Microbiology: Current Research

All submissions of the EM system will be redirected to Online Manuscript Submission System. Authors are requested to submit articles directly to Online Manuscript Submission System of respective journal.
Reach Us +1 (202) 780-3397

Opinion Article - Microbiology: Current Research (2024) Volume 8, Issue 2

Metagenomic profiling of gut microbiota in health and disease.

Yuki Tanaka *

Department of Biomedical Biotechnology, University of Tokyo, Japan

*Corresponding Author:
Yuki Tanaka
Department of Biomedical Biotechnology, University of Tokyo, Japan
E-mail: yuki@u-tokyo.ac.jp

Received: 01-Apr-2024, Manuscript No. AAMCR-24-135731; Editor assigned: 02-Apr-2024, PreQC No AAMCR-24-135731 (PQ) Reviewed:16-Apr-2024, QC No. AAMCR-24-135731 Revised:23-Apr-2024, Manuscript No. AAMCR-24-135731 (R); Published:29-Apr-2024, DOI:10.35841/aamcr-8.2.200

Citation: Tanaka Y. Metagenomic profiling of gut microbiota in health and disease. J Micro Curr Res. 2024; 8(2):200

Visit for more related articles at Microbiology: Current Research


The human gut is a complex ecosystem, home to trillions of microorganisms that play critical roles in maintaining health and influencing disease. The advent of metagenomic profiling has revolutionized our understanding of this microbiota, offering profound insights into its composition, function, and dynamic interactions with the host. This article explores the principles of metagenomic profiling and its implications in health and disease [1].

Metagenomic profiling involves sequencing the collective genomes of microbial communities directly from their natural environment, bypassing the need for culturing. This approach leverages high-throughput sequencing technologies, bioinformatics tools, and vast genomic databases to identify and quantify microbial species, genes, and functional pathways. By analyzing these genetic materials, researchers can gain a comprehensive picture of the microbial ecosystem [2].

The gut microbiota comprises bacteria, archaea, viruses, and fungi, with bacteria being the most extensively studied. Major bacterial phyla include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. These microorganisms contribute to various physiological functions, such as digestion, immune modulation, and protection against pathogens. The diversity and balance of these microbial communities are crucial for maintaining gut health [3].

A healthy gut microbiota is essential for nutrient absorption, production of short-chain fatty acids (SCFAs), synthesis of vitamins, and regulation of the immune system. SCFAs, like butyrate, propionate, and acetate, are key energy sources for colon cells and have anti-inflammatory properties. Moreover, gut bacteria play a pivotal role in the development and function of the immune system, influencing systemic immunity and preventing autoimmune diseases [4].

Dysbiosis, an imbalance in the microbial community, is associated with a variety of diseases. Conditions such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, diabetes, and even mental health disorders like depression and anxiety have been linked to altered gut microbiota. For instance, patients with IBD often exhibit reduced microbial diversity and an overrepresentation of pathogenic bacteria, which may contribute to chronic inflammation [5].

Metagenomic studies have revealed that IBD is characterized by a depletion of beneficial bacteria, such as Faecalibacterium prausnitzii, and an increase in harmful species like Escherichia coli. These microbial shifts can disrupt the gut barrier, leading to an immune response and sustained inflammation. Understanding these microbial changes has opened new avenues for therapeutic interventions, including probiotics, prebiotics, and fecal microbiota transplantation (FMT) [6].

The gut microbiota influences metabolic processes and energy balance. Studies have shown that obese individuals tend to have a higher ratio of Firmicutes to Bacteroidetes compared to lean individuals. This altered ratio affects the efficiency of caloric extraction from food and can promote fat storage. Metagenomic profiling helps in identifying these imbalances and developing strategies to modulate the microbiota for weight management [7].

The gut-brain axis, a bidirectional communication system between the gut and the brain, underscores the influence of gut microbiota on mental health. Dysbiosis has been implicated in conditions such as depression, anxiety, and autism spectrum disorders. Metagenomic profiling enables the identification of microbial metabolites that affect brain function, offering potential biomarkers and targets for treatment [8].

Emerging research suggests that gut microbiota may influence cancer development and response to treatment. Certain bacteria can produce metabolites that promote or inhibit tumor growth. Metagenomic studies have identified specific microbial signatures associated with colorectal cancer, providing insights into microbial-driven carcinogenesis and potential therapeutic targets [9].

Advancements in sequencing technologies, such as next-generation sequencing (NGS) and long-read sequencing, have significantly enhanced the resolution and accuracy of metagenomic profiling. However, challenges remain, including the need for improved bioinformatics tools to handle large datasets, accurate taxonomic classification, and the integration of multi-omics data to understand host-microbe interactions comprehensively [10].


Metagenomic profiling has significantly advanced our understanding of the gut microbiota and its critical role in health and disease. By revealing the intricate relationships between microbes and their host, this technology paves the way for innovative therapeutic approaches and personalized medical strategies. Continued research and technological advancements will undoubtedly enhance our ability to harness the microbiome for improving human health.


  1. Mihajlovic M, Vlajkovic S, Jovanovic P, et al. Primary Mucosal Melanomas: A Comprehensive Review. Int j clinical Exp Pathol. 2012;5(8):739.
  2. Indexed atGoogle scholar

  3. Lian B, Cui CL, Zhou L, et al. The natural history and patterns of metastases from mucosal melanoma: an analysis of 706 prospectively-followed patients. Annals of Oncol. 2017;28(4):868-73.
  4. Indexed atGoogle scholarCross Ref

  5. Furney SJ, Turajlic S, Stamp G, et al. Genome sequencing of mucosal melanomas reveals that they are driven by distinct mechanisms from cutaneous melanoma. J Pathol. 2013;230(3):261-9.
  6. Indexed atGoogle scholarCross Ref

  7. Newell F, Kong Y, Wilmott JS, et al. Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets. Nat Communications. 2019;10(1):1-5.
  8. Indexed atGoogle scholarCross Ref

  9. Lebbé C, Meyer N, Mortier L, et al. Evaluation of two dosing regimens for nivolumab in combination with ipilimumab in patients with advanced melanoma: results from the phase IIIb/IV CheckMate 511 trial. J Clinical Oncol. 2019;37(11):867.
  10. Indexed atGoogle scholarCross Ref

  11. Della-Torre E, Lanzillotta MA, Doglioni C. Immunology of IgG4-related disease. Clinical & Exp Immunol. 2015;181(2):191-206.
  12. Indexed atGoogle scholarCross Ref

  13. Olson CG, Olson NY. Hyper igg4-related disease presenting with orbital tumor and immune deficiency. Case Reports in Immunol. 2021;2021.
  14. Indexed atGoogle scholarCross Ref

  15. Ryu JH, Sekiguchi H, Yi ES. Pulmonary manifestations of immunoglobulin G4-related sclerosing disease. Europ Resp J. 2012 Jan 1;39(1):180-6.
  16. Indexed atGoogle scholarCross Ref

  17. Neild GH, Rodriguez-Justo M, Wall C, et al. Hyper-IgG4 disease: report and characterisation of a new disease. BMC Med. 2006;4(1):1-8.
  18. Indexed atGoogle scholarCross Ref

  19. Chen LY, Mattman A, Seidman MA, et al. IgG4-related disease: what a hematologist needs to know. Haematol. 2019;104(3):444.
  20. Indexed atGoogle scholarCross Ref

Get the App