The document discusses developments in microbiome-based therapeutics. It outlines how advances in omics approaches have improved understanding of the gut microbiome's role in health and disease. Several approaches for microbiome-based therapeutics are discussed, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation. Challenges including determining causative relationships and altering microbial communities are also summarized. The document concludes that more research is still needed but that microbiome therapeutics have significant potential to treat gastrointestinal and other diseases.

1. DEVELOPMENT IN MICROBIOME BASED THERAPEUTICS
Presented by : Y. Veekshith
PC/2021/217
Pharmacology & toxicology
Guide: Dr Manoj Dandekar

2. INTRODUCTION
Microbiome – is a term describe the
genome of all the microorganisms
,symbiotic and pathogenic ,living in and
on all vertebrates.
Intestine – trillion of microbes, (2kg)
Advances in omics based approaches
has opened many areas of research on
the role of intestinal microbiota in
immune system homeostasis that
impact health and diseases.
The dominant phyla in human includes
firmicutes and Bacteroidetes ,
proteobacteria, actinobacteria.

3. MULTIPLE FUNCTIONS OF NEGLECTED ORGAN

4. Gut brain axis
 Bidirectional
 This bidirectional pathway involves
Neuronal system (NTS)
Immune system (cytokines)
Endocrine system ( gut peptides ), sensed
by ENS
HPA axis
 ENS –secondary brain
 80% of neurons in Vagus are sensory
afferent
Cryan JF. Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat. Rev.
Neurosci. 2012;13:701–712. [PubMed] [Google Scholar]

5. Microbiome role in pathogenesis of Alzheimer's
Helicobacter pylori
massive inflammatory mediators
activate Glycogen 3B synthase ALZHEIMERS
Induce hyperphosphorylation of tau protein of Alzheimer's
• Gut microbiota vs amyloid generation in brain;
Enterobacteria species & fungi produce amyloid peptide seeding for aggregation of amyloid in brain
• In case study of 25 Alzheimer's and 25 control groups
decrease in diversity
no of firmicutes
no of Bacteroidetes
• Cultivable butyrate producing bacteria involved in cognitive function has been isolated from microbiota
ALZHEIMERS

6. Winter et al.,2018

7. Dysbiosis in autism
Lee L, Ser H, Khan TM, et al
IDDF2019-ABS-0321 Relationship between autism and gut microbiome: current status and update
Gut 2019;68:A40-A41.

8. Development in microbiome based therapeutics
• The majority of microbiome-based therapies under development
today target either diseases of the gastrointestinal tract, such as ulcerative
colitis and irritable bowel syndrome, or diseases in which a strong link has
been established with the gut microbiome, as is the case for psoriasis and
diseases that involve the gut–brain axis, such as Parkinson’s disease and
other neurological disorders
• For therapies to be rigorously developed as therapeutic treatments, a
better understanding of microbial colonization and kinetics in the
gastrointestinal tract is needed.

9. • Microbiome role in gastric intestinal non gastric
intestinal diseases so we need to target them
• Main challenge in microbiome based therapeutics is
determine cause effective relationship( good
outcome)
• Goal : alter composition by exogenous administration
FECAL MICROBIOTA TRANSPLANTATION
Current successful FDA approved microbiome based intervention – FMT
FMT- function is to replace diseased microorganisms
• 90% efficacy in resolving recurrent infection
LIMITATIONS :
• Inadvertent transplantation of pathobionts
• -ve interaction with recipient existing microbial community
• Variability of different composition & limited long term stabilization of microbial community

10. SECOND GENERATION MICROBIOME BASED THERAPEUTICS TREATMENTS
Probiotics:
Live microbes which when taken adequate amount confer a health effect on host
Acute and chronic inflammation lactic acid bacteria & Bifidobacterium
Amyloid accumulation Alzheimer's
Probiotic SLAB-51 Cocktail alter scfa content AZ mice model
Fermented dairy products contain tryptophan related dipeptide and new lacto peptide
microglial activation cognition
Prebiotic
Selectively fermented ingredients that alter configuration & activity in GIT microbiota that confers positive effect
Alter composition or activity of endogenous microbes
ex insulin in treatment of IBD

11. Engineered strains
Normal flora in host resist pathogen colonization so we use engineered bacteria
 E coli nissle inhibit virulence of vibrio cholera
 Lactobacillus jensenii prevent transmission simian / human immune deficiency in rhesus maca que monkey
modified
cyanovirin N
 Lactococcus lactis for treatment of colitis
 Elafin produce lactic acid bacteria & restore proteolytic homeostasis
 Lactobacillus gasseri deliver GLP1 To treat hyper glycemia
 Modified strain of ECN as therapeutic for phenylketonuria , urea cycle inborn treatment

12. Subtractive approach :
• Removing specific bacteria by antibiotics , phage's
• Specific to targeting activity
• Metagenomic studies of faecal virome that of healthy
and diseased person have revealed that phage variability ,
stability and diversity
• In IBD there is low viral population and bacterial population is high
for localized action
• Phage helps to deliver specific DNA to bacteria to reverse antibiotic resistance
• CRISPER-CAS facilitates future engineering efforts

13. Metabolite based therapeutics as attractive alternative treatment/post biotics
Postbiotics :
preparation of inanimate microorganisms and/ or their components that confer a health benefit on host
• Microbial metabolites affect host physiology and modulate cellular functions of host , these are connection b/w
host and microbiota
• Postbiotics mitigate –ve effect of metabolite pathway
• Post biotics has good potential towards negative effect of dysbiosis
• Examples : short chain fatty acids(scfas) , lipopolysaccharides etc
 scfas (anti-inflammatory activity) altered in IBD
 organic acid taurine decreases intestinal inflammation
Advantages
• Toxicity is low as there are large in no
• Follow p/k parameters
• Metabolite are pleiotropic and cell specific
Challenges
• Pleotropic ( alter other functioning )

