Strain-specific and functional alterations of the human gut microbiome in cancer: A reanalysis of shotgun metagenomics data
(2025) MOBN03 20242Degree Projects in Molecular Biology
- Abstract
- Human gut microbiome plays significant role in maintaining health and homeostasis of the host immune system by modulating immune metabolism, metabolic functions and acting as a barrier against pathogens. Therefore, characterizing the gut microbiome is vital for understanding its role in cancer as several studies have leveraged the strong correlation between gut microbiome dysbiosis and various types of cancer. This study re-analyzed the whole genome shotgun raw DNA sequencing data from a published cohort consisting of six different types of cancer patients and matched healthy controls to investigate gut microbiome alterations at strain level. We employed reference-based approach to study of the alteration of the gut microbiome in cancer at... (More)
- Human gut microbiome plays significant role in maintaining health and homeostasis of the host immune system by modulating immune metabolism, metabolic functions and acting as a barrier against pathogens. Therefore, characterizing the gut microbiome is vital for understanding its role in cancer as several studies have leveraged the strong correlation between gut microbiome dysbiosis and various types of cancer. This study re-analyzed the whole genome shotgun raw DNA sequencing data from a published cohort consisting of six different types of cancer patients and matched healthy controls to investigate gut microbiome alterations at strain level. We employed reference-based approach to study of the alteration of the gut microbiome in cancer at the strain level using a multi-integrated pipeline to assess taxonomic diversity, phylogenetic structure and functional profiles of microbial communities in cancer vs control. Our findings illustrate significant alterations in gut microbiome in different cancer groups, specifically in lymphoma and leukemia that is indicated by reduced alpha diversity as well as significantly different beta diversity across several different cancer groups. We also observed enrichment of Faecalibacillus intestinalis in control aligning with previous research while enrichment of other species in cancer was observed that was not previously reported such as Escherichia coli, Clostridium innocuum. Interestingly, we found a signature of cancer in the strains of some species that were not found to be differentially enriched in cancer. Importantly, we also did gene level analysis that was absent from original study and identified the presence of certain key functional genes in cancer, for example antibiotic resistance genes and toxin/antitoxin systems. This in turn highlight the need to uncover hidden microbial signatures in cancer which may contribute to the development of targeted therapies and may pave the way for next generation probiotics. It also highlights the limitations of reference-based method which can be complemented with an alternative assembly-based approach. (Less)
- Popular Abstract
- Our gut is home for trillions of microbes responsible for maintaining overall health mainly by regulating nutrient absorption, metabolizing drugs and serve as a protective barrier against pathogens. However, there are several commensals which can act as opportunistic pathogen under any stressful conditions thereby altering the composition of gut microbiome. One such condition that we will be going to address is cancer. In this project, I explored the alteration of gut microbiome in different cancer groups and are there significant relationships between gut microbiome and cancer.
We start with re-analyzing whole genome shotgun raw DNA sequencing data from already published cohort. Previous studies had mostly looked at changes in the gut... (More) - Our gut is home for trillions of microbes responsible for maintaining overall health mainly by regulating nutrient absorption, metabolizing drugs and serve as a protective barrier against pathogens. However, there are several commensals which can act as opportunistic pathogen under any stressful conditions thereby altering the composition of gut microbiome. One such condition that we will be going to address is cancer. In this project, I explored the alteration of gut microbiome in different cancer groups and are there significant relationships between gut microbiome and cancer.
We start with re-analyzing whole genome shotgun raw DNA sequencing data from already published cohort. Previous studies had mostly looked at changes in the gut microbiome at species level. Our study analyzed data at a deeper level as it looked at changes in the gut microbiome not just at species level but also at strain level as well trying to identify presence of key functional genes such as those associated with antibiotic resistance using reference-based method.
Our results show clear differences in composition of the gut microbiota between different cancer groups and matched healthy controls, especially in the case of leukemia and lymphoma that were not clearly studied previously. For instance, the presence of key species belonging to genera Clostridium and Enterobacter as well as presence of Escherichia coli in all cancers except leukemia was found, possibly suggesting their role in cancer. Interestingly, based on our analysis, we found signature of cancer at the strain level that was not detectable at the species level.
At functional level, our results indicate significant differences between cancer and control group. However, to complement our findings and to overcome the limitations of reference-based method we plan to use assembly-based approach which will be continued in future. (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9213107
- author
- Ahmad, Ramsha
- supervisor
- organization
- course
- MOBN03 20242
- year
- 2025
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9213107
- date added to LUP
- 2025-09-24 15:13:20
- date last changed
- 2025-09-24 15:13:20
@misc{9213107,
abstract = {{Human gut microbiome plays significant role in maintaining health and homeostasis of the host immune system by modulating immune metabolism, metabolic functions and acting as a barrier against pathogens. Therefore, characterizing the gut microbiome is vital for understanding its role in cancer as several studies have leveraged the strong correlation between gut microbiome dysbiosis and various types of cancer. This study re-analyzed the whole genome shotgun raw DNA sequencing data from a published cohort consisting of six different types of cancer patients and matched healthy controls to investigate gut microbiome alterations at strain level. We employed reference-based approach to study of the alteration of the gut microbiome in cancer at the strain level using a multi-integrated pipeline to assess taxonomic diversity, phylogenetic structure and functional profiles of microbial communities in cancer vs control. Our findings illustrate significant alterations in gut microbiome in different cancer groups, specifically in lymphoma and leukemia that is indicated by reduced alpha diversity as well as significantly different beta diversity across several different cancer groups. We also observed enrichment of Faecalibacillus intestinalis in control aligning with previous research while enrichment of other species in cancer was observed that was not previously reported such as Escherichia coli, Clostridium innocuum. Interestingly, we found a signature of cancer in the strains of some species that were not found to be differentially enriched in cancer. Importantly, we also did gene level analysis that was absent from original study and identified the presence of certain key functional genes in cancer, for example antibiotic resistance genes and toxin/antitoxin systems. This in turn highlight the need to uncover hidden microbial signatures in cancer which may contribute to the development of targeted therapies and may pave the way for next generation probiotics. It also highlights the limitations of reference-based method which can be complemented with an alternative assembly-based approach.}},
author = {{Ahmad, Ramsha}},
language = {{eng}},
note = {{Student Paper}},
title = {{Strain-specific and functional alterations of the human gut microbiome in cancer: A reanalysis of shotgun metagenomics data}},
year = {{2025}},
}