The document discusses the author's quest to create a field guide to microbes. It describes the challenges in doing so given microbes' small size and high diversity. The author discusses using DNA sequencing and phylogenetic trees to identify microbes and determine their functions and relationships. Examples are given of using DNA to study human microbiomes, forensic analysis, and microbial communities. The need for a comprehensive field guide is argued to better understand the roles and identification of microbes.
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuksJonathan Eisen
This document discusses the need for a phylogeny-driven genomic encyclopedia of eukaryotes. It notes that current sources of information on sequenced eukaryotic genomes, such as Wikipedia and GOLD, are disorganized and lack phylogenetic context. The document then analyzes genomic data from the poorly studied protist Collodictyon using 18S and 28S ribosomal DNA sequencing and phylogenomic trees inferred from 124 genes. The analysis finds that Collodictyon is closely related to Diphylleia and occupies a very early divergence in the eukaryote tree of life, either alone or as the sister group to Malawimonas. This suggests Collodictyon represents an important new lineage for
UC Davis EVE161 Lecture 14 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics and microbial phylogenomics. The lecture discusses the history and development of metagenomics, which involves studying the collective genomes of microbes in an environment. It reviews key papers on metagenomics and the discovery of proteorhodopsin and the SAR11 lineage of bacteria from environmental samples. The slides also discuss previous findings on marine microbes from rRNA studies and introduce two new lineages of alpha- and gamma-proteobacteria identified from an analysis of 16S rRNA genes cloned from Sargasso Sea bacterioplankton DNA.
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuksJonathan Eisen
This document discusses the need for a phylogeny-driven genomic encyclopedia of eukaryotes. It notes that current sources of information on sequenced eukaryotic genomes, such as Wikipedia and GOLD, are disorganized and lack phylogenetic context. The document then analyzes genomic data from the poorly studied protist Collodictyon using 18S and 28S ribosomal DNA sequencing and phylogenomic trees inferred from 124 genes. The analysis finds that Collodictyon is closely related to Diphylleia and occupies a very early divergence in the eukaryote tree of life, either alone or as the sister group to Malawimonas. This suggests Collodictyon represents an important new lineage for
UC Davis EVE161 Lecture 14 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics and microbial phylogenomics. The lecture discusses the history and development of metagenomics, which involves studying the collective genomes of microbes in an environment. It reviews key papers on metagenomics and the discovery of proteorhodopsin and the SAR11 lineage of bacteria from environmental samples. The slides also discuss previous findings on marine microbes from rRNA studies and introduce two new lineages of alpha- and gamma-proteobacteria identified from an analysis of 16S rRNA genes cloned from Sargasso Sea bacterioplankton DNA.
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
American Gut Project presentation at Masaryk Universitymcdonadt
The document discusses the microbiome and how microbes outnumber human cells in the human body. It provides several references from scientific studies published between 2001-2015 that examine the microbiome composition in different human and environmental populations using genetic sequencing and analysis techniques. It also discusses challenges and variations in microbiome analysis methods and highlights some key researchers and projects investigating the human microbiome.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
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 discusses the analysis of microbial communities through sequencing of the 16S rRNA gene. It presents WATERS, a workflow system that automates and bundles various software tools for analyzing 16S rRNA sequence data. The goals of WATERS are to simplify the analysis process for users without specialized bioinformatics expertise and to facilitate reproducibility through tracking of data provenance. WATERS guides users through the typical sequence analysis steps of alignment, chimera filtering, OTU clustering, taxonomy assignment, phylogeny tree building, and ecological analyses and visualization. By integrating existing tools into a single automated workflow, WATERS aims to reduce the effort required for 16S rRNA data analysis and allow researchers to focus on biological interpretation of results.
