2023-07-31 17:59:03
All the mysteries of the organism pass through the flora and fauna of our intestinal system. Or not. The truth is that for any pathology there is always evidence in the microbiome. And the time has come when scientists have said that not everything is so and that “if we constantly repeat falsehoods about minor details, can our accuracy be trusted when we cover more important matters?”
This is how emphatic Alan Walker and Lesley Hoyles are in a Perspective article in Nature Microbiology. In the same they have dissected the explosin of recent research on the human microbiome and have brought to the table inaccuracies that lack a solid evidence base.
From all this analysis they have summarized 12 persistent or emerging myths and misconceptions where they describe their factual inaccuracies. This surge in interest has also generated hype and entrenched some misconceptions. Statements on this subject can be repeated to be considered fact, without strong supporting evidence and with ambiguity regarding the original source.
Walker and Hoyles, researchers from the Universities of Aberdeen and Nottingham, say that demystifying and correcting misconceptions, even relatively minor ones, is important to avoid unproductive research projectsencourage critical thinking, and preserve public confidence in microbiome science.
1. New field. Although the most prosperous advances date from 15 years ago, the first investigations on microorganisms associated with humans occurred more than a hundred years ago. The Escherichia coli bacterium was described as early as 1885.
2. Joshua Lederberg coined the term “microbiome.” The Nobel Prize-winning microbiologist is not responsible for the naming in 2001, because microbiota is a basic microbiological term in common use for at least 50 years.
3. There are 1012 bacterial cells per gram of human feces. Through some complex tests it has been determined that it usually ranges between 1010 and 1011 microbial cells per gram of wet weight of feces.
4. It weighs between one and two kilos. At most it reaches 500 grams. This is because the majority of the human microbiota resides in the colon, and “these microorganisms usually represent less than half the weight of fecal solids.”
5. It outnumbers human cells by a ratio of 10:1. It is one of the most repeated misconceptions. It has been shown to originate from an “end of the envelope” calculation in the 1970s, when in reality the ratio is closer to 1:1. It should be noted that “the ratio is likely to vary from person to person and depends on factors such as the size of the host’s body and the amount of fecal material carried in the colon.”
6. It is inherited from mother to son. Although some microorganisms are transferred during childbirth, proportionally few species of microbiota are truly “inherited” and persist from birth to adulthood in offspring. “Each adult ends up with a unique microbiota configuration, even identical twins raised in the same home.”
7. Most diseases are characterized by a pathobiome. This concept has been “loosely” defined as detrimental interactions between microbial communities and their host that lead to disease. Unfortunately, “this term is too simplistic and inherently flawed.” There is no evidence that it has a characteristic role in “most” diseases.
8. The firmicutes-bacteroidetes ratio is altered in obesity. This commonly used but erroneous statement about two of the five families of bacteria present in the microbiota “derives primarily from rodent-based research and from findings in underpowered or single human studies.” However, as with many other studies reporting links between specific microbiota profiles and disease, “reproducibility is poor.”
9. The microbiome is functionally redundant. This argument stems from studies showing that while “the taxonomic composition of human metagenomes can vary enormously”. Although there are important functions that are conserved in many different species of human microbiota, such as the production of short-chain fatty acids, “there are many key functions that are only carried out by a relatively small number of microbiota species.”
10. Sequencing is unbiased. Although sequence-based methods have been transformative for microbiome research, they are not perfect.
11. Need for a standardized methodology. This view is prevalent in the microbiome field and is sensibly based on a desire to make it easier and more robust to compare results from different studies.
12. Most of the human microbiota is ‘uncultivable’. While cultivation is undeniably labor intensive, “it has its own biases and often requires expensive specialized equipment and media, there are clear advantages to having microorganisms in culture.” These include enabling mechanistic experiments, verifying genomic predictions, and developing them as novel therapies.
Reactions from the scientific community
Toni Gabaldn, ICREA research professor and head of the Comparative Genomics group at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC-CNS), explains to SMC that “the field of microbiome study (like other fields in rapidly expanding) suffers from the existence of dogmas and simplifications assumed early on based on very limited information and that we have to correct and modulate as we learn more. One of the most important qualities of science is its ability to self-correct.”
Joining him, also at SMC, Rob Knight, director of the Microbiome Innovation Center and professor at the University of California, San Diego, points out that “the lack of replication of microbiome associations with disease is an important issue, but it has “more nuanced than described in the article. To be useful as a clinical test, a microbe or microbiome pattern need not cause disease, but simply act as an accurate marker of disease.”
There are other experts who state that “this type of article does not provide new results, but it can help the field to advance more precisely and focus efforts on priority research questions”, as Mireia Valls-Colomer, an expert microbiologist in the field, argues. study of the impact of the intestinal microbiome on health, researcher at the Computational Metagenomics Laboratory of the University of Trento (Italy).
But, as Michael Woodworth, researcher in microbial therapeutics, Associate Professor of Medicine, Emory University School of Medicine, stresses, “Many of these myths have already been highlighted by earlier writers, but they need to be consolidated to discourage their perpetuation.
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