Abstract
The coronavirus (COVID-19) pandemic has disrupted clinical trials globally, with unique implications for research into the human gut microbiome. In this mini-review, we explore the direct and indirect influences of the pandemic on the gut microbiome and how these can affect research and clinical trials. We explore the direct bidirectional relationships between the COVID-19 virus and the gut and lung microbiomes. We then consider the significant indirect effects of the pandemic, such as repeated lockdowns, increased hand hygiene, and changes to mood and diet, that could all lead to longstanding changes to the gut microbiome at an individual and a population level. Together, these changes may affect long term microbiome research, both in observational as well as in population studies, requiring urgent attention. Finally, we explore the unique implications for clinical trials using faecal microbiota transplants (FMT), which are increasingly investigated as potential treatments for a range of diseases. The pandemic introduces new barriers to participation in trials, while the direct and indirect effects laid out above can present a confounding factor. This affects recruitment and sample size, as well as study design and statistical analyses. Therefore, the potential impact of the pandemic on gut microbiome research is significant and needs to be specifically addressed by the research community and funders.
Highlights
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) and has resulted in a global pandemic, as well as subsequent restrictions of public and private life
While clinical trials worldwide have been challenged as a consequence, there are unique implications for the rapidly evolving gut microbiome research
The gut microbiome is the vast diverse population of an estimated 100 million−100 trillion microorganisms and their genes that populate the gastrointestinal tract [1]. They play essential roles in the immune and metabolic pathways, thereby influencing maintenance of health and the pathogenesis of disease [2]. This complex system can be disturbed by disease or lifestyle changes, mechanisms that become highly relevant in the context of the COVID-19 pandemic
Summary
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) and has resulted in a global pandemic, as well as subsequent restrictions of public and private life. We propose that there are direct interactions between the gut microbiome and COVID-19, as well as indirect associations through the lifestyle changes induced by lockdowns and increased hygiene (see Figure 1) that need to be considered for ongoing and future microbiome studies. These range from experimental and observational, to longitudinal and population studies, as well as clinical trials using Faecal Microbiota Transplantation, FMT. Elderly and immunocompromised populations are known to have reduced microbiota diversity Since many of these vulnerable patients have had worse clinical outcomes for COVID-19, this strengthens the possibility that the gut microbiome is affecting clinical progression. If these have changed during the lockdown or have been adversely lengthened, this may have detrimental impacts on subsequent analysis and comparisons
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