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The document summarizes research that screened metagenomic libraries from Puerto Rican forests for protease activity. Culture-independent metagenomic techniques were used to study the uncultured microbial genetics. Two libraries containing 14,000 and 600,000 clones were screened, identifying 20 potential clones producing protease enzymes, which are undergoing further analysis. Proteases have important industrial biotechnology applications.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
Nonhumans: Don't Neglect Their MicrobiomesJonathan Eisen
This document discusses the importance of animal microbiomes. It notes that animals are covered in clouds of microbes that form their microbiome, which is likely involved in many important animal phenotypes. Reasons for the growing focus on animal microbiomes include advances in culture-independent techniques and sequencing that have revealed greater microbial diversity than previously appreciated. Understanding animal microbiomes could provide insights into processes like health, disease transmission, and mutualistic relationships with microbes.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
This document summarizes metagenomic approaches for studying soil microbiomes. It discusses soil as the most complex ecosystem with immense biodiversity. Metagenomic techniques allow exploration of soil nutrient dynamics without culturing by sequencing DNA directly from environmental samples. Co-occurrence analysis can reveal relationships between microbial taxa and genes over space and time. Reference databases are needed but current soil references represent only a small fraction of microbes found globally. Single cell genomics provides isolates and genomes for previously uncultured microbes. Collaboration is important for addressing complex questions about soil microbial communities using multi-omics approaches.
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
American Gut Project presentation at Masaryk Universitymcdonadt
The document discusses the microbiome and how microbes outnumber human cells in the human body. It provides several references from scientific studies published between 2001-2015 that examine the microbiome composition in different human and environmental populations using genetic sequencing and analysis techniques. It also discusses challenges and variations in microbiome analysis methods and highlights some key researchers and projects investigating the human microbiome.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
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 discusses the analysis of microbial communities through sequencing of the 16S rRNA gene. It presents WATERS, a workflow system that automates and bundles various software tools for analyzing 16S rRNA sequence data. The goals of WATERS are to simplify the analysis process for users without specialized bioinformatics expertise and to facilitate reproducibility through tracking of data provenance. WATERS guides users through the typical sequence analysis steps of alignment, chimera filtering, OTU clustering, taxonomy assignment, phylogeny tree building, and ecological analyses and visualization. By integrating existing tools into a single automated workflow, WATERS aims to reduce the effort required for 16S rRNA data analysis and allow researchers to focus on biological interpretation of results.
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The document summarizes research that screened metagenomic libraries from Puerto Rican forests for protease activity. Culture-independent metagenomic techniques were used to study the uncultured microbial genetics. Two libraries containing 14,000 and 600,000 clones were screened, identifying 20 potential clones producing protease enzymes, which are undergoing further analysis. Proteases have important industrial biotechnology applications.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
Nonhumans: Don't Neglect Their MicrobiomesJonathan Eisen
This document discusses the importance of animal microbiomes. It notes that animals are covered in clouds of microbes that form their microbiome, which is likely involved in many important animal phenotypes. Reasons for the growing focus on animal microbiomes include advances in culture-independent techniques and sequencing that have revealed greater microbial diversity than previously appreciated. Understanding animal microbiomes could provide insights into processes like health, disease transmission, and mutualistic relationships with microbes.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
This document summarizes metagenomic approaches for studying soil microbiomes. It discusses soil as the most complex ecosystem with immense biodiversity. Metagenomic techniques allow exploration of soil nutrient dynamics without culturing by sequencing DNA directly from environmental samples. Co-occurrence analysis can reveal relationships between microbial taxa and genes over space and time. Reference databases are needed but current soil references represent only a small fraction of microbes found globally. Single cell genomics provides isolates and genomes for previously uncultured microbes. Collaboration is important for addressing complex questions about soil microbial communities using multi-omics approaches.
Genome sequencing and the development of our current information libraryZarlishAttique1
This document provides information about genome projects and the development of current information libraries. It discusses different types of genome projects conducted on organisms from all domains of life. These include projects on humans, plants, animals, fungi, bacteria, archaea, and viruses. It also describes the methods used in genome projects, such as genome assembly, annotation, and high-throughput sequencing techniques including de novo sequencing and resequencing. Genome annotation methods and tools are also outlined. The document concludes by noting the tremendous progress made in high-throughput sequencing capabilities, allowing for rapid sequencing of many genomes.
