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Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.

Antemortem diagnosis of neuroborreliosis in horses has been hindered by both the low sensitivity of PCR testing for

Abstract Young adults are increasingly using non-cigarette products, such as hookahs, since they are perceived as healthier alternatives to cigarette smoking. However, hookah users are exposed to not only carcinogenic compounds but also microorganisms that may play an active role in the development of both infectious and chronic diseases among users. Nevertheless, existing hookah research in this area has focused only on microorganisms that may be transferred to users through the smoking apparatus and not on bacterial communities associated with hookah tobacco. To address this knowledge gap, we conducted time-series experiments on commercially available hookah brands (Al Fakher (flavors: two apple, mint, and watermelon) and Fumari (flavors: white gummy bear, ambrosia, and mint chocolate chill)) stored under three different temperature and relative humidity conditions over 14 days. To characterize bacterial communities, the total DNA was extracted on days 0, 5, 9, and 14, PCR-amplified for the V3V4 region of the bacterial 16S rRNA gene, sequenced on the Illumina HiSeq platform, and analyzed using R. Diversity (alpha and beta) analyses revealed that the microbiotas of Fumari and Al Fakher products differed significantly and that flavor had a significant effect on the hookah microbiota. Overall, Pseudomonas, Bacillus, Sphingomonas, and Methylobacterium were the predominant bacterial taxa across all products. Additionally, we observed compositional differences between hookah brands across the 14-day incubation. These data suggest that the bacterial communities of hookah tobacco are diverse and differ across brands and flavors, which may have critical implications regarding exposures to specific bacteria among hookah users. Key points • Commercial hookah products harbor diverse bacterial communities. • Brands and flavors impact the diversity of these communities. • Research on their viability and transmission to users’ respiratory tracts is needed. Graphical abstract

Antemortem diagnosis of neuroborreliosis in horses has been hindered by both the low sensitivity of PCR testing for Borrelia burgdorferi in CSF and the low specificity of serum:CSF ELISA ratios used to determine intrathecal antibody production against the bacterium. PCR testing of the CSF of an adult horse with acute neurologic disease for the B. burgdorferi flagellin gene was negative. However, we enriched B. burgdorferi DNA through nucleic acid hybrid capture, followed by next-generation sequencing, and identified B. burgdorferi in the CSF of the horse, confirming a diagnosis of neuroborreliosis.

Despite ongoing improvements in regimens to prevent allograft rejection, most cardiac and other types of allografts eventually succumb to chronic vasculopathy, interstitial fibrosis, or endothelial changes, and eventually graft failure. Adaptive immune-mediated damage is considered the primary cause of long-term graft failure, though the events leading to chronic rejection are still poorly understood. Gut microbiota is a known driving force in immune dysfunction. We previously showed that gut microbiota dysbiosis profoundly influences the outcome of vascularized cardiac allografts and subsequently identified biomarker species or “bacterial determinants” associated with these differential graft outcomes (anti-inflammatoryBifidobacterium pseudolongum(Bifido) and pro-inflammatoryDesulfovibrio desulfuricans(Desulfo)). In this study, we further detailed the multifaceted immunomodulatory properties of the pro-tolerogenic bacterial species over time, using our clinically relevant model of allogenic heart transplantation. This model simultaneously accounts for the immunomodulatory properties of antibiotics and tacrolimus immunosuppression, in addition to bacterial determinants. We observed thatBifidoinduced an early anti-inflammatory phenotype within 7 days, whileDesulforesulted in a pro-inflammatory phenotype, defined by alterations in leukocyte distribution and lymph node (LN) structure. These effects were further modulated by inhibition of myeloid cell migration by CCR2 inhibition, supporting the notion that bacterial determinants regulate innate immunity which subsequently influences adaptive immunity. Indeed,in vitroresults showed thatBifidoandDesulfoacted directly on primary innate immune cells. However, by 40 days after treatment, these two bacterial determinants were associated with mixed effects in their impact on LN architecture and immune cell composition. These dynamic effects suggest a critical role for early bacterial determinant-triggered immunological events such as innate immune cell engagement and LN architectural changes in the subsequent modulation of pro-tolerant versus pro-inflammatory immune responses in organ transplant recipients.

