This document summarizes the key points of an article on the diversity and composition of bacteria in indoor environments. It finds that the bacterial communities found indoors are less diverse than outdoors, and that mechanically ventilated rooms contain less diverse communities than window ventilated rooms. Certain building attributes like ventilation source, airflow rates, humidity and temperature are correlated with the diversity and types of bacteria present. Rooms with lower airflow and humidity have higher abundances of potential human pathogens. The study suggests that building design and operation can manage the indoor microbiome and species that may colonize the human microbiome.
Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agricult...Jonathan Eisen
Slides for talk on "Microbiomes in Food and Agriculture" by JonathanEisen - note - not all slides were used in talk. These were there to stimulate discussion ...
Microbiomes in Agriculture, Food, Health and the EnvironmentJonathan Eisen
The document outlines an agenda for a meeting on microbiomes in agriculture, food, health and the environment. The meeting will include four panels discussing the impacts of human and animal microbiomes on food and health, the impacts of microbiomes on plants and agriculture, and the impacts of microbiomes on the environment. It also includes background information on microbiomes and their importance in various contexts.
The Rise of the Microbiome - talk by Jonathan Eisen for AHCJ15Jonathan Eisen
This document discusses the rise of research on the human microbiome. It provides five reasons for the recent increased interest: 1) increased appreciation of microbial diversity, 2) seeking new areas of research after the human genome was sequenced, 3) advances in DNA sequencing and analysis techniques, 4) understanding the functions of microbes in and on the human body, 5) sequencing costs decreasing drastically. It also outlines some of the major challenges in microbiome research, like complexity from host and environmental factors, and gaining public understanding. Finally, it discusses opportunities in the field, such as improving reference databases, analysis methods, model systems like rice, whole systems approaches, education, citizen science, and more.
Jonathan Eisen Talk for #UCDavis #HostMicrobe on Phylogeny & MicrobiomesJonathan Eisen
The document discusses approaches to studying microbiome diversity using phylogeny. It begins by showing the rise in publications on the microbiome over time. It then discusses how phylogeny-driven approaches can be used to study microbiome diversity at various sites in the human body. The approaches involve constructing phylogenetic trees of microbial sequences from samples to determine diversity and relationships between microbes.
Ecological Disturbance of the Human Gut MicrobiomeAnne M. Estes
Set of slides discussing the importance of microbes for human health. Made to accompany the hands-on activity "Modeling the Dynamic Digestive System Microbiome" published: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v16i2.908
Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and th...Jonathan Eisen
The document discusses the complexity of microbiome studies due to the high diversity of microbes found in and on the human body. It notes that only about 25% of the cells in the human body are human, with the rest being thousands of microbial species. These microbes play essential roles in human health like helping extract nutrients from food and protecting against pathogens. The microbiome is established early in life during birth and through breastfeeding, and continues to be influenced by environmental exposures throughout life.
This document summarizes a lecture given by Dr. Larry Smarr on his research exploring the human microbiome. Some key points:
- Dr. Smarr has been studying the microbial universe inside the human body for 40 years, since microbiology began as a frontier science.
- Advances in DNA sequencing have enabled the sequencing of human and microbial genomes, revolutionizing our understanding of the microbiome.
- The human microbiome is essential to health and disease, with 99% of our genes located in microbes rather than human cells.
- Dr. Smarr's own microbiome was studied before and after colonoscopy and colon surgery, showing dramatic shifts and recovery periods.
- Fecal microbiota trans
Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agricult...Jonathan Eisen
Slides for talk on "Microbiomes in Food and Agriculture" by JonathanEisen - note - not all slides were used in talk. These were there to stimulate discussion ...
Microbiomes in Agriculture, Food, Health and the EnvironmentJonathan Eisen
The document outlines an agenda for a meeting on microbiomes in agriculture, food, health and the environment. The meeting will include four panels discussing the impacts of human and animal microbiomes on food and health, the impacts of microbiomes on plants and agriculture, and the impacts of microbiomes on the environment. It also includes background information on microbiomes and their importance in various contexts.
The Rise of the Microbiome - talk by Jonathan Eisen for AHCJ15Jonathan Eisen
This document discusses the rise of research on the human microbiome. It provides five reasons for the recent increased interest: 1) increased appreciation of microbial diversity, 2) seeking new areas of research after the human genome was sequenced, 3) advances in DNA sequencing and analysis techniques, 4) understanding the functions of microbes in and on the human body, 5) sequencing costs decreasing drastically. It also outlines some of the major challenges in microbiome research, like complexity from host and environmental factors, and gaining public understanding. Finally, it discusses opportunities in the field, such as improving reference databases, analysis methods, model systems like rice, whole systems approaches, education, citizen science, and more.
Jonathan Eisen Talk for #UCDavis #HostMicrobe on Phylogeny & MicrobiomesJonathan Eisen
The document discusses approaches to studying microbiome diversity using phylogeny. It begins by showing the rise in publications on the microbiome over time. It then discusses how phylogeny-driven approaches can be used to study microbiome diversity at various sites in the human body. The approaches involve constructing phylogenetic trees of microbial sequences from samples to determine diversity and relationships between microbes.
Ecological Disturbance of the Human Gut MicrobiomeAnne M. Estes
Set of slides discussing the importance of microbes for human health. Made to accompany the hands-on activity "Modeling the Dynamic Digestive System Microbiome" published: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v16i2.908
Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and th...Jonathan Eisen
The document discusses the complexity of microbiome studies due to the high diversity of microbes found in and on the human body. It notes that only about 25% of the cells in the human body are human, with the rest being thousands of microbial species. These microbes play essential roles in human health like helping extract nutrients from food and protecting against pathogens. The microbiome is established early in life during birth and through breastfeeding, and continues to be influenced by environmental exposures throughout life.
This document summarizes a lecture given by Dr. Larry Smarr on his research exploring the human microbiome. Some key points:
- Dr. Smarr has been studying the microbial universe inside the human body for 40 years, since microbiology began as a frontier science.
- Advances in DNA sequencing have enabled the sequencing of human and microbial genomes, revolutionizing our understanding of the microbiome.
