Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
Tracking Immune Biomarkers and the Human Gut Microbiome: Inflammation, Croh...Larry Smarr
Larry Smarr presented on tracking immune biomarkers and the human gut microbiome in relation to inflammation, Crohn's disease, and colon cancer. He turned his own body into a "genomic observatory" by tracking over 100 of his own blood and stool biomarkers and sequencing his gut microbiome multiple times. His research found high levels of inflammation and an abundance of Fusobacteria in his microbiome when inflammation was highest. Following antibiotic and steroid therapy, inflammation and Fusobacteria were greatly reduced. This integrated personal omics approach provides insights into the links between inflammation, gut microbes, and colon cancer risk.
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
The document summarizes a talk given by Dr. Larry Smarr on his research tracking extensive health data on himself over many years. Some key points:
1) Smarr collected over a billion data points defining his body, including DNA sequencing, medical images, and daily biomarkers, revealing episodic inflammation related to his Crohn's disease.
2) Analysis of his gut microbiome via metagenomic sequencing showed many typically abundant bacterial species were severely depleted compared to healthy individuals.
3) Tracking changes over time demonstrated the coupled dynamics of his immune system and gut microbiome in response to therapies, similar to ecological models of invasive species dominating after natives are disturbed.
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 document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
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.
Using Supercomputers and Gene Sequencers to Discover Your Inner MicrobiomeLarry Smarr
This keynote talk discusses research using supercomputers and gene sequencing to study the human microbiome. The human microbiome contains 100 trillion microorganisms and their genes outnumber human genes 300 to 1. The speaker has been collecting data from his own body over 7 years to study his microbiome and immune system interactions. Collaborating researchers have sequenced his gut microbiome over time as well as samples from autoimmune disease patients. Supercomputers are needed to analyze the massive amount of sequencing data and reveal details of microbial ecology and genetics in health and disease. Studying the human microbiome will revolutionize medicine in the next decade.
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
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.
Interactions of the Immune System with the Gut Microbiome in Inflammatory Bo...Larry Smarr
Larry Smarr presented on his research quantifying interactions between his immune system, gut microbiome, and genetics in relation to his diagnosis of Crohn's disease. Over many years, he collected over 150 biological variables from blood and stool samples, and obtained genomic and metagenomic sequencing. Analysis revealed periods of chronic inflammation correlated with shifts in bacterial abundance and invasive strains. Treatment with antibiotics and immunosuppressants reduced inflammation and allowed rare bacteria to decrease while more beneficial firms increased. The research aims to better understand coupled human-microbiome dynamics and how genetics may predispose individuals to conditions like inflammatory bowel disease.
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeLarry Smarr
This document summarizes Dr. Larry Smarr's talk on modeling the human immune system and gut microbiome dynamics. It discusses how the growing diversity of gut bacteria after birth helps train the immune system. In health, constant feedback between the immune system and microbiome leads to homeostasis, but in diseases like Crohn's, this balance fails. The talk demonstrates this dysbiotic state using data from Dr. Smarr's own gut microbiome and biomarkers over five years. It reviews efforts to computationally model this important biological system.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
Stability in Health vs. Abrupt Changes in Disease in the Human Gut Microbiome...Larry Smarr
The document summarizes research on analyzing changes in human gut microbiome composition over time using 16S rRNA gene sequencing and the UniFrac metric. It presents findings that:
1) A healthy person's gut microbiome composition generally remains stable over periods of 60 days based on samples from multiple body sites.
2) In contrast, for people with C. difficile infections, their gut microbiome composition can abruptly shift to a healthy state within days after a fecal microbiota transplant from a healthy donor.
3) Analysis of one individual's gut microbiome samples over 3.5 years found the composition abruptly shifted between two distinct stable states that correlated with changes in symptoms and weight, before and after a
Machine Learning Opportunities in the Explosion of Personalized Precision Med...Larry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on machine learning opportunities in personalized precision medicine using massive datasets from individuals. Some key points:
- Smarr has tracked over 100 of his own blood biomarkers and microbiome over time, revealing health issues like chronic inflammation.
- Analysis of Smarr's microbiome alongside others revealed major shifts between healthy and disease states that can be classified using machine learning.
- Further analysis of microbial proteins identified which were over or under abundant in disease, helping characterize Smarr's own condition.
