Background
The human gastrointestinal tract is a large interface between the host, environmental factors, and antigens in the human body. The gut microbiota represents ten times the number of nucleated human cells and harbors two orders of magnitude more genomic content than the human genome [
1]. Members of the gut microbiota form a complex, mutually beneficial relationship, which substantially contributes to human metabolic processes via their extended gene pool and their encoded enzymes [
2,
3]. Among the most predominant enzymes expressed by several members of the human gut microbiota are azoreductases, which catalyze the reduction of azo-bonds, activating pharmaceutical dosage forms or degrading food additives [
4‐
7].
Among azo compounds whose reduction is largely mediated by the gut microbiota are (i) azo-antibacterial pro-drugs based on sulfanilamide (e.g., prontosil and neoprontosil), (ii) a range of 5-aminosalicylic acid pro-drugs used in the treatment of ulcerative colitis and inflammatory bowel conditions [
8,
9], and (iii) drug-delivery systems that target the colon depending on the azoreductase enzymes produced by the large intestinal microbiota [
6]. Thus, the metabolism and bioavailability of such drugs are largely affected by the azo-reducing capability of the gut microbiota, and compositional changes in the gut microbial community lead to differential human responses toward these drugs. Personalized therapeutics, classically based on an individual’s genetics, is being expanded to the association between the microbiome and bioavailability, treatment outcome, and toxicity of a given drug. Pharmacomicrobiomics [
5,
10] and toxicomicrobiomics [
11,
12], as subfields of precision medicine, are becoming necessary for developing new preventive and therapeutic strategies [
13,
14]. One of the most attractive enzymes for pharmacomicrobiomic studies is the group of azoreductases [
4,
7].
Several researchers have isolated, purified, and biochemically characterized different azoreductases from aerobic and anaerobic microorganisms, some of which are members of the human gut microbiota. They identified their encoding genes, and described their catalytic activity, cofactor requirement, and biophysical characteristics (e.g., [
15‐
21]). However, less attention was given to define the relative abundance of azoreductase-producing microbes within the human gut and to relate compositional variations in the gut microbiota to their azo-reducing activity. Accordingly, this study aimed to explore the composition of the fecal microbiomes of a group of adults with no diagnosed diseases and try to relate their microbial community composition to their azo-reducing activity.
Discussion
The human gut contains trillions of metabolically active microbial cells that enrich the human gene pool with millions of genes, and their encoded enzymes. Azoreductases (expressed by several members of the human gut microbiota) greatly affect metabolism of azodyes, extensively used in food and pharmaceuticals. Thus, the gut microbiota composition is expected to affect the metabolism of many drugs and azodye-containing compounds, and administering these azodye-containing drugs/xenobiotics to different populations, without taking their gut microbiota composition in consideration, might affect the metabolism and bioavailability of such drugs.
In this study, the core microbiome of 16 stool samples, collected from the same neighborhood to reduce variations based on diet and lifestyle, was defined by 16S rRNA amplicon sequencing. This analysis, with an admittedly small sample size, is intended to be a pilot comparative analysis of microbiome structure to relate gut microbial communities to their overall azo-reducing activity. In spite of the deluge of microbiome studies in the past few years, only a handful gut microbiome studies were conducted in Egypt (e.g., [
22‐
26]), and none of them focused on xenobiotic-degrading phenotypes.
Early microbiome studies reported that Firmicutes and Bacteroidetes dominated in the gut (~ 90% relative abundance), but to highly variable degrees [
27,
28], and suggested the Firmicutes-to-Bacteroidetes ratio as a significant a biomarker for the human gut microbiota status [
29], as the coexistence of Bacteroidetes and Firmicutes in the gut implies minimized competition for resources [
30]. Another important biomarker of the gut microbiota status/health is the
Prevotella-to-
Bacteroides ratio, which was suggested as a predictor for successful body fat loss, notably on diets high in fiber and whole grain [
31,
32].
In our study, the microbiome profile of the fecal samples had a typical gut microbiome signature, as Firmicutes and Bacteroidetes constituted ~ 92% of microbial populations. A key finding of the study is that high azo-reducing activity positively correlated with phylum Firmicutes but negatively with phylum Bacteroidetes. This might be because the genomes of Firmicutes are rich in azoreductase-encoding genes [
4]. However, Proteobacteria supersede Firmicutes as azoreductase producers; yet their relative abundance did not significantly or consistently vary within different stool samples, which might be due to their lower overall relative abundance in the gut microbiota in comparison to Firmicutes and Bacteroidetes. Consequently, high azo-reducing stool samples had a higher Firmicutes-to-Bacteroidetes median ratio than low- or non-degraders.
