Here we report that fungal members of the human microbiota, S. cerevisiae but not R. aurantiaca,
can exacerbate intestinal disease and increase gut barrier permeability. Transcriptome analysis of
germfree animals mono-associated with S. cerevisiae or R. aurantiaca revealed that yeast colonization
most robustly impacted intestinal barrier and metabolism. Indeed, animals colonized with S.
cerevisiae have greater intestinal leakage during colitis and increase permeability of intestinal
epithelial cell lines. A fecal metabolomic screen from germfree mice mono-associated with S.
cerevisiae or R. aurantiaca demonstrated that S. cerevisiae colonization enhanced host purine
Presented by:
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February 10th-11th 2016 | San Diego, California, USA
metabolism leading to greater uric acid production. Elevated levels of uric acid are detected in the
serum of animals colonized with S. cerevisiae during colitis. Treatment with uric acid alone is
sufficient to induce worsened disease and increase gut permeability. Importantly, animals treated
with allopurinol, a clinical drug used to reduce uric acid levels, protects from worsened colitis.
Supporting our data in mice, there is a significant positive correlation between elevated uric acid and
ASCA antibodies in human sera. Thus, intestinal yeast species can potentiate oxidative metabolites to
negatively impact the course of IBD and highlights the importance of this kingdom to host health.
June Round, University of Utah School of Medicine
14:35
Regulation of sugar metabolism in human gut bacteria by novel transcription factor
Andrzej Joachimiak, Argonne National Laboratory
15:00
15:30
Afternoon Networking Break: Coffee, Tea & Refreshments in the Exhibition Hall
Part 2: Functions of the Human Microbiome
Bacteriophage Adherence to Mucus (BAM) Immunity: How Phage and the Microbiome form Innate
and Acquired Immune Systems on Mucosal Surfaces
Bacteriophage Adherence to Mucus (BAM) Immunity is a novel, microbiome-derived, phagemediated immunity active at mucosal surfaces. Phage stick to mucin glycoproteins via hypermutable,
immunoglobulin-like domains displayed on their capsids and protect the underlying epithelial cells
from invading bacteria. The complexity of these interactions between phage, microbes and the
macrobial host are just starting to be de-convoluted. Using an organ-on-a-chip approach, we show
that mucus-binding phage have a subdiffusive hunting pattern that resulted in more frequent host
interactions than non-mucus-adherent phages moving by normal Brownian diffusion. A supporting
theory and experiments show that subdiffusion as a more efficient phage search strategy at low
bacterial concentrations found deeper within mucus layers. These findings extend previous
observations that phage form an acquired and adaptive immune system on mucosal surfaces and for
phage manipulation of microbiomes.
15:55
Forest Rohwer, San Diego State University
Metagenomic Assembly and Strain-Level Tracking of the Fecal Resistome
Assemblages of genes that encode resistance to antibiotics within human, animal, insect and
environmental metagenomes are known as “resistomes”. Healthy human gut resistomes have been
described from the metagenomes of the Human Microbiome and MetaHIT Projects, Yanomani
Amerindians, Hadza Hunter-Gathers and others. While most studies report resistance potential as a
tally or fraction of antibiotic resistance genes within a metagenome, we are using deep metagenomic
sequencing and assembly, combined with resistance gene annotation to map antibiotic genes to
specific genomes within a fecal sample. Further, we are associating resistance genes with mobile
genetic elements on these genomes. Our goal is to identify genetic exchange communities of
elements and organisms capable of spread of antimicrobial resistance.
