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Specific Microbiome projects

American Gut Project

American Gut Project

American Gut is a project in which scientists aim to work with non-scientists both to help them (AKA, you) understand the life inside their own guts and to do science. Science is coolest when it informs our daily lives and what could possibly be more daily than what goes on in your gut? One of the big questions the American Gut scientists hope to figure out is what characterizes healthy and sick guts (or even just healthier and sicker guts) and how one might move from the latter to the former. Such is the sort of big lofty goals these scientists dream about at night (spirochetes rather than sugarplums dancing through their heads), but even the more ordinary goals are exciting. Even just beginning to know how many and which species live in our guts will be exciting, particularly since most of these species have never been studied, which is to say there are almost certainly new species inside you, though until you sample yourself (and all the steps that it takes to look at a sample happen— the robots, the swirling, the head scratching, the organizing of massive datasets), we won’t know which ones. Not many people get to go to the rainforest to search for, much less discover, a new kind of monkey, but a new kind of bacterium, well, it is within (your toilet paper’s) reach.


 

Human Oral Microbiome Database (HOMD)

Human Oral Microbiome Database (HOMD)

The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with comprehensive information o­n the approximately 700 prokaryote species that are present in the human oral cavity. Approximately 54% are officially named, 14% unnamed (but cultivated) and 32% are known o­nly as uncultivated phylotypes. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference scheme. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Genome sequences for oral bacteria determined as part of this project, the Human Microbiome Project, and other sequencing projects are being added to the HOMD as they become available. Genomes for 400 oral taxa (58% of taxa o­n HOMD) are currently available o­n HOMD. The HOMD site offers easy to use tools for viewing all publically available oral bacterial genomes.


 

CardioBiome

CardioBiome

The Project CardioBiome is focused in developing a bioinformatics platform integrated with the Electronic Health Record for human microbiome analysis. AMI (Acute Myocardial Infarction) will be taken as a proof of concept.

The ministry of Industry through their Agency CDTI has granted $1 M to the consortium CardioBiome in which Era7 Bioinformatics has the task of developing a cloud based bioinformatics platform for the analysis of 16S data from human microbiomes and for facilitating the integration with EHR (Electronic Health Record) following standards like HL7, FHIR and SMART.

The Project will be focused on Acute Myocardial Infarction as proof of concept and more than 4000 samples from patients will be sequenced. The general interest in getting genomics data integrated with health care pipelines and EHR should be complemented with the integration of 16S metagenomics results since these results will be very important as useful biomarkers for prevention, diagnosis and follow-up of many diseases.


 

JCVI Human Microbiome Studies (HMS)

JCVI Human Microbiome Studies (HMS)

You can find here some information about the J. Craig Venter Institute specific projects. This is the Overview about them taken from JCVI website:

As a leading genomics research organization, the J. Craig Venter Institute has numerous projects and programs that are focused on this emerging research area to identify and characterize the human microbiome — the microbial populations that natively inhabit the human body — and to determine its role in health and disease. JCVI led the foray into this field with a seminal publication in 2006 and has since developed many active areas of research with various clinical sites. Here we outline these projects which investigate the relationship between human health and disease and how this correlates with changes in the human microbiome.  


 

MetaSUB: Metagenomics & Metadesign of Subways & Urban Biomes

MetaSUB: Metagenomics & Metadesign of Subways & Urban Biomes

Building a Molecular Portrait of Cities

Subway surfaces define the daily commute for billions of people each year, and yet there is almost nothing known about the impact of surface type, season, commuter type, or subway design on their commute. We aim to bring a molecular view of the cities to improve their design, use, and impact on health.


 

The Microbiome Quality Control project (MBQC)

The human microbiome has the potential to become one of the most important new tools for personalized health and precision medicine. In order to transition from a basic research environment to the clinic, technologies and computational methods for assessing human-associated microbial communities must be standardized and quality controlled. Inspired by progress in related areas such as the gene expression microarray (MAQC), the MBQC is a collaborative effort to comprehensively evaluate methods for measuring the human microbiome. This includes tools for sampling human-associated microbes at different body sites, techniques and protocols for handling human microbiome samples, and computational pipelines for microbiome data processing.

Variables evaluated during the MBQC-base:

  • Samples
  • Handling:
    • Extraction
    • 16S amplification
    • Sequencing
  • Bioinformatics

More information about the MBQC project:


 

Gut microbiota for health

Gut microbiota for health

Launched in 2012 by the Gut Microbiota and Health section of the European Society for Neurogastroenterology and Motility (ESNM), the “Gut Microbiota for Health” platform’s mission is to share knowledge and promote debate regarding gut microbiota. Our goal is to raise awareness of and interest in the gut’s bacterial community and its importance for our health and quality of life both among the scientific and medical community and society in general.


