art_3A10.1186_2F2049-2618-2-16.pdf

MEETING REPORT

Open Access

Human microbiome science: vision for the future,

Bethesda, MD, July 24 to 26, 2013

Jacques Ravel

, Martin J Blaser

, Jonathan Braun

, Eric Brown

, Frederic D Bushman

, Eugene B Chang

Julian Davies

, Kathryn G Dewey

, Timothy Dinan

, Maria Dominguez-Bello

, Susan E Erdman

, B Brett Finlay

Wendy S Garrett

, Gary B Huffnagle

12,13

, Curtis Huttenhower

, Janet Jansson

, Ian B Jeffery

, Christian Jobin

17,18

Alexander Khoruts

, Heidi H Kong

, Johanna W Lampe

, Ruth E Ley

, Dan R Littman

23,24

, Sarkis K Mazmanian

David A Mills

26,27

, Andrew S Neish

, Elaine Petrof

, David A Relman

30,31

, Rosamond Rhodes

Peter J Turnbaugh

, Vincent B Young

12,13

, Rob Knight

and Owen White

Abstract

A conference entitled

‘

Human microbiome science: Vision for the future

’

was organized in Bethesda, MD from

July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at

providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss

gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes

what is needed for human microbiome research to move forward and deliver medical translational applications.

Introduction

Each of us consists of about 40 trillion human cells [1]

and about 22,000 human genes [2], but as many as 100

trillion microbial cells [3] (the microbiota) and 2 million

microbial genes [4] (the metagenome). Understanding

the microbial side of ourselves may therefore be critic-

ally important for understanding human biology, includ-

ing drug responses [5-8], susceptibility to infectious [9]

and chronic [10] disease, and perhaps even behavior

[11]. Since the inception of the Human Microbiome Pro-

ject (HMP) in 2007 [4,12], the fundamental understand-

ing of the human microbiome has grown at an ever

accelerating pace [13]. Together, the HMP healthy co-

hort study [14,15], and the many associated studies,

which provide more details on methodology, bioinfor-

matics analyses, and additional cohorts, have led to over

350 publications (http://www.ploscollections.org/hmp).

This work has set the stage for rapid advances, some

with high potential for translational studies, in under-

standing the mechanisms governing the similarities and

differences in the microbes we share, their association

with diseases, but more importantly, the functional roles

microbiota play in health and disease.

Meeting goals and objectives

To understand the current state of human microbiome

research, and to identify key areas for progress going for-

ward, we held a conference in Bethesda, MD from July

24 to 26, 2013, entitled

‘

Human Microbiome Science:

Vision for the Future

’

. This conference, which was sup-

ported in part from a grant by NIH to the University of

Maryland School of Medicine, together with corporate

sponsors including Roche, Qiagen, Illumina, Life Tech-

nologies, MoBio, Metabolon, and the BioMed Central

journal

Microbiome

, sought to provide an overview of

cutting-edge work in NIH-supported microbiome re-

search, and to identify obstacles as well as opportunities

for progress in this challenging field of research. The

meeting was organized by a trans-NIH working group,

including 28 participants (programme staff) from 14 (of

the 27) NIH Institutes, Centers and Offices, together

with four scientific advisory members funded by the Hu-

man Microbiome Project. The meeting was attended by

269 participants (and an additional 250 with webcast)

from academia, national labs, a range of government agen-

cies including NIH, Environmental Protection Agency

(EPA), US Department of Agriculture (USDA), Food and

* Correspondence:

jravel@som.umaryland.edu

Institute for Genome Sciences, Department of Microbiology and

Immunology, University of Maryland School of Medicine, 801 W. Baltimore

Street, Baltimore, MD 21201, USA

Full list of author information is available at the end of the article

Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and

reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain

Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,

unless otherwise stated.

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Drug Administration (FDA), US Agency for International

Development (USAID), Office of Science and Technology

Policy (OSTP), US Army, National Science Foundation

(NSF), and National Aeronautics and Space Administra-

tion (NASA), and involved 37 speakers from a broad

range of disciplines including microbiology, immunology,

medicine, infectious disease, ecology, and computer sci-

ence. The broad expertise of the organizing committee

and the participants underscores the way in which mi-

crobes pervade the human body and our environment,

and microbiome research may soon pervade the biomed-

ical research enterprise.

Over the course of this 3-day meeting, there were pre-

sentations and discussions aimed towards:

–

Recognizing that the study of the human

microbiome, in disease and in health, is of relevance

to the missions of all NIH Institutes and Centers;

–

Increasing awareness across all NIH Institutes and

Centers of gaps, needs, and challenges faced by the

broad microbiome research community to drive

future research and investments;

–

Facilitating coordination between the NIH Institutes

and Centers to promote coherent oversight for

policies and approaches that will maximally benefit

microbiome-related biomedical research;

–

Identifying areas where common resources or

partnerships would benefit microbiome-related bio-

medical research;

–

Exploring how NIH and other government funding

agencies could collaborate to integrate the

microbiome into studies of human health and more

broadly into studies of human interactions with

their physical and microbial environment;

–

Fostering understanding of the current state of

microbiome research, and shaping an overall vision

for future directions of the field over the next 10

years.

