As one of the most widely used assays in biological research,an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process.To speed up the colony counting,a machine learn...As one of the most widely used assays in biological research,an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process.To speed up the colony counting,a machine learning method is presented for counting the colony forming units(CFUs),which is referred to as CFUCounter.This cellcounting program processes digital images and segments bacterial colonies.The algorithm combines unsupervised machine learning,iterative adaptive thresholding,and local-minima-based watershed segmentation to enable an accurate and robust cell counting.Compared to a manual counting method,CFUCounter supports color-based CFU classification,allows plates containing heterologous colonies to be counted individually,and demonstrates overall performance(slope 0.996,SD 0.013,95%CI:0.97–1.02,p value<1e-11,r=0.999)indistinguishable from the gold standard of point-and-click counting.This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.展开更多
AIM： In order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract （LDT） in healthy volunteers, a specific technique was developed for collecting mucous of...AIM： In order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract （LDT） in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum. METHODS： A polyethylene tube was designed to go through the colonoscope channel with a No. 8 French tube. In order to avoid internal contamination, the distal extremity was protected with a membrane of microfilm after being sterilized in ethilene oxid. To facilitate the aspiration of a precise volume, its interior was coated with silicone. One hundred rnicrolliter （0.1 mL） sample of mucous was collected and transferred into an Eppenddorff tube containing nine hundred rnicrolliter （0.9mL） of VMGA-3 （viable medium of Goteborg）. This procedure was repeated at each site of the LDT with a new sterilized catheter. RESULTS： All sites revealed the ＂non pathogenic＂ anaerobic bacteria Veillonella sp （average 10s colony forming units/mL-CFU/mL）, allowing to conclude an environment of low oxidation-reduction potential （redox） in the LDT. It was also characterized the presence of Klebisiella sp with significant statistical predominance （SSP） in the ileum. Enterobacter sp was found with SSP in the sigrnoid colon, Bacteroides sp non-pigmented （npg） and Ecoli with SSP in the sigrnoid colon and rectum, Enterococcus sp and Lactobacillus sp with SSP in the rectum, all in a mean concentration of 10s CFU/mL CONCLUSION： This procedure is feasible and efficient and can point out a similar distribution of the aerobic and anaerobic bacteria with the presence of biological markers of normal microbiota in the LDT.展开更多
基金This research was funded by a VPR Special Research Grant entitled Potential of a Site-Specific DNA Interstrand Crosslink.
文摘As one of the most widely used assays in biological research,an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process.To speed up the colony counting,a machine learning method is presented for counting the colony forming units(CFUs),which is referred to as CFUCounter.This cellcounting program processes digital images and segments bacterial colonies.The algorithm combines unsupervised machine learning,iterative adaptive thresholding,and local-minima-based watershed segmentation to enable an accurate and robust cell counting.Compared to a manual counting method,CFUCounter supports color-based CFU classification,allows plates containing heterologous colonies to be counted individually,and demonstrates overall performance(slope 0.996,SD 0.013,95%CI:0.97–1.02,p value<1e-11,r=0.999)indistinguishable from the gold standard of point-and-click counting.This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.
文摘AIM： In order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract （LDT） in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum. METHODS： A polyethylene tube was designed to go through the colonoscope channel with a No. 8 French tube. In order to avoid internal contamination, the distal extremity was protected with a membrane of microfilm after being sterilized in ethilene oxid. To facilitate the aspiration of a precise volume, its interior was coated with silicone. One hundred rnicrolliter （0.1 mL） sample of mucous was collected and transferred into an Eppenddorff tube containing nine hundred rnicrolliter （0.9mL） of VMGA-3 （viable medium of Goteborg）. This procedure was repeated at each site of the LDT with a new sterilized catheter. RESULTS： All sites revealed the ＂non pathogenic＂ anaerobic bacteria Veillonella sp （average 10s colony forming units/mL-CFU/mL）, allowing to conclude an environment of low oxidation-reduction potential （redox） in the LDT. It was also characterized the presence of Klebisiella sp with significant statistical predominance （SSP） in the ileum. Enterobacter sp was found with SSP in the sigrnoid colon, Bacteroides sp non-pigmented （npg） and Ecoli with SSP in the sigrnoid colon and rectum, Enterococcus sp and Lactobacillus sp with SSP in the rectum, all in a mean concentration of 10s CFU/mL CONCLUSION： This procedure is feasible and efficient and can point out a similar distribution of the aerobic and anaerobic bacteria with the presence of biological markers of normal microbiota in the LDT.
