Using Technology to Study

the Human Gut Microbiome

50 points
Due: Monday, March 4 at 11:59 pm

General Overview of the Gut Microbiome

The human gut is home to as many as 100 trillion bacterial cells that make up the microbiome. Many of
these bacteria use substrates from food such as dietary fiber, whole grains and other food components
to produce short chain fatty acids (SCFAs) during the process of fermentation. The SCFA products from
fermentation can be used as an energy source for bacteria or other tissues and cells in the body. The
microbiome is also responsible for the production of metabolites and signaling molecules that may
come from bacterial metabolism of other dietary components. We still don’t fully understand how these
metabolites impact human health and disease.

While every human has gut bacteria, the type of bacteria and the diversity of the bacteria differs
between individuals. For example, research tells us that individuals with obesity have a different gut
bacteria profile compared to non-obese individuals. The current belief is that there is no one particular
“healthy gut microbiome” but rather a spectrum of microbiota that contribute to good health. A healthy
diet with adequate fiber and fermented foods such as yogurt, kefir, and kimchi is thought to be
important in the establishment and maintenance of gut microbiota that supports good health. Other
factors such as antibiotic treatment, radiation therapy, surgery, and some diseases are known to reduce
beneficial bacteria in the large intestine.

Studying the human gut microbiome is complex; however, multiple technologies exist to help
characterize gut bacteria in humans. Although there are various technologies, the two examples that will
be introduced in this assignment are 16S sequencing and whole genome shotgun sequencing (WGS).
These new technologies have spawned companies, such as DayTwo, that analyze individuals’
microbiomes by sequencing rRNA from stool samples and create personalized nutrition
recommendations.

Assignment Instructions
1. Gather background information.
You will become familiar with two technologies (16S sequencing and WGS) that are commonly used to
study the interaction between nutrition and the gut microbiome. To help you understand the basics of
these two technologies, watch the following YouTube videos:
• Illumina MiSeq 16S sequencing (minutes 2:50-4:50)

• Shotgun sequencing (full two minutes)

Then, READ the following:

• Pages 138-140 (Gut Microbiota, Probiotics & Prebiotics) in your course textbook
• Pages 1-3, 6&9 in this paper: Human Microbiome FAQ
Finally, please WATCH the following:
• “Technology and the Human Gut Microbiome” by Dr. Abby Johnson

2. Prepare and write your essay.

Your essay should do the following:

• Summarize similarities and differences of 16S sequencing and WGS technologies.

• Identify one positive and one negative societal impact of the services performed by companies
like DayTwo. Discuss health, social, and economic aspects for each impact.

• Describe two challenges that DayTwo and similar companies might face as research and
technology in the area of the human gut microbiome and nutrition continue to advance.

• Support your statements/opinions with current, reliable references formatted in AMA style.
Your references must include peer-reviewed journal articles.
Essays should be one page, single-spaced, 500-700 words, and have 1-inch margins.