Overview: the human microbiome project

In the first session Dr. Owen White (University of

Maryland School of Medicine, Baltimore, MD, USA)

(Figure 1A) set the stage for the conference, noting that

the meeting was a unique opportunity for microbiome re-

searchers both to reflect on past successes and to define the

direction that the field could take going forward. His intro-

duction was followed by a presentation by Dr. Francis

Collins (Director of the National Institutes of Health,

Bethesda MD, USA) (Figure 1B), who opened with a his-

torical perspective of the Human Microbiome Project

(HMP). He presented an overview of how the microbiome

is uniquely positioned to enhance the mission of the NIH

because of the many associations between the state of

themicrobiomeandawiderangeofdiseasesfrom

gastrointestinal diseases and conditions, to cancer and even

mental illnesses. Dr. Eric Green (Director of National Hu-

man Genome Research Institute, NHGRI) (Figure 1C)

followed with a report on the state and the many accom-

plishments of the HMP. The HMP aimed to survey the

microbiome in humans through taxonomic and metage-

nomic analyses. He highlighted

the central healthy cohort

of volunteers who were intensively sampled, and several

demonstration projects that focused on diseases at sites

such as the GI track, the skin or the urogenital track. These

projects generated over 3.5 Tbp of data and 8 million

unique microbial genes were catalogued. These datasets

(sequence data, strains, clini

cal phenotypes, nucleic acid ex-

tracts, and even cell lines) are publicly available through re-

positories and coordinated through a Data Analysis and

Coordination Center (DACC) hosted at the Institute for

Genome Sciences at the University of Maryland School of

Medicine [13]. Overall, the HMP has led to over 350 peer-

reviewed scientific publications. The HMP has supported

the development of new bioinformatics and technological

tools, which altogether facilitate the study of the human

microbiome for the scientific community. Human micro-

biome studies

’

ethical, legal and social implications (ELSI)

were also evaluated, mirroring the Human Genome Project.

Dr. David Relman (Stanford University) (Figure 2A) gave

thefirstofthreekeynoteaddresseson

‘

Diversity, Stability

and Resilience of the Human Microbiome

’

, highlighting the

larger role the human microbiome plays in both health and

disease. He presented recent work from his laboratory on

the profound effects of antibiotics in reshaping the human

microbiome, and on the value of applying (and perhaps de-

veloping) ecological theory for understanding these com-

plex ecosystems and their contributions to human biology

[16]. In particular, he raised the issue of resilience, an

ecological concept that refers to the amount of disturb-

ance that a system can withstand without changing its

self-organizing processes or services [17]. He empha-

sized the need for better tools to define resilience and

evaluate the stability of, and harm to human-associated

microbial communities.

Dr. Rosamond Rhodes (Icahn School of Medicine at

Mount Sinai, New York) discussed the ethical, legal, and

social implications surrounding the study of the human

microbiome. In particular, she spoke on issues related to

subject identification from knowledge of microbiome se-

quence data - issues that are in so many ways analogous

to those faced by scientists studying the human genome

sequence. These issues impact the way microbiome sci-

ence is and will be performed in the future, especially

biobanking. Importantly, they highlight the need to bet-

ter protect the privacy of subjects involved in micro-

biome research.

The session was closed by Dr. Robbie Barbero, Office of

Science and Technology Policy, (OSTP), who described

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the role of OSTP in supporting cross-agency collaboration

to meet

‘

Grand Challenges

’

that address important societal

needs with a combination of research, technology, and

policy inputs. He described several successful Grand Chal-

lenges to date, and asked the microbiome community to

consider whether a microbiome-focused Grand Challenge

might be appropriate at this point in time, especially given

the pervasive impact of microbes in the environment and

in our bodies.

Basic biology of the microbiome

This session consisted of three exciting talks describing

what we know about how the microbiome develops and

changes over time, elaborating on the theme developed

earlier by Dr. David Relman. Dr. Ruth Ley (Cornell Uni-

versity) described the changes in the gut microbiota

throughout pregnancy, as well as those experienced by

newborns in the first few years of life [18]. She presented

exciting new work that aims at linking host genetic vari-

ations and the composition of the human microbiome.

For example, in a cohort of more than 1,000 twin adults,

heritablegeneraofBacteriaandArchaeawereidentified.

Understanding the contributi

on of human genetic varibility

in shaping the composition of the human microbiome

will govern the way we will be able to manipulate these

microbial communities to maintain or restore health

and cure diseases.

Dr. Jacques Ravel (Institute for Genome Sciences, Uni-

versity of Maryland School of Medicine) discussed the

ecological principles that govern the dynamics of the hu-

man microbiome (resilience, resistance and persistence)

and how one can gain better understanding of these dy-

namic systems using descriptive microbial community

compositional surveys [19], gene composition and whole

community gene expression or even metabolite analysis.

Each of these analyses often reveals different intrinsic

ABC

Figure 2

Keynote speakers.

Dr. Jonathan Braun, University of California Los Angeles,

(A)

highlighted the challenges in translating microbiome

sciences. Dr. David Relman, Stanford University,

(B)

discussed the larger role the human microbiome plays in both health and disease. Dr. Maria

Dominguez-Bello, New York University,

(C)

discussed aspects of the modern versus ancestral microbiome.

B

A

D

C

Figure 1

Dr. Owen White (A), one of the organizers of the meeting introduced Dr. Francis Collins (B), Director of the National Institutes

of Health, who gave an historical perspective on the Human Microbiome Project.

Dr. Eric Green

(C)

, Director of the National Human

Genome Research Institute discussed the many successes of the Human Microbiome Project. Dr. Jesse Goodman

(D)

, Chief Scientist at the US

Food and Drug Administration discussed the regulatory aspects concerning the microbiome, including the challenges associated with

fecal transplants.

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dynamic patterns when applied to the same community.

His presentation stressed the pitfalls that could result

from

a priori

application of principles that might govern

microbial community at a given body site to another

site. Discussing the vaginal microbiota he introduced a

new concept that the intensity of dynamic changes (that

is, frequency and duration of change in microbiota com-

position) could represent an increased risk for acquisi-

tion and transmission of sexually transmitted infections.