A renewed need for a genomic field guide to microbesJonathan Eisen
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
This document discusses the rise of big data in modern microbiology due to advances in DNA sequencing technologies. It notes that while sequencing is now much cheaper and faster, analyzing the large volumes of sequencing data presents new computational challenges. Methods like digital normalization are helping to scale down datasets for assembly. While sequencing is revealing vast unknown diversity in communities like soil, connecting patterns in the data to biological functions and mechanisms remains difficult. Collaboration and data sharing will be important to advance the field.
This document discusses challenges and opportunities for analyzing metagenomic sequencing data from environmental samples. It notes that next-generation sequencing has led to an exponential increase in the amount of sequencing data produced but challenges remain for data analysis and interpretation. Methods discussed to help analyze large metagenomic datasets include computational techniques like de novo assembly to compress data size and digital normalization to scale datasets for assembly. Experimental partitioning of samples into bacterial, viral and other fractions is also presented as a way to gain insights from metagenomic data. The talk emphasizes that continued method development is needed to fully leverage the massive amounts of sequencing data now possible from microbial communities.
Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 ...GigaScience, BGI Hong Kong
This document summarizes the First International EMP meeting and the Earth Microbiome Project's pilot study. The EMP aims to catalog microbial diversity globally by sequencing 10,000 environmental samples. So far over 60,000 samples have been pledged from over 50 researchers worldwide. Analysis of initial samples shows robust seasonal patterns in species richness. The EMP also aims to correlate taxonomic data with environmental parameters and functional gene profiles to better understand microbial communities and predict assemblages.
Rapidly decreasing costs of DNA sequencing and increases in computational power have led to an era of "big data" in microbiology. The collection and analysis of massive datasets from metagenomic studies presents both opportunities and challenges. Key opportunities include understanding microbial community dynamics and interactions at an unprecedented scale. However, challenges include developing computational methods to efficiently analyze large, diverse datasets and training the next generation of microbiologists to work in this new "big data" environment. Overcoming these challenges will require collaborative efforts across disciplines as well as a culture change toward open data sharing and reproducible research.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
The document summarizes Dr. Larry Smarr's presentation about the CAMERA project, which uses supercomputers and networks to explore microbial genomic data from ocean samples. The CAMERA infrastructure provides researchers worldwide with access to over 1 billion base pairs of metagenomic sequence data through an online portal. Analysis of this data has expanded knowledge of microbial biodiversity and gene families, providing insights into evolution and relationships between microbes and human health.
The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.
This presentation will give you an in-depth look at modern techniques and appliations of biotechnology. It will get you thinking about the potential for biotechnology to change your lives in the future. Please take Cornell Notes on the following slides.
Quantifying Your Superorganism Body Using Big Data SupercomputingLarry Smarr
1) The document discusses a lecture given by Dr. Larry Smarr on quantifying his own "superorganism" body using big data and supercomputing.
2) Over many years, Smarr collected massive amounts of biological and medical data on himself, including microbial genome sequencing of stool samples.
3) Analyzing this personal data using supercomputers revealed Smarr had an undiagnosed autoimmune disease (inflammatory bowel disease), disruptions to his gut microbiome, and periodic inflammation.
This document provides an overview of genome sequencing. It discusses the history of genome sequencing, from early sequencing of small viruses in the 1970s to larger genomes like yeast and the human genome. The document outlines different sequencing technologies over time, from Sanger sequencing to newer single-molecule approaches. It also summarizes key genome projects like ENCODE and 1000 Genomes that have provided insights into non-coding regulatory elements and human genetic variation.
Exploring Our Inner Universe Using Supercomputers and Gene SequencersLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on his research exploring the human microbiome using supercomputers and gene sequencers. He began by researching astrophysics but has recently applied those methods to study the microbes within the human body. Through deep genome sequencing of his own stool samples over time and large-scale computational analysis, he was able to map changes in his gut microbiome that provided insights into an undiagnosed autoimmune disease. His research demonstrates how quantitative analysis of the microbiome using advanced technologies can lead to new understandings of health and disease.
