Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses.

The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.

Disease Burden and Treatment Patterns Among US Patients with Hidradenitis Suppurativa: A Retrospective Cohort Study.

INTRODUCTION: Hidradenitis suppurativa (HS) is a chronic, autoinflammatory skin disease associated with many comorbidities. One biologic (adalimumab) is approved for HS. This study assessed the sociodemographic characteristics, comorbidities, treatment patterns, healthcare resource utilization (HCRU) and associated costs of patients with HS following biologic approval. METHODS: This non-interventional, retrospective cohort study involved adult (≥ 18 years) and adolescent (12-17 years) patients diagnosed with HS in the United States (US) using Optum's de-identified Clinformatics® Data Mart Database during the period 1 January 2016 to 31 December 2018. RESULTS: Of 42,843 identified patients, 10,909 met the incident HS patient criteria (10,230 adults, 628 adolescents, 51 patients aged <12 years). Patients were mostly diagnosed by a general practitioner/pediatrician (adults: 41.6%; adolescents: 39.6%) or dermatologist (adults: 22.1%; adolescents: 30.6%). Commonly reported Charlson comorbidities at pre-index in adult patients were diabetes without complications (20.4%), chronic pulmonary disease (16.4%) and diabetes with complications (9.0%), and the most frequent Elixhauser comorbidities were uncomplicated hypertension (38.3%), obesity (22.5%), uncomplicated diabetes (19.0%) and depression (17.4%). The burden of comorbidities generally increased over time after diagnosis in both adults and adolescents. HS-related surgical procedures were uncommon in the 2-years post-index period: an incision and drainage procedure was reported in 7.6% of adults and 6.4% of adolescents. Patients were predominantly treated with both topical and systemic antibiotic treatments (adults: 25.0% and 65.1%, respectively; adolescents: 41.7% and 74.5%, respectively). Biologic prescription was higher in adults than adolescents (3.5% vs. 1.8%). Total healthcare costs for adult and adolescent patients in the 2-years post-index period were US$42,143 and US$16,057, respectively, with outpatient costs accounting for the majority of these costs (US$20,980 and US$8408, respectively). CONCLUSION: In adult and adolescent patients with HS, comorbidity burden continues to increase after diagnosis. All-cause and HS-specific HCRU and costs are high in adults and adolescents with HS. These findings support the need for a multidisciplinary comprehensive care strategy for patients with HS.

A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.

Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.

BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables. RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well. CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.

Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography.

To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.

Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica.

Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.

Microbial Species-Area Relationships in Antarctic Cryoconite Holes Depend on Productivity.

The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.

Fungal communities living within leaves of native Hawaiian dicots are structured by landscape-scale variables as well as by host plants.

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape-scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome.

Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes.

Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.

Structure of bacterial and eukaryote communities reflect in situ controls on community assembly in a high-alpine lake.

Recent work suggests that microbial community composition in high-elevation lakes is significantly influenced by microbes entering from upstream terrestrial and aquatic habitats. To test this idea, we conducted 18S and 16S rDNA surveys of microbial communities in a high-alpine lake in the Colorado Rocky Mountains. We compared the microbial community of the lake to water entering the lake and to uphill soils that drain into the lake. Utilizing hydrological and abiotic data, we identified potential factors controlling microbial diversity and community composition. Results show a diverse community entering the lake at the inlet with a strong resemblance to uphill terrestrial and aquatic communities. In contrast, the lake communities (water column and outlet) showed significantly lower diversity and were significantly different from the inlet communities. Assumptions of neutral community assembly poorly predicted community differences between the inlet and lake, whereas "variable selection" and "dispersal limitation" were predicted to dominate. Similarly, the lake communities were correlated with discharge rate, indicating that longer hydraulic residence times limit dispersal, allowing selective pressures within the lake to structure communities. Sulfate and inorganic nitrogen and phosphorus concentrations correlated with community composition, indicating "bottom up" controls on lake community assembly. Furthermore, bacterial community composition was correlated with both zooplankton density and eukaryotic community composition, indicating biotic controls such as "top-down" interactions also contribute to community assembly in the lake. Taken together, these community analyses suggest that deterministic biotic and abiotic selection within the lake coupled with dispersal limitation structures the microbial communities in Green Lake 4.

