Monmouth Microbiome Initiative

NMI

"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

http://cen.acs.org/articles/94/web/2016/05/White-House-announces-microbiome-initiative.html

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

Data Processing/Data

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

Signup

American Gut Project is a part of the Microsetta Project

The American Gut Project: Overview and How to Get Involved

How to Sequence Your Microbiome with American Gut

Researchers

Rob Knight, University of California San Diego; Ted Talk

Frank Oliaro - Shedd Aquarium

Jack Gilbert, Argonne National Laboratory

AGP Publications

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

Microbiome: Gut Bugs and You | Warren Peters

Shedd Aquarium Microbiome Project

Aquarium Microbiome Project

Food Related Projects

Sour Dough Starter/Bread

Sour Dough Project - NC State

Vegetable List

Vegetable List (Wikipedia)

Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet (cited 97 times, June 2021)

Sauerkraut - Sandor Katz

Video Series: Fermentation Workshop