- The human microbiome is essential to health and disease, with 99% of our genes located in microbes rather than human cells.
- Dr. Smarr's own microbiome was studied before and after colonoscopy and colon surgery, showing dramatic shifts and recovery periods.
- Fecal microbiota trans
The document discusses the normal flora of the human body, including resident and transient flora. It notes that the largest population of normal flora bacteria is found in the colon, with over 400 identified species including Bacteroides fragilis as the most common. The document outlines both beneficial and harmful effects of normal flora, and discusses probiotics which can support normal flora when it is suppressed.
The document discusses the concept of the human microbiome. It defines the microbiome as the genetic material within a microbiota, or the collection of microorganisms in a specific niche. The human microbiome is dynamic and changes based on factors like development, diet, antibiotics, and disease. The Human Microbiome Project aims to characterize the human microbiome and analyze its roles in health and disease. Recent research has shown links between the gut microbiome and conditions like obesity, autism, diabetes, and responses to cancer immunotherapy treatments.
The Human Microbiome Project aims to map the microbial makeup of healthy humans through genome sequencing techniques. It was launched in 2008 by the NIH with a budget of $115-150 million over 5 years. The goals are to develop a reference set of microbial genome sequences, explore relationships between microbes and disease, and establish a repository. The study involves selecting subjects, sampling sites like skin and stool, isolating and sequencing microbial DNA, and creating a database of normal human microbiome variation. Potential benefits include medical evaluations, furthering scientific knowledge, and helping relate microbes to conditions like obesity and diabetes. Applications include tracking microbiome evolution over time and identifying factors distinguishing healthy and diseased microbiomes.
The document discusses the human microbiome, which refers to the trillions of microorganisms that inhabit various parts of the human body. It notes that the microbiome contains over 100 trillion bacterial cells and has more genes than the human genome. The largest and most dense microbiome is located in the gut, where microbes help break down nutrients and support human metabolism. While microbiome compositions vary between individuals and change over time, they perform similar important functions for human health.
What do we actually know about the 100 trillion bacteria that live on and inside our bodies? Alexandra Carmichael, formerly of Quantified Self, CureTogether, and 23andMe, gave this talk at SXSW in Austin on March 16th, 2015.
The document discusses the human microbiome, which is the collection of microbes that live on and inside the human body. It describes some of the microbes commonly found in different areas of the body like the nose, mouth, skin, gut, and urogenital tract. It also discusses how antibiotics and other drugs can disrupt the normal balance of microbes and allow potentially harmful ones to grow. The human microbiome varies between individuals and is an area of ongoing research.
This document discusses the human microbiome, which refers to the microorganisms that inhabit different areas of the human body. It notes that the microbiome develops immediately after birth and includes bacteria, yeasts and protozoa. The microbiome plays an important role in health, such as immune system development, but can also contribute to diseases. The document then describes the types of microbes typically found in different body sites like the gut, skin, respiratory and genitourinary tracts.
Microbes are our Friends.. The effective way of microbes treating our diseases and fighting with the pathogens is very effective. The human microbiome project is a current topic the researchers are focusing now. We think we are humans but the research of Human Microbiome Project states that we are 1% Humans 99% microbes. The highlights of this project is fecal transplantation and effective way of killing pathogens with the positive microbes.
The way we treat our body will treat you back and the antigens which are entered in to our body will greatly fight with microbes to survive and make the human body safe and healthy.
Finally Microbes are us and we are them
The document outlines the history of plant tissue culture from 1832 to the present. Some of the key events include Theodor Schwann presenting the idea that cells can grow outside the body in 1832. In 1898, Gottlieb Haberlandt made the first attempt at plant tissue culture but cells did not divide. Later researchers like White and Skoog added growth hormones like auxin and vitamins, enabling cell division. Techniques like cell suspension cultures and protoplast isolation were developed in the 1950s-60s, allowing for mass plant cell production. Somatic embryogenesis and regeneration methods enabled cloning in the 1970s. Today, tissue culture is used commercially and allows for disease-free propagation of plants.
Looking for Microbiome Testing centers in Australia? Have you by any chance searched for Allele Microbiome? If not, you could certainly look them over.
This document discusses how probiotics can help maintain a healthy balance of bacteria in the digestive system and prevent disease. It explains that probiotics are live microorganisms that resemble beneficial bacteria naturally found in the gut. Consuming probiotics through foods or supplements can help boost immunity, aid digestion, and reduce the risk of conditions like diarrhea, urinary tract infections, and irritable bowel syndrome. Maintaining high levels of good bacteria is important for overall health and wellness.
The microbiome refers to the microorganisms that normally inhabit various areas of the human body. These microbes, known as the normal flora, include bacteria and yeasts that colonize skin, mouth, intestines, and vagina. The normal flora derive benefits from the host without causing harm. They occupy receptor sites and provide colonization resistance against pathogenic microbes. Important members of the normal flora include Staphylococcus epidermidis on the skin, viridans streptococci in the mouth, and a diverse mix of anaerobic and facultative bacteria in the colon. Lactobacilli in the vagina help maintain acidity that inhibits pathogens.
The Role of the Skin Microbiome in Atopic Dermatitis (Eczema)Laura Berry
Presented at the 3rd Microbiome R&D and Business Collaboration Congress: Asia. To find out more, visit: www.global-engage.com
Using modern genomic techniques Niranjan Nagarajan, Associate Director and Group Leader at A*STAR, has identified key perturbations in the resident skin microflora that could act as triggers for eczema flares. Niranjan presents a new form of the hygiene hypothesis for explaining the increasing incidence of eczema and revealing, in the process, novel therapeutic targets for this disease.
"In Gut We Trust" The Microbiome & WellbeingJoeFitAsia
The document discusses the microbiome, which refers to the microorganisms that live in and on the human body. It notes that the microbiome contains trillions of cells and plays an important role in human health and disease. Specifically, it affects body weight, nutrition absorption, and risk of chronic diseases. It also influences conditions like allergies, asthma, and the development of the immune system.