This document discusses the intersection of biology and computer science known as bioinformatics. It begins with an introduction to bioinformatics and its rationale, including the enormous size of biological data and the computational challenges involved. Examples are given of biological questions that can be addressed with computational methods, such as genome assembly, gene finding, and disease classification. Opportunities in the field are noted, such as using deep learning for genome analysis. The talk aims to illustrate how in silico and in vivo approaches can be merged to tackle problems in modern biology.
This document discusses methods for analyzing microbial diversity in soil without culturing. It notes that while culturing methods have provided access to some microbes, they represent only about 1% of soil microbes due to physiological constraints. Molecular methods like 16S rRNA gene sequencing reveal far greater phylogenetic diversity in soil. The document reviews various culture-independent methods like DNA-DNA hybridization, PCR amplification, and gene expression cloning that provide insights into the phylogenetic and functional diversity of uncultured soil microbes, opening possibilities for discovering novel products. It suggests both culturable and unculturable microbes likely contribute to untapped natural product resources.
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
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 document contains slides from a lecture on fungi. The slides cover various topics about fungi, including their phylogenetic diversity, forms, and life cycles. Key points include that fungi have chitin in their cell walls, absorb nutrients from outside their bodies, and can have both single-celled and multicellular stages. The slides also discuss the different life cycles of groups like chytrids, which have flagellated spores and gametes to aid dispersal.
These lecture slides, by Dr Sidra Arshad, offer a simplified look into the mechanisms involved in the regulation of respiration:
Learning objectives:
1. Describe the organisation of respiratory center
2. Describe the nervous control of inspiration and respiratory rhythm
3. Describe the functions of the dorsal and respiratory groups of neurons
4. Describe the influences of the Pneumotaxic and Apneustic centers
5. Explain the role of Hering-Breur inflation reflex in regulation of inspiration
6. Explain the role of central chemoreceptors in regulation of respiration
7. Explain the role of peripheral chemoreceptors in regulation of respiration
8. Explain the regulation of respiration during exercise
9. Integrate the respiratory regulatory mechanisms
10. Describe the Cheyne-Stokes breathing
Study Resources:
1. Chapter 42, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 36, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 13, Human Physiology by Lauralee Sherwood, 9th edition
Summer is a time for fun in the sun, but the heat and humidity can also wreak havoc on your skin. From itchy rashes to unwanted pigmentation, several skin conditions become more prevalent during these warmer months.
- Video recording of this lecture in English language: https://youtu.be/Pt1nA32sdHQ
- Video recording of this lecture in Arabic language: https://youtu.be/uFdc9F0rlP0
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Are you looking for a long-lasting solution to your missing tooth?
Dental implants are the most common type of method for replacing the missing tooth. Unlike dentures or bridges, implants are surgically placed in the jawbone. In layman’s terms, a dental implant is similar to the natural root of the tooth. It offers a stable foundation for the artificial tooth giving it the look, feel, and function similar to the natural tooth.
The skin is the largest organ and its health plays a vital role among the other sense organs. The skin concerns like acne breakout, psoriasis, or anything similar along the lines, finding a qualified and experienced dermatologist becomes paramount.
5-hydroxytryptamine or 5-HT or Serotonin is a neurotransmitter that serves a range of roles in the human body. It is sometimes referred to as the happy chemical since it promotes overall well-being and happiness.
It is mostly found in the brain, intestines, and blood platelets.
5-HT is utilised to transport messages between nerve cells, is known to be involved in smooth muscle contraction, and adds to overall well-being and pleasure, among other benefits. 5-HT regulates the body's sleep-wake cycles and internal clock by acting as a precursor to melatonin.
It is hypothesised to regulate hunger, emotions, motor, cognitive, and autonomic processes.
Travel Clinic Cardiff: Health Advice for International TravelersNX Healthcare
Travel Clinic Cardiff offers comprehensive travel health services, including vaccinations, travel advice, and preventive care for international travelers. Our expert team ensures you are well-prepared and protected for your journey, providing personalized consultations tailored to your destination. Conveniently located in Cardiff, we help you travel with confidence and peace of mind. Visit us: www.nxhealthcare.co.uk
Nano-gold for Cancer Therapy chemistry investigatory projectSIVAVINAYAKPK
chemistry investigatory project
The development of nanogold-based cancer therapy could revolutionize oncology by providing a more targeted, less invasive treatment option. This project contributes to the growing body of research aimed at harnessing nanotechnology for medical applications, paving the way for future clinical trials and potential commercial applications.