Dr. Frederic Bushman (University of Pennsylvania) then

spoke about his work on understanding the dynamics of

the human gut virome (the set of viruses that targets

bacteria and humans). Although immense progress has

been made in understanding the bacteria that inhabit

the human body, especially through 16S rRNA gene se-

quencing and reference genome approaches, studies of

the human virome have lagged behind. Analysis of the

composition of the gut virome shows that, at least over

2.5 years, the dynamics of the virome is subject-specific

and may be important for predicting health, and that the

vast majority of viral diversity in the human gut is still

uncharacterized and rapidly evolving [20,21]. These

studies suggest that a targeted effort to understand viral

diversity may be needed given their likely importance for

the gut ecosystem as a whole.

State of the art microbiome tool

s, technologies, approaches

Microbiome studies rely on the development of novel

and robust technologies, approaches and analytical tools.

Dr. Janet Jansson (Lawrence Berkeley National Laboratory)

described cutting-edge research that combines multi-omics

approaches for in-depth char

acterization of gut community

function in health and disease. Taking examples from her

own work and those of environmental scientists, she

demonstrated the limitations of 16S rRNA gene-based

community survey which often shows high variation be-

tween subjects, while functionally the communities are

more similar. She advocated for applying metaproteomics

combined with metabolomics to gain more accurate in-

sights into the function of the community and often the

host as well [22,23]. The addition of these multiple layers of

omics data provides substantially greater insight into pos-

sible mechanisms, and when joined with time-series data

can be critical for understanding which differences are

causes and which are effects of processes at other levels.

However, she stressed that computational tools for func-

tional assignment and for omics

’

data integration are still

in their infancy and desperately needed. Dr. Dan Littman

(New York University) spoke about approaches for study-

ing the interaction of the host immune system and the

microbiome, noting the importance of specific commensals

in inducing inflammatory T cell responses [24]. He specific-

ally highlighted an association of

Prevotella copri

colo-

nization with the autoimmune response in rheumatoid

arthritis [25,26]. Dr. Curtis Huttenhower (Harvard School

of Public Health) described novel bioinformatics tools for

reconstructing the biomolecular networks driving emer-

gent phenotypes in the microbiome and their influences

on human health [27]. These

computational methods

provide the initial steps to integrate multi-omic data,

generate mechanistic hypotheses, and identify action-

able molecular targets for therapy. He also discussed the

need for improved study designs to effectively scale

microbiome investigations to epidemiological popula-

tions, which along with principled methods for meta-

analysis will aid in ensuring reproducible translational

results.

Dr. Rob Knight (University of Colorado at Boulder) de-

scribed the challenges in moving from associative studies

that link microbes to disease towards studies of causality

using either germ-free mice models or epidemiological

criteria for causation. He also discussed the challenges of

integrating human microbiome datasets that use different

methodologies and different subject populations. He dis-

cussed the critical aspect of the effect size of each meta-

data element. For example, because age and body site can

have large effects even in studies that use very different

methods, it is essential to control for technical variability

when examining serial samples from the same patient or

sub-site analysis (for example, stool

versus

lumen). He also

showed the utility of the HMP dataset [14,15] as a data

frame for integrating dynamics of time series datasets such

as during infant development and for understanding re-

mission of

Clostridium difficile-

associated disease after

fecal microbiota transplantation (FMT). Dr. Owen White

(University of Maryland School of Medicine) closed the

session by discussing integration of large datasets such as

those from Human Microbiome Project into accessible re-

sources such as the HMP DACC, which he leads [13]. He

emphasized the need for adoption of standards such as

those developed by the Genomic Standards Consortium

to enable systematic analysis of these integrated datasets

[28]. At present, privacy concerns make it difficult to ob-

tain and harmonize data from different projects, especially

because a considerable amount of data resides in dbGAP

(the access-controlled Database of Genotypes and Pheno-

types). He stressed that open resources will go a long way

towards making the controlled-access data more re-

usable. Finally, he described OSDF (the Open Science

Data Framework); an open-source project that provides

methods for accessing large volumes of data on distri-

buted file systems, including cloud computing resources,

which are increasingly gaining importance as the volume

of data expands.

The first day concluded with an open discussion facili-

tated by Ed Young, a science writer and blogger, between

the day

’

s speakers and the conference participants. A wide

range of topics was covered including: the potential of

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microbiome data to impact health; the need for improved

reusability of the resources generated through investment

by NIH and other agencies; and the importance of expand-

ing microbiome studies to understand the functional role

of the microbiome in disease. To date, most microbiome

studies have mostly been associative (associate one or more

organisms with a disease state), and the need for studies

that are designed to address causality was also discussed.

Many audience members were interested in issues of sub-

ject identifiability via the

microbiome and how a micro-

biome can be changed in a specific desired direction; both

of these topics are areas of intense scientific interest, how-

ever, at present a clearer picture is still emerging.

The modern

versus

the ancestral microbiome

In the second keynote, Dr. Maria Gloria Dominguez-Bello

(New York University) (Figure 2B) spoke about the mo-

dern versus ancestral microbiome [29,30]. She described

how modern practices including hygiene, antibiotics, and

limited exposure to livestock have likely affected the com-

position of the human microbiome. She showed that

people living more ancestral lifestyles, without antibiotics

and vaccines, such as a previously uncontacted group of

the Yanomamö Amerindian tribe in Venezuela, have a

profoundly different microbiome as compared to western

peoples. Their microbiomes exhibit high diversity not just

in the gut, but at all body sites surveyed. She concluded

her presentation with a description of a fascinating project

that aims to collect not just biological samples, but envir-

onmental samples including household surfaces, water,

soil, air, domestic pets and livestock along gradients of

Westernization in both South America and Africa. Such

studies may be critical for understanding the role of mi-

crobes, or their loss, in several so-called

‘

Western diseases

’

which are a high cost burden on the US health system.