The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities.

Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.

Targeted ITS1 sequencing unravels the mycodiversity of deep-sea sediments from the Gulf of Mexico.

Fungi from marine environments have been significantly less studied than terrestrial fungi. This study describes distribution patterns and associated habitat characteristics of the mycobiota of deep-sea sediments collected from the Mexican exclusive economic zone (EEZ) of the Gulf of Mexico (GoM), ranging between 1000 and > 3500 m depth. Internal Transcribed Spacer 1 (ITS1) amplicons were sequenced by Illumina MiSeq. From 29 stations sampled across three annual campaigns, a total of 4421 operational taxonomic units (OTUs) were obtained, indicating a high fungal richness. Most OTUs assignments corresponded to Ascomycota, unidentified fungi and Basidiomycota. The majority of the stations shared a mere 31 OTUs, including the worldwide reported genera Penicillium, Rhodotorula and Cladosporium. Both a transient and a conserved community were identified, suggesting their dependence on or adaptation to the habitat dynamics, respectively. The differences found in fungal richness and taxonomic compositions were correlated principally with latitude, carbon and carbonates content, and terrigenous content, which could be the potential drivers that delimit fungal distribution. This study represents an expansion of our current knowledge on the biogeography of the fungal community from deep-sea sediments, and identifies the geographic and physicochemical properties that delimit fungal composition and distribution in the GoM.

A Developing Symbiosis: Enabling Cross-Talk Between Ecologists and Microbiome Scientists.

Like all interactions, the success of cross-discipline collaborations relies on effective communication. Ecology offers theoretical frameworks and lexicons to study microbiomes. Yet some of the terms and concepts borrowed from ecology are being used discordantly by microbiome studies from their traditional definitions. Here we define some of the ecological terms and concepts as they are used in ecology and the study of microbiomes. Where applicable, we have provided the historical context of the terms, highlighted examples from microbiome studies, and considered the research methods involved. We divided these concepts into four sections: Biomes, Diversity, Symbiosis, and Succession. Biomes encompass the interactions within the biotic and abiotic features of an environment. This extends to the term "microbiome," derived from "biome," and includes an environment and all the microbes within it. Diversity encompasses patterns of species richness, abundance, and biogeography, all of which are important to understanding the distribution of microbiomes. Symbiosis emphasizes the relationships between organisms within a community. Symbioses are often misunderstood to be synonymous with mutualism. We discard that implication, in favor of a broader, more historically accurate definition which spans the continuum from parasitism to mutualism. Succession includes classical succession, alternative stable states, community assembly frameworks, and r/K-selection. Our hope is that as microbiome researchers continue to apply ecological terms, and as ecologists continue to gain interest in microbiomes, each will do so in a way that enables cross-talk between them. We recommend initiating these collaborations by using a common lexicon, from which new concepts can emerge.

Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica.

Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We extracted DNA and chlorophyll a from the sediments and water of these samples to describe biodiversity and quantify proxies for biomass. Contrary to our expectation, we found that cryoconite holes with greater richness and biomass showed less partitioning of phylotypes by the sediments versus the water, perhaps indicating that the probability of sediment microbes being mixed into the water is higher from richer sediments. Another explanation may be that organisms from the water were compressed by freezing down to the sediment layer, leaving primarily relic DNA of dead cells to be detected higher in the frozen water. Further evidence of this explanation is that the dominant sequences unique to water closely matched organisms that do not live in cryoconite holes or the Dry Valleys (e.g., vertebrates); so this cryptic biodiversity could represent unknown microbial animals or DNA from atmospheric deposition of dead biomass in the otherwise low-biomass water. Although we cannot rule out spatial niche partitioning occurring at finer scales or in melted cryoconite holes, we found no evidence of partitioning between the sediments and water in frozen holes. Future work should include more sampling of cryoconite holes at a finer spatial scale, and characterizing the communities of the sediments and water when cryoconite holes are melted and active.

