This seminar presentation explores the dynamic and interdisciplinary field of Microbiome Engineering, highlighting its pivotal role in modern biotechnology. Microbiomes—complex communities of microorganisms and their genetic materials—exist in diverse environments like soil, human gut, and oceans. The presentation defines microbiome engineering as the strategic modification of these microbial communities using synthetic biology, genetic tools, and ecological principles to benefit health, agriculture, and the environment. The PPT categorizes microbiome engineering into four major types: plant, soil, rhizospheric, and human, each with unique mechanisms and influencing factors. It details the growing integration of microbiome studies into biotechnology applications, such as probiotics for gut health, biofertilizers in agriculture, and biofuels in industry. A comprehensive section on tools and techniques covers CRISPR-Cas systems, recombinant DNA technology, synthetic biology, and microbiome modulation methods like probiotics, prebiotics, and fecal microbiota transplantation. The seminar further outlines the vast applications of microbiome engineering—ranging from disease diagnostics and immune modulation in human health to enhancing crop yields, stress tolerance, and biocontrol in agriculture. Environmental and industrial applications like bioremediation, waste-to-energy conversion, and climate change mitigation are also discussed. Two insightful case studies are included: one demonstrating how Bacillus sp. PM31 improves maize growth under salinity stress, and the other showing how synthetic microbiomes derived from wild rice enhance sulfur utilization in cultivated rice. These studies underscore the practical potential of microbiome manipulation. The presentation concludes by emphasizing microbiome engineering's transformative potential, while also acknowledging challenges such as environmental variability, lab-to-field gaps, and the need for ethical oversight. It advocates for continued research and responsible innovation to unlock the full benefits of this promising field for sustainable development.

1. WELCOME

2. VASANTRAO NAIK MARATHWADA KRISHI
VIDYAPEETH, PARBHANI
MASTER SEMINAR
Presented by
MUNDE AKSHATA DAYANANDRAO
[Reg. No: 2023/MBB/08/ML]
Research Guide
Dr. A. A. Bharose
Associate Dean And Principal,
VDCOAB Latur
VILASRAO DESHMUKH COLLEGE OF AGRICULTURAL
BIOTECHNOLOGY, LATUR 413 512

3. NAME OF TOPIC
Microbiome Engineering

4. List of Content
4
 Introduction
 Types of microbiome Engineering and its mechanism
 Overview of Biotechnology and microbiomes
 Role of microbes in traditional and modern biotechnology
 Tools and Techniques
 Applications of Microbiome in human health
 Applications of Microbiome in Agriculture
 Applications of Microbiome Engineering in Environment and Industry
 Future Prospects of Microbiome Engineering
 Case study
 Conclusion
 Challenges of microbiome engineering
 Summary
 Reference

5. INTRODUCTION
 Importance of microbiome in natural and engineered systems
 Definition of Microbiomes
A microbiome refers to the entire community of microorganisms (such as bacteria, fungi, viruses,
and archaea) that inhabit a particular environment, along with their genetic material. These
environments can include the human body (e.g., gut, skin, mouth), soil, oceans, and other
ecosystems.
 Microbiome = Microorganisms + Their genetic material + Their environment
System Type Role of Microbiome Example
Natural System
Nutrient cycling, plant
health, ecosystem balance
Soil and ocean
microbiomes
Engineered System
Waste treatment, industrial
production, medicine
Bioreactors, probiotics

6.  Definition of Microbiome Engineering
 Microbiome engineering is the application of synthetic biology, genetic engineering, and
ecological principles to modify the structure and function of microbial communities in natural
or artificial environments.
Field Application Example
Human Health
Engineered probiotics for treating IBD (Inflammatory bowel
Disease) or infections
Agriculture Nitrogen-fixing or drought-resistant soil microbiomes
Environmental Technology Bioremediation of oil spills using tailored microbes
Industry Microbial production of biofuels or bioplastics
 Applications of Microbiome Engineering:

7. Types of microbiome Engineering AND ITS MECHANISM
1. Plant microbiome engineering
Microbial communities associated with the plant which can live and interact
with different tissues such as roots, shoots, leaves, flowers, and seeds.