Sarah K. Highlander, J. Craig Venter Institute, La Jolla, CA
16:10
Imaging microbial nutrient acquisition in the plant microbiome
Presented by:
For Sponsorship Opportunities, email [email protected]
For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
One of the key challenges in microbial ecology is determining the ecophysiology of microorganisms in
complex communities. Isotope-labeling experiments provide a powerful means to directly measure
the activities of uncultivated microbes in-situ, as well as quantitatively measure nutrient transfers
between cell types, symbionts and consortia. We are using novel stable isotope techniques to track
microbial nutrient acquisition in the plant rhizosphere, which is the portion of the plant microbiome
that directly surrounds plant roots in soil. The rhizosphere is loosely analogous in function to the
human gut, where the plant acquires the majority of its nutrients in collaboration with the
surrounding soil microbial community. In this zone, we can track the movement of carbon and
nitrogen between the plant host and microbial community using the stable isotopes 13C and 15N, as
well as the fate of these compounds in the soil matrix. To do so, our group has developed 'Chip-SIP',
which combines nanometer-scale isotope imaging using NanoSIMS with phylogenetic microarrays to
determine the isotopic enrichment of microbial populations. Using this isotope array, we have
tracked movement of 13C from labeled plant exudates and 15N from labeled root litter into the soil
microbial community (bacteria, fungi, microfauna), and linked this data to 16S profiles and gene
transcripts. We have also used NanoSIMS to directly image microbial cells in-plantae, where we’ve
documented the transport of 15N by a symbiotic fungi (arbuscular mycorrhizae) to the host plant.
We’re currently using this method with isotopically-labeled water (H218O), which allows us to detect
and characterize all active microorganisms, as water is universally required by microorganisms for
activity. Finally, we are using spatially resolved spectroscopy (STXM/NEXAFS) to determine the
chemical fate of microbial cells in soil, which allows us to classify the compounds sorbed to minerial
surfaces at the nanometer scale (e.g., lipids, amino sugars, phospholipids). These techniques allow
precise, high-resolution, quantitative measurement of molecular and isotopic patterns in undisturbed
samples, and are equally promising techniques for studying host-microbe and microbe-microbe
interactions in the human microbiome.
Jennifer Pett-Ridge, Lawrence Livermore National Laboratory
Conflict food – do genetic conflicts of interest between host and microbiome explain the health
16:25
impacts of junk food?
Humans have a complex relationship with the multitudes of genomes that make up the microbiome.
Cooperation between host and commensal microbes is important in preventing pathogens from
establishing an infection. Conflicts between the human genome and microbiome, on the other hand,
may contribute to chronic diseases such as obesity and metabolic syndrome. Because foods have
powerful and predictable effects on microbiota composition and function, they may also drive
cooperation or conflict in the microbiome.
The conflict food hypothesis proposes that unhealthy foods cause increasing divergence of fitness
interests between host and microbiome. With this perspective, conflict foods are those that select for
exploitative populations of microbes that increase their fitness at the expense of their host’s fitness.
Healthy foods are those that select for microbial communities and functions that are aligned with and
promote human fitness. This presentation investigates the evidence for the conflict food hypothesis
and its implications for nutrition and public health.
Joe Alcock, University of New Mexico
16:45
Diversity and Function of the Skin Microbiome
The human skin harbors an abundant microbial ecosystem with bidirectional metabolic exchanges
supporting symbiotic and commensal functions. Sequence- based analysis of microbial community
structure and organization of the human microbiome has yielded valuable insight into the microbial
diversity and function of its different body niches. Metagenomic analyses of the diverse skin sites in
Presented by:
For Sponsorship Opportunities, email [email protected]
For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
healthy humans demonstrate that contrasting forces of the skin’s biogeography and individual
characteristics shape the skin microbiome and the dynamics of its bacteria, fungi, and viruses.
However, shifts in the ecological properties of the skin microbiome are significantly associated with
skin disease, disease severity, and other physiologic host factors such as age or primary
immunodeficiency. Understanding the function, structure, and dynamics of the microbiome is
important to design therapeutics that precisely target the pathogen of interest, yet spare the
surrounding beneficial microbiota.
Julia Oh, The Jackson Lab
17:10
Close of Conference Day One.
