Gut Microbiome and Its Impact on Health and Diseases

291 Pages·2020·4.813 MB·English

by  Debabrata Biswas, Shaik O. Rahaman

Debabrata Biswas
Shaik O. Rahaman  Editors
Gut Microbiome
and Its Impact
on Health and
Diseases
Gut Microbiome and Its Impact on Health
and Diseases
Debabrata Biswas • Shaik O. Rahaman
Editors
Gut Microbiome
and Its Impact on Health
and Diseases
Editors
Debabrata Biswas Shaik O. Rahaman
Department of Animal and Avian Sciences Department of Nutrition and Food Science
University of Maryland, College Park University of Maryland, College Park
College Park, MD, USA College Park, MD, USA
Center for Food Safety and Security
Systems
University of Maryland
College Park, MD, USA
Molecular and Cellular Biology, Biology
Program
University of Maryland, College Park
College Park, MD, USA
ISBN 978-3-030-47383-9 ISBN 978-3-030-47384-6 (eBook)
https://doi.org/10.1007/978-3-030-47384-6
© Springer Nature Switzerland AG 2020
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Contents
Contribution of Human and Animal to the Microbial
World and Ecological Balance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Zajeba Tabashsum, Zabdiel Alvarado-Martinez, Ashely Houser,
Joselyn Padilla, Nishi Shah, and Alana Young
Determinants of the Gut Microbiota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Arunachalam Muthaiyan
Effects of Diet on Human Gut Microbiome
and Subsequent Influence on Host Physiology and Metabolism . . . . . . . . 63
Bryna Rackerby, Daria Van De Grift, Jang H. Kim, and Si Hong Park
Probiotics and Prebiotics on Intestinal Flora and Gut Health . . . . . . . . . . 85
Mengfei Peng, Nana Frekua Kennedy, Andy Truong, Blair Arriola,
and Ahlam Akmel
Role of the Gut Flora in Human Nutrition and Gut Health . . . . . . . . . . . . 105
Zabdiel Alvarado-Martinez, Stephanie Filho, Megan Mihalik,
Rachel Rha, and Michelle Snyder
Gut Microbiome in Inflammation and Chronic Enteric Infections . . . . . . 133
Arpita Aditya, Catherine Galleher, Yeal Ad, Mitchell Coburn,
and Aaron Zweig
Role of Gut Microbiome in Colorectal Cancer . . . . . . . . . . . . . . . . . . . . . . 153
Xiaolun Sun
Gut Microbiota and Risk for Atherosclerosis:
Current Understanding of the Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . 167
Bidisha Dutta, Chitrine Biswas, Rakesh K. Arya, and Shaik O. Rahaman
v
vi Contents
Gut Microbiome and Its Role in Enteric Infections
with Microbial Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Catherine Galleher, Kyah van Megesen, Audrey Resnicow,
Josiah Manning, Lourdes Recalde, Kelly Hurtado,
and William Garcia
Antibiotic Therapy and Its Effect on Gut Microbiome
in Obesity and Weight Loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
Paola I. Bonilla-Carrero, Hannah Mader, Nathan Meier, Isis Olivas,
Bridget Boyle, and P. Bonilla-Carrero
Impact of Gut Microbiota on Host by Exploring Proteomics . . . . . . . . . . . 229
Thomas E. Angel and Uma K. Aryal
Modulation of Gut Flora and Its Application
in Food Animal Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Zajeba Tabashsum, Vinod Nagarajan, and Debabrata Biswas
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Contribution of Human and Animal
to the Microbial World and Ecological
Balance
Zajeba Tabashsum, Zabdiel Alvarado-Martinez, Ashely Houser,
Joselyn Padilla, Nishi Shah, and Alana Young
1 Introduction
More than 300 years ago, Antonie van Leeuwenhoek observed morphologically
diverse microbes in human plaque, leading to the discovery of a complex microbiota
that exists within the environment, as well as in animal and human bodies (Lane
2015). That was the beginning of understanding that microbes are a part of this
world, and from then, the idea of microbes playing crucial roles in every sphere of
life has become more prominent. The collection of all microbes present in a system
is known as the microbiome of that system, which includes beneficial, neutral, and
harmful microbes. The various microbes that can be found inhabiting different envi-
ronments as part of their microbiome, like people, plants, animals, soil, bodies of
water, and the atmosphere, have proven to be extremely important for, in turn, shap-
ing and maintaining the health and balance of the microbiome of a host, which is
why it has now become the subject of further studies (McFall-Ngai et al. 2013). It has
been reported that the microbiome is closely related with various parts of human
Zabdiel Alvarado-Martinez, Ashely Houser, Joselyn Padilla, Nishi Shah, and Alana Young have
contributed equally with all other contributors.
