A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic

Abstract

The COVID-19 pandemic poses a great challenge to global public health. The extraordinary daily use of household disinfectants and cleaning products, social distancing and the loss of everyday situations that allow contact between individuals, have a direct impact on the transfer of microorganisms within the population. Together, these changes, in addition to those that occur in eating habits, can affect the composition and diversity of the gut microbiota. A two-time point analysis of the fecal microbiota of 23 Metropolitan Buenos Aires (BA) inhabitants was carried out, to compare pre-pandemic data and its variation during preventive and compulsory social isolation (PCSI) in 2020. To this end, 23 healthy subjects, who were previously studied by our group in 2016, were recruited for a second time during the COVID-19 pandemic, and stool samples were collected from each subject at each time point (n = 46). The hypervariable region V3-V4 of the 16S rRNA gene was high-throughput sequenced. We found significant differences in the estimated number of observed features (p < 0.001), Shannon entropy index (p = 0.026) and in Faith phylogenetic diversity (p < 0.001) between pre-pandemic group (PPG) vs. pandemic group (PG), being significantly lower in the PG. Although no strong change was observed in the core microbiota between the groups in this study, a significant decrease was observed during PCSI in the phylum Verrucomicrobia, which contributes to intestinal health and glucose homeostasis. Microbial community structure (beta diversity) was also compared between PPG and PG. The differences observed in the microbiota structure by unweighted UniFrac PCoA could be explained by six differential abundant genera that were absent during PCSI. Furthermore, putative functional genes prediction using PICRUSt infers a smaller predicted prevalence of genes in the intestinal tryptophan, glycine-betaine, taurine, benzoate degradation, as well as in the synthesis of vitamin B12 during PCSI. This data supports the hypothesis that the microbiome of the inhabitants of BA changed in the context of isolation during PCSI. Therefore, these results could increase the knowledge necessary to propose strategic nutraceutical, functional food, probiotics or similar interventions that contribute to improving public health in the post-pandemic era.

Effects of physical distancing by COVID-19 pandemic on diet quality, neurological and immunological markers, and fecal microbiota of Brazilian older women

“…However, the F/B ratio presents high variability among studies, since Mariat et al (100) reported 0.6, while Vaiserman et al (103) detected 1.42 for older adults and, in the present study, the F/B ratio decreased 52.5% (4.36 ± 5.35 to 2.29 ± 1.65) after physical distancing (medium effect size), which could be related to increase in age-associated Bacteroidetes, as described by Martinez et al (102). This result is discordant with Aguilera et al (19), which showed that F/B ratio in the pre-pandemic period was 1.01 ± 0.38 and, after five years (during the physical distancing period), it increased to 1.47 ± 0.96. The age of participants, methodological approaches and interval between sampled periods may justify the differences between these results.…”

“…In fact, these alterations contribute to microbiome imbalance with deleterious consequences for the host ( 16 ), increasing dysbiosis of gut microbiome in older adults. There is a paucity of information about the microbiome of South American populations, since most studies were performed in European, Asian and North American populations, that differ in genetic background, eating habits and environmental factors ( 19 ).…”

“…To the best of our knowledge, there are no studies about changes in microbiota composition associated with physical distancing in older women, which hampers a better discussion of the present results. The closest study was performed by Aguilera et al ( 19 ), that compared the gut microbiome of adults from Buenos Aires (Argentina) between 3 and 5 months of physical distancing. Although the initial samples were collected in 2016, the authors showed that five genera ( Desulfovibrio , Streptococcus , Anaerostipes , Oscillospiraceae , and Eubacterium ) were lost of the core microbiome, while three other genera ( Erysipelotrichaceae , CAG-352 and Akkermansia ) became part of the core microbiome after physical distancing.…”

“…In addition, physical activity acts on brain health inducing positive changes as the enhancement of neurogenesis, angiogenesis, and synaptogenesis, caused by neurotrophins and growth factors, such as the brain-derived neurotrophic factor (BDNF) (14,15). Some authors (16)(17)(18)(19) suggested that physical distancing for pandemic control decreases social connectedness and is associated with extensive hygiene habits, use of household disinfectants and cleaning products, travel barriers, and changes in habits which could significantly impact on the transfer of microorganisms within the population, and microbiome composition. This disruption in microbial sharing and inability for reinoculation (17) could be associated with loss of bacterial diversity causing dysbiosis with deleterious consequences for the host (16) impacting human health over the long term (17), mediating pathogen susceptibility and nosocomial infections (18).…”

Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications

“…Current pandemic control measures have been proposed to have large, uneven and potentially long-term detrimental effects on the human microbiome globally with strict implementation of social distancing, extensive hygiene measures, restricted travel and other measures that influence overall microbial loss 157 . A small study comparing pre-pandemic gut microbiota of 23 healthy individuals from Buenos Aires, Argentina, and its variation during social isolation found a significant ( P <0.05) decrease in phylogenetic diversity and in the phylum Verrucomicrobiota, which contributes to intestinal health and glucose homeostasis, during isolation 158 . The COVID-19 pandemic has been associated with a markedly lower Actinobacteria (Actinomycetota) richness, higher Bacteroidetes (now known as Bacteroidota) richness, and an altered abundance of antibiotic-resistance genes in faecal samples collected from 32 healthy individuals before and during the first wave of the pandemic 159 .…”