Dietary intake of sun dried raisins for a continuous period of 14-days did not alter overall microbiota composition but affected the prevalence of OTUs across study participants at various taxon levels. Some of the observed changes are suggestive of potential health benefits. For instance, we observed a significant increase of OTUs matching
Faecalibacterium prausnitzii after raisin intake. Higher levels of
F. prausnitzii have been correlated with reduced chronic inflammation and fewer colon polyps [
29,
30]. Consistent with our findings, intake of inulin, which is also present in raisins [
14], has previously been shown to increase of
F. prausnitzii levels [
31]. Furthermore, the majority of OTUs matching Ruminococcaceae significantly increased during both intervention time-periods as did multiple OTUs matching
Bacteroidetes spp. Both of these taxa are known to contribute to the degradation of complex carbohydrates resulting in the production of SCFA that contribute to maintaining a balanced gut ecosystem. Our results are consistent with previous studies that reported an increased production of SCFA in fecal samples when raisins are either incubated in vitro or when consumed by humans [
12,
15]. We did not detect a consistent increase in Bifidobacteria or Lactic Acid Bacteria, often considered beneficial gut microbes. This could partially be due to amplification bias as Kuczynski et al. reported that 16S rDNA Illumina primers are less efficient in amplifying
Bifidobacterium spp. [
32]. The significant decrease in OTUs matching
Klebsiella sp., an opportunistic pathogen, may suggest a reduced risk of subclinical enteric inflammation or reduced potential for urinary tract infections [
33‐
35]. This observation is consistent with previous reports that polyphenolic compounds of grapes can reduce opportunistic pathogens in the gut [
36,
37]. While overall we detected no change in
Prevotella sp. prevalence we observed a specific OTU matching
Prevotella sp. that decreased during both weeks of raisin consumption. Previous studies have reported an increase in
Prevotella sp. as a potential health benefit correlating with increased intake of fibers and other plant derived food [
38,
39]. While many studies correlate
Prevotella sp. with improved gut health [
4,
40], others suggest that some species such as
Prevotella copri correlate with chronic inflammation, rheumatoid arthritis, and cardiovascular disease [
38,
41,
42]. This example illustrates the difficulty in attributing changes in specific OTUs at the family and even genus level to relevant health benefits.
When compared to baseline, the number of OTUs that significantly changed was greater during the week 1 than week 2. This could indicate that introducing raisins has mostly short-term effects on microbiota. Alternatively, this observation is consistent with reports by participants that indicate reduced compliance during week 2 due to an aversion to consume the required amount of raisins.
Our study was limited by the small number of participants that exhibited a wide range of age, BMI, dietary habits and underlying microbiota composition [
43‐
45]. These large inter-individual variations reduced our power to observe raisin intake associated effects and likely attenuated the true extent of the effect of raisins on gut microbiota. Furthermore, because this was a pilot study with a small sample size we did not adjust for multiple testing in our exploratory analysis. Although we observed several changes in OTUs across study participants who consumed raisins during the study period, without a confirmatory study with a larger sample size these results should be interpreted with caution.