Difference between revisions of "Monmouth Microbiome Initiative"
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'''''"Today (May 13, 2016), the White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, is announcing the National Microbiome Initiative (NMI). The NMI aims to advance understanding of microbiomes in order to aid in the development of useful applications in areas such as health care, food production, and environmental restoration."''''' | '''''"Today (May 13, 2016), the White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, is announcing the National Microbiome Initiative (NMI). The NMI aims to advance understanding of microbiomes in order to aid in the development of useful applications in areas such as health care, food production, and environmental restoration."''''' | ||
| − | Taken from https://www.whitehouse.gov/blog/2016/05/13/announcing-national-microbiome-initiative | + | :Taken from https://www.whitehouse.gov/blog/2016/05/13/announcing-national-microbiome-initiative |
| + | ::http://cen.acs.org/articles/94/web/2016/05/White-House-announces-microbiome-initiative.html | ||
| − | + | Seminal articles of interest: | |
| − | [[: | + | [[:Media:507.full.pdf|A unified initiative to harness Earth’s microbiomes (2015)]] |
| − | ::''Despite their centrality to life on Earth, we know little about how microbes (''Viruses, bacteria, archaea, microscopic fungi, and protists'') interact with each other, their hosts, or their environment. Although DNA sequencing technologies have enabled a new view of the ubiquity and diversity of microorganisms, this has mainly yielded snapshots that shed limited light on microbial functions or community dynamics. Given that nearly every habitat and organism hosts a diverse constellation of microorganisms—its “microbiome”— such knowledge could transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more (see the photo). We propose an interdisciplinary Unified Microbiome Initiative (UMI) to discover and | + | ::''Despite their centrality to life on Earth, we know little about how microbes (''Viruses, bacteria, archaea, microscopic fungi, and protists'') interact with each other, their hosts, or their environment. Although DNA sequencing technologies have enabled a new view of the ubiquity and diversity of microorganisms, this has mainly yielded snapshots that shed limited light on microbial functions or community dynamics. Given that nearly every habitat and organism hosts a diverse constellation of microorganisms—its “microbiome”— such knowledge could transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more (see the photo). We propose an interdisciplinary Unified Microbiome Initiative (UMI) to discover and advance tools to understand and harness the capabilities of Earth’s microbial ecosystems.'' |
| − | advance tools to understand and harness the capabilities of Earth’s microbial ecosystems.'' | ||
::http://science.sciencemag.org/content/350/6260/507 | ::http://science.sciencemag.org/content/350/6260/507 | ||
| − | + | [[:Media:1915.full.pdf|Host-Bacterial Mutualism in the Human Intestine (2005, Highly cited)]] | |
| − | |||
| − | [[: | ||
::''The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.'' | ::''The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.'' | ||
==Proposed Monmouth College involvement== | ==Proposed Monmouth College involvement== | ||
| − | :1) Biochemistry Research (Sturgeon/Moore | + | :1) Biochemistry Research (Sturgeon/Moore) |
::[[hollow_fiber_system|The Hollow Fiber System]] | ::[[hollow_fiber_system|The Hollow Fiber System]] | ||
::''[[Microbial_Biotransformation_of_Endogenous_and_Exogenous_Biomolecules|Microbial Biotransformation of Endogenous and Exogenous Biomolecules'']] (Sturgeon/Kieft Summer Research 2016) | ::''[[Microbial_Biotransformation_of_Endogenous_and_Exogenous_Biomolecules|Microbial Biotransformation of Endogenous and Exogenous Biomolecules'']] (Sturgeon/Kieft Summer Research 2016) | ||