In addition, the median
Prevotella-to-
Bacteroides ratio was higher in the high azo-reducing group, but did not reach statistical significance owing to high within-group variability. Although some
Bacteroides species are known for their azo-reducing activity [
33,
34], while no azoreductases have been described in
Prevotella species,
Prevotella might be relatively enriched in some high azo-reducing samples just because of its inverse correlation with
Bacteroides, whereas the actual activity was due to the members of phylum Frimicutes in such samples. It is often the case that when
Bacteroides is high in a sample,
Prevotella is low, and vice versa [
35]. Another interpretation of the high variability in
Prevotella relative abundance among azo-reducers, might be that an azoreductase activity is yet to be discovered in some
Prevotella species, or that the activity is strain specific, and thus cannot be resolved by 16S rRNA analysis.
At the genus level, significant variation in alpha diversity was observed with the Simpson diversity index, while richness was not significantly different. This result suggests that evenness, rather than number of taxa is what differentiates the groups. Beta diversity of samples classified according to their azo-reducing activity (and estimated by the weighted UniFrac method) indicated no particular clustering patterns. A possible interpretation is that, although Firmicutes seemed to clearly have an effect on the final azoreductase activity, different genera of Firmicutes were dominant in different samples, and no particular clustering of taxa was observed; yet, the presence of any of these genera seemed to encode enough azoreductases.
The
Fusobacterium-to-
Bifidobacterium ratio is considered as a biomarker for dysbiosis of the gut microbiota. Patients with colorectal cancer were reported to have a decrease in the relative abundance of
Bifidobacterium coupled with increases in
Faecalibacterium prausnitzii abundance [
36,
37]. Unsurprisingly, in this study,
Faecalibacterium species was nil in 10 samples and of negligible value in the other six samples, as all our samples were collected from subjects with no reported diseases (other than obesity in one subject).
Finally, we performed multivariate analysis of relative abundances of different bacterial taxa and gut microbiome biomarkers with age, sex, and BMI of participants to rule out that the observed associations were caused by a confounding factor. Invariably, azo-reducing activity was found as a key player in the relative abundance of Firmicutes and one of the significant covariates with Bacteroidetes relative abundance, and consequently the Firmicutes-to-Bacteroidetes ratio. BMI, on the other hand, was a key covariate with Bacteroidetes and Actinobacteria. These results are in accordance with Kim et al.’s report that phylum Actinobacteria was positively associated with body weight [
38]. In addition an investigation of gut microbiota of lean and obese twins observed higher levels of Actinobacteria in obese subjects [
39]. Kim et al. also reported that age significantly increased the proportions of both class Coriobacteriia and family Coriobacteriaceae in phylum Actinobacteria [
38], whereas La-ongkham et al. observed that the relative abundance of the phylum Actinobacteria in the adult subjects was significantly higher by approximately 2.3 times than that in the elderly group [
40]. Here, age was found as a significant covariate with Chao 1 richness and with Actinobacteria relative abundance, but not with that of the three other major phyla.
Conclusion
In conclusion, we analyzed the fecal microbiomes of 16 adult Egyptian volunteers in a pilot study to relate composition of microbial communities to their azo-reducing activity. Major taxa usually associated with the human gut environment were observed, indicating a typical gut microbiome signature. Despite the small sample size, using multivariate followed by univariate analyses indicated statistically significant trends. The microbiome profiling indicated variations in the Firmicutes-to-Bacteroides and Prevotella-to-Bacteroides ratios among samples with different azo-reducing grades, suggesting the relative abundance of phylum Firmicutes as the most striking factor that may have affected the final azo-reducing activity. Additionally, samples with different azo-reducing grades significantly differed in evenness.
The major limitations of this work are the small sample size and the absence of evidence of causality behind observed statistical associations. Future studies should address these limitations by analyzing larger cohorts; by combining and comparing samples from different human populations at different geographical locations, representing different diets and lifestyles; and by using animal models or ex vivo models of the gut microbiota to allow investigating causality (e.g., by experimentally altering the Firmicutes-to-Bacteroidetes ratio and measuring the azoreductase activity). Additionally, shotgun metagenomics, metaproteomics, metabonomics, and functional metagenomics strategies (reviewed and compared in [
12]) are all likely to provide insight into the mechanism of microbiome members involvement in the azoreduction process.
Moreover, the results of this study highlight the importance of characterizing azoreductase-producing gut bacteria, notably among Bacteroides and Prevotella species, which have not been as studied as Firmicutes and Proteobacteria, and which may have important strain-level variations. Such studies will help increase our knowledge about the fate of azodye-containing drugs or chemicals, and about differential human responses to them. These results will also guide the development of more efficient drugs and dosage forms, and will contribute to efforts for implementing microbiome testing in precision medicine and toxicology.
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