- Smarr's microbiome appeared to undergo an abrupt shift between two stable states correlated with a change in symptoms and drug therapy.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Linking Phenotype Changes to Internal/External Longitudinal Time Series in a ...Larry Smarr
This document summarizes Dr. Larry Smarr's presentation on quantifying physiological data from his own body over the past decade. Some key points:
- Smarr has gathered longitudinal time series data on over 200 biomarkers and microbiome samples to study phenotype changes from his autoimmune disease.
- Sensors have tracked daily metrics like weight, activity levels, and symptoms, revealing oscillations and episodes of inflammation.
- Imaging and biomarker analysis identified the specific location and nature of his Crohn's disease.
- Analysis of his microbiome samples over time uncovered a shift in microbial ecology that correlated with changes in drugs and symptoms.
- Expanding this type of personalized, quantitative approach could transform medicine by deeply characterizing individuals
Tracking Immune Biomarkers and the Human Gut Microbiome: Inflammation, Croh...Larry Smarr
Larry Smarr presented on tracking immune biomarkers and the human gut microbiome in relation to inflammation, Crohn's disease, and colon cancer. He turned his own body into a "genomic observatory" by tracking over 100 of his own blood and stool biomarkers and sequencing his gut microbiome multiple times. His research found high levels of inflammation and an abundance of Fusobacteria in his microbiome when inflammation was highest. Following antibiotic and steroid therapy, inflammation and Fusobacteria were greatly reduced. This integrated personal omics approach provides insights into the links between inflammation, gut microbes, and colon cancer risk.
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
The document summarizes a talk given by Dr. Larry Smarr on his research tracking extensive health data on himself over many years. Some key points:
1) Smarr collected over a billion data points defining his body, including DNA sequencing, medical images, and daily biomarkers, revealing episodic inflammation related to his Crohn's disease.
2) Analysis of his gut microbiome via metagenomic sequencing showed many typically abundant bacterial species were severely depleted compared to healthy individuals.
3) Tracking changes over time demonstrated the coupled dynamics of his immune system and gut microbiome in response to therapies, similar to ecological models of invasive species dominating after natives are disturbed.
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 document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
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.
Using Supercomputers and Gene Sequencers to Discover Your Inner MicrobiomeLarry Smarr
This keynote talk discusses research using supercomputers and gene sequencing to study the human microbiome. The human microbiome contains 100 trillion microorganisms and their genes outnumber human genes 300 to 1. The speaker has been collecting data from his own body over 7 years to study his microbiome and immune system interactions. Collaborating researchers have sequenced his gut microbiome over time as well as samples from autoimmune disease patients. Supercomputers are needed to analyze the massive amount of sequencing data and reveal details of microbial ecology and genetics in health and disease. Studying the human microbiome will revolutionize medicine in the next decade.
Quantifying Your Dynamic Human Body (Including Its Microbiome), Will Move Us ...Larry Smarr
Invited Presentation Microbiology and the Microbiome and the Implications for Human Health Analytic, Life Science & Diagnostic Association (ALDA) 2016 Senior Management Conference
Half Moon Bay, CA
October 3, 2016
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.
Interactions of the Immune System with the Gut Microbiome in Inflammatory Bo...Larry Smarr
Larry Smarr presented on his research quantifying interactions between his immune system, gut microbiome, and genetics in relation to his diagnosis of Crohn's disease. Over many years, he collected over 150 biological variables from blood and stool samples, and obtained genomic and metagenomic sequencing. Analysis revealed periods of chronic inflammation correlated with shifts in bacterial abundance and invasive strains. Treatment with antibiotics and immunosuppressants reduced inflammation and allowed rare bacteria to decrease while more beneficial firms increased. The research aims to better understand coupled human-microbiome dynamics and how genetics may predispose individuals to conditions like inflammatory bowel disease.
The Systems Biology Dynamics of the Human Immune System and Gut MicrobiomeLarry Smarr
This document summarizes Dr. Larry Smarr's talk on modeling the human immune system and gut microbiome dynamics. It discusses how the growing diversity of gut bacteria after birth helps train the immune system. In health, constant feedback between the immune system and microbiome leads to homeostasis, but in diseases like Crohn's, this balance fails. The talk demonstrates this dysbiotic state using data from Dr. Smarr's own gut microbiome and biomarkers over five years. It reviews efforts to computationally model this important biological system.
The document summarizes a seminar given by Dr. Larry Smarr on supercomputing the human microbiome. Some key points:
- The human microbiome contains 100 trillion microorganisms and their DNA contains 300 times as many genes as human DNA.
- Dr. Smarr has been collecting extensive data from his own body over 7 years to study his personal microbiome and immune system interactions using high performance computing.