The document discusses the skin microbiome and its role in atopic dermatitis (eczema). It notes that the skin hosts trillions of bacteria that create an ecosystem. Factors like location on the body, moisture levels, and individual characteristics can influence the types of microbes present. In eczema, skin barrier defects allow overgrowth of bacteria like Staphylococcus aureus that secrete toxins exacerbating inflammation. Studies show shifts in skin microbiota during eczema flares and treatment. A healthy microbiome including species like Staphylococcus epidermidis promotes skin immunity, while dysbiosis may increase eczema risk.
This document summarizes research on bacterial protein acetylation and its role in cellular control mechanisms and symbiotic relationships between organisms. Protein acetylation was previously thought to be specific to eukaryotic histones but recent studies have found acetylated proteins in E. coli and S. enterica mitochondria, suggesting bacteria have additional cellular control pathways involving protein acetylation. The document also discusses how symbiotic bacteria like Spiroplasma can protect fruit flies from nematodes and be inherited, demonstrating how symbiosis allows organisms to adapt without needing the strongest individual traits. This new understanding of bacterial protein acetylation and symbiosis could enable new treatment approaches involving engineered bacteria.
This document outlines major developments in biotechnology from 8000 BCE to present day, including early uses of microbes in food production, discovery of antibiotics and vaccines, understanding of genetics and DNA, and advances like recombinant DNA techniques, monoclonal antibodies, stem cells, cloning, sequencing the human genome, and creating synthetic organisms. It shows how biotechnology has evolved from early applications to become a complex scientific field utilizing living systems to address problems.
Timeline of Biotech development from 2003 to 2017Zohaib HUSSAIN
This document provides a timeline of key developments in biotechnology from 2003 to 2017. It discusses advances in areas like food/agriculture such as drought-resistant crops, medicine/physiology such as the discovery of RNA interference and stem cell reprogramming, and the history of the field including the sequencing of the rice genome in 2005 and 3D bioprinting in 2010. The timeline highlights over 50 specific discoveries, approvals, and other milestones that expanded the use and understanding of biotechnology over a 15 year period.
This document provides an overview of the history of biotechnology from ancient to modern times. It describes how early civilizations first domesticated plants and animals for food production, and how techniques like fermentation were used to preserve foods. Advances in microscopy allowed for the discovery of microorganisms and laid the foundations for modern genetics research. Figures like Mendel, Watson, Crick and others contributed key findings that enabled recombinant DNA technology and genetic engineering. Modern biotechnology now allows for manipulation of genetic material.
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
This document provides an overview of the issues surrounding antibiotic resistance and proposes having an open discussion on new perspectives and metaphors for understanding the relationship between humans and microbes. It summarizes a workshop that brought together scientists, artists, and others to discuss questioning traditional assumptions and generating new insights about microbial ecology, human health, and antibiotic usage. The workshop aimed to initiate a multidisciplinary dialogue on developing a more holistic understanding of these complex topics.
The document discusses the normal flora of the human body, including resident and transient flora. It notes that the largest population of normal flora bacteria is found in the colon, with over 400 identified species including Bacteroides fragilis as the most common. The document outlines both beneficial and harmful effects of normal flora, and discusses probiotics which can support normal flora when it is suppressed.
The document discusses the concept of the human microbiome. It defines the microbiome as the genetic material within a microbiota, or the collection of microorganisms in a specific niche. The human microbiome is dynamic and changes based on factors like development, diet, antibiotics, and disease. The Human Microbiome Project aims to characterize the human microbiome and analyze its roles in health and disease. Recent research has shown links between the gut microbiome and conditions like obesity, autism, diabetes, and responses to cancer immunotherapy treatments.
The Human Microbiome Project aims to map the microbial makeup of healthy humans through genome sequencing techniques. It was launched in 2008 by the NIH with a budget of $115-150 million over 5 years. The goals are to develop a reference set of microbial genome sequences, explore relationships between microbes and disease, and establish a repository. The study involves selecting subjects, sampling sites like skin and stool, isolating and sequencing microbial DNA, and creating a database of normal human microbiome variation. Potential benefits include medical evaluations, furthering scientific knowledge, and helping relate microbes to conditions like obesity and diabetes. Applications include tracking microbiome evolution over time and identifying factors distinguishing healthy and diseased microbiomes.
The document discusses the human microbiome, which refers to the trillions of microorganisms that inhabit various parts of the human body. It notes that the microbiome contains over 100 trillion bacterial cells and has more genes than the human genome. The largest and most dense microbiome is located in the gut, where microbes help break down nutrients and support human metabolism. While microbiome compositions vary between individuals and change over time, they perform similar important functions for human health.
What do we actually know about the 100 trillion bacteria that live on and inside our bodies? Alexandra Carmichael, formerly of Quantified Self, CureTogether, and 23andMe, gave this talk at SXSW in Austin on March 16th, 2015.
The document discusses the human microbiome, which is the collection of microbes that live on and inside the human body. It describes some of the microbes commonly found in different areas of the body like the nose, mouth, skin, gut, and urogenital tract. It also discusses how antibiotics and other drugs can disrupt the normal balance of microbes and allow potentially harmful ones to grow. The human microbiome varies between individuals and is an area of ongoing research.
This document discusses the human microbiome, which refers to the microorganisms that inhabit different areas of the human body. It notes that the microbiome develops immediately after birth and includes bacteria, yeasts and protozoa. The microbiome plays an important role in health, such as immune system development, but can also contribute to diseases. The document then describes the types of microbes typically found in different body sites like the gut, skin, respiratory and genitourinary tracts.
Microbes are our Friends.. The effective way of microbes treating our diseases and fighting with the pathogens is very effective. The human microbiome project is a current topic the researchers are focusing now. We think we are humans but the research of Human Microbiome Project states that we are 1% Humans 99% microbes. The highlights of this project is fecal transplantation and effective way of killing pathogens with the positive microbes.
The way we treat our body will treat you back and the antigens which are entered in to our body will greatly fight with microbes to survive and make the human body safe and healthy.
