BIOLOGY CRITICAL ANALYSIS

Submitted to:
Sir Albin Tabamo

Submitted by:
Lieka Isabel P. Mero
11 - Mars
ABSTRACT

Over the history of research, numerous fields of study have been shown to have
importance in the realm of science. One particular field of science is microbiome research.
Many studies have been conducted regarding the different categories within microbial
communities – however archaea have been constantly overlooked, due to its difficult biology.
The study, titled “Exploring the Archaeome: Detection of Archaeal Signatures in the Human
Body”, by Pausan, M., et al., aims to uncover the overlooked microorganisms, where archaea
was detected in five different body sites using amplicon sequencing. Compared to the
“universal” approach, the method utilized in the study detected 81 RSVs (archaeal ribosomal
sequence variants), a groundbreaking step up from the initial detection of only one RSV. The
results from this study would not only be useful for the human archaeome, but could be
stepping stone for the research of archaea in the future.

INTRODUCTION

In the introduction, the researchers state the evidence and reasons as to why human
archaeome is constantly overlooked and understudied – primer mismatches of “universal
primers”, low abundance of the DNA in samples, improper extraction methods, and the
incompleteness of the 16S rRNA gene reference databases. Most of the reasons stated are due
to methodological issues while processing samples, which is a commonly identified mistake
that can influence microbiome studies. Despite these observed issues, archaea are the most
common microorganisms in the human body, most located in the oral cavity and the
gastrointestinal tract. The researches utilized standard operational procedures, and optimized
methods to reach the target goal.

METHODOLOGY

The researchers attempted to experiment with 27 different 16S rRNA gene-targeting

primer pair combinations suitable for NGS amplicon sequencing with the goal of detecting
the archaeal diversity. For the selection of samples and DNA extraction, samples from body
sites such as the respiratory tract, the digestive tract, and skin swabs were collected. Many
microbiome studies have been published utilizing these samples already. In order to properly
detect archaea located in the human samples, numerous different primer pairs were used
alongside three “universal” primers. The differences of archaeal diversity were calculated and
processed using the Wilcoxon Rank Test, a statistical hypothesis test used for locating a set of
samples or to compare them. For identifying the differences of archaeal diversity according to
body location, ANOVA, analysis of variance, was utilized. For displaying results, RSV tables
were used for taxon abundance, and the taxonomic profiles were for generating bar graphs.
RESULTS AND DISCUSSION

After the experiment concluded, the results shown were proven to meet the objectives
of the study – different phyla of archaea were seen and detected throughout the body. 12
different primer pairs in total were evaluated, which proves the optimization of the primers.
The study emphasized how big of a difference the primer pairs had on the archaeal
community composition, and the conclusion that archaea-specific procedures are more
efficient compared to the existing universal approaches. All primers showed a high coverage
for each phyla and genera, which displays the pin-point accuracy and efficiency of the
methodology the researchers chose to implement.

Even after years of research and studies, there can be fields of science that are only
beginning to be uncovered. Scientists do not have enough knowledge on Archaea yet, even
after being acknowledged as a separate domain of life for more than forty years. Many
aspects of it remain unexplored – how archaeal communities interact with each other, how it
is affected by disease and how it affects disease. For the longest time, they have been
classified as difficult to study, so scientists don’t study them – which creates the problem of
archaea continuing to not be studied. Archaea needs to be studied, as it is a part of our human
body, and to understand our body more, we need to try to understand the different organisms
living in it.

This study is important, and integral to the study of human archaeome - it lays down
the groundwork for future research, while providing large amounts of information itself. It
was well-written, the researchers were clear with their vision, and they executed it properly.
This will be a stepping stone for future research regarding this topic.