In response to metagenomics data from fecal samples, Casey D. Morrow, a doctor, and colleagues from the University of Alabama at Birmingham, developed a microbiome fingerprint technique calledWSS that identifies single strains of certain gut bacteria. They have found that specific strains in adults tend to remain stable in the long run, unless perturbed by events likeantibioticsorobesity surgery. Another discovery suggests that a donor fecal transplant strain for treatment of drug-resistant Clo
Morrow and Hyunmin Koo, Ph.D., modified the fingerprint technique to include identifying single-nucleotide variants in KEGG metabolic pathways of a particular strain. These variants may identifie sub-strains of a Bacteroides vulgatus strain. For example, Morrow and Koo investigated 23 different KEGG metabolic pathways in that bacteria.
Medications have applied this vast analysis to investigate sub-strain fluctuations over longer periods of time, such as days or weeks, in two key gut bacteria B. vulgatus and Bacteroides uniformis. This analysis suggests that sub-strain dynamics might even result in a dysbiosis in the microbial strain community.
Both Bacteroides species are found in high abundance in the gut flora, and they may be keystone species and organisms that aid in the creation of an entire ecosystem.
In the journalScientific Reports, Koo and Morrowsstudy, An Early Evidence of microbial strain dysbiosis in the Human gastrointestinal microbial community of certain healthy individuals and hospitalized COVID19 patients.
According to the study of single-nucleotide variants in KEGG metabolic pathways, most individuals showed a different sub-strain PKS pattern between the two time points.
The UAB researchers then tracked metagenomics data from six healthy individuals that were tested every few days for three to ten weeks, once again analysing sub-strains by single-nucleotide variation in 23 KEGG metabolic pathways. Three individuals showed a different sub-strain at every time point, while three showed sub-strains had PKS patterns that appeared, disappeared and reappeared at different times.
Two of three hospitalized COVID-19 patients were also assessed yearly.
We suggest that gut microbial communities under strain, such as those found in COVID-19 hospitalized patients, might be in a state indicating the potential shift in which the dominant strain might be outcompeted by a minor strain, according to Koo. Disruptions of the gut microbial community resulting from a strain variation may, in turn, alter the community structure and the functions in metabolism and colonization resistance.
As a result of a vital transition, a system becomes a condition relating to autocorrelation, where patterns will be repeated between time points. It is possible that the shared KEGG metabolic pathway clusters represent a state of autocorrelation in the gut microbial strain community that suggests a strain change.