Finally Microbes are us and we are them
The document outlines the history of plant tissue culture from 1832 to the present. Some of the key events include Theodor Schwann presenting the idea that cells can grow outside the body in 1832. In 1898, Gottlieb Haberlandt made the first attempt at plant tissue culture but cells did not divide. Later researchers like White and Skoog added growth hormones like auxin and vitamins, enabling cell division. Techniques like cell suspension cultures and protoplast isolation were developed in the 1950s-60s, allowing for mass plant cell production. Somatic embryogenesis and regeneration methods enabled cloning in the 1970s. Today, tissue culture is used commercially and allows for disease-free propagation of plants.
Looking for Microbiome Testing centers in Australia? Have you by any chance searched for Allele Microbiome? If not, you could certainly look them over.
This document discusses how probiotics can help maintain a healthy balance of bacteria in the digestive system and prevent disease. It explains that probiotics are live microorganisms that resemble beneficial bacteria naturally found in the gut. Consuming probiotics through foods or supplements can help boost immunity, aid digestion, and reduce the risk of conditions like diarrhea, urinary tract infections, and irritable bowel syndrome. Maintaining high levels of good bacteria is important for overall health and wellness.
The microbiome refers to the microorganisms that normally inhabit various areas of the human body. These microbes, known as the normal flora, include bacteria and yeasts that colonize skin, mouth, intestines, and vagina. The normal flora derive benefits from the host without causing harm. They occupy receptor sites and provide colonization resistance against pathogenic microbes. Important members of the normal flora include Staphylococcus epidermidis on the skin, viridans streptococci in the mouth, and a diverse mix of anaerobic and facultative bacteria in the colon. Lactobacilli in the vagina help maintain acidity that inhibits pathogens.
The Role of the Skin Microbiome in Atopic Dermatitis (Eczema)Laura Berry
Presented at the 3rd Microbiome R&D and Business Collaboration Congress: Asia. To find out more, visit: www.global-engage.com
Using modern genomic techniques Niranjan Nagarajan, Associate Director and Group Leader at A*STAR, has identified key perturbations in the resident skin microflora that could act as triggers for eczema flares. Niranjan presents a new form of the hygiene hypothesis for explaining the increasing incidence of eczema and revealing, in the process, novel therapeutic targets for this disease.
"In Gut We Trust" The Microbiome & WellbeingJoeFitAsia
The document discusses the microbiome, which refers to the microorganisms that live in and on the human body. It notes that the microbiome contains trillions of cells and plays an important role in human health and disease. Specifically, it affects body weight, nutrition absorption, and risk of chronic diseases. It also influences conditions like allergies, asthma, and the development of the immune system.
The document discusses the skin microbiome and its role in atopic dermatitis (eczema). It notes that the skin hosts trillions of bacteria that create an ecosystem. Factors like location on the body, moisture levels, and individual characteristics can influence the types of microbes present. In eczema, skin barrier defects allow overgrowth of bacteria like Staphylococcus aureus that secrete toxins exacerbating inflammation. Studies show shifts in skin microbiota during eczema flares and treatment. A healthy microbiome including species like Staphylococcus epidermidis promotes skin immunity, while dysbiosis may increase eczema risk.
This document summarizes research on bacterial protein acetylation and its role in cellular control mechanisms and symbiotic relationships between organisms. Protein acetylation was previously thought to be specific to eukaryotic histones but recent studies have found acetylated proteins in E. coli and S. enterica mitochondria, suggesting bacteria have additional cellular control pathways involving protein acetylation. The document also discusses how symbiotic bacteria like Spiroplasma can protect fruit flies from nematodes and be inherited, demonstrating how symbiosis allows organisms to adapt without needing the strongest individual traits. This new understanding of bacterial protein acetylation and symbiosis could enable new treatment approaches involving engineered bacteria.
This document outlines major developments in biotechnology from 8000 BCE to present day, including early uses of microbes in food production, discovery of antibiotics and vaccines, understanding of genetics and DNA, and advances like recombinant DNA techniques, monoclonal antibodies, stem cells, cloning, sequencing the human genome, and creating synthetic organisms. It shows how biotechnology has evolved from early applications to become a complex scientific field utilizing living systems to address problems.
Timeline of Biotech development from 2003 to 2017Zohaib HUSSAIN
This document provides a timeline of key developments in biotechnology from 2003 to 2017. It discusses advances in areas like food/agriculture such as drought-resistant crops, medicine/physiology such as the discovery of RNA interference and stem cell reprogramming, and the history of the field including the sequencing of the rice genome in 2005 and 3D bioprinting in 2010. The timeline highlights over 50 specific discoveries, approvals, and other milestones that expanded the use and understanding of biotechnology over a 15 year period.
This document provides an overview of the history of biotechnology from ancient to modern times. It describes how early civilizations first domesticated plants and animals for food production, and how techniques like fermentation were used to preserve foods. Advances in microscopy allowed for the discovery of microorganisms and laid the foundations for modern genetics research. Figures like Mendel, Watson, Crick and others contributed key findings that enabled recombinant DNA technology and genetic engineering. Modern biotechnology now allows for manipulation of genetic material.
Opening up Scientific and Scholarly CommunicationJonathan Eisen
The document discusses the history and goals of the Public Library of Science (PLoS), an organization founded in 2000 to promote open access scientific publishing. PLoS circulated an open letter calling for freely accessible scientific literature and launched their own open access journals, PLoS Biology and PLoS Medicine, after not enough publishers supported open access. The document also describes the author's personal experience with lack of access to scientific papers delaying treatment for his stillborn son, which reinforced his views that limiting access is unethical and counterproductive to advancing scientific knowledge.
This document provides an overview of the issues surrounding antibiotic resistance and proposes having an open discussion on new perspectives and metaphors for understanding the relationship between humans and microbes. It summarizes a workshop that brought together scientists, artists, and others to discuss questioning traditional assumptions and generating new insights about microbial ecology, human health, and antibiotic usage. The workshop aimed to initiate a multidisciplinary dialogue on developing a more holistic understanding of these complex topics.
