Additional file 13 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle
Creators: name: Teseo, S.
name: Otani, S.
name: Brinch, C.
name: Leroy, S.
name: Ruiz, P.
name: Desvaux, M.
name: Forano, E.
name: Aarestrup, F. M.
name: Sapountzis, P.
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 13: Supplementary Results 3. There are two main approaches to identify zoonotic and animal pathogens in fecal (or other) samples: a culture-based approach that typically isolates microbial strains and then examines their virulence potential using PCR or sequencing (individual genome sequencing) and a shotgun metagenomic approach that examines all sequencing reads against a set of known virulence genes (e.g. VFdb database). A common controversy between the two methods is that the metagenomic approach likely overestimates the diversity of community members and the diversity of virulence or other microbial genes, while the culture-based approach underestimates it. However, many microbes cannot be cultivated simply because their niches are too specific. As a result of that, in any given sample there is always a number of impossible-to-cultivate microbes that will not be detected. On the other hand, shotgun metagenomic approaches are also prone to errors because they identify any sequences that are present in the samples regardless of whether they come from microbes that are present in the sample or sequences from dead microbes. Despite how the tendency to miscalculate gene diversity of the two approaches is in opposite directions, it has always been assumed that their results (when examining the same samples) should largely be in agreement. Fifteen of the samples that we used, originating from composite samples of feces, had been used for shotgun metagenomics sequencing [26] and for isolating Escherichia strains and independent genome sequencing [23]. Therefore, we took advantage of that unique opportunity to test the above hypothesis. Using the metagenomic reads from the fifteen samples as well as the genome sequences from the 150 Escherichia isolates (for each fecal sample ten Escherichia isolates were genome sequenced; [23]), we mapped the predicted ORFs from both datasets to the entire VFdb database (not the pathogenic subset we used in the manuscript but the entire dataset). This showed that in the fifteen independent comparisons an average of 76% (ranging from 38% to 89%) of the Escherichia annotations were identical to the ones from genome sequences coming from the Escherichia isolates. In the venn diagrams presented here, the light green circle represents the genes coming from Escherichia isolates (culture-based approach) and the purple circle illustrate the genes identified using the shotgun metagenomic approach (metaG). The numbers inside the circles show the unique number of annotations to each group as well as the common. At the bottom right of each Venn diagram, the percentage (inside the parentheses) shows the count of common annoatation/total Escherichia annotations present in the metagenome (i.e. the Escherichia annotation that can be found in the metagenome and originate from Escherichia strains that could also be isolated).