Z. Tabashsum (*) · Z. Alvarado-Martinez
Molecular and Cellular Biology, Biology Program, University of Maryland,
College Park, MD, USA
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
e-mail: [email protected]
A. Houser
Molecular and Cellular Biology, Biology Program, University of Maryland,
College Park, MD, USA
J. Padilla · N. Shah · A. Young
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
© Springer Nature Switzerland AG 2020 1
D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and
Diseases, https://doi.org/10.1007/978-3-030-47384-6_1
2 Z. Tabashsum et al.
health and disease, such as metabolism, intestinal homeostasis, and immune devel-
opment (Tasnim et al. 2017). Though each individual’s microbiome is unique, a con-
sistent and diverse gut microbiota is considered to be optimal for maintaining health.
The gut microbiota is responsible for producing metabolites that aid physiological
and metabolic processes, as well as adjusts local and systemic immune responses
that lead to the development of protective immunity against pathogens, while simul-
taneously maintaining immune lenience toward commensals (Tasnim et al. 2017).
On the other hand, imbalance of the gut microbiota (dysbiosis) can disrupt vital
health-promoting activities and has been associated with diseases like gastrointesti-
nal, cardiovascular, autoimmune, and metabolic disorders (Jandhyala 2015). Due to
such phenomenon, the gut microbiome is considered as a vital organ, and disruption
of the balance within the microbial ecosystem can lead to severe chronic diseases and
future health consequences.
We are still figuring out the ecological processes of a steady and wide-ranging gut
microbiome that is comprised of bacteria, archaea, fungi, and viruses, which in them-
selves include a very diverse bacteriophage community (Tasnim et al. 2017). The
microbiota can be permanent (residents), or transient (hitchhikers), but the transmis-
sion routes of the microbes are essential for establishing and maintaining the micro-
bial diversity in the human or animal host’s gut; however, the patterns of transmission
are not entirely understood. Researches on the influence of environmental factors on
the diversity and richness of the human gut microbiota and the process of gut micro-
biota transmission are still at beginning stages (Hasan and Yang 2019). Many vari-
ables outside the host, like geography, weather, and habitat, as well as factors within
the host, like personal habits, hygiene, and food, can influence the process of mold-
ing the microbiome, which adds many layers of complexity in studies seeking to
understand its composition and how it relates to its surroundings.
Overall, the microbiome plays a crucial role wherever they inhabit, ultimately
forming a big part of that ecosystem. However, researchers are still in the early verge
of figuring out the microbiome’s broad role in the health of the host/environmental
balance and the extent of problems that can occur from an interruption in the regular
interactions between the microbiome and its host/environment.
2 Microbial Ecosystem
Microorganisms take up a significant portion of all living beings, exceeding even that
of animals, in addition to being highly diverse, which can be seen across multiple
ecosystems. The estimated number of prokaryotic cells, which are primary microbe
on Earth, is between 4.2 × 1030 and 6.4 × 1030 (Editorial 2011). Eukaryotic microor-
ganisms are also prominent, which leads us to the idea that life on Earth is primarily
microbial (Oren 2009). The microbes differ morphologically, metabolically, and
phylogenetically. Cell size and shape are far more limited for prokaryotes, with most
species being described as rod-shaped or coccoid-shaped with a length of 1–5 μm.
However, some giant prokaryotes have been found that dwarf most eukaryotic
Contribution of Human and Animal to the Microbial World and Ecological Balance 3
microorganisms but are not as prevalent. Prokaryotes also differ morphologically by
displaying stalks and other appendages as well as spiral shapes (Young 2007). The
true diversity of the microbial world becomes apparent when the metabolic poten-
tials of these microbes are compared. Prokaryotic microorganisms can use carbon
dioxide, acetate, or organic compounds as their carbon source when performing dif-
ferent metabolic processes, such as photoautotrophy, photoheterotrophy, aerobic het-
erotrophic metabolism, denitrification, sulfate reduction, dissimilatory metal
reduction, chemoautotrophic sulfur oxidation, nitrification, methanogenesis, and fer-
mentation. In the case of some eukaryotic microorganisms, they can use carbon diox-
ide or organic compounds as their carbon source during photoautotrophy, aerobic
heterotrophic metabolism, and fermentation (Oren 2009). The presence of these vari-
ous types of metabolisms shows how microorganisms have evolved to enable life,
even under distinctively different and possibly even adverse conditions. Newly
developed molecular technology such as sequencing of the small-unit ribosomal
RNA has aided in expanding the current knowledge that is had about the diversity of
the microbial world (IOM 2009). The ever-growing database of the living beings on
earth has shown that only a few branches in the Eukarya domain contain multicel-
lular organisms, while all other branches in the Eukarya, Archaea, and Bacteria
domains are microorganisms (Oren 2009).
