Background and Aims: Changes in the esophageal microbiome have been reported in children with eosinophilic esophagitis (EoE), but few data exist for adults. We aimed to determine whether the esophageal microbiome differs in adults with and without EoE. Methods: In a prospective cohort study, adults undergoing outpatient endoscopy were enrolled as incident EoE cases or non-EoE controls. Clinical, endoscopic, and histologic data were collected. An esophageal biopsy was utilized for microbiome analysis. Bacterial DNA was extracted and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Analyses were performed comparing microbiome features for cases and controls, and within cases for disease features, with correction for multiple hypothesis testing. Results: A total of 24 incident EoE cases (mean age 40 years; 63% male; 100% white; 97 eos/hpf) and 25 controls (mean age 48, 36% male; 76% white; 1 eos/hpf) were analyzed. Principal coordinate analysis ordination failed to distinguish cases from controls. There were no microbiome differences within EoE cases based on clinical phenotype, presence of atopy, or endoscopic features. Use of proton pump inhibitors (PPIs), however, was significantly associated with 5 taxa including SR1 at the phylum level and Burkholderia at the genus level. Conclusions: There were no significant differences in the esophageal microbiome between newly diagnosed EoE cases and non-EoE controls in adults, or within EoE cases based on clinical features. However, given the strong rationale for the esophageal microbiome in EoE pathogenesis, future studies should explicitly consider the presence of PPIs as a confounding feature.

Wastewater treatment plants (WWTPs) are thought to be potential incubators of antibiotic resistance. Persistence of commonly used antibiotics in wastewater may increase the potential for selection of resistance genes transferred between bacterial populations, some of which might pose a threat to human health. In this study, we measured the concentrations of ten antibiotics in wastewater plant influents and effluents, and in surface waters up- and downstream from two Charlotte area treatment facilities. We performed Illumina shotgun sequencing to assay the microbial community and resistome compositions at each site across four time points from late winter to mid-summer of 2016. Antibiotics are present throughout wastewater treatment, and elevated concentrations of multiple antibiotics are maintained in moving stream water downstream of effluent release. While some human gut and activated sludge associated taxa are detectable downstream, these seem to attenuate with distance while the core microbial community of the stream remains fairly consistent. We observe the slight suppression of functional pathways in the downstream microbial communities, including amino acid, carbohydrate, and nucleic acid metabolism, as well as nucleotide and amino acid scavenging. Nearly all antibiotic resistance genes (ARGs) and potentially pathogenic taxa are removed in the treatment process, though a few ARG markers are elevated downstream of effluent release. Taken together, these results represent baseline measurements that future studies can utilize to help to determine which factors control the movement of antibiotics and resistance genes through aquatic urban ecosystems before, during, and after wastewater treatment.

Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify phenotypically resistant cultivable portions of these bacterial communities and characterized the composition of the culturable subset of these populations. Resistant taxa were more abundant in raw sewage and wastewater before the biological aeration treatment stage. While some antibiotic-resistant bacteria (ARB) were detectable downstream of treated wastewater release, these organisms are not enriched relative to effluent-free upstream water, indicating efficient removal during treatment. Combined culture-dependent and -independent analyses revealed a stark difference in community composition between culturable fractions and the environmental source material, irrespective of culturing conditions. Higher proportions of the environmental populations were recovered than predicted by the widely accepted 1% culturability paradigm. These results represent baseline abundance and compositional data for ARB communities for reference in future studies addressing the dissemination of antibiotic resistance associated with urban wastewater treatment ecosystems.

Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.