Networking & Welcome Drink Reception in the Exhibition Hall
POSTER SESSION
Conference Day Two: Thursday February 11th, 2016
08:30
Registration for Conference and Exhibition Hall Opens for All Attendees
09:00
Establishing causal connections between gut microbiota composition and human disease
The composition of the gut microbiota is thought to have dramatic effects on the development and
progression of a variety of diseases. However, identifying the specific bacteria that preferentially
affect disease susceptibility and severity in humans remains a major challenge. In response to this
problem, we recently developed a novel technology that uses the host’s own immune response to the
microbiota as a guide to identify specific members of the gut microbiota that preferentially modulate
disease development. Using this approach, we could identify and isolate specific bacterial strains from
IBD patients that selectively conferred susceptibility to severe colitis when transplanted into germfree mice. These studies thus: (i) establish a new strategy for the identification of disease- and
immune-modulating members of the microbiota in humans; (ii) identify potentially disease-driving
members of the intestinal microbiota in humans with IBD; and (iii) begin to establish causal, rather
than correlative, connections between specific changes in the microbiota and human disease. Future
studies using similar approaches will allow us to elucidate the precise role of microbiota composition
in human health and disease, and will eventually enable the development of novel and specific
microbiota-targeted therapeutics.
Noah W. Palm, Yale University School of Medicine
09:10
New proteomic insights into host-microbe interactions
The intestinal microbiota have profound and diverse effects on host physiology, but the precise nature
of host-microbe interactions remains difficult to measure. Specific microbial sub-populations,
enumerated through 16S sequencing, are often correlated with health and disease states. This
approach cannot directly report dynamic host responses to perturbations to the microbiota as
mediated by diet, pharmaceuticals, or opportunistic infections, however. We previously developed a
mass spectrometry technique, “host-centric proteomics of stool,” which directly measures proteins
secreted or shed into the GI in response to changing intestinal ecosystems. With this approach, we
quantified host responses to antibiotic-associated infections in mice, and are extending these
observations to humans. These efforts are enhanced by novel software we developed which enables
unprecedented depths of protein discovery from virtually any organism, even in the absence of paired
Presented by:
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For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
metagenomic sequencing. With it, we are able to quantify dynamic host, microbial and dietary
interactions directly from stool.
9:35
Josh Elias, Stanford University, USA
Activity-Based Protein Profiling of Drug Metabolism in the Gut Microbiome
The broad diversity of microbes residing in the human body greatly extends the synthetic and metabolic
capacity of the human genome. Emerging studies also show the diverse metabolic functions encoded by
trillions of microbes within the intestinal tract can mediate the chemical transformation of xenobiotics,
such as pharmaceuticals and environmental contaminants associated with energy production. Still, the
impact that xenobiotic exposures have on the microbiome, and in turn how perturbed microbiomes
influence host susceptibility to environmental or drug agents is poorly understood, yet may be a critical
component of individual variability to xenobiotic toxicity, drug bioavailability, efficacy, and interactions.
In our research, we are using activity-based protein profiling to evaluate the hypothesis that
perturbations in the composition of the gut microbiome influence susceptibility by altering host
metabolic capacity toward xenobiotics. Our approach enables the direct measurement of functionally
active enzymes of the host and microbiome important to drug metabolism and disposition. Due
principally to the high complexity of mammalian microbiomes, our understanding of their specific
protein activities is largely based on inference from metagenomics and transcriptomic data. Activitybased probes (ABPs) we have or are developing offer the potential to transform this approach, by
permitting the direct and selective capture and fluorescence imaging or proteomic profiling of the
metabolically active subset of microbes and proteins within the microbiome.
Aaron Wright, PNNL
10:00
Antibiotics, Pedatric Dysbiosis, and Disease
Antibiotics are by far the most common medications prescribed for children. Recent epidemiological
data suggests an association between early antibiotic use and disease phenotypes in adulthood.
Antibiotic use during infancy induces imbalances in gut microbiota, called dysbiosis. The gut
microbiome’s responses to antibiotics and its potential link to disease development are especially
complex to study in the changing infant gut. Here, we synthesize current knowledge linking antibiotics,
dysbiosis, and disease and propose a framework for studying antibiotic-related dysbiosis in children.