- Analyzing microbiome data requires massive computing resources, such as millions of core hours on supercomputers. This reveals details of microbial ecology and genetics in health and disease.
- Computational analysis of microbiome sequencing data from many subjects shows major shifts in microbial populations between healthy and
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemLarry Smarr
1) Dr. Larry Smarr reported on results from a decade of self-quantification, including longitudinal measurements of his gut microbiome and over 100 biomarkers, to better understand the interactive dynamics of the human-microbiome system in health and disease.
2) Analysis found that Smarr's gut microbiome was unstable with high levels of E. coli, unlike healthy individuals, and computational analysis linked this dysbiosis to chronic inflammation identified in his biomarkers.
3) Smarr underwent robotic colon resection surgery in 2016, and analysis found his gut microbiome changed more dramatically after surgery than from colonoscopy or typical differences between individuals, eventually achieving a healthy post-surgical state.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Recent advances now allow sequencing these microbial genomes and analyzing massive datasets to map the dynamics of the immune-microbial system and its connection to disease states. A key focus is generating high-resolution time series data of the gut microbiome and immune variables from large cohorts to understand how they influence conditions like inflammatory bowel disease. There is potential to design gut microbes as sensors of disease states by programming them to detect specific conditions.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
Exploring the Dynamics of The Microbiome in Health and DiseaseLarry Smarr
Remote Invited Provocateur Lecture
2017 Innovation Lab on Quantitative Approaches to Biomedical Data Science:
Challenges in our Understanding of the Microbiome
San Diego, CA
June 19, 2017
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Larry Smarr
This document summarizes a lecture on inflammation, the gut microbiome, bacteriophages, and the initiation of colorectal cancer. The lecturer discusses his personal experience with Crohn's disease and extensive self-monitoring. Analysis of his microbiome data over time revealed shifts correlated with inflammation levels. Certain bacteria like Fusobacterium nucleatum and E. coli were found at highest levels during peak inflammation. The lecturer's genetic analysis revealed SNPs linked to autoimmune disease that may have predisposed him to Crohn's. The lecture explores the role of the microbiome in mediating inflammation and cancer initiation in the gut.
Individual, Consumer-Driven Care of the Future: Taking Wellness One Step FurtherLarry Smarr
Calit2 Director Larry Smarr gives the closing keynote address to the 2nd annual Learning Conference on Integrated Delivery Systems in San Diego on May 7, 2014.
Measuring the Human Brain-Gut Microbiome-Immune System Dynamics: a Big Data C...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on measuring the human brain-gut microbiome-immune system dynamics and the challenges of analyzing big data related to these systems. It discusses how understanding the interactions between human genetics, behavior, and the human microbiome is important for understanding human health and disease. As an example, it details Dr. Smarr's own research into his Crohn's disease, analyzing his gut microbiome, immune markers, genetics, and symptoms over time. It shows how computational analysis of metagenomic sequencing data from many healthy and IBD patients can reveal differences in microbial ecology and gene families between health and disease states.
Quantifying the Time Progression of a Human Autoimmune Disease using Genome S...Larry Smarr
Larry Smarr has been collecting extensive data on his own health for over 5 years to study his diagnosis of Crohn's disease. Analysis of this data using genome sequencing and supercomputers has demonstrated the episodic evolution of his coupled immune-microbial system. High resolution metagenomic sequencing at JCVI and computational analysis with several CPU-decades of supercomputer time at SDSC has revealed the complex time-varying dynamics of Smarr's microbial ecology, shedding light on the autoimmune disease process. Comparisons to data from healthy individuals and those with IBD from the NIH Human Microbiome Project provide insights into how inflammation can alter the gut microbiome.
Machine Learning in Healthcare by Mehrdad YazdaniData Con LA
Abstract:- Using Machine Learning to Identify Major Shifts in Human Gut MicrobiomeProtein Family Abundance in Disease Inflammatory Bowel Disease (IBD) is an autoimmune condition that is observed to be associated with major alterations in the gut microbiome taxonomic composition. Here we classify major changes in microbiome protein family abundances between healthy subjects and IBD patients. We use machine learning to analyze results obtained previously from computing relative abundance of ~10,000 KEGG orthologous protein families in the gut microbiome of a set of healthy individuals and IBD patients. We develop a machine learning pipeline, involving the Kolomogorv-Smirnov test, to identify the 100 most statistically significant entries in the KEGG database. Then we use these 100 as a training set for a Random Forest classifier to determine ~5% the KEGGs which are best at separating disease and healthy states. Lastly, we developed a Natural Language Processing classifier of the KEGG description files to predict KEGG relative over- or under- abundance. As we expand our analysis from 10,000 KEGG protein families to one million proteins identified in the gut microbiome, scalable methods for quickly identifying such anomalies between health and disease states will be increasingly valuable for biological interpretation of sequence data.