Lyme Disease Transmission Risk: Seasonal Variation in the Built Environment.

Seasonal variation in spatial distribution and pathogen prevalence of Borrelia burgdorferi in blacklegged ticks (Ixodes scapularis) influences human population risk of Lyme disease in peri-urban built environments. Parks, gardens, playgrounds, school campuses and neighborhoods represent a significant risk for Lyme disease transmission. From June 2012 through May 2014, ticks were collected using 1 m² corduroy cloths dragged over low-lying vegetation parallel to walkways with high human foot traffic. DNA was extracted from ticks, purified and presence of B. burgdorferi assessed by polymerase chain reaction amplification. Summer is reported as the time of highest risk for Lyme disease transmission in the United States and our results indicate a higher tick density of 26.0/1000 m² in summer vs. 0.2/1000 m² to 10.5/1000 m² in spring and fall. However, our findings suggest that tick infection rate is proportionally higher during the fall and spring than summer (30.0⁻54.7% in fall and 36.8⁻65.6% in spring vs. 20.0⁻28.2% in summer). Seasonal variation in infected tick density has significant implications for Lyme disease transmission as people are less likely to be aware of ticks in built environments, and unaware of increased infection in ticks in spring and fall. These factors may lead to more tick bites resulting in Lyme infection.

Phosphorus, not nitrogen, limits plants and microbial primary producers following glacial retreat.

Current models of ecosystem development hold that low nitrogen availability limits the earliest stages of primary succession, but these models were developed from studies conducted in areas with temperate or wet climates. Global warming is now causing rapid glacial retreat even in inland areas with cold, dry climates, areas where ecological succession has not been adequately studied. We combine field and microcosm studies of both plant and microbial primary producers and show that phosphorus, not nitrogen, is the nutrient most limiting to the earliest stages of primary succession along glacial chronosequences in the Central Andes and central Alaska. We also show that phosphorus addition greatly accelerates the rate of succession for plants and for microbial phototrophs, even at the most extreme deglaciating site at over 5000 meters above sea level in the Andes of arid southern Peru. These results challenge the idea that nitrogen availability and a severe climate limit the rate of plant and microbial succession in cold-arid regions and will inform conservation efforts to mitigate the effects of global change on these fragile and threatened ecosystems.

Temporal dynamics of gut microbiota in triclocarban-exposed weaned rats.

Widely used as an antimicrobial in antibacterial bar soaps, triclocarban (3,4,4'-trichlorocarbanilide; TCC) is effective against Gram-positive bacteria but shows little efficacy against Gram-negative strains, potentially altering the composition of indigenous microflora within and on the human body. To date, the consequence of continuous or previous nonprescription antimicrobial exposure from compounds in personal care products on commensal microflora is still elusive. Previous research has shown that TCC exposure during gestation and lactation induced dysbiosis of gut microbial communities among exposed dams and neonates. However, the impact of antimicrobial exposure specifically after discontinuation of the use of TCC on the gut microbiota has not been investigated. In this study, weaned Sprague Dawley rats (postnatal day, PND 22) were provided ad lib access to TCC-supplemented diet (0.2% w/w or 0.5% w/w) for 4 weeks (phase I) followed by a 4-week washout period (phase II) to determine gut microflora changes both during continuous exposure to TCC and to determine the potential rebound following TCC withdrawal. Fecal samples were collected at baseline (PND 22) prior to TCC exposure and throughout phase I and phase II. The V4 region of 16S rDNA was sequenced from extracted total fecal DNA with the MiSeq platform. Exposure to both 0.2% w/w and 0.5% w/w TCC was sufficient to alter diversity of microbiota during phase I of treatment. This effect was further prolonged into phase II, even when TCC exposure was discontinued. Collectively, these data highlight the impact of both continuous and prior TCC exposure on gut microbial ecology and shed light onto the potential long-term health risk of daily nonprescription antimicrobial personal care product use.