Gastrointes nal Microbiome – A Pharmacological approach to

next-genera on therapeu cs of Diseases and Disorders

Fa ma Ali1 , Suchismita Majumdar Dhar2

1
Research Student, Innovation Hub, Birla Industrial and Technological Museum, Kolkata under National
Council of Science Museums, Govt of. India
2
Biotechnology Mentor, Innovation Hub, Birla Industrial and Technological Museum, Kolkata under
National Council of Science Museums, Govt of. India

1
fatima99ali55@gmail.com, Contact no - 9903897001
2
suchismita.biotech@gmail.com, Contact no – 9804173248
Corresponding Author: Suchismita Majumdar Dhar

Abstract: An alteration of intestinal microflora significantly contributes to the pathogenesis of

different inflammatory and autoimmune disorders. There is emerging an interest on the role of
selective modulation of microflora in inducing benefits in inflammatory intestinal disorders and
other neurodegenerative diseases by relatively new approaches such as engineered probiotics,
prebiotics, synbiotic, and fecal microbiota transplantation (FMT). New insights have raised an
interest in FMT for the management of extra-intestinal disorders associated with gut microbiota.
This review shows that it is an exciting time to adopt the methods of Translational Science of
FMT application to unexpected health disorders, including metabolic diseases, neuropsychiatric
disorders, autoimmune diseases, allergic disorders, and tumors.

Keywords: Gastrointestinal Microbiome, Microbiota, Dysbiosis, Autoimmune diseases, Allergic

disorders, Neurological disorders, Metabolic diseases, Extra-Intestinal Tumors, Prebiotics,
Genetically engineered Probiotics, Synbiotics, Fecal Microbiota Transplantation,
Next-generation microbiota therapeutics, Translational Science.

Introduction
The human intestinal microflora, known as “microbiota”, includes 100 trillion (1014) bacteria,
quadrillion viruses, fungi, parasites, and archaea for a total weight of about 1 kg [1].The stomach
and small intestine are colonized only by a few species of bacteria, mainly because of the acid
environment, the presence of bile and pancreatic secretions, and the peristaltic activity limiting
bacteria stable colonization [2]. On the contrary, the colon harbours about 1012 microorganisms.
Where every individuals' microbiota composition varies dramatically and geographically, a
conserved set of bacterial functional gene profiles are present in all healthy individuals, implying
that our microbiome plays an important role in physiological gut functioning. [2]
Composition: Colonization of human gut starts few days after birth. Pattern of intestinal
microbiota may be firstly influenced by type of delivery and type of diet and, later, by immune
stimulaton and environmental factors, becoming more stable after the first two years[2], even
though it can be modified under some circumstances, such as diarrhea, antibiotic treatment, or
dietary interventions. Bacteria in stomach, duodenum, and jejunum are mostly represented by
oropharyngeal origin aerobic gram-positive ones, whereas in the ileum coliforms are the
predominant species. Post ileocecal valve harbours a growth of bacterial anaerobic species,
mainly Bacteroides, Bifidobacteria, Clostridi and Lactobacilli. Alterations in the complex
physiological bacterial population are associated with negative functional outcomes or diseases,
known as dysbiosis, which is linked to variety of ailments, including obesity and its associated
metabolic disturbances. [3]

