Pilot Project to Expand the Number of Sequences of Culturable Microbes from the
Human Body
George Weinstock, Richard Gibbs
Human Genome Sequencing Center, Baylor College of Medicine
Richard Wilson, Jeffrey Gordon, Sandra Clifton
Genome Sequencing Center, Washington University
Bruce Birren, Chad Nusbaum
The Broad Institute of MIT and Harvard
Summary
We propose a Human Microbiome Pilot Project (HMPP) to generate key data that are
needed to design a cost effective large scale Human Microbiome Project. Specifically,
this pilot will:
1. Create reference genome sequences of representatives of divisions (superkingdoms) of
bacteria and archaea in targeted human host habitats to assist assembly and/or
interpretation of metagenomic sequence data.
2. Define the quality of the sequence and annotation required for these references and the
appropriate technologies with which to produce it.
3. Collect data needed to design effective largescale metagenomic sampling methods,
including:
4. Determine the extent and nature of diversity within members of individual `species' in
a single host's habitats, and between different hosts
5. Define the variation in prevalence of these different phylotypes and hence the required
sensitivity of sampling methods.
6. Establish the relative levels of bacterial, archaeal and eukaryotic microbes and viruses
in these communities.
7. Explore new methods for storing, displaying, and analyzing these data as necessary to
enable rapid progress to a full scale Human Microbiome Project.
The project will be performed by the three NHGRIfunded Genome Centers with
coordination and advice from the NHGRI staff and an HMPP Advisory Panel. The
project will also coordinate with other groups engaged in human microbiome work and
with data repositories that are involved in collecting and presenting human microbiome
data.
2
Introduction
The collection of trillions of microorganisms resident in the human body form complex
communities primarily concentrated in a few body sites (Table 1) (Paustian, 2006
Tierno, 2001). These communities contribute to our normal postnatal development, play a
significant role in defining our physiology, and vary according to gender, age,
environment, diet, and disease states. The key determinants and the degree of variation
are not well understood.
Table 1. The Normal Human Microbiota
Body Site bacteria/ml or #
gram species
Respiratory ?
3 4
Nose 10 10
10
Oral 10 total >700
8 10
Saliva 10 10
12
Gingival crevice 10
11
Tooth surface 10
14
Gastrointestinal 10 total >1000
Tract
0 4
Stomach 10 10
4 7
Small intestines 10 10
11 12
Colon (feces) 10 10
12
Skin 10 total ?
5
Surface 10
Urogenital ?
9
Vagina 10
13
Human cells 10 total
While most thinking about the microbial origins of causes of disease has focused on
invasion by pathogens, increasing attention is being paid to the idea that the normal
microbiota affects predisposition to and can be a critical contributor to a number of
pathologic states. Some of the better understood examples, such as dental caries,
gingivitis, and vaginitis, result from changes in the composition of the oral and vaginal
microbiota with associated host inflammatory responses. These can be thought of as
"ecological diseases" which result from alteration of the normal balance of microbes in a
community.
More novel mechanisms are being discovered as well. For example, recent studies
(Turnbaugh et al., 2006 Ley et al., 2006) show a correlation between the abundance of
3
different bacterial divisions in the gut and obesity. In this case, the amount of energy
harvested from the diet is affected by the microbial community structure. Additional
discussion of the importance of the gut microbiota was presented in a previous white
paper to the NHGRI (Gordon et al., 2005). One hopes that an understanding of the
connection between microbial communities and human health will lead to new therapies
and diagnostics. Therapies could involve manipulating the composition of microbial
communities, or the human genes and gene products whose expression and activities are
found to be regulated by the microbiota, or using the chemical entities produced by
microbial communities as therapeutic agents. Diagnostics could involve the ideas
borrowed from ecology, such as "sentinel species" organisms whose population
dynamics are particularly sensitive to environmental changes (eg, changes in host
physiology) and indicative of impending conditions.
As recognition of the importance of the normal microbiota of the human body has grown
in recent years, several concepts have emerged. First is the idea that a microbial
community is an important operational element itself. Although many organisms within a
community cannot be cultured in isolation, they exist in the community environment,
which includes not only microbial neighbors but also the host habitat. This community
("biome"), can be thought of as a unit analogous to an organ, and its genome as a
"metagenome" (using meta to denote something of a higher order) comprising the
genomes of the included community organisms. This microbial metagenome
(microbiome) has been referred to as the "second human genome" and the concept has
been suggested of the human as a "superorganism" whose genetic and metabolic
landscape is an amalgamation of microbial and human components (Gill et al., 2006).