Host immune system/microbiome interactions

Dr. Sarkis Mazmanian (Caltech) discussed how specific

bacterial genes control how some gut bacteria colonize the

intestinal tract [31]. Focusing on

Bacteroides

species in

mice, he presented data demon

strating that a unique class

of microbial polysaccharide utilization loci is responsible

for species-specific saturable colonization of the crypt chan-

nels in the gut. These commensal colonization factors (ccf)

loci in

Bacteroides fragilis

and

Bacteroides vulgatus

enable

species-specific physical inte

ractions with the host that me-

diate stable and resilient gut colonization; ccf mutants are

defective in horizontal transmission. These studies stress

the importance of species-specific genes that, if absent,

could affect the establishment of a healthy microbiome. Dr.

Eugene Chang (University of Chicago) discussed the effects

of the gut microbiome on host epithelial functions and re-

sponses [32,33], focusing on the pouchitis model that has

been extremely informative in his HMP demonstration

project. Dr. Susan Erdman (Massachusetts Institute of

Technology)presentedherworkonanimalmodelsshow-

ing that specific microbial exposures affect host hormones,

including oxytocin [34], interrelated with host immune

cell functioning. She showed that prior exposures to gut

microbes alter the immune system and potency of T

regulatory (Treg) lymphocytes, lowering risk for sys-

temic diseases including cancer later in life. These stu-

dies highlighted microbe-endocrine-immune linkages

and possible mechanisms for transmitting the effects of

maternal microbial exposures to offspring, including be-

havioral benefits such as improved social interactions.

Microbiome and disease associations

Dr. Heidi H Kong (NIH, NCI, Dermatology Branch) dis-

cussed how skin microbiota can influence host skin im-

munity and vice versa. For example, Yasmine Belkaid

and co-workers [35] showed that applying the skin com-

mensal

S. epidermidis

on germ-free mice can restore the

ability to control skin infections by the parasite

Leish-

mania major

. These findings have potential implications

for the development of rational tissue-specific adjuvant

and vaccine approaches. In addition to highlighting the

importance of studying fungal communities as well as

bacterial communities, she discussed work demonstrat-

ing the alterations of the skin microbiome in patients

with atopic dermatitis (AD) and primary immunodefi-

ciencies [36]. The notable differences in the skin micro-

biomes of these patient populations may reflect how the

host can modulate its skin microbiome and potentially

elicit episodes of skin disease. Since AD is often linked

with asthma and hay fever, understanding the triggers of

AD may allow scientists to develop strategies to prevent

and treat these other diso

rders. Dr. Gary Huffnagle

(University of Michigan) described the major challenges

associated with sampling the lungs, a body site previ-

ously believed to be sterile [37,38]. It is now known that

a low-abundance microbiota exists in the lung and that

when diseased, the microbial load increases, comprising

numerous taxa not found in the mouth or throat. This

indicates that there are sele

ctive pressures in the lungs

for bacterial persistence, colonization and growth that

uniquely shape the bacterial community of this body

site. Dr. Vincent Young (University of Michigan)

reviewed Koch

’

s Postulates and their implications for

moving beyond a

‘

classical

’

infectious disease model and

towards an understanding of the role of both com-

mensal and pathogenic microbes in the development

of inflammatory bowel disease. In particular, unders-

tanding the interactions of normal gut bacteria with the

host mucosa is critical to understanding how dysre-

gulation of these normal interactions can trigger the ab-

normal host response that characterizes inflammatory

bowel disease [32].

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Functional interactions between host and microbiome

Microbes are important modulators of host phenotypes. It

is critical to better understand the mechanisms governing

this modulation. Dr. Andrew Ne

ish (Emory University) dis-

cussed how the microbiome controls epithelial cell prolife-

ration, focusing on the role of microbes in stimulating

reactive oxygen species (ROS) production in the gut epi-

thelium [39,40]. In Nox1 and Frp1 null mice, and dNox

knockout

Drosophila,

the dynamics of crypt cell prolif-

eration are substantially altered, suggesting that signal-

ing to host cells via reactive oxygen species stimulated

by commensal bacteria is important. Dr. Peter Turnbaugh

(Harvard University) spoke about the impact of gut mi-

crobes on drug metabolism; for example, how certain

strains of the gut bacterium

Eggertella lenta

carry a cyto-

chrome operon that causes in

activation of the cardiac drug

digoxin [7]. These and other st

udies highlight the important

role of the microbiome in altering the outcome of thera-

peutics. A better understanding of these interactions may

someday allow us to devise strategies to improve drug effi-

cacy and reduce side effects. Dr. Wendy Garrett (Harvard

School of Public Health) discussed how microbial me-

tabolites, in particular short-chain fatty acids which are

the major end products of bacterial fermentation of

dietary polysaccharides, regulate the size and function of

the colonic Treg pool, and can protect mice against colitis

[41,42]. Thus, short-chain fatty acids may act as a trans-

ducer of the gut microbiome into a reliable signal that can

regulate immune homeostasis and function in the colon.