My Remembrances of Mike Norman Over The Last 45 YearsLarry Smarr
Mike Norman has been a leader in computational astrophysics for over 45 years. Some of his influential work includes:
- Cosmic jet simulations in the early 1980s which helped explain phenomena from galactic centers.
- Pioneering the use of adaptive mesh refinement in the 1990s to achieve dynamic load balancing on supercomputers.
- Massive cosmology simulations in the late 2000s with over 100 trillion particles using thousands of processors across multiple supercomputing sites, producing petabytes of data.
- Developing end-to-end workflows in the 2000s to couple supercomputers, high-speed networks, and large visualization systems to enable real-time analysis of extremely large astrophysics simulations.
Metagenics How Do I Quantify My Body and Try to Improve its Health? June 18 2019Larry Smarr
Larry Smarr discusses quantifying his body and health over time through extensive self-tracking. He measures various biomarkers through regular blood tests and analyzes his gut microbiome by sequencing stool samples. This revealed issues like chronic inflammation and an unhealthy microbiome. Smarr then took steps like a restricted eating window and increasing plant diversity in his diet, which reversed metabolic syndrome issues and correlated with shifts in his microbiome ecology. His goal is to continue precisely measuring factors like toxins, hormones, gut permeability and food/supplement impacts to further optimize his health.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in cyberinfrastructure development through regional networks. It provides data showing the importance of MSIs like historically black colleges and universities (HBCUs) in educating underrepresented minority students in STEM fields. Regional networks can help equalize opportunities by assisting MSIs in overcoming barriers to resources through training, networking infrastructure support, and helping institutions obtain necessary staffing and funding. Strategies mentioned include collaborating with MSIs on grants and addressing issues identified in surveys like lack of vision for data use beyond compliance. The goal is to broaden participation in STEAM fields by leveraging the success MSIs have shown in supporting underrepresented students.
Global Network Advancement Group - Next Generation Network-Integrated SystemsLarry Smarr
This document summarizes a presentation on global petascale to exascale workflows for data intensive sciences. It discusses a partnership convened by the GNA-G Data Intensive Sciences Working Group with the mission of meeting challenges faced by data-intensive science programs. Cornerstone concepts that will be demonstrated include integrated network and site resource management, model-driven frameworks for resource orchestration, end-to-end monitoring with machine learning-optimized data transfers, and integrating Qualcomm's GradientGraph with network services to optimize applications and science workflows.
Wireless FasterData and Distributed Open Compute Opportunities and (some) Us...Larry Smarr
This document discusses opportunities for ESnet to support wireless edge computing through developing a strategy around self-guided field laboratories (SGFL). It outlines several potential science use cases that could benefit from wireless and distributed computing capabilities, both in the short term through technologies like 5G, LoRa and Starlink, and longer term through the vision of automated SGFL. The document proposes some initial ideas for deploying and testing wireless edge computing technologies through existing projects to help enable the SGFL vision and further scientific opportunities. It emphasizes that exploring these emerging areas could help drive new science possibilities if done at a reasonable scale.
The Asia Pacific and Korea Research Platforms: An Overview Jeonghoon MoonLarry Smarr
This document provides an overview of Asia Pacific and Korea research platforms. It discusses the Asia Pacific Research Platform working group in APAN, including its objectives to promote HPC ecosystems and engage members. It describes the Asi@Connect project which provides high-capacity internet connectivity for research across Asia-Pacific. It also discusses the Korea Research Platform and efforts to expand it to 25 national research institutes in Korea. New related projects on smart hospitals, agriculture, and environment are mentioned. The conclusion discusses enhancing APAN and the Korea Research Platform and expanding into new areas like disaster and AI education.
Panel: Reaching More Minority Serving InstitutionsLarry Smarr
This document discusses engaging more minority serving institutions (MSIs) in the National Research Platform (NRP). It provides data showing that MSIs serve a disproportionate number of underrepresented minority students and are important producers of STEM graduates from these groups. The NRP can help broaden participation in STEAM fields by providing MSIs access to advanced cyberinfrastructure resources, new learning modalities, and opportunities for collaborative research between MSIs and other institutions. Regional networks also have a role to play in helping MSIs overcome barriers and attracting them to collaborative grants. The goal is to tear down walls between research and teaching and reinvent the university experience for more inclusive learning and innovation.
