Designing a healthy habitat:
Exploring the urban microbial landscape
Project Team:
PI , Uri Hershberg
Biomedical Engineering, Drexel University
TR Muth
Microbiologist, Brooklyn College
Gail Rosen
Microbiome and Computational analysis, Drexel University
Nicole Koltick
Architecture + Interiors, Material research, Drexel University
Yvonne Michael
Epidemiologist, Drexel University
Diana Nicholas
Architecture + Interiors, Drexel University
*Our project was mentioned in The Scientist
METROPOLOME:
RESEARCHERS TAKE ADVANTAGE OF RAPID AND CHEAP DNA SEQUENCING TECHNOLOGIES TO MAP THE BACTERIAL MICROBIOME OF NEW YORK CITY
December 1, 2013
Project Synopsis:
To fully understand and prevent the spread of disease in human society we must first understand how the native bacterial populations behave in the urban environments where most of us live. A 'hotbed' of such activity are the environments where children spend their days. These environments are always mixed use. Children sleep, eat and play in them. Moreover, children are one of the main vectors and sufferers of endemic infections. To get at this important issue we have created a multidisciplinary team of researchers, including expertise in microbiology, architecture/design, bioinformatis and epidemiology, who will study the bacterial population and behaviors in day care centers considering multiple social and biological levels. Our underlying hypothesis in this study is that human behavior / design influences the bacterial world in more subtle ways than simply through cleaning. We would like to test how the design of environments and the daily use we make of them influence the bacterial biome, both in terms of specific bacterial dynamics and in terms of the stability and diversity of biomes. To test this hypothesis and achieve our ultimate outcome we will ask questions across several scales of design, biology and human interaction. This will include general comparisons of stability and diversity in biomes where we feel there is a difference in human behavior, either through design parameters or because of different day-to-day use. We will also attempt to create specific scenarios of simple behaviors, which we believe will categorically change the stability and diversity of biomes and (ultimately) the spread of disease. We feel that a daycare is an ideal example for such a study as it is an environment where people - eat / sleep / play and defecate (hopefully not in the same space) and is populated by small children, a population where our ultimate outcome is of paramount importance. As a control to such spaces we will also look at a space that is not as tightly controlled but shares much of the same uses and age groups – The Smith play house. This Philadelphia institution hosts children year round as a play area. it is thus home to a population of children and adults that are similar in average characteristics to those found in a daycare but exhibit a faster turnover of their populations during the day and follow a much less regimented and repetitive schedule. Our study of the day cares and the Smith play-house will follow three related aims -
AIm 1 : Spatio temporal comparison of biome change and diversity in the built environment. – To characterize the spatio temporal spread of the microbiome and its diversity we will collect bacterial samples at several temporal scales: (i) during the day; (ii) for several days a week; (iii) for a whole season; and along usage specific spatial determinants: (i) in regions with different specific defined usage (ii) in the interface between regions. These samples will all be sequenced by 16s assay to identify diversity and changes in diversity.
Aim 2: Comparing planned and specific interaction in the built environment. In this aim we will focus on human interactions in the built environment. Our main focus is the number of interactions, their types and their consistency / repetitiveness throughout. We will measure the characteristics of interaction through direct observational studies based on pre-determined criteria. To contextualize these findings we will compare the actual observed interactions with the planned use of the spaces, and the scheduled behaviors planned in them. In considering these behaviors we will differentiate between students, staff and guests.
Aim 3 : Combining the human and biome scales through the design of the built environment. We will use the actual built environment and the design element from which it is comprised to combine between the human and biome levels. We will asses the effects of design at the materials level, the local design of specific structures and their use and the overall design and programing of the buildings.
These will from a urban built ‘geography’ and coordinate system in which we will place the biome / human interactions. In doing so we will compare to what degree the more controlled environments of the daycares show similar dependencies on design with the more open Smith Play house.
One of the strengths of our proposal is that the actual experiments that need to be employed are relatively simple. Much of the data could be collected by student in the different disciplines we combine. We envision much of our data collection as forming the labs in a set of loosely related classes in Biology, (microbiology and bioinformatics), Epidemiology and Architecture. At the undergraduate level these will be separate course focused on the form of research methodology done in each modality. At the same time we will include teaching modules which will help inform teacher and daycare student of the bacterial world. Finally, senior undergrads and grad students will have a combined seminar in which they will design and pursue specific research questions within the study of the built environment. In this fashion we will create a new generation of students in our different fields with a greater appreciation for their specific research methodologies and how they can be applied to studies of the urban environment, at different scales of biology and human interaction.
