The "Fingerprinting" method for tracking single strains of specific gut bacteria

The "Fingerprinting" method for tracking single strains of specific gut bacteria ...

Researchers at the University of Alabama at Birmingham developed a microbiome fingerprint technique calledWSS that identifies single strains of certain gut bacteria. These findings have shown that particular strains in adults tend to be stable over time unless perturbed by events likeantibioticsorobesity surgery. Moreover, a donor fecal transplant strain used to treat 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 States, have refined the fingerprint technique to include studying single-nucleotide variants in KEGG metabolic pathways of a particular strain. These variants can also identify sub-strains of a Bacteroides vulgatus strain. For example, Morrow and Koo used the following 23 different KEGG metabolic pathways to identify sub-strains of a particular strain.

In two key gut bacteria B. vulgatus and Bacteroides uniformis, they have now applied this extensive analysis to monitor sub-strain dynamics. They believe that this slowing down of the intrinsic rates of strain variation in sick patients may result in a dysbiosis in the human strain community.

Both of the Bacteroides species are found in the gut flora, and they may be keystone plants, organisms that may assist define an entire ecosystem.

In the journalScientific Reports, Koo and Morrowsstudy, A Study of Early Anxiety of microbial strain dysbiosis in certain healthy individuals and hospitalized COVID19 patients.

In general, Koo and Morrow 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 determine if they had shown different KEGG metabolic sub-strain patterns. In general, most cases showed a different sub-strain PKS pattern between the two time points of each individual.

At some point, UAB researchers tracked metagenomics records from six healthy individuals who were tested every few days over three to ten weeks, 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 times.

Two of three hospitalized COVID-19 patients were found to be having a similar PKS pattern.

We suggest that gut microbial communities under stress, such as those found in COVID-19 hospitalized patients, might be in a state indicating the potential shift in which the dominant strain would be outcompeted by a minor strain, according to Koo. Disruptions of the gut microbial community causing a disturbance might, in turn, affect the community structure and impact the functions in metabolism and colonization resistance.

As a result of a critical transition, a system can enter a condition related to autocorrelation, and where patterns would be repeated between time periods. It is possible that the shared KEGG metabolic pathway clusters represent a state of autocorrelation in the gut microbial strain community, which implies a strain change.

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