We recommend future studies into the microbiome-mediated effects of antibiotics focused on four
types of dysbiosis: loss of keystone taxa, loss of diversity, shifts in metabolic capacity, and blooms of
pathogens. Establishment of a large and diverse baseline cohort to define healthy infant microbiome
development is essential to advancing diagnosis, interpretation, and eventual treatment of pediatric
dysbiosis. This approach will also help provide evidence-based recommendations for antibiotic usage in
infancy.
10:25
Dan Knights, University of Minnesota
Intestinal microbial communities associated with acute enteric infections and disease recovery
The intestinal microbiome represents a complex network of microbes that are important for human
health and preventing pathogen invasion. Studies that examine differences in intestinal microbial
communities across individuals with and without enteric infections are useful for identifying microbes
that support or impede intestinal health.
Presented by:
For Sponsorship Opportunities, email [email protected]
For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections (n = 200)
and 75 healthy family members to identify differences in intestinal community composition. Stools
from 13 patients were also examined post-infection to better understand how intestinal communities
recover. Patient communities had lower species richness, evenness, and diversity versus uninfected
communities, while principle coordinate analysis demonstrated close clustering of uninfected
communities, but not the patient communities, irrespective of age, gender, and race. Differences in
community composition between patients and family members were mostly due to variation in the
abundance of phyla Proteobacteria, Bacteroidetes, and Firmicutes. Patient communities had
significantly more Proteobacteria representing genus Escherichia relative to uninfected communities,
which were dominated by Bacteroides. Intestinal communities from patients with bloody diarrhea
clustered together in the neighbor-joining phylogeny, while communities from 13 patients’ postinfection had a significant increase in Bacteroidetes and Firmicutes and clustered together with
uninfected communities.
These data demonstrate that the intestinal communities in patients with enteric bacterial infections
get altered in similar ways. Furthermore, preventing an increase in Escherichia abundance may be an
important consideration for future prevention strategies.
Rob Britton, Baylor College of Medicine
10:50
Morning Networking Break: Coffee, Tea & Refreshments in the Exhibition Hall
11:20
Fermented Foods as Experimentally Tractable Microbial Ecosystems
Microbial communities of fermented foods have provided humans with tools for preservation and
flavor development for thousands of years. These simple, reproducible, accessible, culturable, and
easy-to-manipulate systems also provide opportunities for dissecting the mechanisms of microbial
community formation. Fermented foods can be valuable models for processes in less tractable
microbiota.
Rachel Dutton, UCSD
11:45
Speaker TBC
12:10
Speaker TBC
12:35
Networking Lunch
Part 3: Applications of the Human Microbiome
14:00
Restoring and preserving man-microbe symbiosis
Man builds as a microbe-host symbiosis from birth on. Maintenance of symbiosis is key to the
preservation of its health and well-being. Yet this recognition comes after more than 60 years
during which our microbiota has had to cope with drastic changes in birth management,
nutrition and clinical practices. This has come with an uncontrolled increase in incidence of
immune-mediated diseases. As we get to recognize dysbiosis as an alteration of man-microbe
symbiosis, “how to preserve and restore man microbe symbiosis?” is a very timely question.
As a central component of human health, the intestinal microbiome may help in several ways
that we will illustrate:
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February 10th-11th 2016 | San Diego, California, USA
1: as a stratifying tool for personalization of nutrition and therapies, allowing to account for
non-responders as well as predicted risk of onset and aggravation of chronic disorders, i.e. via
quantitative metagenomics.
2: as a source of novel drugs and drug-targets, i.e. via functional metagenomics unraveling
novel microbe-cell crosstalk mechanisms
3: as a target for modulation, aiming at a preventive or curative outcome, i.e. via functional
nutrition
4: as a drug of its own, as per organ transplantation, for ecological restoration, management of
infectious risk or prevention of dissemination of resistance.
Metagenomics has revolutionized our perception of the importance of the intestinal microbiota
for human health and yet more is needed to eventually get the most from our gut.