The annual report of the Carl R. Woese Institute for Genomic Biology (IGB) summarizes the events of 2014. The report includes stories about IGB research accomplishments, partnerships, education initiatives, and community outreach. It also intersperses stories about notable world events to highlight connections between ongoing IGB work and global issues. The report demonstrates how the IGB brings together diverse expertise and collaborations to conduct transdisciplinary research aimed at addressing societal challenges.
This document is an issue of the LSF Magazine that focuses on the microbiome. It includes several articles that discuss the history and current state of microbiome research, such as Ian's gut experiment, the American Gut Project, environmental metagenomics, and probiotic philosophy. It also profiles prominent microbiome researchers like Ananda Chakrabarty. Additionally, it provides updates on Life Sciences Foundation events and partnerships related to documenting the history of biotechnology and genomics.
The concept of the human microbiome was first suggested by Joshua Lederberg, who coined the term ‘‘microbiome, to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space’’
1
CHAPTER 1 Microbiology: Then and Now
CHAPTER 2 The Chemical Building Blocks of Life
CHAPTER 3 Concepts and Tools for Studying Microorganisms
CHAPTER 4 Cell Structure and Function in the Bacteria and Archaea
CHAPTER 5 Microbial Growth and Nutrition
CHAPTER 6 Metabolism of Microorganisms
CHAPTER 7 Control of Microorganisms: Physical and Chemical Methods
1 Foundations of Microbiology
P A R T
n 1676, a century before the Declaration of Independence, a Dutch
merchant named Antony van Leeuwenhoek sent a noteworthy let-
ter to the Royal Society of London. Writing in the vernacular of his
home in the United Netherlands, Leeuwenhoek described how he used a simple
microscope to observe vast populations of minute, living creatures. His reports
opened a chapter of science that would evolve into the study of microscopic
organisms and the discipline of microbiology. At that time, few people, including
Leeuwenhoek, attached any practical significance to the microorganisms, but
during the next three centuries, scientists would discover how profoundly these
organisms influence the quality of our lives and the environment around us.
We begin our study of the microorganisms by exploring the grassroot devel-
opments that led to the establishment of microbiology as a science. These devel-
opments are surveyed in Chapter 1, where we focus on some of the individuals
who stood at the forefront of discovery. Today we are in the midst of a third Golden Age of microbiology and our
understanding of microorganisms continues to grow even as you read this book. Chapter 1, therefore, is an important
introduction to microbiology then and now.
Part 1 also contains a chapter on basic chemistry, inasmuch as microbial growth, metabolism, and diversity
are grounded in the molecules and macromolecules these organisms contain and in the biological processes they
undergo. The third chapter in Part 1 sets down some basic concepts and describes one of the major tools for study-
ing microorganisms. Much as the alphabet applies to word development, in succeeding chapters we will formulate
words into sentences and sentences into ideas as we survey the different groups of microorganisms and concentrate
on their importance to public health and human welfare.
Although most microorganisms are harmless—or even beneficial, some cause infectious disease. We will concentrate
on the bacterial organisms in Chapter 4, where we survey their structural frameworks. In Chapter 5, we build on these
frameworks by examining microbial growth patterns and nutritional requirements. Chapter 6 describes the metabolism
of microbial cells, including those chemical reactions that produce energy and use energy. Part 1 concludes by consider-
ing the physical and chemical methods used to control microbial growth and metabolism (Chapter 7).
I
Cells of Vibrio cholerae, transmitted to
humans in contaminated water and food, are
the cause of cholera.
62582_CH01_001_034.pdf 162582.
The document discusses open science and open access. It provides examples of open science like open access publishing, open notebooks, prepublication data release, and open source software. It discusses three aspects of open science: cost, restrictions, and timing. It discusses the costs of publishing, creative commons licenses, and examples of organizations that promote open access like the Public Library of Science (PLoS) and how they circulated an open letter to encourage open access. Overall, the document discusses the history and concepts of open science and open access.
Toward Novel Human Microbiome Surveillance Diagnostics to Support Public HealthLarry Smarr
The document discusses ongoing research into understanding the human microbiome and its role in health and disease. It outlines how sequencing costs have dropped dramatically, enabling analysis of both human and microbial genomes. Several studies are highlighted that use microbiome profiling to differentiate between healthy individuals and those with various forms of inflammatory bowel disease.
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome composition and function can change with health status, diet, medications and other
Discovering the 100 Trillion Bacteria Living Within Each of UsLarry Smarr
This document provides a summary of a lecture on the human microbiome given by Dr. Larry Smarr. Some key points:
- The human microbiome refers to the trillions of bacteria that live within the human body. Each person contains 100 trillion bacteria, outnumbering human cells.
- Research into the microbiome is a rapidly growing field that provides insights into health and disease. The microbiome plays a role in processes like drug metabolism and immunity.
- The microbiome is established early in life and influenced by factors like birth method and antibiotic use in the first years. This early development can impact future health.
- Microbiome imbalances are linked to diseases like inflammatory bowel disease. New treatments are
The Human Microbiome, Supercomputers,and the Advancement of MedicineLarry Smarr
The keynote presentation discusses the importance of the human microbiome and how understanding its dynamics can advance medicine. It notes that the human microbiome contains tens of trillions of microbial cells and hundreds of times as many genes as human cells. Understanding the microbiome as an ecology rather than focusing on single pathogens is crucial. The presentation describes research tracking one person's microbiome and biomarkers over time, finding shifts between healthy and diseased states. It advocates developing tools to manage the microbiome and new therapies like fecal transplants. National initiatives now recognize the microbiome's importance in health and disease.
Science consists of observing the natural world through careful observation and experimentation. While scientific progress influences society, it also regularly challenges ethical values, requiring discussion on adapting new technologies. One area requiring bioethical discussion is biotechnology, as it can affect humans, other species and the environment, with benefits but also risks like gene modification and cloning. There are commonly accepted ethical principles like autonomy, non-maleficence, beneficence and justice that can guide choices, but science also requires rules and consideration of impacts on all life and nature's balance.
