Khannous-Lleiffe, O. | Search bioRxiv

bioRxiv2023

Stability of Oral and Fecal Microbiome at Room Temperature: Impact on Diversity

When collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing, are not always feasible. It is fundamental to study the impact of temporary room temperature (RT) storage and shipping on the microbiome diversity obtained in different types of samples. We performed a pilot study aimed at validating the sampling protocol based on the viability of the 16S rRNA gene sequencing in microbiome samples. Fecal and oral samples from five participants were collected and preserved in different conditions: a) 70% ethanol; b) in a FIT tube for stool samples; and c) in a chlorhexidine solution for oral wash samples. Four aliquots were prepared per sample, which were stored at RT, and frozen at days 0, 5, 10 and 15, respectively. In terms of alpha diversity, the maximum average decrease in 5 days was 0.3%, 1.6% and 1.7% for oral, stool in ethanol and stool in FIT, respectively. Furthermore, the relative abundances of the most important phyla and orders remained stable over the two weeks. The stability of fecal and oral samples for microbiome studies preserved at RT with 70% ethanol, chlorhexidine and in FIT tubes was verified for a 15-day window, with no substantial changes in terms of alpha diversity and relative abundances.

microbiology↗

bioRxiv2020

Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome

Heart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of the cardiac ventricular filling and/or ejection of blood capacity. Sleep fragmentation (SF) involves a series of short sleep interruptions that lead to fatigue and contribute to cognitive impairments and dementia. Both conditions are known to be associated with increased inflammation and dysbiosis of the gut microbiota. In the present study, male mice were distributed into four groups, and subjected for four weeks to either HF, SF, both HF and SF, or left unperturbed as controls. We used 16S metabarcoding to assess fecal microbiome composition before and after the experiments. Evidence for distinct alterations in several bacterial groups and an overall decrease in alpha diversity emerged in HF and SF treatment groups. Combined HF and SF conditions, however, showed no synergism, and observed changes were not always additive, suggesting that some of the individual effects of either HF or SF cancel each other out when applied concomitantly. IMPORTANCEThe study demonstrates the potential of the gut microbiome as a source of molecular markers for the diagnosis, prevention, and treatment of both heart failure and sleep fragmentation conditions in isolation. Our results provide the first evidence of an antagonistic effect of the presence of both conditions in the gut microbiome dysbiosis, showing an attenuation of the alterations that are observed when considering them separately.

microbiology↗