Cancer remains one of the leading causes of death worldwide, prompting the need for innovative treatment methods. Nanotechnology offers promising new approaches, including the use of gold nanoparticles (nanogold) for targeted cancer therapy. Nanogold particles possess unique physical and chemical properties that make them suitable for drug delivery, imaging, and photothermal therapy.
Osteoporosis - Definition , Evaluation and Management .pdfJim Jacob Roy
Osteoporosis is an increasing cause of morbidity among the elderly.
In this document , a brief outline of osteoporosis is given , including the risk factors of osteoporosis fractures , the indications for testing bone mineral density and the management of osteoporosis
Travel vaccination in Manchester offers comprehensive immunization services for individuals planning international trips. Expert healthcare providers administer vaccines tailored to your destination, ensuring you stay protected against various diseases. Conveniently located clinics and flexible appointment options make it easy to get the necessary shots before your journey. Stay healthy and travel with confidence by getting vaccinated in Manchester. Visit us: www.nxhealthcare.co.uk
June 2024 Oncology Cartoons By Dr Kanhu Charan Patro
"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February 2, 2014.
1. !
!
The Quest for a Field Guide to the Microbes
!
Jonathan A. Eisen
@phylogenomics
University of California, Davis
!
Talk for Science in the River City
January 28, 2014
2. The Quest for A Field Guide to the Microbes
Part I:
!
My Obsessions
35. Field Guides
• What should be included
•
•
•
•
•
Catalog of types of organism
Functional diversity
Biogeography (space and time)
Niche information
Means for identification
• Provides a guide to interpret normal
states and abnormalities
39. The Quest for A Field Guide to the Microbes
Part III:
!
A Micro Bit
about Microbes
40. The Microbe Challenge
• Microbes are small
• But diversity and numbers
are very high
• Appearance not a good
indicator of type or function
• Field observations of limited
value
77. Who is Out There?
DNA
extraction
PCR
Makes lots of
copies of the
rRNA genes
in sample
PCR
Phylogenetic tree
rRNA1
Sequence alignment = Data matrix
Yeast
C
A
C
A
C
T
A
C
A
G
T
E. coli
Humans
A
Yeast
E. coli
rRNA1
A
G
A
C
A
G
Humans
T
A
T
A
G
T
Sequence
rRNA genes
rRNA1
5’ ...TACAGTATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
80. The Tree of Life
2006
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
!60
81. The Tree of Life
2006
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
82. Who is Out There?
DNA
extraction
PCR
Makes lots of
copies of the
rRNA genes
in sample
PCR
Phylogenetic tree
rRNA1
Sequence alignment = Data matrix
rRNA2
Yeast
C
A
C
A
T
A
C
A
G
T
A
G
A
C
A
G
Humans
T
A
T
A
G
T
Yeast
T
A
C
A
G
T
rRNA1
5’ ...ACACACATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
C
E. coli
Humans
A
rRNA2
E. coli
rRNA1
Sequence
rRNA genes
rRNA2
5’ ...TACAGTATAGGTG
GAGCTAGCGATCGAT
CGA... 3’
