Are these patterns unique to the Central Coast or reflective of broader environmental microbiome dynamics?
The patterns observed in this study are likely not unique to the Central Coast. Similar differences in soil microbiomes associated with land use and production practices have been reported in other studies. In addition, environmental factors such as soil temperature and moisture are known to influence soil microbiome composition across a range of agricultural systems and geographic regions.
How do stress factors from seasonality influence gene transfer?
This study was not designed to evaluate the effects of seasonal stress factors on gene transfer, so no conclusions can be drawn regarding that relationship from these data.
In the vineyard-produce site, did you also test for mitochondrial DNA in the STEC negative samples?
Yes. For all soil samples from either wine-grape vineyards or produce fields that were included in the subset of samples subjected to metagenomic sequencing, the analysis included mitochondrial DNA identification, regardless of STEC status.
Is both E. coli O157 and nonO157 STEC pathogenic to humans? Have we investigated if non-O157 STEC is causing health problems? Are they becoming pathogenic?
Both E. coli O157 and non-O157 STEC can cause illness in humans. Disease severity can vary depending on the strain and the individual infected, ranging from mild gastrointestinal illness to severe disease, including bloody diarrhea and hemolytic uremic syndrome (HUS). While E. coli O157 is historically the most recognized STEC associated with severe outbreaks, some non-O157 STEC strains can also cause serious human illness.
Is there a reason to examine microbiomes of enriched samples?
Yes. In many environmental samples, E. coli is present at very low relative abundance compared to other microorganisms, making detection difficult in unenriched, culture-independent samples. Enrichment increases the relative abundance of E. coli, improving the ability to detect STEC-associated targets such as Shiga toxin genes and to further characterize the E. coli population associated with STEC-positive samples.
Was previous BSAAO use, or field crop history considered for differences in metagenomic analysis? Was the history of BSAAO application noted for soil transects?
To our knowledge, untreated BSAAO was never used in the produce farms that were included in the study. Treated BSAAO, if present, was sampled on participating produce farms, vineyard and compost sites. The history of treated BSAAO use was not recorded for soil transects.
What percent of STEC were EHEC?
We do not yet know the percentage of STEC isolates that meet the criteria for EHEC classification, as additional characterization and analysis are still in progress.
What specific characteristics in the sample are you looking for further analysis using metagenomics?
Further metagenomic analyses will focus on differences in microbiome composition and diversity among samples, as well as potential associations between microbiome profiles and environmental or weather-related factors.
You found 12 O157 strains, but how many times were O157 positives in samples found?
There were a total of 83 samples that tested positive for E. coli O157 across the different sample matrices.