Nontraditional irrigation water sources (e.g., recycled water, brackish water) may harbor human pathogens, including Vibrio spp., that could be present in a viable-but-nonculturable (VBNC) state, stymieing current culture-based detection methods. To overcome this challenge, we coupled 5-bromo-2′-deoxyuridine (BrdU) labeling, enrichment techniques, and 16S rRNA sequencing to identify metabolically-active Vibrio spp. in nontraditional irrigation water (recycled water, pond water, non-tidal freshwater, and tidal brackish water). Our coupled BrdU-labeling and sequencing approach revealed the presence of metabolically-active Vibrio spp. at all sampling sites. Whereas, the culture-based method only detected vibrios at three of the four sites. We observed the presence of V. cholerae, V. vulnificus, and V. parahaemolyticus using both methods, while V. aesturianus and V. shilonii were detected only through our labeling/sequencing approach. Multiple other pathogens of concern to human health were also identified through our labeling/sequencing approach including P. shigelloides, B. cereus and E. cloacae. Most importantly, 16S rRNA sequencing of BrdU-labeled samples resulted in Vibrio spp. detection even when our culture-based methods resulted in negative detection. This suggests that our novel approach can effectively detect metabolically-active Vibrio spp. that may have been present in a VBNC state, refining our understanding of the prevalence of vibrios in nontraditional irrigation waters.

The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to B. pseudolongum type strain ATCC25526 of porcine origin using a combination of in vitro and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to host responses of immune modulation and changes in intestinal B. pseudolongum strains. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.

Previous studies have characterized bacterial communities in menthol versus non-menthol cigarettes. However, these studies evaluated commercial cigarettes, for which levels of chemical constituents are largely unknown, and therefore, could not assess the impact of varying nicotine and menthol concentrations on tobacco bacterial communities. To address this knowledge gap, we performed time-series experiments using SPECTRUM research cigarettes with varying nicotine and menthol levels. Cigarettes were incubated under three storage conditions for 14 days. Cigarette tobacco was then sub-sampled (n = 288), DNA extracted, and subjected to PCR amplification of the V3V4 region of the 16S rRNA gene, followed by Illumina HiSeq sequencing. Sequences were analyzed using QIIME and R. Incubation under varying conditions did not affect bacterial diversity. However, significant differences in bacterial communities were observed across varying nicotine concentrations in menthol and non-menthol products. For example, Pseudomonas spp. was negatively correlated with nicotine concentrations in menthol cigarettes. A significantly higher relative abundance of P. veronii and P. viridiflava was observed in menthols versus non-menthols, while a significantly higher relative abundance of Bacillus foraminis and B. coagulans was found in non-menthols versus menthols. Additional bacteria (e.g., Staphylococcus spp., Jeotgalicoccus psychrophilus, and B. flexus) significantly changed in relative abundance between days 0 and 14. Our findings demonstrate that nicotine and menthol levels have a significant impact on the relative abundance of potential bacterial pathogens present in cigarettes. Future work is needed to demonstrate whether these tobacco-associated bacteria could be transferred to users while smoking, ultimately contributing to adverse respiratory impacts. KEY POINTS: • Varying nicotine levels changes bacterial composition of research cigarettes. • Mentholation affects the tobacco bacterial microbiome. • SPECTRUM research cigarettes are dominated by Pseudomonas and Bacillus.