 

NASA: Study of the Impact of Long-Term Space Travel on the Astronauts' Microbiome (Microbiome) - 07.14.16

NASA: Study of the Impact of Long-Term Space Travel on the Astronauts' Microbiome (Microbiome) - 07.14.16

You can see here information about this research project of NASA with the goal of analyzing the changes in human immune system and microbiome during space travels.

International Space Station Science for Everyone

Science Objectives for Everyone

The Microbiome experiment investigates the impact of space travel on both the human immune system and an individual’s microbiome (the collection of microbes that live in and on the human body at any given time). To monitor the status of the crewmembers' microbiome and immune system and their interaction with the unique environment of the International Space Station (ISS), we will take periodic samples from different parts of the body and the surrounding ISS environment. As part of this study, the likelihood and consequences of alterations in the microbiome due to extreme environments, and the related human health risk, will be assessed.


 

The Michigan Microbiome Project

The Michigan Microbiome Project

The Michigan Microbiome Project (MMP) was recently initiated by faculty members of multiple departments in the Medical School at the University of Michigan. It’s mission is to elucidate principles underlying the structure, functions and dynamics of the human microbiome. The goal is to manage microbiomes for the benefit of human health. These objectives will be met by both observational and interventional studies in several human cohorts.

Measuring body fat

One part of the MMP is introducing microbiome analysis into the ongoing Weight Management Program in the Department of Internal Medicine: Metabolism, Endocrinology & Diabetes.

In this project, we will look for correlations between the composition of the gut microbial community, metabolites generated by these microbes, and phenotypic characteristics of the hosts that are already being measured. We will also study the effects of dietary supplements that stimulate certain microbes on weight management and other health outcomes.


 

Coral Microbiome Portal

Coral Microbiome Portal

The Coral Microbiome Portal (CMP) database brings together next generation sequencing data of coral-associate microorganisms from studies conducted thoughout the world’s reefs, with the goal of enhancing knowledge and advancing understanding of coral-microbial relationships.

The data are hosted on the CMP portal on the Marine Biological Laboratory’s VAMPS (The Visualization and Analysis of Microbial Population Structures) website, and are accessible for download, analysis, and visualization by anyone with a web browser.

https://vamps.mbl.edu/portals/coral_microbe/coral.php

 


 

The Seagrass Microbiome Project!

Seagrasses are unique in being the only kinds of flowering plants that live entirely in a marine environment.  Seagrass meadows are of great scientific and practical interest for many reasons. For example, they provide foraging and nursery habitat for many marine species, including sea turtles, fish, diverse invertebrates, and epiphytic algae (e.g.,Harbone et al. 2006). They also serve important roles in nutrient cycling in the ocean (Touchette & Burkholder 2000a, Touchette & Burkholder 2000b) and as a physical anchoring system that protects the coastline from the erosive kinetic energy of waves and tides (Christianen et al. 2013). Many seagrass based ecosystems are under severe threats globally (Orth et al. 2006; Waycott et al. 2009) due to factors such as global climate change, pollution, human encroachment, and invasion of exotic species.

The Seagrass Microbiome Project is collaboration among Jonathan Eisen and Jay Stachowicz at the University of  California, Davis and Jessica Green at the University of Oregon, with funding from the Gordon and Betty Moore Foundation.


 

Shedd Aquarium Microbiome Project

Shedd Aquarium Microbiome Project

The Shedd Aquarium Microbiome Project is the world’s first comprehensive look at microbiomes in a controlled aquarium ecosystem and how they influence complex environmental conditions and animal health.

Shedd Aquarium along with Argonne National Laboratory, the University of Illinois, Illinois Institute of Technology and the United States Department of Agriculture started this project to explore the unique relationships between the countless unseen living organisms that share our exhibit environments with the animals that live there. 

 


 

The Brazilian Microbiome Project (BMP)

The Brazilian Microbiome Project (BMP)

 

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known.  Our goal is to co-ordinate and standardize these, together with future projects. There is no prioritization of specifics taxonomic groups.

 


 

The Home Microbiome Study

The Home Microbiome Study

Most of us are aware of the bacteria on the surfaces we come in contact with. The doorknob for the bathroom, coins and paper currency in our pockets, handrails in subway cars, computer keyboards and mice at the library… the list of built environments on which microbes thrive is nearly endless

 


 

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