Diet and the microbiome

Dr. Ian Jeffery (University Co

llege Cork, Ireland) presented

the ElderMet project that studie

s diet-gut microbiota inter-

actions as it relates to the health of the elderly [43]. In this

project, comparisons of elderly subjects living in the com-

munity, residential-care or hos

pital settings were performed

using a combination of dietary assessment, gut microbial

characterization using 16S rRNA gene surveys, and NMR-

based metabolomic analyses. Differences in diet and living

situation were highly correlated with differences in the gut

microbiota composition and function. Within these popula-

tions the microbiota was asso

ciated with health outcomes

in the individuals such as fra

ilty and inflammatory markers.

Over the long term, diet was associated with changes in gut

microbiota and therefore dietary modulation of the micro-

biota may have an impact on health of the elderly. This

work could lead to carefully desi

gned dietary interventions

to promote healthier aging. Dr. Kathryn Dewey (University

of California, Davis) reviewed what is known about the

influence of diet in early life on the microbiome. She

discussed the key role of breastfeeding, noting that the

microbial composition of breast milk may be influenced

by the mother

’

s weight and mode of delivery, and that

prebiotics in human milk promote the growth of beneficial

gut bacteria. Although many studies have compared breast-

fed to formula-fed children, it is still unclear which spe-

cific aspects of breastfeeding have an effect on the gut

microbiome. Introduction of solid foods, the types of solid

foods consumed, and certain nutrients such as iron and

fatty acids influence the diversity and composition of gut

bacteria. However, there is little information on how

dietary composition or nutrient intake affects the

microbiome of children and the health consequences of

differences in the gut microbiome. A new project enti-

tled the Breast Milk, Gut Microbiome, and Immunity

(BMMI) Project aims to discover new ways to promote

healthy growth in infants and children, and will address

some of these important questions. Dr. Johanna Lampe

(Fred Hutchinson Research Center and University of

Washington) discussed how a range of dietary compo-

nents are metabolized by bacter

ia, potentially impacting

human health [44]. For example, bacterial metabolites

can act as nutrients for host cells (for example, short-

chain fatty acids), act as signaling molecules, or be gen-

otoxic (as in the case of nitrites and hydrogen sulfide)

or beneficial to host cells (for example, isothiocyanates

and flavonoids). Of particular interest in studies of car-

diovascular disease is the bacterial conversion of choline

to trimethylamine, which is subsequently converted to

trimethylamine N-oxide (TMAO) in the liver.

Translational research and the microbiome

The third day was dedicated to strategies for moving be-

yond basic association between microbiome and disease

by exploiting the microbiome to improve human

health. The third keynote was given by Dr. Jonathan

Braun (UCLA) (Figure 2C) who noted that the key to

translating microbiome science was to identify plaus-

ible mechanisms to explain how bacteria might affect

the host, as well as therapeutic targets for modulating

bacterial activity. He highlighted a number of diseases

that were either caused by pathogenic microbes or by a

‘

pathogenic

’

microbial ecosystem, including

Clostridium

difficile

-associated colitis, inflammatory bowel disease,

Type 1 diabetes, lymphoma, atherosclerosis, and elements

of behavior and cognition. The main challenges are to un-

tangle the relationships among the complex networks of

microbial species, their functions and products and how

they mediate effects on the host (and vice versa) [45]. Un-

derstanding the properties that drive these networks is key

to designing reliable interventions. This presentation was

followed by Dr. Jesse Goodman (FDA, Chief Scientist)

(Figure 1D) who covered regulatory aspects concerning

the microbiome, in particular the FDA

’

s decision to re-

quire an IND (Investigational New Drug) application ap-

proval for all FMT other than those for treating

C. difficile

infections. In his presentation he also reviewed the regu-

latory issues surrounding probiotics not covered by the

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GRAS (Generally Recognized as Safe) guidelines, for ex-

ample, microbial strains isolated from traditionally con-

sumed fermented foodstuffs. He stressed that the FDA

’

mission was to get effective therapies and diagnostics

into the hands of consumers as rapidly as possible, how-

ever, within the microbiome space methods for demon-

strating safety and efficacy are still in their infancy and

very much evolving.

Body/microbiome axis

Dr. Ted Dinan (University College Cork, Ireland) discussed

his work on the microbiome-gut-brain axis where he uses

germ-free mice to demonstrate that the lack of gut mi-

crobes affects sociability, decreases memory, and increases

stress responses. He discussed the role that bacteria play

in producing neurotransmitters, such as norepinephrine,

serotonin, or dopamine, as well as how certain probiotic

bacteria can actually modulate the effects of neurotrans-

mitters. In particular, he presented data showing how spe-

cific strains of

Lactobacillus rhamnosus

modulate stress

and this effect appears to be mediated through the vagus

nerve in mice [46]. He cautioned that identifying psycho-

biotics (a live organism that, when ingested in adequate

amounts, produces a health benefit in patients suffering

from psychiatric illness) should involve rationally designed

screening strategies of very large numbers of putative mi-

crobial strains, and that, just as is the case with chemical

drugs, most strains are expected to have no effect on most

disorders. Dr. Martin Blaser (New York University) spoke

about both epidemiological evidence linking antibiotic use

and the risk for obesity [47]. He presented experimental

evidence in mice that sub-therapeutic antibiotic treatment

as well as pulsed full-dose antibiotic treatment modifies

body composition, growth, and immune status, leading to

increased adiposity. These results, together with the use of

antibiotics as growth promoters in livestock, suggest that

the obesity epidemic in humans may be in part attribut-

able to modifications of the gut microbiota by antibiotics,

especially in early in life. Dr. Stanley Hazen (Cleveland

Clinic) discussed links between microbes and cardiovas-

cular disease, and in particular the role of bacteria in

converting choline to TMAO, which in turn promotes

atherosclerosis [48]. This model, supported by careful

work in mice and in human subjects, suggests a direct

and specific mechanistic link between gut microbes and

cardiovascular disease. Dr. Christian Jobin (University

of Florida School of Medicine) presented his work on

gut microbiome and colorectal cancer [49], stressing the

importance of mechanistic studies identifying specific

bacterial genes involved in the causal pathway to cancer.