While an increasing number of studies have evaluated tobacco microbiomes, comparative microbiome analyses across diverse tobacco products are non-existent. Moreover, to our knowledge, no previous studies have characterized the metabolically-active (live) fraction of tobacco bacterial communities and compared them across products. To address these knowledge gaps, we compared bacterial communities across four commercial products (cigarettes, little cigars, cigarillos and hookah) and one research cigarette product. After total DNA extraction (n = 414) from all samples, the V3V4 region of the 16S rRNA gene was sequenced on the Illumina HiSeq platform. To identify metabolically-active bacterial communities within these products, we applied a coupled 5-bromo-2'-deoxyuridine labeling and sequencing approach to a subset of samples (n = 56). Each tobacco product was characterized by its signature microbiome, along with a shared microbiome across all tobacco products consisting of Pseudomonas aeruginosa, P. putida, P. alcaligenes, Bacillus subtilis, and Klebsiella pneumoniae. Comparing across products (using Linear discriminant analysis Effect Size (LEfSe)), a significantly higher (p 0.05) relative abundance of Klebsiella and Acinetobacter was observed in commercial cigarettes, while a higher relative abundance of Pseudomonas and Pantoea was observed in research cigarettes. Methylorubrum and Paenibacillus were higher in hookah, and Brevibacillus, Lactobacillus, Bacillus, Lysinibacillus, and Staphylococcus were higher in little cigars and cigarillos. Across all products, the majority of the metabolically-active bacterial communities belonged to the genus Pseudomonas, followed by several genera within the Firmicutes phylum (Bacillus, Terribacillus, and Oceanobacillus). Identification of some metabolically-active pathogens such as Bacillus cereus and Haemophilus parainfluenzae in commercial products is of concern because of the potential for these microorganisms to be transferred to users' respiratory tracts via mainstream smoke. Future work is warranted to evaluate the potential impact of these tobacco bacterial communities on users' oral and lung microbiomes, which play such an important role on the spectrum from health to disease.

Background: The beneficial effects attributed to Bifidobacterium are thought to arise from their host immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. Results: We have shown that B. pseudolongum UMB-MBP-01, a murine isolate, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to B. pseudolongum type strain ATCC25526 of porcine origin using a combination of in vitro and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to host responses of immune modulation and changes in intestinal B. pseudolongum strains. Conclusion: Our study demonstrated a single probiotic bacterial strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome in response to prophylactic supplementation strains and the intestinal responses, and advances our understanding of the mechanisms which drive the strain-specific association between prophylactic Bifidobacterium and health benefit.

Acne and rosacea, despite their similar clinical presentations, follow distinct clinical courses, suggesting that fundamental differences exist in their pathophysiology. We performed a case-control study profiling the skin microbiota in rosacea and acne patients compared to matched controls. Nineteen rosacea and eight acne patients were matched to controls by age ± 5 years, sex and race. DNA was extracted from facial skin swabs. The V3V4 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq and analysed using QIIME/Metastats 2.0 software. The mean relative abundance of Cutibacterium acnes in rosacea with inflammatory papules and pustules (20.454% ±16.943%) was more similar to that of acne (19.055% ±15.469%) than that of rosacea without inflammatory papules and pustules (30.419% ±21.862%). C acnes (P = .048) and Serratia marcescens (P = .038) were significantly enriched in individuals with rosacea compared to acne. Investigating the differences between the skin microbiota in acne and rosacea can provide important clues towards understanding the disease progression in each condition.

Background Associations between acne and gastrointestinal comorbidities suggest that microbial dysbiosis and intestinal permeability may promote inflammatory acne, a condition often managed with oral antibiotics. Objective We performed a case-control study to investigate the skin and gut microbiota in 8 acne patients before and after receiving oral minocycline compared to controls matched by age ±5 years, sex, and race. Methods DNA was extracted from stool samples and facial skin swabs. Sequencing of the V3V4 region of the bacterial 16S rRNA gene was performed using Illumina MiSeq and analyzed using QIIME/MetaStats 2.0 software. Results Acne patients included 7 female and 1 male, ages 20~32. Shannon diversity was not significantly different between the skin (p=0.153) or gut (p

Purpose of review The microbiota plays an important role in health and disease. During organ transplantation, perturbations in microbiota influence transplant outcome. We review recent advances in characterizing microbiota and studies on regulation of intestinal epithelial barrier function and mucosal and systemic immunity by microbiota and their metabolites. We discuss implications of these interactions on transplant outcomes. Recent findings Metagenomic approaches have helped the research community identify beneficial and harmful organisms. Microbiota regulates intestinal epithelial functions. Signals released by epithelial cells or microbiota trigger pro-inflammatory or anti-inflammatory effects on innate and adaptive immune cells, influencing the structure and function of the immune system. Assessment and manipulation of microbiota can be used for biomarkers for diagnosis, prognosis, and therapy. Summary The bidirectional dialogue between the microbiota and immune system is a major influence on immunity. It can be targeted for biomarkers or therapy. Recent studies highlight a close association of transplant outcomes with microbiota, suggesting exciting potential avenues for management of host physiology and organ transplantation.

BackgroundStaphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Few data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection.MethodsWe performed 2 matched case–control studies (colonization cohort—neonates who did and did not acquire S. aureus colonization; bacteremia cohort—neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in 2 intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge and cultured for S. aureus, and the nasal microbiome was characterized using 16S rRNA gene sequencing.ResultsIn the colonization cohort, 43 S. aureus–colonized neonates were matched to 82 controls. At 1 week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank-sum test P < .05) and differed in beta diversity (omnibus MiRKAT P = .002) even after adjusting for birth weight (P = .01). The bacteremia cohort included 10 neonates, of whom 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared with colonized neonates and controls.ConclusionsThe association of increased S. aureus abundance and decrease of microbiome diversity suggest the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.

Multiple studies have demonstrated that cigarettes harbor bacterial pathogens. Yet, to our knowledge, there are no published data to date on whether or not these microorganisms can be aerosolized and transmitted to the respiratory tract of users. To address this knowledge gap, we characterized cigarette bacterial communities and evaluated whether or not they could be aerosolized in mainstream smoke. Filtered and unfiltered cigarettes were tested. Non-smoked tobacco leaf, enriched non-smoked tobacco leaf extract and enriched mainstream smoke extract samples (n = 144) were incubated on trypticase soy agar, and resulting bacterial colonies were sequenced. Total DNA was also extracted, followed by PCR amplification of the 16S rRNA gene, sequencing and analysis using UCHIME, QIIME and R packages. The predominant bacterial genera cultured from the mainstream smoke of unfiltered cigarettes were Bacillus, Terribacillus, Paenibacillus and Desulfotomaculum. Culturable bacteria were not recovered from the smoke of filtered products. However, sequencing data demonstrated no significant differences in bacterial community diversity in the smoke of filtered versus unfiltered cigarettes, suggesting that other non-culturable bacteria may be aerosolized in mainstream smoke as well. Our study provides novel evidence that tobacco-associated bacterial communities are viable, can be aerosolized in mainstream smoke, and could potentially be transferred to the oral cavity and respiratory tract of smokers.

Background Staphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Few data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection. Methods We performed 2 matched case–control studies (colonization cohort—neonates who did and did not acquire S. aureus colonization; bacteremia cohort—neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in 2 intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge and cultured for S. aureus, and the nasal microbiome was characterized using 16S rRNA gene sequencing. Results In the colonization cohort, 43 S. aureus–colonized neonates were matched to 82 controls. At 1 week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank-sum test P < .05) and differed in beta diversity (omnibus MiRKAT P = .002) even after adjusting for birth weight (P = .01). The bacteremia cohort included 10 neonates, of whom 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared with colonized neonates and controls. Conclusions The association of increased S. aureus abundance and decrease of microbiome diversity suggest the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.

Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities., Graphical abstract, Highlights • Cities possess a consistent “core” set of non-human microbes • Urban microbiomes echo important features of cities and city-life • Antimicrobial resistance genes are widespread in cities • Cities contain many novel bacterial and viral species, This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.