Panel: The Global Research Platform: An OverviewLarry Smarr
The document provides an overview of the Global Research Platform (GRP), an international collaborative partnership creating a distributed environment for data-intensive global science. The GRP facilitates high-performance data gathering, analytics, transport up to terabits per second, computing, and storage to support large-scale global science cyberinfrastructure ecosystems. It aims to orchestrate research across multiple domains using international testbeds for investigating new technologies related to data-intensive science. Examples of instruments generating exabytes of data that would benefit include the Korea Superconducting Tokamak, the High Luminosity LHC, genomics, the SKA radio telescope, and the Vera Rubin Observatory.
Panel: Future Wireless Extensions of Regional Optical NetworksLarry Smarr
CENIC is a non-profit organization that operates an 8,000+ mile fiber optic network connecting over 12,000 sites across California, including K-12 schools, universities, libraries, and research organizations. It has over 750 private sector partners and contributes over $100 million annually to the California economy. CENIC's network enables research and education collaborations, innovation, and economic growth statewide. It also operates a wireless research network called PRP that connects wireless sensors to supercomputers, supporting applications like wildfire modeling.
Global Research Platform Workshops - Maxine BrownLarry Smarr
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EPOC and NetSage provide engagement and network monitoring services to support research and education. NetSage collects anonymized network flow data to help understand traffic patterns and troubleshoot performance issues. It provides dashboards and analysis to answer common questions from network engineers and end users. Examples of NetSage deployments and use cases were shown for the CENIC network, including top sources and destinations of traffic, debugging slow flows, and analyzing international traffic patterns by country over time.
The document discusses accelerating science discovery with AI inference-as-a-service. It describes showcases using this approach for high energy physics and gravitational wave experiments. It outlines the vision of the A3D3 institute to unite domain scientists, computer scientists, and engineers to achieve real-time AI and transform science. Examples are provided of using AI inference-as-a-service to accelerate workflows for CMS, ProtoDUNE, LIGO, and other experiments.
Democratizing Science through Cyberinfrastructure - Manish ParasharLarry Smarr
This document summarizes a presentation by Manish Parashar on democratizing science through cyberinfrastructure. The key points are:
1) Broad, fair, and equitable access to advanced cyberinfrastructure is essential for democratizing 21st century science, but there are significant barriers related to knowledge, technical issues, social factors, and balancing capabilities.
2) An advanced cyberinfrastructure ecosystem for all requires integrated portals, access to local and national resources through high-speed networks, diverse allocation modes, embedded expertise networks, and broad training.
3) Realizing this vision will require a scalable federated ecosystem with diverse capabilities and incentives for partnerships to meet growing needs for cyberinfrastructure and
Panel: Building the NRP Ecosystem with the Regional Networks on their Campuses;Larry Smarr
This document summarizes a panel discussion on building the National Research Platform ecosystem with regional networks. The panelists discussed how their regional networks are connecting to and using the Nautilus nodes of the NRP. Examples included using NRP for deep learning and computer vision research at the University of Missouri, challenges of adoption in Nevada and potential solutions, and Georgia Tech's new involvement through the Southern Crossroads regional network. The regional networks see opportunities to expand NRP access and training to enable more researchers in their regions to take advantage of the platform.
Open Force Field: Scavenging pre-emptible CPU hours* in the age of COVID - Je...Larry Smarr
The document discusses Open Force Field (OpenFF), an open-source project that enables rapid development of molecular force fields through automated infrastructure, open data and software, and an open science approach. OpenFF provides access to large quantum chemical datasets, runs quantum chemistry calculations on pre-emptible cloud resources with minimal human intervention, and facilitates easy iteration and testing of new force field hypotheses through an open development model.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
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Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires services like CloudBank and Kubernetes federation.
Panel: Open Infrastructure for an Open Society: OSG, Commercial Clouds, and B...Larry Smarr
The document discusses open infrastructure for an open society and the role of commercial clouds. It describes how the National Research Platform (NRP), Open Science Grid (OSG), and Open Science Data Federation (OSDF) provide open infrastructure through open source components that anyone can contribute to and use. It then discusses how Southwestern Oklahoma State University leveraged NRP resources on their campus and engaged students and local teachers. Finally, it outlines the pros and cons of commercial clouds, noting they provide huge capacity and variety but are very expensive for regular use. Facilitating science users on clouds requires tools for account management, documentation, and integrating cloud resources through HTCondor and Kubernetes.