Using IL10-/- germ-free mice which develop colitis-

associated colorectal cancer after exposure to microbes,

he identified the polyketide colibactin, produced by

coli

, which appears to play a substantial inflammation-

dependent role in colorectal cancer development in

mice and humans. These studies have started to un-

tangle the role of inflammation, gut microbiota, and

specific bacterial genes in the development of cancer.

Dr. Julian Davies (University of British Columbia, Canada)

ended the session with a discussion of the wealth of che-

mical products that microbes produce, and of the im-

portance of mining this wealth using rational genomic

approaches for identifying microbial secondary meta-

bolites with therapeutic activities. He noted that the

microbiome itself represents a great source of novel and

potentially bioactive natural products [50].

Probiotics, microbiome vaccines, and fecal transplants

The final session turned to methods for directly manipulat-

ing the microbiome. Dr. Alexander Khoruts (University of

Minnesota) covered the remarkable efficacy (approximately

90% remission rates) of fecal mi

crobiota transplantation

(FMT) in curing recurrent

Clostridium difficile

infection

(CDI). The potential mechanisms of action are starting to

be elucidated and involve ec

ological, immunological, and

metabolic (bile acids) components - all are proposed to

lead to

C. difficile

colonization resistance. He noted that

many challenges remain before widespread implementa-

tion of FMT can become a reality in routine clinical

practice. Dr. Elaine Petrof (Queen

’

s University, Canada)

provided a complementary approach for FMT using

synthetic stool made of defined communities of bacteria

cultured from human feces but grown in the laboratory,

rather than samples from don

ors. She described the suc-

cessful treatment of two CDI patients using a defined

synthetic stool comprising 33 bacterial isolates [51].

This approach holds substantial promise for improving

patient and physician acceptability of FMT. Dr. David

Mills (University of California, Davis) discussed the role

of milk-oriented prebiotics and probiotics in identifying

compounds and bacteria that could form the next gen-

eration of rationally-designed prebiotics and probiotics

to improve and support infant health. He described the

rich diversity in oligosaccharides found in human breast

milk and noted that the typ

es of glycans found in breast

milk help to shape the composition of the infant gut

microbiota, specifically different species of

Bifidobacter-

ium

[52]. This information could be used to design syn-

biotic formulations comprised of specific human milk

oligosaccharides and bacteria to drive a healthy infant

gut. Ultimately, understanding the co-evolution of milk

glycans, the immune system, and gut bacteria in infancy

may be critical in improving human health in infants

and may be among the first translational models for

modulation of the gut microbiota. Finally, Eric Brown

(representing the Brett Finlay Lab, University of British

Columbia, Vancouver, Canada) spoke about gut micro-

biota and vaccine efficacy. In developing countries vaccine

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efficacy is lower and the gut microbiota is different from

that in developed countries. He suggested a link between

the impact of diet and malnutrition on the composition of

the gut microbiota and vaccine efficacy. He highlighted a

need for studies to explore ways to manipulate the gut

microbiota to improve vaccine response, including pro-

biotics and/or prebiotics. Understanding the basis for

vaccine failure in developing countries is a key issue

in global public health. Further, developing tests for

the maturation of the infant microbiota and immune

system, which could be used to improve public health

strategies and vaccine efficacy could have a large bene-

ficial effect.

The meeting closed with another floor discussion mod-

erated by Ed Yong, which gave participants a final chance

to share their thoughts about the workshop and about the

future of human microbiome research. He led discussions

on the impact of antibiotics on the gut microbiota and

long-term health, as well as on ways to better understand

mechanisms of action driving the benefit associated with

manipulation of the microbiota.

Gaps, needs, and challenges: a framework for the future

of human microbiome studies

A key objective of this meeting was to identify gaps,

needs and challenges specific to each individual re-

search project presented, and the field as a whole.

In addition, the meeting organizers aimed to expand

microbiome research by incl

uding specialists in other

disciplines who could benefit from a microbiome

focus. Not surprisingly, speaker responses to the ques-

tions of gaps, needs, and challenges varied, neverthe-

less, some themes emerged:

Causation and the need for prospective longitudinal studies

A challenge in microbiome

research is to move beyond

identification of microbiota

community structures that

correlate with disease stat

es to establishing a causal

link between structural changes and the functions of

microbiota in disease. Prospective longitudinal studies

in humans were recommended to help better under-

stand the drivers of microbiome dynamics with respect

disease risk and to develop predictive models of sus-

ceptibility that could sugge

st better health practices

(Relman, Ravel). Prospective long-term follow up of

intervention trials are also needed to identify the con-

sequences of differences in microbiome structure and

function in early life (Blaser, Dewey, Knight). In mice,

multi-generational studies that monitor transfer of

microbiota to offspring ove

r generations with changes

in diet, antibiotics, or environment are important for

testing cause/effects relationships between allergic,

autoimmune, and behavioral disorders and the micro-

biome (Mazmanian). Impro

ved clinical phenotyping

and clean study design are essential to successful micro-

biome studies (Chang). Understanding links between host

genetics and the microbiome may also require a longitu-

dinal component, as some phenotypes develop only at

specific ages (Ley).

Improved understanding of microbial ecosystems of the

human body

We need more robust knowledge of ecological networks

within microbial ecosystems and their stability over time

within individuals (Braun). Characterization of microbial

succession and colonization, and of the natural history

of microbes and the disorders they cause, was noted as a

potential means to correct dysbiosis or influence meta-

bolism of drugs (Mazmanian, Ley, Turnbaugh, Chang).