Exploring the urban microbial landscape
Project Team:
PI , Uri Hershberg
Biomedical Engineering, Drexel University
TR Muth
Microbiologist, Brooklyn College
Gail Rosen
Microbiome and Computational analysis, Drexel University
Nicole Koltick
Architecture + Interiors, Material research, Drexel University
Yvonne Michael
Epidemiologist, Drexel University
Diana Nicholas
Architecture + Interiors, Drexel University
*Our project was mentioned in The Scientist
METROPOLOME:
RESEARCHERS TAKE ADVANTAGE OF RAPID AND CHEAP DNA SEQUENCING TECHNOLOGIES TO MAP THE BACTERIAL MICROBIOME OF NEW YORK CITY
December 1, 2013
Project Synopsis:
To fully understand and prevent the spread of disease in human society we must first understand how the native bacterial populations behave in the urban environments where most of us live. A 'hotbed' of such activity are the environments where children spend their days. These environments are always mixed use. Children sleep, eat and play in them. Moreover, children are one of the main vectors and sufferers of endemic infections. To get at this important issue we have created a multidisciplinary team of researchers, including expertise in microbiology, architecture/design, bioinformatis and epidemiology, who will study the bacterial population and behaviors in day care centers considering multiple social and biological levels. Our underlying hypothesis in this study is that human behavior / design influences the bacterial world in more subtle ways than simply through cleaning. We would like to test how the design of environments and the daily use we make of them influence the bacterial biome, both in terms of specific bacterial dynamics and in terms of the stability and diversity of biomes. To test this hypothesis and achieve our ultimate outcome we will ask questions across several scales of design, biology and human interaction. This will include general comparisons of stability and diversity in biomes where we feel there is a difference in human behavior, either through design parameters or because of different day-to-day use. We will also attempt to create specific scenarios of simple behaviors, which we believe will categorically change the stability and diversity of biomes and (ultimately) the spread of disease. We feel that a daycare is an ideal example for such a study as it is an environment where people - eat / sleep / play and defecate (hopefully not in the same space) and is populated by small children, a population where our ultimate outcome is of paramount importance. As a control to such spaces we will also look at a space that is not as tightly controlled but shares much of the same uses and age groups – The Smith play house. This Philadelphia institution hosts children year round as a play area. it is thus home to a population of children and adults that are similar in average characteristics to those found in a daycare but exhibit a faster turnover of their populations during the day and follow a much less regimented and repetitive schedule. Our study of the day cares and the Smith play-house will follow three related aims -
AIm 1 : Spatio temporal comparison of biome change and diversity in the built environment. – To characterize the spatio temporal spread of the microbiome and its diversity we will collect bacterial samples at several temporal scales: (i) during the day; (ii) for several days a week; (iii) for a whole season; and along usage specific spatial determinants: (i) in regions with different specific defined usage (ii) in the interface between regions. These samples will all be sequenced by 16s assay to identify diversity and changes in diversity.
Aim 2: Comparing planned and specific interaction in the built environment. In this aim we will focus on human interactions in the built environment. Our main focus is the number of interactions, their types and their consistency / repetitiveness throughout. We will measure the characteristics of interaction through direct observational studies based on pre-determined criteria. To contextualize these findings we will compare the actual observed interactions with the planned use of the spaces, and the scheduled behaviors planned in them. In considering these behaviors we will differentiate between students, staff and guests.
Aim 3 : Combining the human and biome scales through the design of the built environment. We will use the actual built environment and the design element from which it is comprised to combine between the human and biome levels. We will asses the effects of design at the materials level, the local design of specific structures and their use and the overall design and programing of the buildings.
These will from a urban built ‘geography’ and coordinate system in which we will place the biome / human interactions. In doing so we will compare to what degree the more controlled environments of the daycares show similar dependencies on design with the more open Smith Play house.
One of the strengths of our proposal is that the actual experiments that need to be employed are relatively simple. Much of the data could be collected by student in the different disciplines we combine. We envision much of our data collection as forming the labs in a set of loosely related classes in Biology, (microbiology and bioinformatics), Epidemiology and Architecture. At the undergraduate level these will be separate course focused on the form of research methodology done in each modality. At the same time we will include teaching modules which will help inform teacher and daycare student of the bacterial world. Finally, senior undergrads and grad students will have a combined seminar in which they will design and pursue specific research questions within the study of the built environment. In this fashion we will create a new generation of students in our different fields with a greater appreciation for their specific research methodologies and how they can be applied to studies of the urban environment, at different scales of biology and human interaction.