A new study found over 600 different viruses in samples from showerheads and toothbrushes, with no two samples being the same.

A recent published in Frontiers in Microbiomes investigated toothbrush and showerhead microbiomes to understand microbial composition in biofilm-based and frequently moist built environments.

Background

Built environments, including human-created and occupied environments, are critical to human health and well-being. Occupant behavior, cleanliness, personal hygiene, food choices, and geographic location impact the microbiome in these spaces.

Toothbrushes and shower heads are biofilm-dominated habitats with potential for human exposure. Bacteriophages, or viral organisms that infect bacterial organisms with high specificities for their host, influence microbial community composition and function via host infections and horizontal gene transfer.

Previous research has revealed differences between microbiomes from various human-constructed habitats and parts of a single type of indoor environment. In-depth research on viromes, particularly bacteriophages in specific built environments, is required to assess better the ecological interactions between viruses and bacteria that shape the built environment microbiota.

About the study

In the present study, researchers investigated microbial differences in toothbrush and showerhead biofilms and explored their interactions with environmental biofilms.

The researchers created a network of viral contigs and probable bacterial hosts from showerhead and toothbrush microbiomes. Volunteers sampled biofilms from showerheads and toothbrushes. The team obtained the showerhead samples from throughout the United States and the toothbrush samples from within 100 miles of Northwestern University.

Ninety-two showerhead samples and 36 toothbrush samples underwent amplicon and metagenomic sequencing. Using bioinformatic methods, researchers detected phages in these settings and investigated their interactions with bacterial populations. They investigated the possible functions of phages in toothbrush and showerhead microbiomes.

 The researchers identified potential phage contigs and examined viral contigs for completeness. They aligned the viral contigs to form viral operational taxonomic units (vOTU). They quantified the number of vOTUs across samples. They predicted open reading frames (ORFs) in vOTUs with above-medium quality and assigned taxonomies.

Researchers used several phage host matching methods to identify the most likely host for vOTUs. They used the Virulence Factor Database to identify antibiotic resistance genes and virulence factors in vOTU nucleotide sequences. They used principal coordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA).

Results

The researchers found 362 medium-quality, 232 high-quality, and 22 complete vOTUs. The top 15 most prevalent vOTUs in showerhead and toothbrush samples did not overlap, indicating that the two home biofilm types contain unique virus populations. Even viromes from the same sample type share few taxa. The showerhead information showed that only the home water source could significantly but poorly predict the variation in the viral composition.

Metadata gathered from toothbrush microbiomes revealed that no factor was significantly related to the composition of the toothbrush viral community. Although the recorded environmental parameters had negligible effects on the bacterial and viral communities in the sample sets, there was a strong correlation between the bacterial and viral community compositions in toothbrush and showerhead biofilms. However, the viral community richness did not correspond with the Simpson or Shannon indices.

Of the 614 high-quality vOTUs with enough coverage, the team found 532 associated with 32 families of bacteria, with only Caulobacteraceae, Sphingomonadaceae, and Burkholderiaceae detected in showerheads and toothbrushes. Low values for average nucleotide identity (ANI) compared to reference genetic sequences and numerous unknown or hypothetical ORFs suggest that these habitats are home to numerous unique and uncharacterized phages.

With bacterial taxonomy assignments, the toothbrush environments contain human microbiome-related taxa such as Streptococcus, Veillonella, and Klebsiella. Showerhead biofilms contain species distinct from Mycobacterium (Mycobacteroides and Mycolicibacterium) and genera widespread in soil or drinking water (Aquabacterium, Sphingopyxis, and Sphingobium).

Mycobacteriophages have shown a significant level of genetic diversity. Searching the ORFs against antibiotic resistance and virulence factor databases yielded few results, indicating that these viruses are unlikely to transport cargo with known negative human health impacts. However, the wide range of phage taxa and functional genes need more research to comprehend their implications for human health, biotechnology, and therapies.

Conclusions

The study found that microbiomes, particularly viral communities in home bathrooms, are different and distinctive, implying a limited connection between these compartments in built environments. The bacterial hosts’ sensitivity to environmental conditions may influence the viral makeup and abundance.

The primary features of viromes are significant disparity and genetic content diversity. There is no indication that viral contigs containing antibiotic resistance genes or virulence factors pose a problem in these constructed settings. Longitudinal sampling is required to improve understanding of the dynamics of host-phage interactions in these environments.