BACKGROUND: The efficacy of antibiotics in rosacea treatment suggests a role for microorganisms in its pathophysiology. Growing concern over the adverse effects of antibiotic use presents a need for targeted antimicrobial treatment in rosacea. OBJECTIVE: We performed a case–control study to investigate the skin microbiota in patients with rosacea compared to controls matched by age, sex, and race. METHODS: Nineteen participants with rosacea, erythematotelangiectatic, papulopustular, or both, were matched to 19 rosacea-free controls. DNA was extracted from skin swabs of the nose and bilateral cheeks of participants. Sequencing of the V3V4 region of the bacterial 16S ribosomal RNA gene was performed using Illumina MiSeq and analyzed using QIIME/MetaStats 2.0 software. RESULTS: Compared with controls, skin microbiota in erythematotelangiectatic rosacea was depleted in Roseomonas mucosa (p = 0.004). Papulopustular rosacea was enriched in Campylobacter ureolyticus (p = 0.001), Corynebacterium kroppenstedtii (p = 0.008), and the oral flora Prevotella intermedia (p = 0.001). The highest relative abundance of C. kroppenstedtii was observed in patients with both erythematotelangiectatic and papulopustular rosacea (19.2%), followed by papulopustular (5.06%) and erythematotelangiectatic (1.21%) rosacea. C. kroppenstedtii was also associated with more extensive disease, with the highest relative abundance in rosacea affecting both the cheeks and nose (2.82%), followed by rosacea sparing the nose (1.93%), and controls (0.19%). CONCLUSIONS: The skin microbiota in individuals with rosacea displays changes from that of healthy skin, suggesting that further studies examining a potential role for the skin microbiota in the pathophysiology of rosacea may be warranted.

A quenching agent is commonly added to chlorinated, reclaimed water during sample collection to prevent chlorine-mediated die-off of viable microbiota. However, the effect of quenching on downstream 16S rRNA-based bacterial community analyses is unclear. We conducted a side-by-side comparison of 16S rRNA sequencing data from reclaimed water samples quenched with sodium thiosulfate and non-quenched samples. Our data showed that 16 S rRNA processing and sequencing methods, and resulting bacterial profiles, were not negatively impacted by quenching.

This case-control study investigates the association between nasal microbial profiles and odds of infection after elective surgical procedures., Key Points Question Can characterization of microbiota present on preoperative nasal swab estimate risk for postoperative infection in patients undergoing elective surgical procedures? Findings In this case-control study, 167 patients were classified to nasal microbial profile cluster 1 and 30 patients to cluster 2 based on 16S ribosomal RNA gene sequencing. Classification to cluster 2 was associated with statistically significantly higher odds of infection (ie, deep surgical site infection, bacteremia, or pneumonia) after surgical procedure, independent of covariates, including nasal carriage of Staphylococcus aureus on preoperative culture and intrasample microbial diversity (ie, α diversity). Meaning These findings suggest that the nasal microbiome is an independent risk factor associated with infectious outcomes after elective surgical procedures., Importance The association of the nasal microbiome with outcomes in surgical patients is poorly understood. Objective To characterize the composition of nasal microbiota in patients undergoing clean elective surgical procedures and to examine the association between characteristics of preoperative nasal microbiota and occurrence of postoperative infection. Design, Setting, and Participants Using a nested matched case-control design, 53 individuals who developed postoperative infection were matched (approximately 3:1 by age, sex, and surgical procedure) with 144 individuals who were not infected (ie, the control group). The 2 groups were selected from a prospective cohort of patients undergoing surgical procedures at 2 tertiary care university hospitals in Baltimore, Maryland, who were at high risk for postoperative infectious complications. Included individuals were aged 40 years or older; had no history of autoimmune disease, immunocompromised state, immune-modulating medication, or active infection; and were scheduled to undergo elective cardiac, vascular, spinal, or intracranial surgical procedure. Data were analyzed from October 2015 through September 2020. Exposures Nasal microbiome cluster class served as the main exposure. An unsupervised clustering method (ie, grades of membership modeling) was used to classify nasal microbial samples into 2 groups based on features derived from 16S ribosomal RNA gene sequencing. The microbiome cluster groups were derived independently and agnostic of baseline clinical characteristics and infection status. Main Outcomes and Measures Composite of surgical site infection, bacteremia, and pneumonia occurring within 6 months after surgical procedure. Results Among 197 participants (mean [SD] age, 64.1 [10.6] years; 63 [37.7%] women), 553 bacterial taxa were identified from preoperative nasal swab samples. A 2-cluster model (with 167 patients in cluster 1 and 30 patients in cluster 2) accounted for the largest proportion of variance in microbial profiles using grades of membership modeling and was most parsimonious. After adjusting for potential confounders, the probability of assignment to cluster 2 was associated with 6-fold higher odds of infection after surgical procedure (odds ratio [OR], 6.18; 95% CI, 3.33-11.7; P