| Line 30: | Line 28: | ||
==Education== | ==Education== | ||
| + | :[[Introduction_to_Bacterial_genomes|Introduction to Bacterial genomes]] | ||
| + | :[https://www.futurelearn.com/courses/the-human-microbiome Future Learn: The Human Microbiome] | ||
| + | :[https://www.coursera.org/learn/microbiome Corsera: Gut Check] | ||
| + | :[https://www.classcentral.com/course/edx-how-to-analyze-a-microbiome-21572 EdX: How to analyze a microbiome] | ||
| + | :[https://www.pbs.org/video/nova-wonders-whats-living-in-you-fnbfuy/ NOVA Wonders What's Living in You?] | ||
| + | ==Processing Data== | ||
| − | |||
| − | :[https:// | + | ====unconfirmed==== |
| + | :[https://docs.qiime2.org/2022.2/ Qiime 2] <--pronounced "chime" | ||
| + | ::[https://docs.qiime2.org/2021.4/install/native/ installation - MAC] | ||
| + | :::''(Note: Qiime is a UNIX based application which means it runs natively on Linux and MAC computer; PC need to install an emulator] | ||
| + | ::[https://view.qiime2.org/ Qiime 2 View] | ||
| + | |||
| + | [[Data Processing/Data]] | ||
| + | |||
| + | ==Protocols== | ||
| + | :[[Media:Naqib2018.pdf|Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol]] | ||
| + | :[[Media:fmicb-12-637526.pdf|Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities]] | ||
| + | :[[Media:16s-metagenomic-library-prep-guide-15044223-b.pdf|16S Metagenomic Sequencing Library: Preparation Preparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System]] | ||
==[https://microsetta.ucsd.edu/american-gut-project/ American Gut Project]== | ==[https://microsetta.ucsd.edu/american-gut-project/ American Gut Project]== | ||
| Line 46: | Line 60: | ||
===Researchers=== | ===Researchers=== | ||
| − | [https://youtu.be/i-icXZ2tMRM Rob Knight Ted Talk] | + | :[https://youtu.be/i-icXZ2tMRM Rob Knight, University of California San Diego; Ted Talk] |
| + | :[https://www.sheddaquarium.org/about-shedd/leadership/animal-experts/frank-oliaro Frank Oliaro - Shedd Aquarium] | ||
| + | :[https://gilbertlab.com/ Jack Gilbert, Argonne National Laboratory] | ||
===AGP Publications=== | ===AGP Publications=== | ||
| − | [[Media:2018-McDonald.pdf|American Gut: an Open Platform for Citizen Science Microbiome Research, mSystems (2018), 3(3)]] | + | :[[Media:2018-McDonald.pdf|American Gut: an Open Platform for Citizen Science Microbiome Research, mSystems (2018), 3(3)]] |
| + | |||
| + | ==Health References== | ||
| + | *[[:File:The Human Intestinal Microbiome in Health and Disease.pdf]] | ||
| + | *[[:File:Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization.pdf]] | ||
| + | *[[:File:Ghrelin.pdf]] | ||
| + | *[[:File:NAture_energy.pdf]] | ||
| + | *[[:File:pbio.1002533.pdf]] | ||
| + | *[[:File:pnas.1909224116.pdf]] | ||
| + | *[[:File:The gut microbiome in neurological disorders.pdf]] | ||
| + | |||
===Other Videos=== | ===Other Videos=== | ||
| − | [https://youtu.be/IDqMB6C1uys Microbiome: Gut Bugs and You | Warren Peters] | + | :[https://youtu.be/IDqMB6C1uys Microbiome: Gut Bugs and You | Warren Peters] |
| + | |||
| + | ==[https://www.sheddaquarium.org/care-and-conservation/shedd-research/shedd-aquarium-microbiome-project Shedd Aquarium Microbiome Project]== | ||
| + | :[https://youtu.be/ny74u2RGgyg Aquarium Microbiome Project] | ||
| + | |||
| + | ==[https://www.mypsomagen.com Psomagen]== | ||
==Food Related Projects== | ==Food Related Projects== | ||
===Sour Dough Starter/Bread=== | ===Sour Dough Starter/Bread=== | ||
| − | [http://robdunnlab.com/projects/wildsourdough/#makeastarter Sour Dough Project - NC State] | + | :[http://robdunnlab.com/projects/wildsourdough/#makeastarter Sour Dough Project - NC State] |
===Vegetable List=== | ===Vegetable List=== | ||