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Here is the updated list of Top Best Ayurvedic medicine for Gas and Indigestion and those are Gas-O-Go Syp for Dyspepsia | Lavizyme Syrup for Acidity | Yumzyme Hepatoprotective Capsules etc
Osteoporosis - Definition , Evaluation and Management .pdfJim Jacob Roy
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share - Lions, tigers, AI and health misinformation, oh my!.pptxTina Purnat
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Basavarajeeyam is a Sreshta Sangraha grantha (Compiled book ), written by Neelkanta kotturu Basavaraja Virachita. It contains 25 Prakaranas, First 24 Chapters related to Rogas& 25th to Rasadravyas.
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Histololgy of Female Reproductive System.pptxAyeshaZaid1
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Rasamanikya is a excellent preparation in the field of Rasashastra, it is used in various Kushtha Roga, Shwasa, Vicharchika, Bhagandara, Vatarakta, and Phiranga Roga. In this article Preparation& Comparative analytical profile for both Formulationon i.e Rasamanikya prepared by Kushmanda swarasa & Churnodhaka Shodita Haratala. The study aims to provide insights into the comparative efficacy and analytical aspects of these formulations for enhanced therapeutic outcomes.
ABDOMINAL TRAUMA in pediatrics part one.drhasanrajab
Abdominal trauma in pediatrics refers to injuries or damage to the abdominal organs in children. It can occur due to various causes such as falls, motor vehicle accidents, sports-related injuries, and physical abuse. Children are more vulnerable to abdominal trauma due to their unique anatomical and physiological characteristics. Signs and symptoms include abdominal pain, tenderness, distension, vomiting, and signs of shock. Diagnosis involves physical examination, imaging studies, and laboratory tests. Management depends on the severity and may involve conservative treatment or surgical intervention. Prevention is crucial in reducing the incidence of abdominal trauma in children.
Recomendações da OMS sobre cuidados maternos e neonatais para uma experiência pós-natal positiva.
Em consonância com os ODS – Objetivos do Desenvolvimento Sustentável e a Estratégia Global para a Saúde das Mulheres, Crianças e Adolescentes, e aplicando uma abordagem baseada nos direitos humanos, os esforços de cuidados pós-natais devem expandir-se para além da cobertura e da simples sobrevivência, de modo a incluir cuidados de qualidade.
Estas diretrizes visam melhorar a qualidade dos cuidados pós-natais essenciais e de rotina prestados às mulheres e aos recém-nascidos, com o objetivo final de melhorar a saúde e o bem-estar materno e neonatal.
Uma “experiência pós-natal positiva” é um resultado importante para todas as mulheres que dão à luz e para os seus recém-nascidos, estabelecendo as bases para a melhoria da saúde e do bem-estar a curto e longo prazo. Uma experiência pós-natal positiva é definida como aquela em que as mulheres, pessoas que gestam, os recém-nascidos, os casais, os pais, os cuidadores e as famílias recebem informação consistente, garantia e apoio de profissionais de saúde motivados; e onde um sistema de saúde flexível e com recursos reconheça as necessidades das mulheres e dos bebês e respeite o seu contexto cultural.
Estas diretrizes consolidadas apresentam algumas recomendações novas e já bem fundamentadas sobre cuidados pós-natais de rotina para mulheres e neonatos que recebem cuidados no pós-parto em unidades de saúde ou na comunidade, independentemente dos recursos disponíveis.
É fornecido um conjunto abrangente de recomendações para cuidados durante o período puerperal, com ênfase nos cuidados essenciais que todas as mulheres e recém-nascidos devem receber, e com a devida atenção à qualidade dos cuidados; isto é, a entrega e a experiência do cuidado recebido. Estas diretrizes atualizam e ampliam as recomendações da OMS de 2014 sobre cuidados pós-natais da mãe e do recém-nascido e complementam as atuais diretrizes da OMS sobre a gestão de complicações pós-natais.
O estabelecimento da amamentação e o manejo das principais intercorrências é contemplada.
Recomendamos muito.
Vamos discutir essas recomendações no nosso curso de pós-graduação em Aleitamento no Instituto Ciclos.
Esta publicação só está disponível em inglês até o momento.