8. Factors Influencing plant microbiome engineering

9. 2. Soil Microbiome Engineering
Soil microbiome refers to microbial communities in the bulk soil beyond the
rhizosphere and is mainly influenced by agricultural management practices.

10. 3. Human Microbiome Engineering
Human microbiome engineering refers to the intentional manipulation of the
microbial communities that live on and within the human body, particularly
the gut microbiome, to achieve specific health outcomes.

11. 4. Rhizospheric Microbiome Engineering
Engineering the microbiome of the rhizosphere (the soil surrounding
plant roots) to enhance plant growth and nutrient gain.
Barnawal and Heydarian
Aminocyclopropanecarboxylate

12. Overview of Biotechnology and microbiomes
Microbiome engineering holds significant relevance in biotechnology due to its potential to transform health,
agriculture, industry, and the environment.
1. Human Health Probiotics(Microorganisms beneficial for digestive system) and Therapeutics
Gut microbiomes are used to treat diseases like obesity, mental health.
2. Agriculture
 Crop Enhancement:
Modifying soil or plant-associated microbiomes to improve nutrient uptake, increase growth rates.
 Sustainable Farming:
Reducing dependence on chemical fertilizers.
3. Industrial Biotechnology
 Bioprocess Optimization:
Engineering microbial communities for more efficient production of biofuels, bioplastics, and
other valuable compounds.
4. Environmental Applications
 Bioremediation:
Using engineered microbes to clean up oil spills, heavy metals, and other environmental contaminants.

13. Role of microbes in traditional and modern biotechnology
It plays a crucial role due to their versatility, rapid growth, and diverse metabolic capabilities.
1. Role of Microbes in Traditional Biotechnology
Traditional biotechnology refers to the historical use of biological processes for practical purposes, often without
genetic manipulation. Microbes have been central to this since ancient times.
a. Fermentation Yeasts (e.g., Saccharomyces cerevisiae) –
Used in baking, brewing (beer, wine), and ethanol production. Lactic acid bacteria (e.g., Lactobacillus spp.) – Used
in yogurt, cheese, sauerkraut, pickles, and other fermented foods.
b. Bio preservation
Certain microbes produce organic acids, bacteriocins, or alcohol that help preserve food by preventing the growth of
spoilage organisms. (e.g. Lactobacillus and streptococcus)
c. Composting and Organic Waste Degradation
Microorganisms help decompose organic matter, enriching soil fertility and recycling nutrients. (e.g. fungi and
archae)
d. Traditional Antibiotic Production
Fungi (e.g., Penicillium spp.) and bacteria (e.g., Streptomyces spp.) produce natural antibiotics like penicillin and
streptomycin.

14. 2. Role of Microbes in Modern Biotechnology
Modern biotechnology involves the deliberate manipulation of organisms at the
molecular or genetic level.
a. Genetic Engineering and Recombinant DNA Technology
Microbes are genetically modified to produce: Insulin, growth hormones, vaccines
(e.g., E. coli used to produce human insulin)
Enzymes for industry
(e.g., Bacillus spp. producing amylases and proteases)
b. Biopharmaceuticals and Vaccine Development
Engineered bacteria and yeast cells are used to produce monoclonal antibodies
(artificially engineered antibodies that target a single specific antigen) and recombinant
vaccines
(e.g., hepatitis B vaccine produced by Saccharomyces cerevisiae (yeast)).

15. C. Bioremediation
Certain microbes degrade pollutants, heavy metals, and oil spills
(e.g., Pseudomonas putida for oil degradation).
d. Industrial Biotechnology Biofuels
Clostridium and Zymomonas mobilis for bioethanol and biobutanol production.
Bioplastics: Ralstonia eutropha produces polyhydroxyalkanoates (PHAs), a type of biodegradable
plastic.
e. Synthetic Biology
Advanced design of microbial systems for novel functions, such as biosensors, smart
therapeutics, and metabolic pathway engineering.
f. CRISPR Technology
The gene-editing system is derived from microbial immune systems
(e.g., Streptococcus pyogenes provides the Cas9 protein).