83. Who is Out There?
DNA
extraction
PCR
Makes lots of
copies of the
rRNA genes
in sample
PCR
rRNA1
5’...ACACACATAGGTGGAGCTAG
CGATCGATCGA... 3’
Phylogenetic tree
rRNA1
Sequence alignment = Data matrix
rRNA2
rRNA1
Humans
E. coli
Yeast
A
C
A
C
A
C
rRNA2
T
A
C
A
G
C
A
C
T
G
T
rRNA4
C
A
C
A
G
T
E. coli
A
G
A
C
A
G
Humans
T
A
T
A
G
T
Yeast
T
A
C
A
G
T
rRNA2
5’..TACAGTATAGGTGGAGCTAGC
GACGATCGA... 3’
T
rRNA3
rRNA4
rRNA3
Sequence
rRNA genes
rRNA3
5’...ACGGCAAAATAGGTGGATTC
TAGCGATATAGA... 3’
rRNA4
5’...ACGGCCCGATAGGTGGATTC
TAGCGCCATAGA... 3’
84. DNA Sequencing Has Gone Crazy
1977
2010
Sanger sequencing method by F. Sanger
(PNAS ,1977, 74: 560-564)
1983
1953
2000
1990
1980
Approaching to NGS
AAATCGCTAGCGC
CGGCGAGCTAGC
CGAGCGATCGAGC
CGAGCATCGAGTA
PCR by K. Mullis
(Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:263-73)
Discovery of DNA structure
(Cold Spring Harb. Symp. Quant. Biol. 1953;18:123-31)
Human Genome Project
(Nature , 2001, 409: 860–92; Science, 2001, 291: 1304–1351)
1993
Development of pyrosequencing
(Anal. Biochem., 1993, 208: 171-175; Science ,1998, 281: 363-365)
Single molecule emulsion PCR
1998
Founded Solexa
1998
Founded 454 Life Science
2000
454 GS20 sequencer
(First NGS sequencer)
2005
Solexa Genome Analyzer
(First short-read NGS sequencer)
Illumina acquires Solexa
(Illumina enters the NGS business)
2006
2006
ABI SOLiD
(Short-read sequencer based upon ligation)
Roche acquires 454 Life Sciences
(Roche enters the NGS business)
2007
2007
GS FLX sequencer
(NGS with 400-500 bp read lenght)
NGS Human Genome sequencing
(First Human Genome sequencing based upon NGS technology)
2008
2008
Hi-Seq2000
(200Gbp per Flow Cell)
From Slideshare presentation of Cosentino Cristian
http://www.slideshare.net/cosentia/high-throughput-equencing
2010
Miseq
Roche Jr
Ion Torrent
PacBio
Oxford
85. A Thumb Drive DNA Sequencer?
From Oxford Nanopores Web Site
94. Variation May Affect Health
• Microbial community different in many disease
states compared to healthy individuals
• Unclear if this is cause or effect in most cases
99. The Built Environment
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 ISME Journal (2012), 1–11
the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla:
& 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12
Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those
www.nature.com/ismej
found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with
hands. On illustrations of the relative abundance of discriminating suggesting fecal contamination of these surfaces. Floor
Figure 3. Cartoon toilet surfaces, gut-associated taxa were more prevalent, taxa on public restroom surfaces. Light blue indicates low
surfaces dark blue indicates high abundance of taxa. (A) contained several taxa taxa (Propionibacteriaceae, Corynebacteriaceae,
abundance while were the most diverse of all communities and Although skin-associated commonly found in soils. Skin-associated
Staphylococcaceae especially the Propionibacteriaceae, on all surfaces, they were relatively more abundant on surfaces routinely touched with
bacteria, and Streptococcaceae) were abundant dominated surfaces routinely touched with our hands. Certain taxa were more
hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, vagina-associated Lactobacillaceae were widelyBacteroidaceae)in female
common in female than in male restrooms as Ruminococcaceae, Lachnospiraceae, Prevotellaceae and distributed were most
abundant on toilet surfaces. from urine contamination. Use of the SourceTracker algorithm confirmed Nocardioidaceae) taxonomic
restrooms, likely (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and many of our were in low
abundance on all restroom surfaces, they were relatively more abundant on the floor of the surfaces. Overall, theseFigure not drawn to scale.
observations as human skin was the primary source of bacteria on restroom restrooms we surveyed. results demonstrate that
doi:10.1371/journal.pone.0028132.g003
restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear
Bacteria
linkages between communities on or in different body sites and those communities found on restroom surfaces. More of P
show that SourceTracker analysis support the taxonomic
the stallgenerally,were likely dispersed manuallypublicwomen used as we Results of human-associated microbes are commonly found
in), they this work is relevant to the after health field
1
1
1,2
1,2
1,2
Steven W Kembel , Evan Jones , Jeff Kline , Dale Northcutt , Jason Stenson ,
on Coupling these observations with those of the
patterns highlighted above, indicating that human skin was the
the toilet. restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching
1
Bohannan1, G Z Brown1,2 and Jessica L Green1,3
Ann
time, the M Womack , Brendan JM 100
of surfaces.
