Researchers at the University of Alabama at Birmingham previously developed a microbiome fingerprint technique calledWSS that identifies single strains of particular gut bacteria, using metagenomics data. They also found that a donor fecal transplant strain for treatment of drug-resistant Clostridium difficile infections persisted in the recipient for as long as two years after the transplant.
Morrow and Hyunmin Koo, both from the United Kingdom, have refined the fingerprint method to identify single-nucleotide variants in the KEGG metabolic pathways of a particular strain. For example, Morrow and Koo conducted a research on 23 different KEGG metabolic pathways in that bacteria.
In two key gut bacteria B. vulgatus and Bacteroides uniformis, they have now applied this powerful analysis to monitor sub-strain patterns in short periods of time, days or weeks. This finding suggests a decrease in intrinsic rates of strain variation in sick patients. This suggests a shift in the dominant strains of the gut microbiome.
Both of the Bacteroides species are found in the gut flora, and they may be keystone species and organisms that help define an entire ecosystem.
In the journalScientific Reports, Koo and Morrowsstudy, an early indicator of microbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID19 patients.
Researchers from Koo and Morrow first examined previously published metagenomics data from 41 individuals sampled one year apart and 11 individuals sampled 90 days apart. They examined a single dominant strain of B. vulgatus in each individual at the two time points to see if they had shown different KEGG metabolic sub-strain patterns, as detected from an analysis of single-nucleotide variants in KEGG metabolic pathways, or PKS. In general, most individuals showed a different sub-strain P
Metagenomics data from six healthy individuals were then analysed every few days over three to ten weeks again, again analysing sub-strains by single-nucleotide variants 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 time points.
Two of three hospitalized COVID-19 patients were examined multiple times as part of shared PKS patterns.
We suggest that gut microbial communities under strain, such as those found in COVID-19 hospitalized patients, might be in a state indicating the possibility that a dominant strain would be outperforming by a minor strain, according to Koo. Disruptions of the gut microbial community resulting from a strain variation might, in turn, alter the community structure and impact the functions in metabolism and colonization resistance.
While a complex biological system approaches a critical transition, there is a slowing down of intrinsic rates of change, according to Morrow. The system enters a condition that is related to autocorrelation, where patterns would 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 implies a strain change.