This document provides information about the 4th edition of the textbook "Biochemistry" by Donald Voet and Judith G. Voet. It lists the publisher, editors, production staff, and copyright information for the textbook. It also provides a brief preface written by the authors that introduces the intended audience for the textbook and discusses some of its themes and organization. The preface emphasizes that biochemistry is a growing field shaped by experimentation and the efforts of individual scientists, and that it illustrates the unity of life through evolution as well as the importance of control networks and medical applications.
2014 CrossRef Annual Meeting Keynote: Ways and Needs to Promote Rapid Data Sh...Crossref
Keynote address: "Ways and Needs to Promote Rapid Data Sharing" by Laurie Goodman of GigaScience.
Data is the base upon which all scientific discoveries are built, and data availability speeds the rate at which discoveries are made. Given that the overall goal for research is to improve human health and our environment, waiting to release data until after the first publication (sometimes taking years) is unacceptable. There are myriad issues that impede researchers from openly, and most importantly, rapidly sharing data, including lack of incentives: no credit, limited funding benefits, and little impact on career advancement; and cultural issues: the fear of being scooped. However, scientific publishers —the communicators of science and a key mechanism by which a researcher’s productivity is measured— can, and should, play a central role in promoting data sharing. Data citation and publication are just some of the ways we can support and encourage researchers who share data. Here, I will provide examples to help make clear the need for publishers to play an active role in this process and provide potential ways to facilitate our ability to promote open and rapid data sharing. This is not easy; but it is essential.
Essay On Helping Parents At Home In HindiRuth Phillips
1. The document discusses a trade campaign to promote Hot Fire Fuel Injector Cleaner.
2. It references a famous saying that you have to spend money to make money to justify the promotion.
3. The main focus of the promotion will be communicating that the fuel injector cleaner works.
From Me To We: Discovering the Trillions of Microorganisms That are a Part of UsLarry Smarr
The document summarizes a lecture about the human microbiome and its importance in health and disease. It discusses how sequencing DNA has revealed that the human body hosts trillions of microorganisms and that 99% of our genes are microbial. Understanding the microbiome is crucial for medicine as shifts in the microbial ecology can be linked to various diseases. The lecturer discusses his own efforts to track biomarkers and microbiome data over time, revealing how perturbations correlated with disease symptoms and weight changes. Precision approaches analyzing large cohorts will be needed to unravel microbiome dynamics in health and illness.
The document discusses the normal flora or microbiota that colonize the human body. It describes the major sites where microbes normally reside, including the skin, respiratory tract, gastrointestinal tract, and urogenital tract. The gut microbiota plays an important role in digestion and produces vitamins. Antibiotics can disrupt the normal balance of microbes. The Human Microbiome Project aims to characterize the microbes associated with health and disease.
The document discusses the human microbiome and focuses on the gut microbiome. It describes how the gut microbiome is assembled through factors like birth method, diet, disturbances, and succession over time. Community composition impacts functions like energy harvesting and obesity risk. Fecal transplants can cure infections by transferring a healthy gut community. Antibiotics have disrupted gonorrhea populations worldwide by targeting essential processes, but resistance has developed through mechanisms that reduce antibiotic effects.
Similar to Opening up to Diversity talk by @phylogenomics at #UCDPHSA (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Talk by Jonathan Eisen for LAMG2022 meetingJonathan Eisen
The document discusses the history of the Lake Arrowhead Microbial Genomes (LAMG) conference. It reveals that LAMG2020 was cancelled due to a secret plan by organizers who formed an "anti-karyote society" that hates eukaryotes. The meeting was to be renamed the "Big, Large, Enormous" meeting of the Lake Arrowhead Big Large Enormous Anti-Karyote Society. The document also hints that several past LAMG speakers have made cryptic comments indicating involvement in a conspiracy surrounding the conference.
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Phylogenetic and Phylogenomic Approaches to the Study of Microbes and Microbi...Jonathan Eisen
The document discusses Jonathan Eisen's work as a microbiology professor at UC Davis. It provides an overview of his research topics, which include microbial phylogenomics and evolvability, phylogenetic methods and tools, and using phylogenomics to study microbial communities and interactions between microbes and hosts under stress. The document also acknowledges collaborators and funding sources for Eisen's research over the years.
This document summarizes a class on detecting, quantifying, and tracking variations of SARS-CoV-2 RNA from COVID-19 samples. It discusses using quantitative RT-PCR (qRT-PCR) to detect and measure viral RNA levels in samples. Sequencing is used to identify variations in the viral genome over time, and online tools like Nextstrain allow viewing the evolution and global transmission of variants. Genotyping assays are also described that can rapidly screen samples for known single nucleotide variations during PCR.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 8 - COVID RNA DetectionJonathan Eisen
This document summarizes a class on SARS-CoV-2 RNA detection, quantification, and variation. It discusses how qRT-PCR is used to detect and quantify the virus by amplifying and detecting viral RNA. It also covers sequencing to identify variants, how variants evolve over time, and genotyping assays that can screen samples for known single nucleotide variations. Nextstrain and other online tools are presented that use sequencing data to analyze viral phylogenies, track variant distributions globally, and visualize genetic variations across the SARS-CoV-2 genome.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms for those who already suffer from conditions like depression and anxiety.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 5 - COVID VaccinesJonathan Eisen
The document discusses a class on COVID-19 vaccines. It covers topics like vaccine development, current candidates, delivery challenges, and comparisons between vaccines. Moderna and Pfizer mRNA vaccines are highlighted as being similar but having some differences in mRNA region, nanoparticle structure/synthesis, dosage amount, and storage temperature requirements. Other vaccines discussed include Novavax using spike protein nanoparticles, and AstraZeneca and Johnson & Johnson using DNA for spike protein delivered by a modified virus.
EVE198 Winter2020 Class 9 - COVID TransmissionJonathan Eisen
This document discusses modes of SARS-CoV-2 transmission including droplets, aerosols, and surfaces. It emphasizes that surfaces are not as big a risk as initially thought. It provides guidance on limiting transmission from different modes such as distancing, masks, washing hands, cleaning surfaces, and improving ventilation. The focus in 2021 is on droplets and aerosols rather than surfaces.