SOURCES
source of bacteria on all public restroom surfaces
bacteria indicate that routine can
1
Bathroomdistribution of gut-associatedon indoor surfaces, an approach of high-throughput analyses ofpathogen communities to determine
biogeography.Furthermore, we demonstrate that we use use primary be used to track bacterial transmission and test the
By
Biology and the Built Environment Center, Institute of Ecology and Evolution, Department of
sources the bacteria of urine- and fecal-associated bacteria
of dispersal
whichexamined, while the human gut was an important source on or
could
toilets results in
Soil
un to take
swabbing throughout surfaces in While these results are not unexpected,
different the restroom. practices.
Biology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory,
efficacy of hygiene
around the toilet, and urine was an important source in women’s
Water
80
of outside
Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute,
public restrooms,highlight the importance of hand-hygiene when using
restrooms (Figure 4, Table S4). Contrary to expectations (see
they do researchers
Mouth
Santa Fe, NM, USA
om plants
Microbial Biogeography of Public by the SourceTracker 6(11): e28132.
public microbes vary in ST, surfaces could also be potential
restrooms GE, Bates
determined thatCitation: Floressince these Knights D, Lauber CL, Stombaugh J, et al. (2011)above), soil was not identifiedRestroom Surfaces. PLoS ONEalgorithm as
Urine
doi:10.1371/journal.pone.0028132
60
being a major source of bacteria on any of the surfaces, including
ours after
where theyvehicles from dependcome for the transmission of human pathogens. Unfortunately,
Gut
Editor: Mark R. Liles, Auburn University, college students
floors (Figure 4). Although the floor samples contained family-level
previous studies have documented that United States of America are
ing on the surface (chart).frequent users of the studied restrooms)(who not
ere shut
taxa 23, 2011
likely Received September 12, 2011; Accepted November 1, 2011; Published November that are common in soil, the SourceTracker algorithm
the most
are
Buildings are complex ecosystems that house trillions of microorganisms interactingSkin each
with
40
ortion of
other, with humans and with their environment. Understanding the ecological and evolutionary
probably underestimates the relative importance of which permits
always the most ß 2011 Flores et al. This is an[42,43].
Copyright: diligent of hand-washers open-access article distributed under the terms of the Creative Commons Attribution License, sources, like
ORIGINAL ARTICLE
Average contribution (%)
Architectural design influences the diversity and
structure of the built environment microbiome
February 9, 2012
Do
or
Do in
or
ou
t
St
all
in
Fa Sta
uc
et ll ou
So han t
ap
d
dis les
pe
ns
To
T
e
ile oile r
tf
lus t sea
hh t
a
To ndle
ile
tf
lo
Si or
nk
flo
or
processes that determine the diversity and composition of the built environment microbiome—the
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
pant in indoor microbial
community of microorganisms that live indoors—is important for understanding the relationship
20
Funding: This work was supported
Foundation
their Indoor Environment program, and
ecology research,ofPeccia the Howard with funding from the Alfred P. Sloan had no role andstudy design, data collection and analysis, in part bytothe National
between building design, biodiversity and human health. In this study, we used high-throughput
Institutes
Health and
Hughes Medical Institute. The funders
in
decision
publish, or
sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and
preparation of has
thinks that the fieldthe manuscript.
airborne bacterial communities at 0 health-care facility. We quantified airborne bacterial community
a
Competing Interests:
structure and environmental conditions in patient rooms exposed to mechanical or window
wh i c h
yet to gel. And the Sloan The authors have declared that no competing interests exist.