Joel Doré, INRA
14:35
Developing Predictive and Prognostic Markers for Wound Healing
Wound-healing is still a complex area. We look into the different contributions to infection-related
complications and poor healing apparent in acute and chronic wounds, with particular focus on
microbial load, microbial diversity and pathogenic microorganism (bioburden). We have found that
standard cultures offer little predictive or prognostic value for wound outcomes, and better
biomarkers are needed to guide management and treatment of both acute and chronic wound
patients. We have begun longitudinal studies employing culture-independent approaches and the
incorporation of patient clinical data which have the potential to provide more precise information on
how wound microbiomes evolve during the healing process, and also predict specific outcomes – such
as rate of healing or progression to infection-related complication.
Elizabeth Grice, University of Pennsylvania
14:55
Molecular cartography of the human skin surface in 3D
The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the
environment. The molecular composition of this organ is derived from host cells, microbiota, and
external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance
the technologies needed to explore the topographical distribution of skin molecules, using 3D
mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal
that the molecular composition of skin has diverse distributions and that the composition is defined
not only by skin cells and microbes but also by our daily routines, including the application of hygiene
products. The technological development of these maps lays a foundation for studying the spatial
relationships of human skin with hygiene, the microbiota, and environment, with potential for
developing predictive models of skin phenotypes tailored to individual health.
Pieter Dorrestein, UCSD
15:20
The Microbiome-Gut-Brain Axis in Autism
The microbiome-gut-brain axis has been implicated in behavioral disorders as well as functional
gastrointestinal (GI) disorders. While GI symptoms are a significant comorbidity in children with autism
spectrum disorder (ASD) and may contribute to problem behaviors, microbiome studies in individuals
with autism are hampered by multiple confounders that have yielded conflicting results.
Presented by:
For Sponsorship Opportunities, email [email protected]
For Programme Questions, email [email protected]
February 10th-11th 2016 | San Diego, California, USA
Consequently, there is growing interest in defining the role of the microbiome in ASD development,
especially in early childhood when establishment of the gut microbiome and manifestations of clinical
ASD symptoms occur concurrently. The identification of GI issues remains difficult in the ASD
population and in particular the children with limited verbal communication. The development of
stool-based biomarkers would represent a vital tool for both physicians and children with ASD.
Microbiome characterization of GI specimens in children with autism will be discussed and compared
to unaffected siblings, healthy children, and children with functional GI disorders. The identification of
pathophysiologic mechanisms that link disturbances in the microbiome-gut-brain axis with disease
phenotypes in individuals with ASD will also addressed.
Ruth Ann Luna, Texas Children’s Hospital
Anxiety and Depression Increase in a Stepwise Manner in Parallel With Multiple FGIDs and Symptom
15:45
Severity and Frequency
Anxiety and depression occur frequently in patients with functional gastrointestinal disorders (FGIDs),
but their precise prevalence is unknown. We addressed this issue in a large cohort of adult patients
and determined the underlying factors.
In total, 4,217 new outpatients attending 2 hospitals in Hamilton, Ontario, Canada completed
questionnaires evaluating FGIDs and anxiety and depression (Hospital Anxiety and Depression scale).
Chart review was performed in a random sample of 2,400 patients.
Psychiatric comorbidity is common in patients referred to a secondary care center but is often
unrecognized. The prevalence of both anxiety and depression is influenced by gender, presence of
organic diseases, and FGIDs, and it increases with the number of coexistent FGIDs and frequency and
severity of GI symptoms.
Premysl Bercik, McMasters University
16:05
Infectious Diseases, Vaccine Development and CBER/FDA Regulatory Pathways
Regulatory insight into: clinical practice in internal medicine and infectious diseases and conduct of
phase 1 and 2 clinical trials as principal investigator. Infectious diseases, vaccine development and
CBER/FDA regulatory pathways. Formulating vaccine development strategies and identifying
programmatic obstacles. Working with public-private partnerships, national regulatory agencies, CDC
and ACIP in addressing infectious disease vaccine issues and policies.
Wellington Sun, FDA
Speaker TBC
16:30
17:10
Close of Conference.
Presented by:
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