Prof. Marcus Renato de Carvalho
www.agostodourado.com
Novas diretrizes da OMS para os cuidados perinatais de mais qualidade
Quantifying the Time Progression of the Interaction of the Human Immune System with the Gut Microbiome
1. “Quantifying the Time Progression of
the Interaction of the Human Immune System
with the Gut Microbiome”
Research Council Presentation
UC San Diego Health Sciences
March 5, 2014
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information Technology
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
Jacobs School of Engineering, UCSD
http://lsmarr.calit2.net 1
2. Visualizing Time Series of
150 LS Blood and Stool Variables, Each Over 5-10 Years
Calit2 64 megapixel VROOM
3. Only One of My Blood Measurements
Was Far Out of Range--Indicating Chronic Inflammation
Normal Range
<1 mg/L
Normal
27x Upper Limit
Episodic Peaks in Inflammation
Followed by Spontaneous Drops
Complex Reactive Protein (CRP) is a Blood Biomarker
for Detecting Presence of Inflammation
Antibiotics
Antibiotics
4. Adding Stool Tests Revealed
Oscillatory Behavior in an Immune Variable
Normal Range
<7.3 µg/mL
124x Upper Limit
Lactoferrin is a Protein Shed from Neutrophils -
An Antibacterial that Sequesters Iron
Typical
Lactoferrin
Value for
Active
IBD
Hypothesis: Lactoferrin Oscillations
Coupled to Relative Abundance
of Microbes that Require Iron
6. Confirming the Colonic Crohn’s Hypothesis:
Finding the “Smoking Gun” with MRI Imaging
“Long segment wall thickening in the proximal
and mid portions of the sigmoid colon,
extending over a segment of ~16 cm,
with suggestion of intramural sinus tracts.
Edema in the sigmoid mesentery
and engorgement of the regional vasa recta.”
– MRI report, Cynthia Santillan, M.D. UCSD
Jan 2012
Clinical MRI Slice Program
Crohn's disease
affects the thickness
of the intestinal wall.
Having Crohn's disease
that affects your colon
increases your risk
of colon cancer.
Reveals Inflammation in 6 Inches of Sigmoid Colon
Thickness 15cm – 5x Normal Thickness
7. To Map Out the Dynamics of My Microbiome Ecology
I Partnered with the J. Craig Venter Institute
• JCVI Did Metagenomic
Sequencing on Six of My
Stool Samples Over 1.5 Years
• Sequencing on
Illumina HiSeq 2000
– Generates 100bp Reads
– Run Takes ~14 Days
– My 6 Samples Produced
– 190.2 Gbp of Data
• JCVI Lab Manager,
Genomic Medicine
– Manolito Torralba
• IRB PI Karen Nelson
– President JCVI
Illumina HiSeq 2000 at JCVI
Manolito Torralba, JCVI Karen Nelson, JCVI
8. We Downloaded Additional Phenotypes
from NIH HMP For Comparative Analysis
5 Ileal Crohn’s Patients,
3 Points in Time
2 Ulcerative Colitis Patients,
6 Points in Time
“Healthy” Individuals
Download Raw Reads
~100M Per Person
Source: Jerry Sheehan, Calit2
Weizhong Li, Sitao Wu, CRBS, UCSD
Total of 5 Billion Reads
IBD Patients
35 Subjects
1 Point in Time
Larry Smarr
6 Points in Time
9. We Created a Reference Database
Of Known Gut Genomes
• NCBI April 2013
– 2471 Complete + 5543 Draft Bacteria & Archaea Genomes
– 2399 Complete Virus Genomes
– 26 Complete Fungi Genomes
– 309 HMP Eukaryote Reference Genomes
• Total 10,741 genomes, ~30 GB of sequences
Now to Align Our 5 Billion Reads
Against the Reference Database
Source: Weizhong Li, Sitao Wu, CRBS, UCSD
11. We Used SDSC’s Gordon Data-Intensive Supercomputer
to Analyze a Wide Range of Gut Microbiomes
• ~180,000 Core-Hrs on Gordon
– KEGG function annotation: 90,000 hrs
– Mapping: 36,000 hrs
– Used 16 Cores/Node
and up to 50 nodes
– Duplicates removal: 18,000 hrs
– Assembly: 18,000 hrs
– Other: 18,000 hrs
• Gordon RAM Required
– 64GB RAM for Reference DB
– 192GB RAM for Assembly
• Gordon Disk Required
– Ultra-Fast Disk Holds Ref DB for All Nodes
– 8TB for All Subjects
Enabled by
a Grant of Time
on Gordon from SDSC
Director Mike Norman
12. We Recently Used Dell’s Supercomputer to Analyze
An Additional 219 HMP and 110 MetaHIT Samples
• Dell’s Sanger cluster
– 32 nodes, 512 cores,
– 48GB RAM per node
– 50GB SSD local drive, 390TB Lustre file system
• We used faster but less sensitive method with
a smaller reference DB (duo to available 48GB
RAM)
• Only processed to taxonomy mapping
– ~35,000 Core-Hrs on Dell’s Sanger
– 30 TB data
Source: Weizhong Li, UCSD
13. Using Scalable Visualization Allows Comparison of
the Relative Abundance of 200 Microbe Species
Calit2 VROOM-FuturePatient Expedition
Comparing 3 LS Time Snapshots (Left)
with Healthy, Crohn’s, UC (Right Top to Bottom)
14. Lessons From Ecological Dynamics:
Invasive Species Dominate After Major Species Destroyed
”In many areas following these burns
invasive species are able to establish themselves,
crowding out native species.”
