Understanding The Biomass Conversion Processes Through

Community-wide Metabolic Interaction Network of Deep

Biosphere
Submitted by
Dikesh Kumar
(20BT30008)

Bachelor Thesis Project

Under the supervision of

Prof. Pinaki Sar

Department of Bioscience & Biotechnology

Indian Institute of Technology, Kharagpur
Table of
contents
01 02 03
Introduction Research gap Objective

04 05
Methodology Result & Future Scope
01
This study explores the community-wide metabolic

Introduction
interaction networks in the deep biosphere, focusing
on the intricate microbial dynamics and key pathways
that underpin biomass conversion processes, thereby
enhancing our understanding of microbial community
functionality in extreme environments.
01 IntroductionContinued…

● Deep Biosphere and Metabolic

Interactions

● Why is it important to understand?

● How does our study help to

understand this?
● Wood-Ljungdahl pathway

● Acetogenic Bacteria and

Acetogenesis

● 16S rRNA amplicon sequencing

02 Research Gap
1.Insufficient characterization of interspecies metabolic
exchanges and their impact on nutrient cycles within the
deep biosphere’s microbial ecosystems.

2.Inadequate understanding of the survival mechanisms

and metabolic flexibility of extremophilic microorganisms
under varying environmental stresses.
03 Objectives
1.Investigate Community-Wide Metabolic Networks:
Examine the interactions and dynamics within community-
wide metabolic networks to enhance understanding of
biomass conversion processes in the deep biosphere's
microbial communities.

2.Metabolites Analysis : Analyse consumed and produced

metabolites within microbial pathways.
0
4ethodology
M
Steps involved in Metabolic
network Construction

Data Collection

Network Construction
Data Analysis

Metabolic Mapping
 Data Collection

Employ 16S rRNA amplicon sequencing to identify

microbial taxa.

Perform metagenomic sampling to capture

comprehensive genetic diversity.
 Data Analysis

Use QIIME2 to classify and quantify microbial

communities.

Apply PICRUSt2 to predict the functional potential

of microbial consortia.
 Metabolic Mapping

Analyze pathways using MetaCyc to elucidate

metabolic processes.

Integrated MetaCyc data with 16S rRNA amplicon

sequencing results to predict the functional activities
of microbial taxa within the community
 Network Construction

Developed a detailed map of the microbial metabolic

network, showcasing how different organisms' pathways
intersect and influence each other within the community.

Investigated the flow of substrates and products

through the metabolic pathways to understand the
efficiency and regulation of biomass conversion
processes.
0
5esult & Future Scope
R
 Sample Pathway

MetaCyc Analysis

Identified major metabolites associated

with pathways and integrating information
about consumed and produced
metabolites into the dataset.

Source: https://www.researchgate.net/figure/A-typical-MetaCyc-pathway-A-short-pathway-was-
selected-for-this-figure-the-average_fig1_320593085
MetaCyc Analysed Dataset
Sankey Chart for Pathways and Consumed metabolites
 Metabolic Connectivity Network
CALVI
N-PWY
GLYCOLY
SIS-TCA-
GLYOX-
BYPASS

PENTO
-
e5 SE-P-
los
ibu te PWY
D-r spha
acetyl-CoA

o
ph

RIBOS
YN2-
PWY
oxaloacetate

NONO
P42- XIPEN PWY-
PWY T-PWY 7560
D-
3-p glyce
ho ral
sp de
ha hy
te de
oxaloacetate

(S)-malate GLUCO NONM PWY-

PWY-
NEO- EVIPP- 5121
6969
PWY PWY

pyruvate

P42- PWY-
PWY-
PWY 7111
5484
 Future Scope

Extended Environmental Variables Analysis:

•Study impact of temperature, pH, substrate
composition.

Deeper Metabolic Pathway Advanced Omics Techniques:

Characterization: •Implement newer genomics and
•Explore lesser-known pathways and their roles proteomics technologies.
 Reference
1.
s:
Sahu, R. P., Kazy, S. K., Bose, H., Mandal, S., Dutta, A., Saha, A., ... & Sar, P. (2022). Microbial diversity and function in crystalline basement
beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environmental Microbiology, 24(6), 2837-2853.

2. Dutta, A., Dutta Gupta, S., Gupta, A., Sarkar, J., Roy, S., Mukherjee, A., & Sar, P. (2018). Exploration of deep terrestrial subsurface microbiome in
Late Cretaceous Deccan traps and underlying Archean basement, India. Scientific reports, 8(1), 17459.

3. Teske, A., Biddle, J. F., Edgcomb, V. P., & Schippers, A. (2013). Deep subsurface microbiology: a guide to the research topic papers. Frontiers in
microbiology, 4, 122.

4. Sravan, J. S., Tharak, A., & Mohan, S. V. (2021). Status of biogas production and biogas upgrading: A global scenario. In Emerging technologies and
biological systems for biogas upgrading (pp. 3-26). Academic Press.

5. Mondal, Suman, Pritam Kundu, and Amit Ghosh. "Understanding the biomass conversion processes of bovine gut microbiota through community-
wide metabolic interaction network." Bioresource Technology Reports 17 (2022): 100989.

6. Sahu, Rajendra Prasad, et al. "Microbial diversity and function in crystalline basement beneath the Deccan traps explored in a 3 km borehole at
Koyna, western India." Environmental Microbiology 24.6 (2022): 2837-2853.

7. Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., ... & Langille, M. G. (2020). PICRUSt2 for prediction of
metagenome functions. Nature biotechnology, 38(6), 685-688.
Thank
You