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Debunking Myths: The Truth About Human Microbiome
In the vast landscape of human health and medical research, few fields have captivated and puzzled us as much as the enigmatic world of the human microbiome. These trillions of microorganisms living inside and on our bodies hold keys to understanding our health, yet they also harbour a myriad of misconceptions. Over the past two decades, interest in this intriguing field has spiked, but with it comes a troubling surge in hype and misinformation. This has led to a cloud of myths surrounding the human microbiome that often obscure the truth and hinder scientific progress. In this blog post, we’ll dissect twelve myths, bringing you a clear, evidence-based view of the intriguing world of the human microbiome. Join us as we delve into the facts, debunk the myths, and explore the multifaceted reality of this fascinating field based on a recent article appeared in Nature Microbiology.
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Myths and Misconceptions
A nascent field? The truth about microbiome research: Contrary to the belief that microbiome research is in its infancy, it has a rich history, dating back to the late nineteenth century, when microorganisms such as Escherichia coli and bifidobacteria were first isolated and identified. Notable concepts such as the gut-brain axis have been studied for centuries, and the health impacts of key microbiome-associated metabolites were reported over four decades ago.
The origination of the term ‘microbiome’: It is a common misunderstanding that Nobel laureate Joshua Lederberg invented the term ‘microbiome.’ However, it was used in its modern context more than a decade before he began using it in 2001.
The overestimation of bacterial cells in human faeces: The frequently quoted figure of 10^12 bacterial cells per gram of human faeces likely stemmed from dry-weight measurements rather than wet-weight counts. The true figure, as confirmed by methods like direct cell counts, fluorescence in situ hybridization, flow cytometry, and qPCR, ranges between 10^10 and 10^11 cells per wet gram.
Microbiota outnumbering human cells?: The belief that the microbiota outnumbers human cells by a ratio of 10:1 originated from a rough estimate in the 1970s. More detailed analyses show a 1:1 ratio, although this can vary based on factors like body size and the amount of fecal material in the colon.
Inheritance of the microbiota from mother at birth: While some microorganisms are transferred from mother to baby during birth, few persist from birth to adulthood. Most gut microbiota diversity develops after birth, and every adult ends up with a unique microbiota configuration, shaped by environmental exposures, diet, antibiotic therapy, and host genetics.
The oversimplification of the pathobiome concept: The term ‘pathobiome,’ loosely defined as harmful interactions between microbial communities and their host leading to disease, is simplistic and lacks the precision required for clinical practice. Diseases show inconsistent alterations in microbiota, making it challenging to identify specific gut microbiota configurations associated with disease progression.
The myth of the Firmicutes:Bacteroidetes ratio in obesity: The belief that the Firmicutes:Bacteroidetes ratio is altered in obesity primarily stems from rodent research and underpowered human studies. However, there are no reproducible microbial taxonomic signatures of obesity in humans.
Functional redundancy of the gut microbiome: While the taxonomic composition of human metagenomes varies greatly, functional gene prediction profiles remain consistent. However, this perspective fails to capture specialist or less well-characterized functions, making the claim of functional redundancy an oversimplification.
Bias in sequencing: Despite the transformative nature of sequence-based methods for microbiome research, they are not perfect. Biases can be introduced at every step, from sample collection and storage to DNA extraction and data analysis.
Standardized methodologies: more harm than good?: The idea that the microbiome field needs standardized methodologies is sensible but flawed. Each methodology carries its own biases, and what works best may depend on the specific microbial community in a given sample. A diversified approach with increased transparency in methodology reporting is more effective.
The ‘unculturable’ human microbiota: The belief that most human-associated microorganisms cannot be cultivated in the laboratory is not entirely accurate. A reasonably large portion of our bacterial and archaeal microbiota has been successfully cultured, and continued effort is likely to reduce the current gaps in culture collections.
The potential benefits of personalized microbiome medicine: Although the concept of tailoring medical treatments based on an individual’s microbiome composition seems attractive, it’s currently fraught with challenges, mostly due to the vast complexity and variability of the microbiome. However, as our understanding deepens and technology advances, this could be a promising direction for future research.
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Conclusion
In conclusion, while the field of human microbiome research has seen significant progress, it’s also riddled with misconceptions and myths. It’s important to acknowledge that microbiome research is not a nascent field, that Lederberg did not coin the term ‘microbiome’, and that the number of microbial cells has been commonly overestimated. Furthermore, the belief that microbiota is inherited at birth and persists into adulthood is oversimplified, as is the concept of a ‘pathobiome’. The relationship between obesity and the Firmicutes:Bacteroidetes ratio, along with the notion of functional redundancy in the gut microbiome, requires deeper understanding. It’s equally crucial to recognise the biases in sequencing techniques, the limitations of standardised methodologies, and the inaccuracies surrounding the ‘unculturable’ human microbiota. Finally, while personalised microbiome medicine promises immense potential, it is currently a challenging prospect due to the vast complexity and variability of the microbiome.
As we navigate this fascinating yet complex field, it’s incumbent upon us to critically evaluate the information we encounter. Continuous research, coupled with an understanding of the historical context, will be key to dispelling these myths and unveiling the truth about our microbial companions. Remember, as we learn more about our microscopic allies, we uncover more about ourselves and our health.
In light of this, we encourage everyone, from researchers to health professionals to laypeople, to engage in ongoing dialogue and learning about the microbiome. Whether it’s keeping up-to-date with the latest research, participating in scientific discussions, or sharing this knowledge with others, every action contributes to a greater collective understanding of this crucial area of study. Let’s step into a future where the true potentials of the microbiome are fully understood and harnessed for the betterment of human health.
Additional Reading
Cani PD 2018. Human gut microbiome: hopes, threats and promises. Gut 67:1716-1725. http://dx.doi.org/10.1136/gutjnl-2018-316723
Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV & Knight R 2018. Current understanding of the human microbiome. Nature Medicine24(4):392-400. https://doi.org/10.1038/nm.4517.
Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, et al. 2022. The core human microbiome: Does it exist and how can we find it? A critical review of the concept. Nutrients14(14): 2872. https://doi.org/10.3390/nu14142872
Walker AW & Hoyles L 2023. Human microbiome myths and misconceptions. Nature Microbiology 8:1392–1396. https://doi.org/10.1038/s41564-023-01426-7