14. Żółkiewicz J, Marzec A, Ruszczyński M, Feleszko W. Postbiotics-A Step Beyond Pre- and Probiotics. Nutrients. 2020 Jul 23;12(8):2189. doi:
10.3390/nu12082189.PMID: 32717965; PMCID: PMC7468815.
Cell free supernatant:
• Lactobacillus acidophilus & casei has anti-inflammatory and
TNFalpha & IL-10(anti-inflammatory)
• Lactobacillus and bifido bacterium prevent the entry of E.coli
Into enterocytes
Exopolysaccharides:
During growth bacteria produces biopolymers outside of cells
Those get aggregates to form EPS
• Beta glucans
+
dectin1 on macrophages cellular response against virus and bacteria
• Beta glucans + lactobacilli
increase adhesion to intestinal epithelium
Enzymes : released to compact ROS
ex: glutathione peroxidase , peroxide dismutase (SOD)
• genetically produced lactobacillus SOD superior to decrease Crohn's disease
SCFS:
• Energy source to enterocytes & modulate gene expression by inhibiting histone deacetylase

15. Para biotics :
These are inactive and nonviable probiotics provide good health through antioxidant , anti-inflammatory , some metabolic
and immune pathway when taken in particular amount
probiotic + parabiotic
increases stability of probiotics for wide range of temp and prolong self life of probiotic
Proteobiotics :
Metabolites of probiotics that interrupting virulence strategies
Prevent bacterial colonization and prevent development of resistance
example : proteobiotics of lacto bacillus prevent virulence of lactobacillus acidophilus an Entero haemorrhagic E coli
infection

17. Microbiota based therapeutics pose certain challenges
• Consequences of altering the composition of microbial community
• Determining perfect target
• Biosensors are needed to produce microbial therapeutics
• Recombinant engineered microbe – robust and phenotypically stable
• Regulatory questions should be answered
• SOURCE: Reprinted from Advanced Drug Delivery Reviews, 105, Mark Mimee, Robert J. Citorik, and Timothy K. Lu, “Microbiome
therapeutics—Advances and challenges,” 44-54, Copyright 2016, with permission from Elsevier.

18. Global microbiome therapeutics market key
players
• Enterome bioscience
• Maa T pharma
• Open biome
• Second genome
• Seres therapeutics
• Rebiotix

19. Clinical status of drugs
Disease Treatment Phase
Hepatic Encephalopathy Drug: VLS#3 Phase 2
Other : placebo Phase 3
Probiotics
FMT
Disease Treatment phase
Liver cirrhosis Other : FMT Not applicable
Other : standard of care
Post biotics
Disease Treatment Phase
Ulcerative colitis Drug : MS_20 oral soln NA
Other : placebo
Prebiotics
Disease Treatment Phase
Diarrhoea Drug : Zn&Fe fortification Phase 3
Pneumonia Other : pre & pro biotic

20. Conclusion :
As microbiome play key role various pathological conditions like Alzheimer's , IBD
etc
We explored microbiome , Therapeutics was developed accordingly to microbiota
is ongoing process , if we done intense research we get wonder
Therapeutics targeting the human microbiome are undergoing rapid development
and attracting broad interest due to potential benefits
Right from the origin of humans they are with us and helping us , we demystifying
their utility for human health need to be much more evaluated

21. References
• https://www.nap.edu/catalog/24751/the-chemistry-of-microbiomes-proceedings-of-a-seminar-series
• Cryan JF. Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat. Rev. Neurosci. 2012;13:701–
712. [PubMed] [Google Scholar]
• SOURCE: Reprinted from Advanced Drug Delivery Reviews, 105, Mark Mimee, Robert J. Citorik, and Timothy K. Lu, “Microbiome therapeutics—
Advances and challenges,” 44-54, Copyright 2016, with permission from Elsevier.
• Pluta R, Ułamek-Kozioł M, Januszewski S, Czuczwar SJ. Gut microbiota and pro/prebiotics in Alzheimer’s disease. Aging (Albany
NY). 2020; 12:5539-5550. https://doi.org/10.18632/aging.102930
• Żółkiewicz J, Marzec A, Ruszczyński M, Feleszko W. Postbiotics-A Step Beyond Pre- and Probiotics. Nutrients. 2020 Jul 23;12(8):2189. doi: 10.3390/nu12082189.
PMID: 32717965; PMCID: PMC7468815.
• J, Marzec A, Ruszczyński M, Feleszko W. Postbiotics-A Step Beyond Pre- and Probiotics. Nutrients. 2020 Jul 23;12(8):2189. doi: 10.3390/nu12082189. PMID:
32717965; PMCID: PMC7468815.
• 10 Engineering the Microbiome for Human Health Applications - Timothy K. Lu, Mark Mimee, Robert J. Citorik, and Karen Pepper
• Akram W, Garud N, Joshi R. Role of inulin as prebiotics on inflammatory bowel disease. Drug Discov Ther. 2019;13(1):1-8. doi: 10.5582/ddt.2019.01000. PMID:
30880316
• . Reprinted from Advanced Drug Delivery Reviews, 105, Mark Mimee, Robert J. Citorik, and Timothy K. Lu, “Microbiome therapeutics—Advances and challenges,” 44-54,
Copyright 2016, with permission from Elsevier.