16. Tools and Techniques
Microbiome engineering involves the deliberate manipulation of microbial communities to improve health,
agriculture, industry, or the environment. This interdisciplinary field combines microbiology, synthetic biology,
ecology, genomics, and systems biology. Here are the key tools and techniques used in microbiome engineering:
1. Culture-Based Techniques Selective Culturing: Growing specific microbes under defined conditions to
isolate or enrich desirable strains.
• Co-culture Systems: Culturing multiple microbial species together to study their interactions or optimize
community dynamics.

17. 2.Genomic and Metagenomic Tools
I) 16S rRNA Sequencing:
For taxonomic profiling of bacterial communities.
This method targets the 16S rRNA gene, a conserved region in bacterial genomes, to identify and
classify bacteria within a sample.

18. II) Shotgun Metagenomics
Provides comprehensive insight into microbial diversity, functions, and gene content.
Following is the process involved in shout gun metagenomics

19. I.CRISPR-Cas Systems: Precise genome
editing of microbes to introduce beneficial traits.
II.Recombinant DNA Technology: Cloning
genes into plasmids for expression in microbes.
3. Genetic Engineering of Microbes

20. III. Synthetic Biology: Designing and constructing new genetic circuits and pathways in
microbes to control behaviour or functions. It allows for the creation of programmable
biological systems.

21. 4. Microbiome Modulation Techniques
• Probiotics: Probiotics are live beneficial microorganisms that, when administered in
adequate amounts, confer health benefits to the host.
• Prebiotics: Prebiotics are non-digestible food components that selectively stimulate the
growth or activity of beneficial microorganisms in the gut. Supplying nutrients that
selectively feed beneficial microbes.
• Synbiotics: Combination of probiotics and prebiotics.
• Fecal Microbiota Transplantation (FMT): Transferring fecal microbiota from a healthy
donor to a recipient (commonly used in gut microbiome therapy).

22. Applications of Microbiome in human health
│
┌───────────────┼────────────────┐
│ │ │
Gut Health Immune System Disease Diagnostics
│ │ │
▼ ▼ ▼
Maintains Modulates Biomarkers for
digestive immune response early disease
balance and tolerance detection
│ │ │
▼ ▼ ▼
Prevention Reduces risk Personalized
of diarrhoea, of allergies, medicine and
IBS, IBD asthma, etc. treatment plans
┌───────────────┼────────────────┐
│ │ │
Metabolic
Health Mental Health Therapeutics
│ │ │
▼ ▼ ▼
Influences Gut-brain Probiotic and
metabolism axis microbiome-based
and weight communication treatments
management (e.g., mood, for diseases
cognition) (e.g., C. difficile)

23. Applications of Microbiome in Agriculture
│
┌─────────────────────┼──────────────────────┐
│ │ │
Soil Health Plant Growth Promotion Biocontrol of Pathogens
│ │ │
Improves nutrient Enhances nutrient Suppresses harmful
cycling & soil uptake (e.g., nitrogen, microbes (e.g., fungi,
structure phosphorus) bacteria, viruses)
│ │ │
▼ ▼ ▼
Reduces need for Promotes root Reduces chemical
chemical fertilizers development pesticide use
┌─────────────────────┼──────────────────────┐
│ │ │
Stress
Tolerance Crop Yield Improvement Bioremediation
│ │ │
▼ ▼ ▼
Improves plant Increases productivity Degrades pollutants
resilience to under various (e.g., pesticides,
drought, salinity, conditions heavy metals)
and disease
└────────────────────────────────────────────┘
Sustainable Agriculture

24. Applications of Microbiome Engineering
in Environment and Industry
│
┌──────────────────┼──────────────────────┐
│ │ │
Environmental Industrial Waste Management
Applications Applications & Bioremediation
│ │ │
▼ ▼ ▼
Soil and water Biofuel production Degradation of pollutants
quality monitoring using engineered (e.g., oil spills,
and improvement microbes (e.g., algae) plastics, metals)
│ │ │
▼ ▼ ▼
Bioremediation of Biomanufacturing of Waste-to-energy
heavy metals, enzymes, chemicals, conversion using
pesticides and materials engineered consortia
┌──────────────────┼──────────────────────┐
│ │ │
Climate Change Food and Beverage Biofertilizers and
Mitigation Industry Biopesticides
│ │ │
▼ ▼ ▼
Methane-reducing Fermentation Engineered microbial
gut microbiota in optimization (e.g., products to reduce
livestock probiotics, Flavors) chemical input
└────────────────────────────────────────────┘
Toward Sustainable Industry and a
Healthier Environment