| − | [https://en.wikipedia.org/wiki/List_of_vegetables Vegetable List (Wikipedia)] | + | :[https://en.wikipedia.org/wiki/List_of_vegetables Vegetable List (Wikipedia)] |
| − | [[:File:nut1391685.pdf|Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet (cited 97 times, June 2021)]] | + | |
| + | :[[:File:nut1391685.pdf|Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet (cited 97 times, June 2021)]] | ||
====Most Common==== | ====Most Common==== | ||
| + | |||
| + | ===Sauerkraut - Sandor Katz=== | ||
| + | :[[Sauerkraut_Katz|Video Series: Fermentation Workshop]] | ||
| + | |||
| + | ===[https://www.netflix.com/title/80170368 Ugly Delicious]=== | ||
Latest revision as of 15:04, 7 July 2022
"Today (May 13, 2016), the White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, is announcing the National Microbiome Initiative (NMI). The NMI aims to advance understanding of microbiomes in order to aid in the development of useful applications in areas such as health care, food production, and environmental restoration."
Seminal articles of interest:
A unified initiative to harness Earth’s microbiomes (2015)
- Despite their centrality to life on Earth, we know little about how microbes (Viruses, bacteria, archaea, microscopic fungi, and protists) interact with each other, their hosts, or their environment. Although DNA sequencing technologies have enabled a new view of the ubiquity and diversity of microorganisms, this has mainly yielded snapshots that shed limited light on microbial functions or community dynamics. Given that nearly every habitat and organism hosts a diverse constellation of microorganisms—its “microbiome”— such knowledge could transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more (see the photo). We propose an interdisciplinary Unified Microbiome Initiative (UMI) to discover and advance tools to understand and harness the capabilities of Earth’s microbial ecosystems.
- http://science.sciencemag.org/content/350/6260/507
Host-Bacterial Mutualism in the Human Intestine (2005, Highly cited)
- The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.
Proposed Monmouth College involvement
- 1) Biochemistry Research (Sturgeon/Moore)
- The Hollow Fiber System
- Microbial Biotransformation of Endogenous and Exogenous Biomolecules (Sturgeon/Kieft Summer Research 2016)
- 2) Wellness (J. Braun)
- 3) Modeling (Fasano/M. Sostarecz)
- 4) Educational Garden/Raw Food/Soil (Watson/Engstrom)
- Can we track, then model microbe spread through the "fields" (ex. blueberries, raspberries, strawberries, veggie plots)
Goal: Submit an NSF proposal to fund on-campus research activities.
Education
- Introduction to Bacterial genomes
- Future Learn: The Human Microbiome
- Corsera: Gut Check
- EdX: How to analyze a microbiome
- NOVA Wonders What's Living in You?
Processing Data
unconfirmed
- Qiime 2 <--pronounced "chime"
- installation - MAC
- (Note: Qiime is a UNIX based application which means it runs natively on Linux and MAC computer; PC need to install an emulator]
- Qiime 2 View
- installation - MAC
Protocols
- Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol
- Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities
- 16S Metagenomic Sequencing Library: Preparation Preparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System
American Gut Project
- American Gut Project is a part of the Microsetta Project
Researchers
- Rob Knight, University of California San Diego; Ted Talk
- Frank Oliaro - Shedd Aquarium
- Jack Gilbert, Argonne National Laboratory
AGP Publications
Health References
- File:The Human Intestinal Microbiome in Health and Disease.pdf
- File:Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization.pdf
- File:Ghrelin.pdf
- File:NAture_energy.pdf
- File:pbio.1002533.pdf
- File:pnas.1909224116.pdf
- File:The gut microbiome in neurological disorders.pdf