Relman raised several key qu

estions, including: which

aspects of diversity matter most, and do these aspects

mainly occur at the level of organisms, genes, or path-

ways, or between communities? He argued that under-

standing the fitness lands

cape of an individual would

improve our knowledge of resilience and contribute to

strategies for maintenance and restoration of important

ecosystem services. Mazmanian and Knight also noted

that understanding specific and successful colonization

processes would be critical to improve disease outcomes.

Host-microbiome signals and interactions

Presenters noted our poor understanding of the signal-

ing and communication processes between microbiomes

and the host. Improved methods and models systems

are needed. While recognizing the limitations of animal

models, they nevertheless have provided a wealth of in-

formation that have led to our current understanding of

the role of the microbiome in health and disease and

continue to generate novel hypotheses that can be tested

in well-designed human studies. Continued support for

the development of better animal models is critical to

the future of this field. Studies that investigate the mecha-

nisms by which the microbiota influences and is influenced

by the immune system (Littman, Garrett, Chang), or how

hormones, such as estrogen impact the vaginal ecosystems

(Ravel), are desperately needed. Exhaustive identifica-

tion of small molecule, bioactive metabolites, secreted

and cell surface peptides that can influence microbe-to-

host interactions, would be highly desirable (Hutten-

hower, Mills, Jobin).

Analysis approaches and tools

Many concerns regarding the lack of tools for the analysis

’

omic datasets being generated by the microbiome com-

munity were expressed during the meeting. Researchers

need improved methods to perform quantitative measure-

ments of transcripts, proteins, and metabolites (Braun,

Ravel). There is also a lack of consensus as to how much

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diverse

‘

omics

’

data is needed for robust scientific in-

terpretation (Knight). The need for better methods to

integrate large and diverse

‘

omics

’

datasets was fre-

quently mentioned (Young, Jeffrey, Lampe, Jansson,

Huttenhower, Knight) and the sheer volume of infor-

mation should be considered to be

‘

big data

’

problem

(Jansson). The lack of procedures to integrate multiple

omics data types in longitud

inal studies was also iden-

tified (Knight). The overall need for increased interdis-

ciplinary collaboration to generate and interpret data

was noted (Mills, Lampe, Jansson), mainly because of the

different expertise needed to analyze such datasets ex-

ceeds what any individual lab can do. Presenters pointed

out that tools for the analysis, visualization, and manipu-

lation of these large datasets are also needed. Users

would like, for example, to

‘

make meta

’

omics analysis

as easy as microarray analysis

’

(Huttenhower). Specific

systems for analysis of metabolomic, genetic, glycomic

datasets (Mills), or sequences from low-biomass sam-

ples (Kong), and mass spectrometry data (Davies) are

also lacking. Many presentations at the meeting thus

revolved around the generation of diverse

‘

omics

’

data-

sets, and the challenges assoc

iated with integrating that

information.

Standards

Several presenters expressed that more standards are

needed in microbiome research. Standardized protocols

improve reproducibility of microbiome experiments and

ensure translation of results from independent expe-

riments (Braun, Huttenhower, White, Knight). White sug-

gested that software could be developed to improve the

uniformity of data submissions to the NCBI Short Read

Archive and dbGaP. Further, uniform clinical and la-

boratory procedures such

as sampling methods at

different body sites, PCR protocols, and DNA/RNA ex-

traction methods would also improve our ability to

compare data from different research projects (Kong).

It was also noted that non-standardized diets for model

organisms could account for phenotypic differences

between experiments (Mazmanian). Presenters also

cited the challenges associated with non-standard meta-

data associated with micr

obiome work. Most sample

information is not in a standardized format (Knight),

and standardized clinical description of phenotypes is

lacking (Kong). A solution to these metadata issues

would be to utilize softwa

re systems similar to the

PhenX toolkit for describin

g common clinical data ele-

ments [53], in combination with standardized meta-

data deposition practices being enforced by scientific

journals (White). There was a clear need expressed for

collection of data and tools in a single accessible site,

much as the HMP DACC provided for the Human

Microbiome Project.

Conclusions

The meeting was clearly a succes

s, in that it highlighted the

amazing progress in microbiome research funded across a

range of NIH Institute and Centers, focusing on a wide

array of diseases. Additionally, while the speakers re-

sponses to the needs, gaps, and challenges varied, themes

focusing on a few key areas emerged: studies of causality

(mechanistic studies in model organisms and prospective

longitudinal studies), need to integrate more complex

omics and phenotype data, and better standardization of

methods and data. Overall, the diversity and excellence of

talks underscored how much has been done in this field,

in just the past 6 years, and the potential for microbiome

science to produce a revolution in human health.

Abbreviations

AD:

Atopic Dermatitis; DACC: Data Analysis and Coordination Center;

dbGaP: The Database of Genotypes and Phenotypes; ELSI: Ethical, Legal and

Social Implications; EPA: Environmental Protection Agency; FDA: Food and

Drug Administration; FMT: Fecal Microbiota Transplantation; GRAS: Generally

Recognized as Safe; HMP: Human Microbiome Project; NASA: National

Aeronautics and Space Administration; NHGRI: National Human Genome

Research Institute; NIH: National Institutes of Health; NSF: National Science

Foundation; OSTP: Office of Science and Technology Policy; USAID: US

Agency for International Development; USDA: US Department of Agriculture.

Competing interests

The authors declare that they have no competing interests.