The interactions between components of this superorganism are poorly understood and
offer an important area for future research.
The Human Microbiome Project (HMP) has been proposed to further our understanding
of this aspect of human biology. In the broadest terms the HMP would produce reference
sequences for representative genomes of the human microbiota, and perform
metagenomic analyses (sequencing of microbial communities as mixtures of genomes) of
samples obtained from individuals representing different aspects of the human lifecycle
(i.e. males and females of varying ages with various lifestyles and living conditions, and
with physiologic and pathophyisologic states, etc.). The reference sequences would allow
the component organisms to be identified in the metagenomic samples and comparison of
the metagenomic data would allow correlations to be made between the content of
organismal and gene lineages and the human condition, as in the obesity example cited
above.
The HMP is a very complex project, given the genetic/environmental/lifestyle variations
that exist among humans, the variations in the composition of microbial communities that
exist between individuals, the importance of considering space and time when sampling
diversity in a given host habitat, the question of whether the species concept can be
meaningfully applied to the microbial world, technical challenges in deep community
sampling given the enormous range of abundance of different microbial phylotypes
within some host habitats, the inability to culture most members of a microbiota using
4
current methods, and many other issues. Nevertheless, while still at the conceptual stage,
the HMP has gained much momentum over the last year, in part because of the
introduction of a new generation of highly parallel DNA sequencers, and in part by the
development of new computational tools for comparing microbial communities whose
composition has been described by 16S rRNA gene sequencebased enumeration. Within
the NIH, several discussions have been held and most recently the HMP has been
selected for further development as one of the next Roadmap initiatives. In Europe, a
conference was held addressing the idea of an international HMP, and recently the
European Union announced funding for this initiative (Eichinger, 2007). Outside of the
EU, there has been a commitment to the project at the Wellcome Trust Sanger Institute,
and genome centers in China, Japan, and elsewhere have indicated their enthusiasm to
participate with local funding. Despite a need to clarify many technical details, the broad
enthusiasm for the concept indicates that it will eventually become a reality.
Establishing clear pilot studies at the appropriate scale to address key questions is
critically important for the successful design of the HMP. NIH is currently funding
several metagenomic projects. These include a RFA from the National Institute for
Dental and Craniofacial Research (NIDCR) for metagenomic research of the oral cavity
(currently being reissued) and a project at The Institute for Genomic Research (TIGR)
funded by the National Institute for Allergies and Infectious Diseases (NIAID) for
metagenomic studies of the vaginal flora. Last, but not least, the NHGRI approved the
Human Gut Microbiome Initiative at the Genome Sequencing Center at Washington
University in 2005 (Gordon et al., 2005).
These initial projects are important, but not of comparable scale to earlier NHGRI pilot
studies for the Human Genome Project (during 19961998) or the ENCODE project
(currently being completed). In this proposal we seek to expand the existing NHGRI pilot
project, expanding it to include all three NHGRIfunded Genome Centers and broaden
the scope. The need to obtain more information for the HMP through such projects is
becoming pressing as the NIH Roadmap and EU initiatives move forward.
5
Math Boxes Objectives To introduce My Reference Book; and to introduce the t Math Boxes routine. www.everydaymathonline.com ePresentations eToolkit Algorithms EM Facts Family Assessment Common Curriculum Interactive Practice Workshop Letters Management Core State Focal Points Teacher's GameTM Standards Lesson Guide Teaching the Lesson Ongoing Learning …
US-China Education Review B 4 (2011) 579-585 Earlier title: US-China Education Review, ISSN 1548-6613 A Study of the Relationship Between Students' Anxiety and Test Performance on State-Mandated Assessments Rosalinda Hernandez, Velma Menchaca, Jeffery Huerta University of Texas Pan American, Edinburg, USA This study examined whether …
HIGH-EFFICIENCY UPFLOW FURNACE INSTALLER'S INFORMATION MANUAL D ES IG N CE R TI F I ED ATTENTION, INSTALLER! After installing the ATTENTION, USER! Your furnace installer should furnace, show the user how to turn off gas and electricity to give you the documents listed on …
Raven/Johnson Biology 8e Chapter 12 1. A true-breeding plant is one that-- a. produces offspring that are different from the parent b. forms hybrid offspring through cross-pollination c. produces offspring that are always the same as the parent d. can only reproduce with itself The …
Math Skills for Business- Full Chapters 1 U1-Full Chapter- Algebra Chapter3 Introduction to Algebra 3.1 What is Algebra? Algebra is generalized arithmetic operations that use letters of the alphabet to represent known or unknown quantities. We can use y to represent a company's profit or …