25. Future Prospects of Microbiome Engineering
Field Future Prospects
Healthcare -Personalized microbiome-based therapies
- Microbiome editing for disease prevention and
treatment
- Development of next-gen probiotics and
microbiome drugs
Agriculture - Precision microbiome management for crop
yield and resilience
- Engineered biofertilizers and biopesticides
- Climate-smart farming via microbiome
solutions
Environment - Advanced bioremediation using synthetic
microbial consortia
- Pollution and waste degradation
- Carbon capture and ecosystem restoration
through engineered microbes
Food & Nutrition - Microbiome-informed dietary plans
- Functional foods with engineered microbes
- Enhanced fermentation processes for food
preservation and quality

26. Achievements of Microbiome Engineering
 Synthetic Microbial Communities (SynComs):
Researchers are designing and testing synthetic microbial communities (SynComs) to
specifically enhance plant disease resistance and abiotic stress tolerance. This involves rationally
selecting beneficial microbes and understanding their synergistic interactions.
 Sustainable Agriculture:
Microbial modulation promotes eco-friendly practices, enhances soil health, reduces
pollution, supports long-term sustainability, and facilitates chemical-free food production.
Traditional approaches like crop rotation are also being re-examined for their positive impact on soil
microbial diversity.
 Biotechnology & Synthetic Biology:
Synthetic Biology-Enabled Probiotics Utilizing synthetic biology, scientists have engineered
probiotics with enhanced stability and targeted therapeutic delivery capabilities. These advancements
improve the efficacy of probiotics in treating various health conditions.
 DNA Methylation for Microbiome Modulation:
Emerging research highlights the role of bacterial DNA methylation in regulating gene
expression. Harnessing this mechanism offers a reversible and precise method to modulate microbiome
functions without altering the DNA sequence.

27.  Human Health & Medicine
Skin Microbiome as a Vaccine Platform:
Scientists transformed the common skin bacterium Staphylococcus epidermidis into a
topical vaccine platform. In mice, this approach elicited strong and specific antibody responses,
suggesting potential for non-invasive vaccine delivery.
CRISPR-Based Gut Microbiome Editing:
Advancements in CRISPR-Cas systems have enabled precise editing of gut bacteria, allowing
for the removal of harmful gene clusters and the enhancement of beneficial metabolic pathways.
 Agriculture & Environmental Sustainability:
Reducing Methane Emissions in Cattle:
A collaborative project is exploring the use of CRISPR technology to edit the gut microbiome of
cows, aiming to suppress methane-producing archaea. This approach could significantly lower
greenhouse gas emissions from livestock.
Enhancing Soil Health through Composting:
Studies have shown that composting human excrement transitions its microbiome from gut-like to
soil-like, enriching soil microbial diversity and promoting sustainable agriculture practices.

28. 28

29. CASE STUDY I

30. Methodology
1.
2.
3.
4.
5.
Bacteria Collection Bacillus sp. PM31 and Testing
Maize Seed Preparation
Salinity Stress Setup
Plants were grown in pots and watered with different salt concentrations
(0, 300, 600, and 900 mM NaCl).
Measurements Taken
After 21 days, they measured plant height, weight, root length, leaf area,
and water content.
Gene Analysis
Special tests (PCR and qRT-PCR) were done to examine stress-related genes in
both bacteria and plants.

31. ACS Omega
http://pubs.acs.org/journal/acsodf

32. Result
Effect of Bacillus sp. PM31 on plant growth promotion of Zea mays L. under salinity stress.
Growth curve analysis of Bacillus sp. PM31 under salinity stress
ACS Omega http://pubs.acs.org/journal/acsodf

33. CONCLUSION
• The beneficial bacteria Bacillus sp. PM31 can help maize plants grow better
under salt stress (salty soil conditions). When maize plants were treated with this
bacteria
• Their growth improved (taller plants, bigger roots, more biomass).
• They had higher levels of helpful substances (like sugars, proteins, chlorophyll,
antioxidants).
• They showed lower levels of harmful stress indicators (like hydrogen peroxide and
MDA).Malondialdehyde.
• Their stress-fighting genes (APX and SOD) became more active.
• This means that Bacillus PM31 can be used as a natural, eco-friendly solution
(biofertilizer) to help crops survive and grow well in salty soils.

