The Extinction Within Our Guts
Introduction
According to Erica Sonnenburg, senior research scientist in the Department of Microbiology at the Stanford University School of Medicine, for the approximately 180,000 years that humans exclusively foraged for food… their guts [had] up to 50% more bacterial species and twice as many bacterial genes than ours do (Sonnenburg 2016). In addition, global antibiotics consumption rates have increased by 46 percent in the last two decades…(Oxford 2021). There seems to be a connection between the two occurrences which must be further explored. Les Dethlefsen, research scientist from The Relman Lab at Stanford medical school asserts that although most courses of antibiotic treatment have no apparent adverse effects, antibiotics can cause significant changes in gut microbiota that have both short- and long-term health consequences (Dethlefsen and Relman, 2011). However the importance of antibiotics remains, as these medicines have effectively fought infections caused by bacteria for years. Antibiotic development has been one of the greatest medical advances of the 20th century and has drastically changed modern medicine by extending the human lifespan by many years. However, we cannot ignore the downsides as it is important to maintain the balance between use of antibiotics and our microbial ecosystem. Thus, there is an ongoing debate due to the research gaps, on the effects of antibiotics on the composition of the human gut microbiota.
Richness and Diversity
According to Francisco Guarner of Vall d’Hebron research center in Spain and his colleagues, “antibiotic use is associated with reduced microbiota diversity” and it has also shown to “disrupt the balance that exists between the various species of gut microbiota” (Guarner, et al. 2020). This assertion was further supported by a study conducted by the Relman lab at Stanford School of Medicine which researched the effects of a specific antibiotic, ciprofloxacin, on three individuals, concluding that the introduction of this antibiotic reduced the richness and diversity of the gut microbiota rapidly by several units (Dethlefsen, et al. 2010). In addition, the study mentioned that a large portion of the lost value was regained in a few days and richness and diversity also recovered quickly. However, this research failed to mention that although the overall microbial population may potentially rise, the species diversity is decreased after antibiotic therapy. For example, in a study conducted by Suchita Panda, lead researcher at 4D Pharma, tested the effects of broad-spectrum antibiotics on two different gut microbiota and concluded that although the ratio of the microbiota increased, it was due to the multiplication of antibiotic-resistant bacteria, causing richness to decrease significantly (Panda, et al. 2014). Furthermore, numerous common species were undetected even after the gut microbiota’s baseline composition was mostly recovered (Panda, et al. 2014). Dethlefsen and Panda argue for the potential use of probiotics to reverse the current disruptions in diversity and maintain the richness of the gut microbiome. Mirroring this argument, it is necessary to conduct further research on the gut microbiota and the role of probiotics to improve our understanding and resolve this extinction issue.
Health Issues
According to Andres Cubillos-Ruiz PHD, a research scientist at the Wyss Institute for Biologically Inspired Engineering at Harvard University, interventions such as medications lead to dysbiosis, altering of the microbiota’s composition, and “this unbalance can lead to various health issues” (Trafton 2022). In fact, the gut microbes may be the central explanation of the increase in the earlier onset of asthma, allergies, Type 2 diabetes, childhood Crohn’s disease and especially obesity (Sonnenburg 2016). Although the microbial component of obesity is debated profusely, a study performed by Kazushi Sugimoto, researcher at Mie University in Japan, measuring the bacteria in stool samples of obese and non-obese subjects, determined that there was a difference in gut microbiota compositions and that certain bacterial species were significantly associated with each group (Sugimoto 2015) while a similar study conducted by Gerald Lobley, senior researcher at University of Aberdeen in Scotland, concluded that there were no significant changes in the proportion of microbiota in the two groups (Lobley 2008). Considering these contrasting findings, the reliability of the studies is limited and there needs to be further research conducted to close the gap between gut microbiota and obesity correlation. To combat the health complications of antibiotics, probiotics (mixtures of beneficial bacteria) have been proposed as a potential solution by Trafton and Sonnenburg to maintain overall gut health and reduce the susceptibility of disease.
Counteractive Methods
Whether probiotics are an effective method to counter the negative effects of antibiotics, and preserve the diversity and compositions of microbes in the gut is under debate, as there are a myriad of perspectives on the issue. Peera Hemarajata, clinical microbiologist of the Los Angeles County Public Health Laboratories, and her colleagues, proposed probiotics as preventive and therapeutic measures, in order to restore the healthy composition and function of the gut microbiome (Hemarajata, el al. 2013). They reason that mechanisms of probiosis include manipulation of intestinal microbial communities, suppression of pathogens, and immunomodulation which counters against the negative side effects of antibiotics (Hemarajata, el al. 2013). On the other hand, Andres Cubillos-Ruiz PhD ’15, a research scientist at Harvard University, brings up that, standard probiotics fall short of the diversity of native microorganisms and “they cannot accomplish the same functions as the native microbes that you have nurtured throughout your life” (Trafton 2022). Although probiotics can be useful towards short-term health benefits, the long-term consequences are inevitable. Cubillos-Ruiz and his colleagues came up with a solution to prevent this issue by engineering a modified bacteria that can be delivered orally, break down antibiotics that reach the intestinal tract and then be excreted through the digestive tract (Trafton 2022). The experimental trials conducted by the researchers showed that mice that received engineered bacteria maintained a much higher level of microbial diversity compared to mice that received only antibiotics and there is already a version of the treatment being developed to test in high-risk patients (Trafton 2022). From using probiotics to counter the effects of antibiotics, to creating new technology such as engineered bacteria, there is an ongoing search for the most effective solution to approach this issue with many different perspectives.
Conclusion
Despite the positive intentions of antibiotics in fighting infections and illnesses, their usage has been followed by a majority of negative consequences on the gut microbiota. To prevent the further extinction of the gut microbes, we need to develop a wider understanding of the correlation between the composition of the gut bacteria, the effects on its richness and diversity and the resulting diseases due to the implementation of antibiotics. By designing, developing, and translating new antibiotic alternatives, in addition to methodologies that are efficient in conserving and restoring the microbial community after antibiotic-associated perturbations (Panda, et al. 2014), we can improve current strategies to reverse these disruptions in our gut. Our gut ecosystem is malleable and fragile and it is crucial to understand that this microbiome will be bequeathed to our descendants (Sonnenburg 2016). Therefore, the responsibility is now in the hands of those who are aware of this crisis to find a solution for the sake of not only our health but also that of the future generation.
References
Sonnenburg, Erica. “Op-Ed: The Extinction inside Our Guts.” Los Angeles Times, Los
Angeles Times, 25 Feb. 2016. https://www.latimes.com/opinion/op-ed/la-oe-0225-sonnenburg-gut-bacteria-extinction-20160225-story.html
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