EVE198 Fall2020 "Covid Mass Testing" Class 8 VaccinesJonathan Eisen
This document discusses a class on vaccines for COVID-19. It covers topics like vaccine development, current candidate vaccines, challenges with vaccine distribution, and how vaccines are being assessed for safety, effectiveness, costs and production feasibility. Over 100 vaccine candidates are in development using platforms like DNA, RNA, viral vectors and inactivated viruses. Efforts like Operation Warp Speed are coordinating development of nucleic acid, viral vector and protein subunit vaccines. Distribution challenges include vaccine production, storage and logistics, number of doses required, and overcoming vaccine nationalism and hesitancy.
EVE198 Fall2020 "Covid Mass Testing" Class 2: Viruses, COIVD and TestingJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Fall2020 "Covid Mass Testing" Class 1 IntroductionJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
13. Public Library of Science (PLoS)
• Started in 2000 by
• Harold Varmus
• Pat Brown
• Michael Eisen
• First action was to circulate
an open letter on publishing
14. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
15. The Letter
We support the establishment of an online public library that would
provide the full contents of the published record of research and scholarly
discourse in medicine and the life sciences in a freely accessible, fully
searchable, interlinked form. Establishment of this public library would vastly
increase the accessibility and utility of the scientific literature, enhance
scientific productivity, and catalyze integration of the disparate communities of
knowledge and ideas in biomedical sciences.We recognize that the publishers
of our scientific journals have a legitimate right to a fair financial return for
their role in scientific communication. We believe, however, that the
permanent, archival record of scientific research and ideas should neither be
owned nor controlled by publishers, but should belong to the public and should
be freely available through an international online public library.To encourage
the publishers of our journals to support this endeavor, we pledge that,
beginning in September 2001, we will publish in, edit or review for, and
personally subscribe to only those scholarly and scientific journals
that have agreed to grant unrestricted free distribution rights to any
and all original research reports that they have published, through PubMed
Central and similar online public resources, within 6 months of their initial
publication date.
16.
17.
18. J-Can
you get people to sign this and FAX it to me.
1-786-549-0137. Craig and
Claires sigs would be greatly appreciated.
I assume I can put your name on it, no?
I set up a site http://www.publiclibraryofscience.org
to keep lists of
people who have signed.
-M
19. PLoS After the Letter (2003)
• > 25,000 people signed the letter
•Small increase in open access
support
• But not enough
• So PLoS announced the launch of
their own journals
•PLoS Biology
•PLoS Medicine
23. RhoGam
• Supplier
• RhoGAM should be administered within 72 hours of
known or suspected exposure to Rh-positive red
blood cells.
• Wikipedia
• It is given by intramuscular injection as part of
modern routine antenatal care at about 28 weeks of
pregnancy, and within 72 hours after childbirth.[5] It
is also given after antenatal pathological events that
are likely to cause a feto-maternal hemorrhage.[6]
• Question
• What happens if you do it even later?
26. Paywall
You can purchase online access to this
article (and all its versions) for a 24-
hour period. Articles are US $ 29.95,
with some exceptions where prices may
vary. Click "Buy Now" to display the
price
29. Access Blocked - What Next?
• Bought lots of articles
!
• Tried to contact experts
!
• Got friends to get some articles from libraries
!
• Got more and more pissed off
30. Baby Lost
• Benjamin Augustin Eisen stillborn August
29, 2003
31. Lack of Access
• Scientist without access
!
• Would access have helped?
!
• Is limiting access useful or needed?
!
• Goal of much of scientific and medical
research is to spread knowledge
45. The Built Environment
The ISME Journal (2012), 1–11
& 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12
www.nature.com/ismej
ORIGINAL ARTICLE
Architectural design influences the diversity and
structure of the built environment microbiome
Bacteria of Public time, the
Steven W Kembel1, Evan Jones1, Jeff Kline1,2, Dale Northcutt1,2, Jason Stenson1,2,
Ann M Womack1, Brendan JM Bohannan1, G Z Brown1,2 and Jessica L Green1,3
1Biology and the Built Environment Center, Institute of Ecology and Evolution, Department of
Biology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory,
Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute,
Santa Fe, NM, USA
0 Average contribution (%)
Door in
Buildings are complex ecosystems that house trillions of microorganisms interacting with each
other, with humans and with their environment. Understanding the ecological and evolutionary
processes that determine the diversity and composition of the built environment microbiome—the
community of microorganisms that live indoors—is important for understanding the relationship
between building design, biodiversity and human health. In this study, we used high-throughput
sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and
airborne bacterial communities at a health-care facility. We quantified airborne bacterial community
structure and environmental conditions in in
patient out
ventilation and in outdoor air. The phylogenetic Stall Stall diversity handles
rooms exposed to mechanical or window
of airborne bacterial communities was
lower indoors than outdoors, and mechanically Faucet ventilated rooms contained less diverse microbial
communities than did window-ventilated rooms. Bacterial communities in indoor environments
contained many taxa that are absent or rare outdoors, including taxa closely related to potential
human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative
humidity and temperature, were correlated with the diversity and composition of indoor bacterial
communities. The relative abundance of bacteria closely related to human pathogens was higher
indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity.
The observed relationship between building design and airborne bacterial diversity suggests that
we can manage indoor environments, altering through building design and operation the community
of microbial species that potentially colonize the human microbiome during our time indoors.
The ISME Journal advance online publication, 26 January 2012; doi:10.1038/ismej.2011.211
Subject Category: microbial population and community ecology
Keywords: aeromicrobiology; bacteria; built environment microbiome; community ecology; dispersal;
environmental filtering
Introduction
Humans spend up to 90% of their lives indoors
Toilet seat
Toilet flush handle
Sink floor
microbiome—includes human pathogens and com-mensals
interacting with each other and with their
Microbial Biogeography of Public Restroom Surfaces
Gilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4,
Noah Fierer1,5*
Bacteria of Public Restrooms
1 Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America, 2 Department of Computer Science,
University of Colorado, Boulder, Colorado, United States of America, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United
States of America, 4 Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America, 5 Department of Ecology and Evolutionary
Biology, University of Colorado, Boulder, Colorado, United States of America
Abstract
We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the
diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited
by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of
the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla:
Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those
found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with
hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor
surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated
bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more
common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female
restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic
observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that
restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear
linkages between communities on or in different body sites and those communities found on restroom surfaces. More
generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found
on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching
of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine
sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the
efficacy of hygiene practices.
Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces. Light blue indicates low
abundance while dark blue indicates high abundance of taxa. (A) Although skin-associated taxa (Propionibacteriaceae, Corynebacteriaceae,
Staphylococcaceae and Streptococcaceae) were abundant on all surfaces, they were relatively more abundant on surfaces routinely touched with
hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae, Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were most
abundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in low
abundance on all restroom surfaces, they were relatively more abundant on the floor of the restrooms we surveyed. Figure not drawn to scale.
doi:10.1371/journal.pone.0028132.g003
Citation: Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, et al. (2011) Microbial Biogeography of Public Restroom Surfaces. PLoS ONE 6(11): e28132.
doi:10.1371/journal.pone.0028132
Editor: Mark R. Liles, Auburn University, United States of America
Received September 12, 2011; Accepted November 1, 2011; Published November 23, 2011
Copyright: ! 2011 Flores et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported with funding from the Alfred P. Sloan Foundation and their Indoor Environment program, and in part by the National
Institutes of Health and the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or
preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: noah.fierer@colorado.edu
Introduction
More than ever, individuals across the globe spend a large
portion of their lives indoors, yet relatively little is known about the
microbial diversity of indoor environments. Of the studies that
have examined microorganisms associated with indoor environ-ments,
differences in the relative abundances of specific some surfaces (Figure 1B, Table S2). Most notably, were clearly more abundant on certain surfaces restrooms than male restrooms (Figure 1B). Some family are the most common, and often most abundant, found in the vagina of healthy reproductive age women Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces. Communities were PCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) form clusters distinct from surfaces touched with hands.
doi:10.1371/journal.pone.0028132.g002
most have relied upon cultivation-based techniques to
detect organisms residing on a variety of household surfaces [1–5].
Not surprisingly, these studies have identified surfaces in kitchens
and restrooms as being hot spots of bacterial contamination.
Because several pathogenic bacteria are known to survive on
surfaces for extended periods of time [6–8], these studies are of
obvious importance in preventing the spread of human disease.
However, it is now widely recognized that the majority of
microorganisms cannot be readily cultivated [9] and thus, the
communities and revealed a greater diversity of bacteria on
indoor surfaces than captured using cultivation-based techniques
[10–13]. Most of the organisms identified in these studies are
related to human commensals suggesting that the organisms are
not actively growing on the surfaces but rather were deposited
directly (i.e. touching) or indirectly (e.g. shedding of skin cells) by
humans. Despite these efforts, we still have an incomplete
understanding of bacterial communities associated with indoor
environments because limitations of traditional 16 S rRNA gene
cloning and sequencing techniques have made replicate sampling
and in-depth characterizations of the communities prohibitive.
With the advent of high-throughput sequencing techniques, we
can now investigate indoor microbial communities at an
unprecedented depth and begin to understand the relationship
between humans, microbes and the built environment.
the stall in), they were likely dispersed manually after women used
the toilet. Coupling these observations with those of the
distribution of gut-associated bacteria indicate that routine use of
toilets results in the dispersal of urine- and fecal-associated bacteria
throughout the restroom. While these results are not unexpected,
they do highlight the importance of hand-hygiene when using
public restrooms since these surfaces could also be potential
vehicles for the transmission of human pathogens. Unfortunately,
previous studies have documented that college students (who are
likely the most frequent users of the studied restrooms) are not
always the most diligent of hand-washers [42,43].
Results of SourceTracker analysis support the taxonomic
patterns highlighted above, indicating that human skin was the
primary source of bacteria on all public restroom surfaces
examined, while the human gut was an important source on or
around the toilet, and urine was an important source in women’s
restrooms (Figure 4, Table S4). Contrary to expectations (see
above), soil was not identified by the SourceTracker algorithm as
being a major source of bacteria on any of the surfaces, including
floors (Figure 4). Although the floor samples contained family-level
taxa that are common in soil, the SourceTracker algorithm
probably underestimates the relative importance of sources, like
high diversity of floor communities is likely due to the frequency of
contact with the bottom of shoes, which would track in a diversity
of microorganisms from a variety of sources including soil, which is
known to be a highly-diverse microbial habitat [27,39]. Indeed,
bacteria commonly associated with soil (e.g. Rhodobacteraceae,
Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average,
begun to take
of outside
from plants
hours after
were shut
proportion of
the human
back to pre-vious
which
26 Janu-ary
Journal,
mechanically
had lower
diversity than ones with open win-dows.
availability of fresh air translated
proportions of microbes associ-ated
human body, and consequently,
pathogens. Although this
that having natural airfl ow
Green says answering that
clinical data; she’s hoping
hospital to participate in a study
they move around. But to quantify those con-tributions,
Peccia’s team has had to develop
new methods to collect airborne bacteria and
extract their DNA, as the microbes are much
less abundant in air than on surfaces.
In one recent study, they used air fi lters
to sample airborne particles and microbes
in a classroom during 4 days during which
students were present and 4 days during
in indoor microbial
ecology research, Peccia
thinks that the field has
yet to gel. And the Sloan
Foundation’s Olsiewski
shares some of his con-cern.
“Everybody’s gen-erating
vast amounts of
data,” she says, but looking across data sets
can be diffi cult because groups choose dif-ferent
analytical tools. With Sloan support,
though, a data archive and integrated analyt-ical
tools are in the works.
To foster collaborations between micro-biologists,
architects, and building scientists,
the foundation also sponsored a symposium
on the microbiome of the built environment
100
80
60
40
20
Door out
Soap dispenser
Toi l et f lo o r
SOURCES
Soil
Water
Mouth
Urine
Gut
Skin
Bathroom biogeography. By
swabbing different surfaces in
public restrooms, researchers
determined that microbes vary in
where they come from depend-ing
on the surface (chart).
on February 9, 2012