Figure - available from: Frontiers in Microbiology
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Average ROC curve obtained through 20 times repeated 10-fold cross-validation. (A) Average ROC curve obtained through 20 times repeated 10-fold cross-validation on all the training cohorts. (B) Average ROC curve obtained through independent validation on all the independent cohorts using the random forest classifier trained with 20 times repeated 10-fold cross-validation of all the training cohorts. AUC data are shown as (average of AUC) ± SD.
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Background
Colorectal cancer (CRC) is linked to distinct gut microbiome patterns. The efficacy of gut bacteria as diagnostic biomarkers for CRC has been confirmed. Despite the potential to influence microbiome physiology and evolution, the set of plasmids in the gut microbiome remains understudied.
Methods
We investigated the essential features of...
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Citations
... Needless to say, plasmids are generally known to be present in bacteria, archaea, and even some eucaryotic organisms, and they are classified into several classes by their function; however, not much attention is given to this fact in the context of a possible interaction with cells of the human intestine tract. Few studies analyzed meta-genomic data and suggested particular plasmids to be used as biomarkers (27). ...
Introduction
Colorectal cancer (CRC) is one of the leading oncogenic disorders, both in terms of incidence and mortality. The etiology of the disease is certainly multifactorial. Various risk factors like alcohol consumption, smoking, CRC family history, inflammatory bowel disease, hormone therapy, aspirin/nonsteroidal anti-inflammatory drugs use, higher body mass index, consumption of red and/or processed meat, insufficient physical activity, and decreased intake of fruit and vegetables have been pointed out; however, there is not enough support evidence for a single particular causative mechanism. Recently, gut bacterial microbiota has been shown to influence significantly the pathogenesis of CRC. However, little attention is paid to the putative impact of plasmids in gut flora.
Material and methods
We have designed and tested the workflow for semi-selective isolation and amplification of random circular sequences. The exploitation of rolling circle amplification (RCA) with a random hexamers protocol is crucial for the outcome.
Results
Our results suggest that it is possible to isolate and amplify plasmid DNA from gut flora and further process, sequence, and identify them.
Discussion
Little is known about the interactions between bacterial plasmids and human cells. The collection of plasmid sequencing data and the comparison of CRC patients and healthy control sequences can be the first step to elucidating this phenomenon.