Role of Microbiota in diseases

Allergic disorders: The prevalence of allergic diseases has been increasing in modern society
over the past 50 years. A wealth of studies regarding the relationship between allergic diseases
and microbiota has been conducted in both humans and mice. Moreover, accumulating evidence
has suggested early-life antibiotic exposure is involved in the development of atopy, such as
allergic asthma and food allergies, with an altered composition of intestinal microbiota possibly
being involved [1]. The use of FMT seems promising in restoring immune homeostasis by
transferring a complex community of bacteria which is more stable and harbours a greater ability
to colonize [1].
Autoimmune diseases: The incidence of autoimmune diseases has dramatically increased, but
the causes of these conditions remain poorly understood. The onset of rheumatoid arthritis (RA)
is multifactorial and requires both genetic and environmental influential factors, with the
commensal intestinal microbiota playing a major role [1, 4]. Alterations in the intestinal
microbiome can have an extended effect on RA through mucosal immune activation. Previous
reports have implicated Prevotella copri in the pathogenesis of RA. Hashimoto’s thyroiditis (HT)
is a thyroid autoimmune disorder, and a series of studies have been implemented to explore the
link between gut micro-organisms and HT [1-4]. Further work is required to test the hypothesis
that the gut microbiota is an epigenetic factor for triggering HT, and thereby determine whether
FMT is favorable for managing the illness.
Metabolic diseases: There is compelling evidence that the GI microbiota is closely linked to a
series of metabolic conditions. Obesity, diabetes mellitus, and metabolic syndrome are epidemic
in modern society. There have been extensive investigations concerning microbiota reaction
acting as a pivotal role in the pathogenesis of these endocrine diseases in animal models.
Changes in gut microbiota composition have also been reported in obese humans, with a shift in
the ratio of Firmicutes and Bacteroidetes. Recent studies have shown that short chain fatty acid
(including butyrate) producing Clostridiales strains were found to be decreased in patients with
type 2 diabetes mellitus, but non-butyrate producing Clostridiales and pathogens such as
Clostridium clostridioforme were increased. Leaky gut or loss of intestinal integrity may
facilitate the development of cardiometabolic disorders due to alterations in composition and
diversity of gut microbiota. Evidence has recently been generated that demonstrates the gut
microbiota acting as an epigenetic factor driving the progression of non-alcoholic fatty liver
disease (NAFLD), a metabolic syndrome that manifests in the liver. Intestinal dysbiosis promotes
hepatic injury and inflammation through either a breakdown of the intestinal barrier or
translocation of microbial products [2, 4, 5].
Neurological disorders: In the last few years, the importance of GI microbiota impairment in the
etiopathogenesis of pathology such as autism, dementia and mood disorder has been raised. The
evidence of the inflammatory state alteration, highlighted in disorders such as schizophrenia,
major depressive disorder and bipolar disorder, strongly recalls the microbiota alteration, highly
suggesting an important role of the alteration of GI system in neuropsychiatric disorders. A
deeper assessment of the role of gut microbiota in the development of autism spectrum disorder
(ASD), as well as the advancement of the therapeutic approaches for the modulation of gut
microbiota is warranted for a better management of ASD and mood disorders. Recent data show
the strong correlation between dysbiosis and conditions such as obesity, allergies, autoimmune
disorders, IBS, IBD, and psychiatric disorders [1, 3, 6].
Extra-Intestinal Tumors: A strong association has been illustrated between the GI microbiota
and colorectal cancer. Recently, incremental data has suggested that the gut flora (namely
Streptococcus bovis and Helicobacter hepaticus) might be involved in EI tumors. Gold et al
reviewed 8 EI malignancies in 45 cases with Streptococcus bovis bacteremia in a retrospective
study, which suggested that EI malignancy might be warranted in patients with Streptococcus
bovis. In addition, prior work has shown the gut microbiota is also involved in mammary tumors.
Furthermore, Fox et al used a mouse model to examine the hypothesis that specific intestinal
bacteria were associated with hepatocarcinogenesis. The progress of hepatocellular carcinoma
induced by aflatoxin and hepatitis C transgene was promoted by Helicobacter hepaticus
colonization in the intestine. More recently, Yamamoto et al investigated the relationship
between the GI microbiota and lymphoma, using an Atm-/- mouse model and found that the GI
microbiota acted as a potential contributor to lymphoma onset. [1-3]