Authors

’

contributions

OW, JR, and RK wrote the paper. All authors read, edited and approved the

final manuscript.

Acknowledgements

The authors would like to thank Lita Proctor (NHGRI/NIH), for conceiving this

idea to evaluate the status of microbiome research across the NIH, as well as

Christopher Wellington, Nicholas Digiacomo, Sue Dilli, and Michele Giglio for

their invaluable contributions to the organization of the scientific program

and the logistics of the meeting. The conference was supported in part by

grant U01HG004866 from the National Human Genomics Research Institute,

National Institutes of Health. The conference organizers are grateful to

Roche, Qiagen, Illumina, Life Technologies, MoBio, Metabolon, and the

BioMed Central journal

Microbiome

for their financial support of the meeting.

Author details

Institute for Genome Sciences, Department of Microbiology and

Immunology, University of Maryland School of Medicine, 801 W. Baltimore

Street, Baltimore, MD 21201, USA.

Department of Microbiology, Human

Microbiome Program, New York University Langone Medical Center, 550 First

Avenue, Bellevue CD 689, New York, NY 10016, USA.

Department of

Pathology and Laboratory Medicine, David Geffen School of Medicine at

UCLA, Los Angeles, CA 90095, USA.

The Michael Smith Laboratories and

Department of Microbiology and Immunology, University of British

Columbia, Vancouver, BC V6T 1Z4, Canada.

Department of Microbiology,

Perelman School of Medicine at the University of Pennsylvania, Philadelphia,

PA 19104, USA.

Knapp Center for Biomedical Discovery, University of

Chicago, 900 E. 57th Street, Chicago IL 60637, USA.

Department of

Microbiology and Immunology, University of British Columbia, 2350 Health

Sciences Mall, Life Sciences Centre, Vancouver BC V6T 1Z3, Canada.

Department of Nutrition, University of California, One Shields Avenue, Davis,

CA 95616, USA.

Department of Psychiatry, GF Unity, Cork University Hospital,

Cork, Wilton, Ireland.

Division of Comparative Medicine, Massachusetts

Institute of Technology, One Massachusetts Avenue, Cambridge, MA 02139,

USA.

Department of Immunology and Infectious Diseases, Harvard School

of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.

Department of Internal Medicine/Infectious Diseases, Immunology

University of Michigan Medical School, 1500 W. Medical Center Drive, Ann

Ravel

et al. Microbiome

2014,

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Arbor, MI 48109, USA.

Department of Microbiology, Immunology University

of Michigan Medical School, 1500 W. Medical Center Drive, Ann Arbor, MI

48109, USA.

Department of Biostatistics, Harvard School of Public Health,

655 Huntington Avenue, Boston MA 02115, USA.

Earth Sciences Division,

Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA

94720, USA.

Department of Microbiology, The Alimentary Pharmabiotic

Centre, University College Cork, Cork, Ireland.

Department of Infectious

Diseases & Pathology, College of Medicine, University of Florida, 2015 SW

16th Avenue, PO Box 110880, Gainesville, FL 32611, USA.

Department of

Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of

Florida, 2015 SW 16th Avenue, PO Box 110880, Gainesville, FL 32611, USA.

Department of Medicine, Center for Immunology, Room 3-184, Medical

Biosciences Building, 2101 6th S. E, Minneapolis, MN 55416, USA.

Dermatology Branch, Center for Cancer Research, National Cancer Institute,

National Institutes of Health, 10 Center Dr, Bethesda, MD 20814, USA.

Cancer Prevention Program, Public Health Sciences Division, Fred

Hutchinson Cancer Research Center, 1100 Fairview Ave N, PO Box 19024,

Seattle, WA 98109, USA.

Department of Microbiology, Cornell University,

123 Wing Drive, Ithaca, NY 14853, USA.

Department of Pathology,

Molecular Pathogenesis, 540 First Avenue, Skirball Institute, New York, NY

10016, USA.

Department of Microbiology, Molecular Pathogenesis, 540 First

Avenue, Skirball Institute, New York, NY 10016, USA.

Division of Biology &

Biological Engineering, California Institute of Technology, 1200 E. California

Bl, Pasadena, CA 91125, USA.

Department of Food Science and Technology,

University of California, One Shields Avenue, Davis, CA 95616, USA.

Department of Viticulture and Enology, University of California, One Shields

Avenue, Davis, CA 95616, USA.

Department of pathology, Emory University

School of Medicine, 105H whitehead bldg., 615 Francis Street, Atlanta, GA

30322, USA.

Department of Medicine/Infectious Diseases, Gastrointestinal

Diseases Research Unit, Queens University and Kingston General Hospital, 76

Stuart Street, GIDRU wing, Kingston ON K7L 2V7, Canada.

Department of

Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA.

Department of Medicine, Stanford University, Stanford, CA 94305, USA.

Department of Medical Education, Icahn School of Medicine at Mount

Sinai, One Gustave Levy Place, Box 1076, Annenberg 12-42, New York, NY

10029, USA.

FAS Center for Systems Biology, Harvard University, 52 Oxford

St, Cambridge, MA 02138, USA.

Department of Chemistry and Biochemistry,

Howard Hughes Medical Institute, University of Colorado, 215 UCB, Boulder,

CO 80309, USA.

Institute for Genome Sciences, Department of

Epidemiology and Public Health, University of Maryland School of Medicine,

660 W. Redwood Street, Baltimore, MD 21201, USA.

Received: 30 January 2014 Accepted: 12 March 2014

Published: 18 July 2014

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Cite this article as:

Ravel

et al.

Human microbiome science: vision for

the future, Bethesda, MD, July 24 to 26, 2013.

Microbiome

2014

:16.

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