* E-mail: noah.fierer@colorado.edu
ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was
26 JanuFoundation’s Olsiewski
lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial
communities than did window-ventilated rooms. Bacterial communities in indoor environments
Journal,
shares some of his concontained many taxa that are absent or rare outdoors, including taxa closely related to potential
communities and revealed a greater diversity of bacteria on
Introduction
hanically
cern. “Everybody’s genhuman pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative
indoor surfaces than captured using cultivation-based techniques
humidity and temperature, were correlated with the diversity and composition of indoor bacterial
had lower
erating vastMore than ever, individuals across the globe spend a large [10–13]. Most of the organisms identified in these studies are
amounts of
communities. The relative abundance of bacteria closely related to human pathogens was higher
portion of their lives indoors, yet relatively little is known about the
related to human
are
y than ones with openthan outdoors, and higher in rooms withquantify those con- lower relative humidity. looking across data sets 2. Relationship between bacterial communities associated with commensals suggesting that the organisms were
they move around. But to lower airflow rates and data,” she says, but
indoors winFigure
ten public restroom surfaces. Communities
microbial diversity of indoor environments. Of the studies that
not actively
The observed relationship between building design and airborne bacterial can be difficult because groups choose dif- of the unweighted UniFrac distance matrix. Each point represents agrowing on the surfaces but rather were deposited
ility of fresh air translated tributions, Peccia’s team has had to develop diversity suggests that
PCoA
single sample. Note that the floor (triangles) and toilet (as
have examined microorganisms associated with indoor environdirectly (i.e. touching) or indirectly (e.g. shedding of skin cells) by
we can manage indoor environments, altering through building design and operation the community
form
tions of microbes associ- new methods to collect airbornemicrobiomeand our timeanalytical tools. With ments, most have relied upon cultivation-based techniques hands. humans. Despite these efforts, we still have an incomplete
Sloan support, clusters distinct from surfaces touched with to
of microbial species that potentially colonize the human bacteria during ferent indoors.
doi:10.1371/journal.pone.0028132.g002
detect organisms residing on a variety of household surfaces [1–5].
The ISME Journal extract their DNA, 26 January 2012; are much
understanding of bacterial communities associated with indoor
an body, and consequently, advance online publication,as the microbesdoi:10.1038/ismej.2011.211 a data archive and integrated analytthough,
Subject Category: microbial population and community ecology
Not surprisingly, these studies have identified surfaces in kitchens
environments because limitations of traditional 16 S rRNA gene
high diversity
communities is likely due to
of
related
relative abundances of s
pathogens. Although this less abundant in air than on surfaces.
ical tools dispersal;
Keywords: aeromicrobiology; bacteria; built environment microbiome; community ecology;are in the works. and restrooms as being hot of floorof bacterial contamination.the frequencyand sequencingdifferences in the made replicate sampling
spots
cloning
techniques have
e human
ck to pre-
contact
shoes, which would track a diversity
some surfaces (Figure 1B, Table
notably
environmental filtering In one recent study, they used air filters
Because several pathogenic bacteria are known
hat having natural airflow
To foster collaborations between micro- with the bottom aofvariety of to survive on inand in-depth characterizations of abundant onS2). Most surfaces
of microorganisms from
sources including soil, which is
were clearly more the communities prohibitive.
certain
surfaces for extended periods of time [6–8], these studies are of
With the
Green says answering that to sample airborne particles and microbes biologists, architects, and building scientists,in preventing the spread microbial habitat [27,39]. Indeed,advent of high-throughputrestrooms (Figure 1B). Some
known to be a highly-diverse
restrooms than male sequencing techniques, we
obvious importance
of human disease.
can now
bacteria commonly associated with soil (e.g.
family indoor microbial communities at abun
often most an
Introduction
microbiome—includes the foundation and comclinical data; she’s hoping in a classroom during 4 days during which human pathogensalso sponsored a symposium widely recognized that the majority of Rhodobacteraceae, investigate are the most common, andthe relationship
However, it is now
unprecedented depth and begin to understand
mensals interacting with each other and with their
Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average,
found in the vagina of healthy reproductive age w
101. The Microbe Challenge
• Microbes are small
• But diversity and numbers
are very high
• Appearance not a good
indicator of type or function
• Field observations of limited
value