34. CASE STUDY II

35. Methodology
1. Sample collection from different sites
2. DNA extraction by using kit method
3. Shotgun Metagenomics Sequencing and Bioinformatic
analysis of data
4. Data analysis and visualization of it.

36. 36
Result
•Microbial Community Differences:
•Principal Component Analysis (PCA) and diversity indices showed significant differences between wild and
cultivated rice rhizospheres.
•Wild rice had greater microbial diversity and more complex S-cycling networks.
•Functional Verification:
•Synthetic microbiome inoculation significantly enhanced root elongation in both wild and cultivated rice.
Response of rice roots to synthetic microbiome.
a. Root and pot figures of wild and cultivated rice at day 0 and day 7 under different synthetic microbiomes inoculation.
There are 5 pots as biological replicates for each treatment.
b. Difference of root elongation (/mm)

37.  Domestication has simplified the sulfur-cycling microbial community in
rice rhizospheres, reducing microbial diversity and beneficial interactions.
 The study confirms that synthetic microbiomes based on dominant wild rice
microbes can enhance sulfur utilization in cultivated rice.
 The findings suggest that step-by-step construction of synthetic microbiomes
based on functional genes is a promising strategy for improving plant-
microbe interactions and advancing sustainable agriculture.
CONCLUSION

38. CONCLUSION OF MICROBIOME ENGINEERING
 Microbiome engineering holds transformative potential in health,
agriculture, and environmental sustainability.
 By manipulating microbial communities, scientists can improve
disease resistance, enhance nutrient absorption, and develop targeted
therapies. However, the field must navigate ethical, ecological, and
safety challenges to ensure responsible application.
 Continued research, regulation, and public engagement will be
essential in unlocking the full promise of microbiome engineering for
the benefit of humanity and the planet.

39. Challenges of microbiome engineering
1. Effect of abiotic or environmental factors
2. Deeper understanding of the microbial community structure over time
3. Limited ability to harness and manipulate the microbiome in agriculture
4. Nature and mechanisms of microbiota-plant relationship
5. Bridging the lab-field gap

40. Summary
 Microbiome engineering involves manipulating microbial communities to enhance health,
agriculture, industry, and the environment.
 It integrates microbiology, biotechnology, synthetic biology, and ecology using tools like
CRISPR and recombinant DNA.
The seminar covers types of microbiomes—plant, soil, rhizospheric, and human—and their
roles in biotechnology.
 Applications include fermentation, pharmaceuticals, bioplastics, and microbiome
modulation via various techniques.
Case studies feature Bacillus sp. PM31 in maize under salt stress and synthetic microbiomes in
rice.
 Key benefits span gut health, crop yield, bioremediation, and biofuels.
 The seminar concludes with both the promise and challenges of real-world microbiome
engineering.

41. REFERENCES
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mediated salinity stress tolerance in maize (Zea mays L.): a fortunate way toward sustainable agriculture.
ACS Omega 8 (23), 20471–20487.
Bruinsma, J., Fischer, G., Nachtergaele, F., Poulisse, J., Tran, D., Griffee, P., Clarke, L., 2015. Crop
production and natural resource use. World Agric.: Towards 2030, 127–137.
Chaudhary, T., Shukla, P., 2020. Commercial bioinoculant development: techniques and challenges. In:
Shukla, P. (Ed.), Microbial Enzymes and Biotechniques. Springer, Singapore.
Macia, J., Manzoni, R., Conde, N., Urrios, A., de Nadal, E., Sole, R., Posas, F., 2016. Implementation of
complex biological logic circuits using spatially distributed multicellular consortia. PLoS Comput.
Nautiyal, C.S., Srivastava, S., Chauhan, P.S., Seem, K., Mishra, A., Sopory, S.K., 2013. Plant growth-
promoting bacteria Bacillus amyloliquefaciens NBRISN13 modulates gene expression profile of leaf and
rhizosphere community in rice during salt stress. Plant Physiol. Biochem. 66, 1–9.

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