1. Introduction
The gut microbiota (the community of microorganisms, including bacteria, fungi, and viruses, that live within the digestive tract) are important for human health. While genetics influence the human gut microbiota to a small extent, environmental factors including diet and lifestyle are more influential [
1]. The biodiversity hypothesis, an extension of the hygiene hypothesis, posits that human contact with environmental microbiota influences proper development of the immune system, and thus aids in the prevention of immune-mediated diseases [
2]. This hypothesis has been supported by the increase in immune-mediated diseases that has occurred alongside the rise of urbanization and subsequent decrease in human interaction with environmental microbiota, the microorganisms that live in our surroundings [
3,
4].
Additional support for the role of environmental factors influencing the gut microbiota is found in studies that examine gut microbiome composition amongst groups that vary in geography and lifestyle. In a study examining the gut microbiota of urban and rural Russians, the gut microbiome of urban Russians was more similar to that of people living in Western countries than rural Russians, and gut microbial communities were more similar among individuals living within the same rural area [
5]. Another study compared the gut microbiome of Nigerian urban-dwellers and rural subsistence farmers and found differences in the relative abundance of many bacterial taxa between the two groups, and several taxa that were unique to each group [
6]. Research has also examined the relationship between quantity and/or type of greenspace and human microbiota alpha diversity. Alpha diversity quantifies the number of microbial taxa present and/or how even the abundances are among the taxa within a sample; higher microbiota diversity is frequently associated with better health [
7,
8]. A large multi-country study found that people with a high level of vegetation cover near their home had more diverse gut microbiota than those with a low amount of greenspace near their home [
9].
One likely contributor to the differences seen in the aforementioned studies is the extent of exposure to, and the composition of, microorganisms found in soil. Soil has a diverse microbiota, and soil microbiota composition varies geographically [
10,
11]. There are several potential means for soil bacteria to impact the human microbiota, including inhaling soil dust through the nasal passages, and soil bacteria contacting the skin [
12]. To test this experimentally, a pilot study was conducted in which intervention participants rubbed their hands with a soil mixture three times a day for two weeks. There was an increase in the alpha diversity of the intervention participants’ stool microbiome when compared with controls [
13]. To further examine the potential for enhanced soil contact to impact the human microbiota, several studies have examined the effect of nature interventions on the microbiome of young children. For example, one study enhanced the biodiversity of a daycare yard by adding forest floor and sod. Compared with before the intervention, the relative abundance of
Clostridiales and Shannon diversity of
Ruminococcaceae in the children’s gut bacteria increased, and skin bacterial diversity increased [
14]. In another study, a nature-exposure intervention for preschool children did not change the alpha diversity of the gut microbiota, but did change the prevalence of some taxa [
15].
Gardening is a potential strategy for altering the human microbiota via direct contact with soil. It is a popular leisure activity for millions of Americans, as well as worldwide, and provides routine soil exposure even for urban dwellers. There are several pathways by which gardening could result in direct bacterial transfer from soil to humans, including when gardeners touch their mouths or food with dirt on their hands, inhaling dirt through the nasal passages, or consuming the foods harvested from the garden that might have soil or soil residue on them. To date, only a small number of studies have examined the association between gardening and human microbiota. One study found that immediately after gardening, there is a temporary increase in the number of soil bacteria taxa that are found on the skin of the hands, but that this change diminishes over a matter of hours [
16]. Another study examined the gut microbiome across the gardening season, and found increases in some bacterial taxa at the peak of gardening season [
17]. Beyond sole exposure to soil microbiota, gardeners may also experience exposure to microorganisms in compost, which typically consists of decomposed animal manure and/or plant material. The bacterial communities present in compost can vary widely. For example, one study found differing microbial community compositions among composted manure from different types of livestock [
18]. Another study examined a variety of composts, with some solely consisting of plant-based material and others containing manure from various animals. This study found that while there are some bacterial taxa that are prevalent across different types of compost, there are distinct microbial communities based on compost type [
19].
More studies examining how gardening influences the gut microbiome are needed, including on the potential for compost, a commonly used soil amendment, to influence the gut microbiome of gardeners. Our study examines the gut microbiome of gardeners at three time points across a five-month-long gardening season: prior to gardening, after adding compost to their garden plot, and at the peak of harvest. We aimed to (1) examine the gut microbiota composition and diversity across the three time points, and (2) to determine if soil or compost bacteria were present in the gardeners’ gut microbiomes.
4. Discussion
This study investigated the association between soil and compost exposure and gardeners’ gut microbiota, as well as the potential for soil or compost bacteria to transmit to the human gut during gardening. The gut bacterial communities of participants who used P compost had lower Shannon alpha diversity compared to the gut bacterial communities of participants using the other two compost types after soil amendments (
Table 3). In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from the compost compared to the soil (
Figure 6). The results suggested that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota. However, direct evidence of improved health remains to be demonstrated.