Source: Ponderosa Pine Fire Ecology
http://cpluhna.nau.edu/Biota/ponderosafire.htm
15. Almost All Abundant Species (≥1%) in Healthy Subjects
Are Severely Depleted in Larry’s Gut Microbiome
16. Top 20 Most Abundant Microbial Species
In LS vs. Average Healthy Subject
152x
765x
148x
849x
483x
220x
201x
522x
169x
Number Above
LS Blue Bar is Multiple
of LS Abundance
Compared to Average
Healthy Abundance
Per Species
Source: Sequencing JCVI; Analysis Weizhong Li, UCSD
LS December 28, 2011 Stool Sample
17. Comparing Changes in Gut Microbiome Ecology with
Oscillations of the Innate and Adaptive Immune System
Normal
Innate Immune System
Normal
Adaptive Immune System
Time Points of
Metagenomic
Sequencing
of LS Stool Samples
Therapy: 1 Month Antibiotics
+2 Month Prednisone
LS Data from Yourfuturehealth.com
Lysozyme
& SIgA
From Stool
Tests
18. Time Series Reveals Autoimmune Dynamics
of Gut Microbiome by Phyla
Therapy
Six Metagenomic Time Samples Over 16 Months
19. “Arthur et al. provide evidence that inflammation
alters the intestinal microbiota
by favouring the proliferation of genotoxic commensals,
and that the Escherichia coli
genotoxin colibactin promotes colorectal cancer (CRC).”
Christina Tobin Kåhrström
Associate Editor,
Nature Reviews Microbiology
20. E. coli/Shigella Phylogenetic Tree
Miquel, et al.
PLOS ONE, v. 5, p. 1-16 (2010)
Does Intestinal Inflammation Select for
Pathogenic Strains That Can Induce Further Damage?
“Adherent-invasive E. coli (AIEC)
are isolated more commonly
from the intestinal mucosa of
individuals with Crohn’s disease
than from healthy controls.”
“Thus, the mechanisms
leading to dysbiosis might also
select for intestinal colonization
with more harmful members of the
Enterobacteriaceae*
—such as AIEC—
thereby exacerbating inflammation
and interfering with its resolution.”
Sebastian E. Winter , et al.,
EMBO reports VOL 14, p. 319-327 (2013) *Family Containing E. coli
AIEC LF82
21. Chronic Inflammation Can Accumulate
Cancer-Causing Bacteria in the Human Gut
Escherichia coli Strain NC101
22. Phylogenetic Tree
778 Ecoli strains
=6x our 2012 Set
D
A
B1
B2
E
S
Deep Metagenomic
Sequencing
Enables
Strain Analysis
23. We Divided the 778 E. coli Strains into 40 Groups,
Each of Which Had 80% Identical Genes
LS00
1
LS00
2
LS00
3
Median
CD
Median
UC
Median
HE
Group 0: D
Group 2: E
Group 3: A, B1
Group 4: B1
Group 5: B2
Group 7: B2
Group 9: S
Group 18,19,20: S
Group 26: B2
LF82NC101
24. Reduction in E. coli Over Time
With Major Shifts in Strain Abundance
Strains >0.5% Included
Therapy
25. Thanks to Our Great Team!
UCSD Metagenomics Team
Weizhong Li
Sitao Wu
Calit2@UCSD
Future Patient Team
Jerry Sheehan
Tom DeFanti
Kevin Patrick
Jurgen Schulze
Andrew Prudhomme
Philip Weber
Fred Raab
Joe Keefe
Ernesto Ramirez
JCVI Team
Karen Nelson
Shibu Yooseph
Manolito Torralba
SDSC Team
Michael Norman
Mahidhar Tatineni
Robert Sinkovits
UCSD Health Sciences Team
William J. Sandborn
Elisabeth Evans
John Chang
Brigid Boland
David Brenner