Objective To characterize the microbial communities of the anterior nares (nose) and posterior pharynx (throat) of adults dwelling in the community and in nursing homes before and after treatment with intranasal mupirocin. Methods Staphylococcus aureus-colonized adults were recruited from the community (n = 25) and from nursing homes (n = 7). S. aureus colonization was confirmed using cultures. Participants had specimens taken from nose and throat for S. aureus quantitation using quantitative PCR for the nuc gene and bacterial profiling using 16S rRNA gene sequencing over 12 weeks. After two baseline study visits 4 weeks apart, participants received intranasal mupirocin for 5 days with 3 further visits over a 8 week follow-up period. Results We found a decrease in the absolute abundance of S. aureus in the nose for 8 weeks after mupirocin (1693 vs 141 fg/ul, p = 0.047). Mupirocin caused a statistically significant disruption in bacterial communities of the nose and throat after 1 week, which was no longer detected after 8 weeks. Bacterial community profiling demonstrated that there was a decrease in the relative abundance of S. aureus (8% vs 0.3%, pStaphylococcus epidermidis in the nose (21% vs 5%, p Conclusions Decolonization with mupirocin leads to a sustained effect on absolute and relative abundance of S. aureus but not for other bacteria in the nose. This demonstrates that a short course of mupirocin selectively decreases S. aureus in the nose for up to 8 weeks.

The etiology of vulvar lichen sclerosus (LS) remains unclear; however, alterations in cutaneous and gut microbiota may be contributing to the pathogenesis of this inflammatory condition. To explore this hypothesis, we conducted a pilot case-control study, obtaining dermal swab and stool samples from prepubertal girls with vulvar LS (n = 5), girls with nonspecific vulvovaginitis (n = 5), and healthy controls (n = 3). Samples (n = 56) were subjected to total DNA extractions. Resulting DNA was purified, subjected to PCR (targeting the V3V4 region of the 16S rRNA gene), sequenced, and analyzed using QIIME, MetagenomeSeq, and DESeq2 software packages. Our findings showed that there were significant differences in the cutaneous and gut microbiotas of girls with LS compared to controls. On the skin, girls with LS had a statistically significantly higher relative abundance of Porphyromonas spp., Parvimonas spp., Peptoniphilus spp., Prevotella spp., Dialister spp., and Peptostreptococcus spp., but a lower relative abundance of Cornyebacterium compared to the control group. In the gut samples, girls with LS had a significantly higher relative abundance of Dialister spp., Clostridiales spp., Paraprevotella spp., Escherichia coli, Bifidobacterium adolescentis, and Akkermansia muciniphila, and a lower relative abundance of Roseburia faecis and Ruminococcus bromii compared to controls. These results suggest a potential association between cutaneous and gut dysbiosis and pediatric vulvar LS. Future studies involving larger samples sizes are warranted to further evaluate this association.