The current study found that alpha diversity of the gardeners’ gut microbiota did not significantly change over the three time points (
Table 2). This is similar to the findings from Brown et al. who showed that alpha diversity metrics of human fecal bacteria, including observed features and Faith’s phylogenetic diversity, were similar before the gardening season and during the harvesting season [
17]. In our study, we found that participants who used P compost had a significantly lower richness (inverse Simpson index) at T1 and a significantly lower evenness and richness at T2 and T3 (Shannon and inverse Simpson indices) of bacteria than those who used CM compost (
Table 3), suggesting that baseline differences in alpha diversity, and not the type of compost used, were responsible for the observed differences.
When examining specific taxa, we observed that some bacterial taxa significantly changed in gardeners’ stool over the gardening season (
Table 4), though it must be acknowledged that factors like diet were not included in our models. Similarly, Brown et al. found that gardeners had significantly lower abundances of
Romboutsia uncultured,
Terrisporobacter uncultured,
Butyricicoccus uncultured, and
Lachnospiraceae cultured before the gardening season than at peak season [
17]. In our study, an unclassified genus in the
Lachnospiraceae family was significantly different over the three time points. However, the relative abundance of this taxa was similar between any of the two time points when tested using multiple pairwise comparisons. This might be due to the lack of statistical power when comparing people who used different types of compost. In our study, nine people used CM compost, ten used DMP compost, and six used P compost. However, three other taxa that significantly changed in the stools of gardeners over the gardening season (
Dorea, Ruminococcus 1, and
Collinsella) did have significant pairwise differences.
Dorea is a gram-positive non-spore-forming bacteria that belongs to the
Lachnospiraceae family and occurs in human feces [
29]. In the current study, gardeners’ stools had a significantly lower relative abundance of
Dorea at T3 than at T1 or T2. Compared to Italian urban-dwelling controls, a depletion of
Dorea and unclassified
Lachnospiraceae was found in Hadza hunter-gatherers’ fecal samples [
30]. This suggests that these taxa may represent a key difference between industrialized-like and non-industrialized-like gut microbiomes [
31]. Similarly, residents of Norman, Oklahoma who had an urban-industrialized lifestyle were enriched in
Dorea compared to Matses and Tunapuco, individuals of a hunter-gatherer population and a traditional agricultural community, respectively [
32]. This provides evidence that lifestyle is a key factor contributing to differences between industrialized-like and non-industrialized-like gut microbiomes. However, caution must be taken when drawing this conclusion since these analyses did not account for dietary intake by participants.
Compost houses a diverse microbiome, whose composition varies greatly by compost type [
18,
19]. In the present study, the three compost types had different alpha diversity of compost bacteria, but there was no association between soil alpha diversity and the type of compost with which the soil was amended (
Supplementary Table S1). When examining the beta diversity of soil samples by type of compost, we found differences by compost type shortly after compost had been added to the soil (T2), but not later in the season (T3) (
Figure 4). This result suggests that the soil bacteria composition was sensitive to compost additions [
33,
34,
35], but that the compost’s effect on soil bacteria composition may have diminished over time [
36]. Therefore, the environmental microbiomes gardeners are exposed to may differ by type of compost used, and the effects may vary across the gardening season.
According to the FEAST analysis, participants who applied CM compost to their gardens had more gut bacteria that were potentially transferred from the compost compared to those who used DMP or P compost (
Figure 6). Conversely, participants who used DMP or P compost had more soil bacteria that was potentially transferred to their gut bacteria based on the results from the FEAST analysis. CM compost is comprised of only chicken manure, DMP is composed of both cow manure and plant material, and P is solely plant material. Chickens have a monogastric digestive system, which is also found in humans, while cows are ruminants. Thus, the chicken manure compost may contain more bacteria that is viable in the human gut compared to the DMP compost. Alternatively, chicken manure compost may harbor more similar bacteria to those found in the human gut. This requires further study.
In our study, there are some limitations that should be acknowledged. First, the sample size is relatively small, and may not have sufficient power to detect differences across the three time points. The sample size within each compost group is even smaller, resulting in low power to detect differences between compost groups. Thus, a larger sample size is necessary for future studies. Second, inclusion of a control group that does not garden would also be beneficial in order to examine if the gut microbiota changes over the seasons regardless of whether people garden. Each participant had a unique garden, so baseline soil differed by participant. Further, neither participant diet nor extent of time spent gardening or in the garden have been taken into account, and these factors should be analyzed in future research. In this study, only three time points across an entire gardening season were considered. Additional time points throughout the entire gardening season should be considered as the garden, the diet, and the gut are dynamic across time. Further, to truly determine bacterial transfer from soil/compost to the human gut, shotgun whole genome analysis of stool DNA is needed.