The human microbiome is also very dynamic and contains a vast array of micro-
bial species, which contribute to the overall health (both positive and negative) of the
host (Cho and Blaser 2012). The symbiotic relationship between microorganisms
and their host likely originates around the same time animals appeared, about 700
million years ago. Bacteria began to serve as producers of digestible molecules in the
animal gut, thus heavily influencing gut evolution and health (Mcfall-Ngai et al.
2013; Bahrndorff et al. 2016). Microorganisms and their crucial activity in the gut
have become an essential part of a healthy life. Diversity of the gut microbiota is an
important indicator of a healthy gut and the overall health of the humans or animals.
Low diversity of gut microbiota has been closely associated with many diseases spe-
cifically chronic diseases, such as inflammatory bowel disease. The microbiome–
host association indicates that a species-rich gut ecosystem is stronger against
environmental influences because the microbes are functionally related and able to
compensate for any missing species (Valdes et al. 2018). Microorganisms reside not
only the gut but can also be found in different organs and secretions of the host, such
as skin, saliva, stool, and the vagina. Saliva and stool have quite diverse communities
of microbes, similar to the gut. However, it was found that other parts are mostly
populated by simple communities of microbes, such as in the case of the male uri-
nary tract. On the other hand, an increase in microbial diversity in the vagina leads to
health complications, such as bacterial vaginosis (The Human Microbiome Project
Consortium 2012). This emphasizes how the microbial communities and their sym-
biotic relationship with humans have evolved and how microbes have become spe-
cific to a certain type of environment; even within a single organism, the structure
and function of each microbial community are unique.
Due to the dynamic nature of microbial communities, not all microbes will be
present in constant ratios; rather, their numbers are unique and can change within a
4 Z. Tabashsum et al.
community and ecosystem at a given time. Some selection pressures must exist in
order to isolate the best-suited microbial community. For the gut microbial commu-
nity, there must be strict requirements for sustaining or gaining membership. Each of
these microbes produces a variety of enzymes for utilizing available nutrients and
uses their cell-surface molecular paraphernalia to attach to a suitable habitat in which
they can colonize and avoid a reaction-ready immune system (Ley et al. 2006). The
ability for genetic mutations in order to stay well adapted, ability to grow rapidly to
avoid being washed out, and high resistance to stress are some of the mechanisms
that have developed and are crucial for surviving the passage, colonization, and prev-
alence in a new host, even when conditions might be adverse (Ley et al. 2006).
Without such abilities, the microbes would not be able to survive in the gut environ-
ment, much less make significant contributions to the community. These factors will
be essential, especially at the first stages of microbial discrimination, which begins
right after birth.
As mentioned before, upsetting the delicate balance of the microbiome can have
negative effects on overall health of the host. An example of this is the studies that
have shown a possible link between microbiota and cardiovascular disease, based on
data about how some microbes metabolize dietary phosphatidylcholine into the pro-
atherosclerotic metabolite trimethylamine-N-oxide (TMAO) (Koeth et al. 2013). In
another study, Koeth et al. (2013) observed that a group of healthy people challenged
with dietary phosphatidylcholine showed increased plasma levels of TMAO that
were suppressed by prior treatment with antibiotics. These increased plasma TMAO
levels were found to be associated with increased risk for cardiovascular events in
patients with cardiovascular disease risk factors, providing more evidence of a link
between the microbiome and cardiovascular disease (Koeth et al. 2013; Shreiner
et al. 2015). A similar link has been found between microbiota and inflammatory
bowel disease (IBD). IBD is characterized by inappropriate inflammation in the gut
resulting from a combination of environmental and genetic risk factors and is also
associated with alterations in the gut microbiota. Studies found that patients with
IBD had low-diversity gut microbiomes and that the use of antibiotics amplifies the
microbial dysbiosis (Shreiner et al. 2015).
The microbiome is clearly important for human health, so its stability and response
to disturbances are crucial issues to discuss. Relman (2012) reported that the ecology
of human microbiome will be stable as long as the key components of the system
remain in equilibrium after a disturbance, and that the system can be resistant to
future disturbances if they are experienced for a short period, or as long as it allows
enough time for key components to recover to their initial state of equilibrium. As
long as the system is robust enough to resist significant change and maintain certain
parameters within range, it will still be able to operate and exert its beneficial proper-
ties, allowing for some variability without compromising the overall functions.
Disturbance can be defined as an event or process (physical or biological) that causes
abrupt structural changes to the composition of the community. The most well-
known disturbance is antibiotics. Recently, antibiotics have been used in massive
quantities and concentrations relative to their natural occurrence over millions of
years in the environment (Relman 2012). This has led to bacteria becoming resistant
to antibiotics, thus making them much harder to treat. While this is a widely known