Next generation Microbiome therapeutics

Prebiotics: Prebiotics are currently defined as “selectively fermented ingredients that result in
specific changes in the composition and/or activity of the GI microbiota, thus conferring benefits
upon host health”. Some examples of prebiotics are dietary fibers and some types of
oligosaccharides, although only inulin-type fructans and galacto-oligosaccharides fulfill all the
criteria for prebiotic classification [1]. Some polysaccharides can also be found in seaweeds and
microalgae [1, 2]. These food ingredients may modify the gut microbiota, mainly at the level of
individual strain, selectively stimulating growth of health-promoting species already residing in
the colon. Prebiotics can also inhibit the adherence of pathogens to gut epithelium, preventing
them from translocating across the epithelial GI cells. [3-7]

Synbiotics: About 20 years ago, the term “synbiotic” was firstly introduced to describe “a
mixture of probiotics and prebiotics that beneficially affects the host by improving the survival
and implantation of live microbial dietary supplements in the GI tract, by selectively stimulating
the growth or by activating the metabolism of one or a limited number of health-promoting
bacteria, and thus improving host welfare”. Commonly combinations include Bifidobacteria and
fructooligosaccharides (FOS), Lactobacillus rhamnosus GG (LGG) and inulin, and
Bifidobacteria and Lactobacilli with FOS or inulin[1, 6].

Fecal transplantation: Engineering the microbial community as a whole is an alternative strategy

that has seen tremendous clinical success for treatment of recurrent Clostridium difficile
infections. Infusion of stool from healthy donors to diseased patients, termed a fecal microbiota
transplant, boasts greater than 90% efficacy in resolving recurrent infections and is more than
twice as effective as antibiotic treatment alone. In a hepatic injury model, the redefined
microbiota increased survival and protected against cognitive defects associated with
hyperammonemia. [3, 4, 7] Case reports of FMT have also shown favorable outcomes in
Parkinson’s disease, multiple sclerosis, myoclonus dystonia, chronic fatigue syndrome, and
idiopathic thrombocytopenic purpura. FMT is a promising approach in the manipulation of the
intestinal microbiota and has potential applications in a variety of EI conditions associated with
intestinal dysbiosis. [6, 7]

Genetically Engineered Probiotics: Recent efforts seek to augment the natural benefits of
probiotics through recombinant expression of therapeutic biomolecules. Implementation of cells
as vehicles of drug delivery could enable continuous in situ production of biotherapeutics that
could overcome issues such as bioavailability and drug inactivation associated with oral
administration. Administration of therapeutic cells resulted in an increase in survival and a
concomitant decrease in bacterial burden and cholera toxin expression. Similarly, Lactobacillus
jensenii was genetically modified to prevent transmission of human immunodeficiency virus
(SHIV) in a rhesus macaque model. Early work explored the use of Lactococcus lactis
engineered to constitutively secrete recombinant interleukin-10 (IL-10), a potent
anti-inflammatory cytokine depleted in IBD. IL-10-secreting L. lactis were further modified to
produce either the auto-antigen proinsulin or glutamic acid decarboxylase-65 for treatment of
autoimmune diabetes. Recombinant bacteria have also been implemented for treating oral
mucositis, a condition involving ulcerative lesions that is a common side effect of chemotherapy.
Administration of the engineered probiotic increased the numbers of intestinal insulin-producing
cells and decreased hyperglycemia in a rat model. Together, these studies suggest that
recombinant cellular therapies could be viable therapeutic agents to treat inflammatory diseases.
Integration of recombinant microbes into the host microbiome has also seen success in treating
metabolic diseases, such as obesity and diabetes. [4-6]

Subtractive Approaches: Subtractive therapies may employ chemicals, peptides, or even

