The public health response to the coronavirus disease 2019 (COVID-19) pandemic consisted of sudden and sweeping changes in hygiene and lifestyle, including the widespread use of face masks, increased handwashing, the liberal use of disinfectants, restrictions on travel, and social distancing. Though these health directives were intended to prevent transmission of COVID-19, their collateral effects have been theorized to alter the diversity and composition of the human microbiome, including possible ecological disruptions to essential host-commensal niches in the gut [1]. Since the intestinal microbiome is important for host metabolism and immunoregulation, such rapid and large-scale ecological shifts in the human gut have implications for altered susceptibility to diabetes, obesity, and autoimmunity. Nevertheless, the extent of gut microbial disruptions due to pandemic associated lifestyle changes remain largely uncatalogued, and whether such changes could impact host physiology is unknown. As COVID-19 settles into a more endemic phase and future pandemics loom, understanding how public health-directed lifestyle measures may acutely or persistently reshape the ecology and function of the intestinal microbiome is of interest.

In this issue of Digestive Diseases and Sciences, Hosseini et al [2] describe how pandemic-associated environmental and cultural changes may have impacted the small bowel microbiome in the United States. After comparing bacterial communities in duodenal aspirates obtained from COVID-19 negative patients prior to or during the pandemic, the authors observed that the intra-pandemic microbiome was associated with an altered beta diversity, with reductions in the genera Rothia, Pseudomonas, and Escherichia-Shigella and an increase in the uncommon extremophile phylum Deinococcus-Thermus. Cytokine assays on blood samples obtained from patients also revealed that the intra-pandemic group had reduced circulating levels of IL-18.

This study provides the first description of changes in the intra-pandemic small bowel microbiome compared with the pre-pandemic era. Although this investigation is in line with other studies reporting an altered intra-pandemic oral or fecal microbiome [3, 4], this study uniquely provides a first look at changes in the duodenal microbiome, an under-sampled bioniche, whose ecology can be affected by changes in dietary patterns and environmental exposures. This investigation also excludes the potential confounding effect of SARS-CoV-2 viral infection on the microbiome [5] through the recruitment of patients who had no history of COVID-19 and were serologically negative for the infection at the time of sample collection.

By utilizing samples obtained through sterile endoscopic aspiration of luminal fluid, this study surmounts the challenge of accessing the small bowel microbiome. Historically, the duodenal and jejunal compartment have been understudied due to limited accessibility, with most microbial studies relying on fecal samples, an approach that only captures the microbiome populating the terminus of the human gastrointestinal tract. By collecting duodenal samples, these data provide insight into the diversity and taxonomy of the small bowel compartment, an important area for nutrient processing and absorption, as well as an interaction point between food substrates, commensal bacteria, and host epithelium. These data contribute evidence that the proximal microbiome is dominated by gram-positive, facultative anaerobes from the phylum Firmicutes and the family Streptococcacæa, in both pre-pandemic and intra-pandemic conditions, similar to prior studies reporting that gram-positive aerobes and facultative anaerobes are prevalent in the duodenum [6]. Nonetheless, this study extends those observations by suggesting that during the conditions of the pandemic, constituents of the anærobic, gram-negative phylum Fusobacterium were secondarily and relatively more prevalent, with relative increases in the constituent gram-negative anaerobic genera Fusobacterium and Leptotrichia—both traditionally found in the oral cavity. Accordingly, the authors demonstrate that the beta diversity of the intra-pandemic small bowel is significantly altered, underlining that the pandemic lifestyle and the associated shift in extraneous conditions may reshape the proximal intestinal microbiome.

Nevertheless, these taxonomic alterations should be tempered by other challenges inherent to small bowel sampling. Though the authors used an appropriate sterile, endoscopic approach for gaining access to this compartment, samples were obtained only during a single timepoint. The small bowel demonstrates significant intra-individual temporal dynamics, with samples exhibiting variability even within the same individual when obtained during the morning vs evening period [7]. Unlike the colon, which has a relatively stable microbiome, the small bowel is exposed to rapidly fluctuating luminal conditions, with intermittently variable food substrate delivery, inflow of bile and digestive enzymes, and short transit times. Changes in dietary substrates can rapidly change intestinal diversity [8]. As this study only assessed a single timepoint per individual, with no assessment of dietary intake, the diversity and taxonomic indices only provides a single snapshot of a dynamic ecosystem, likely underestimating true population fluxes and trends during the intra- and pre- pandemic period.

The statistical methodologies used in this study do provide appropriate assessment of microbial sequences by utilizing rarefaction, normalization, and a negative binomial generalized linear model. Such an approach can adjust for the complexity, sparsity, and over-dispersed nature of microbiome data. Yet, the model used in this study does not effectively handle zero-inflation [9], potentially attributing statistical significance to very low abundance organisms. The authors note that although the phylum Deinococcus-Thermus was significantly more prevalent in the intra-pandemic group, this phylum was not present in the core duodenal set identified in this study, suggesting that any significant changes in relative abundance should be tempered by its overall rarity across samples. Nevertheless, the expansion of this phylum during pandemic conditions is of interest, since a similar expansion of this extremophile was noted in the oral cavities of non-COVID infected pandemic patients [10]. Overall, such observations are analogous to the concept that repeated handwashing, changes in hygiene, and broad use of antibiotics can disrupt human microbial diversity.

Though this study provides correlative evidence that the intra-pandemic microbiome may be altered, there is limited information on whether individuals sampled during the pandemic demonstrated a lifestyle distinct from individuals in the pre-pandemic period. The study reports no data on comparative social exposures, frequency of travel, dietary patterns, or hygienic practices between the two periods. Furthermore, since analyses were not performed within the same individual across both periods, it remains possible that any observed taxonomic shifts are secondary to the high level of inter-individual variability present in the small bowel microbiome, rather than true lifestyle-associated shifts.

Nonetheless, this study provides novel evidence reporting alterations in the composition of the small bowel microbiome among COVID-19 negative individuals in the intra-pandemic era. Although the microbiome was largely similar to the expected distributions of microbes in the duodenum, there was an increased relative prevalence of specific gram-negative, obligate anaerobes and a small expansion in an extremophilic phylum. By choosing COVID-19-negative individuals, the authors were able to remove the potential confounding effect of viral infection on small bowel composition, and the use of sterile collection of duodenal aspirates provided unique insight into a rarely sampled yet important bioniche in the human gastrointestinal tract.

Still, to more definitively explore how such rapid shifts in human behavior may influence the small bowel microbiome, future studies should examine longitudinal samples obtained within the same individual across timepoints. Detailed exposure and dietary records alongside pairwise, longitudinal assessments may provide valuable insight into the stability of these intestinal populations. Shotgun metagenomics of the small bowel microbiome can additionally reveal functional contributions of the bacterial gene pool to host metabolism, potentially highlighting links between microbial shifts and aberrant nutrient uptake and resource utilization. As the current pandemic eases into a chronic endemic state, and as future pandemics are likely to further alter hygienic and lifestyle practices, the development of registries surveying healthy individuals across such varying conditions will provide a more comprehensive understanding of the structural and functional contribution of these multiple microbial compartments to human health and disease.