replicating entities to remove bacteria from the gut with varying degrees of specificity. In
medicine, this is currently accomplished through the use of antibiotics, which tend to be
broad-spectrum in nature, exhibiting activity towards many different bacteria. The development
of targeted antimicrobials, such as bacteriocins and bacteriophages, could yield more effective
subtractive therapies. Bacteriophage therapy is a highly specific method of killing bacteria
through the use of natural or engineered viral parasites. Bacteriophages, or phages, are viruses
that infect bacteria and use cellular resources to produce progeny, generally killing the bacterial
host in the process. Engineered phages, or those modified to carry additional or alternative
functions to those naturally occurring, may prove useful for therapeutics as design can be
informed by new knowledge. Phages have also been used as DNA delivery agents to reverse
antibiotic resistance or to exert broad-spectrum [4] or sequence-specific [4, 5] antimicrobial
activity. Additionally, genome engineering and tools such as CRISPR-Cas and assembly methods
including Gibson and yeast assembly should prove useful for the development of new phages
with augmented capabilities in modulating microbial communities. [4-6]
Conclusion: The Science of Translation of Gut Microbiota therapeutics by FMT, prebiotics and
probiotics has significantly made a major impact on the perspectives of treating various disorders
and diseases. Consideration of the successes of FMT in treating IBS, CDI, IBD and obesity
related diseases have encouraged new researches and studies to engage in the treatment of
wide-spread diseases and disorders that go beyond the GI tract. It is well established that the
gastrointestinal microbiota plays a critical role in GI development and function while regulating
host inflammatory responses and immune homeostasis. It seems likely that the future roles of
probiotics and prebiotics will go beyond traditional gastrointestinal illnesses, particularly as the
role of the microbiota and the CNS and other organs is better understood. Novel applications in
the future may include the treatment of chronic immune disorders, tumors and anxiety-like
behaviors or psychiatric illness with microbiota therapeutics.

Abbreviations: FMT- Fecal Microbiota Transplantation, RA- Rheumatoid arthritis, HT-

Hashimoto’s thyroiditis, NAFLD- Non-alcoholic fatty liver disease, ASD- Autism spectrum
disorder, IBS- Irritable bowel syndrome, IBD- Inflammatory bowel disease, GI-Gastrointestinal,
CNS - Central Nervous System, CDI- Clostridium difficile Infection, EI - Extra-Intestinal.

Acknowledgement: We would like to acknowledge the constant support and guidance provided
by our lab In-Charge Sri. Sudipto Saha, Curator, BITM and would also like to express our
sincere gratitude to Sri. Sk. E Islam, Director, BITM.
References and notes:
[1] Meng-Que Xu, Hai-Long Cao, Wei-Qiang Wang, S. Wang, Xiao-Cang Cao, F. Yan, Bang-Mao Wang,
2015, “Fecal microbiota transplantation broadening its application beyond intestinal disorders,” World J
Gastroenterol., 21(1), pp. 102-111.
[2] A. Gallo, G. Passaro, A. Gasbarrini, R. Landolfi, M. Montalto, 2016, “Modulation of microbiota as
treatment for intestinal inflammatory disorders: an uptodate,” World J Gastroenterol., 22(32), pp.
7186-7202.
[3] C. A. Marotza , A. Zarrinpar, 2016, “Treating Obesity and Metabolic Syndrome with Fecal
Microbiota Transplantation,” Yale Journal of Biology and Medicine., pp.383-388.

[4] M. Mimee, R. J. Citorik, and Timothy K. Lu1, 2016 “Microbiome Therapeutics – Advances and
Challenges,” Adv Drug Deliv Rev., pp. 44–54.

[5] F. Mangiola, G. Ianiro, F. Franceschi, S. Fagiuoli, G. Gasbarrini, A. Gasbarrini, 2016, “Gut

microbiota in autism and mood disorders”, World J Gastroenterol., 22(1), pp. 361-368.

[6] B. Petschow, Jo¨ el Dor´ e, P. Hibberd, T. Dinan, G. Reid, M. Blaser,

P. D. Cani, F. H. Degnan, J. Foster, G. Gibson, J. Hutton, T. R. Klaenhammer, R. Ley, M. Nieuwdorp,
B. Pot, D. Relman, A. Serazin, and M. E. Sanders, 2013, “Probiotics, prebiotics, and the host
microbiome: the science of translation,” Ann. N.Y. Acad. Sci., pp. 1–17.

[7] A. Y. Wang, J. Popov, Nikhil Pai, 2016, “Fecal microbial transplant for the treatment of pediatric
inflammatory bowel disease,” World J Gastroenterol., 22(47), pp.10304-10315.