Tobacco smoking is still the leading cause of preventable diseases and death in the USA and throughout the globe. Under Section 904(a)(3) of the US Federal Food, Drug, and Cosmetic Act, tobacco manufacturing companies need to report on quantities of harmful and potentially harmful constituents (HPHCs) in all tobacco products. While the extensive HPHC list of 2012 includes 93 chemicals, which are categorized as carcinogenic, respiratory, cardiovascular, or reproductive toxicants or addictive compounds, it fails to include microorganisms (bacteria and fungi) that have been shown to contribute to adverse health outcomes among tobacco users. Nevertheless, over the last 50 years, researchers have studied microorganisms in a variety of tobacco products using both culture-based and culture-independent techniques. In this mini-review, we provide an overview of this body of research, detailing the bacterial and fungal microbiomes residing in commercial tobacco products. Overall, studies have characterized over 89 unique bacterial genera and 19 fungal genera in cigarettes, cigars, cigarillos, hookah, and smokeless tobacco. The most predominant bacterial genera are Bacillus, Pseudomonas, and Staphylococcus. Fungal genera identified have included Aspergillus, Penicillium, Mucor, Alternaria, Cladosporium, Streptomyces, and Candida, to name a few. While some of the identified microorganisms are known human pathogens, others are potential opportunistic pathogens. Given the vast array of microorganisms that are present across diverse types of tobacco products, future research should be focused on the viability of these microorganisms, as well as their ability to transfer to the user’s respiratory tract, potentially contributing to adverse health outcomes. Key points • Commercial tobacco products harbor diverse bacterial and fungal communities. • Some of these microorganisms are known or opportunistic human pathogens. • Research on their viability and transmission to users’ respiratory tracts is needed.

Background The ability of Cutibacterium acnes strains to form biofilms has been correlated with their virulence. Objective This study examined biofilm and skin microbiota in acne patients in order to understand their role in the development of acne lesions. Methods Thin sections of punch biopsy specimens of (i) uninflamed comedones, (ii) inflammatory lesions, and (iii) uninvolved adjacent skin of acne patients were examined. Epiflourescence and confocal laser scanning microscopy were used for biofilm detection, and pyrosequencing with taxonomic classification of 16s rRNA gene amplicons was used for microbiota analysis. Results Of the 39 skin specimens from patients with mild-moderate acne (n = 13) that were studied, nine (23%) contained biofilm. Among these specimens, biofilm was most frequently detected in comedones (55.6%) and less frequently in inflammatory papules (22.2%) and uninvolved skin (22.2%). Comedones demonstrated the highest mean alpha diversity of all the lesion subtypes. The relative abundance of Staphylococcus was significantly higher in comedones (11.400% ± 12.242%) compared to uninvolved skin (0.073% ± 0.185%, P = 0.024). Conclusions The microenvironment of the comedone differs from that of inflammatory lesions and unaffected skin. The increased frequency of biofilm in comedones may account for the lack of host inflammatory response to these lesions.

The increasing use of reclaimed water for irrigation in areas lacking access to advanced wastewater treatment and reclaimed water distribution systems calls for an examination of irrigation-site-based treatment technologies that can improve the quality of this alternative water source. To address this need, we investigated the impact of zero-valent iron (ZVI)-sand filtration on the bacterial community structure and functional potential of conventionally treated reclaimed water utilized in downstream applications. Over a 2-month period, reclaimed water was collected from a tertiary wastewater treatment plant in the Mid-Atlantic, U.S. and trucked to our greenhouse facility. The water was stored in rain barrels and then filtered through one ZVI-sand filter every 5 days. Filtrate was then subjected to enumeration, phylotyping, shiga toxin screening, and antimicrobial susceptibility testing of Escherichia coli. Aliquots of filtrate were also DNA extracted, and purified DNA was subjected to 16S rRNA gene sequencing and metagenomic shotgun sequencing. The genera Dechloromonas, Desulfotomaculum, Leptonema, and Thermomonas, which contain denitrifying and sulfate reducing species, commonly used in bioremediation, and known to increase the inherent reactivity of ZVI, were significantly more relatively abundant in ZVI-sand filtered reclaimed water compared to reclaimed water. The concentration of E. coli in ZVI-sand filtered reclaimed water was significantly lower compared to that of reclaimed water, and cefoxitin- and tetracycline-resistant E. coli were undetectable after ZVI-sand filtration. ZVI-sand filtration reduced the occurrence of human as well as plant pathogenic genera (Aeromonas, Mycobacterium, Shewanella, Acidovorax, Agrobacterium, and Clavibacter) but increased the proportion of Azospira, a nitrogen fixing bacterial genera, in the microbial community. Our exploratory functional analysis showed a modest non-significant increase in the proportion of open reading frames for genes associated with iron uptake, oxidative stress, as well as defense and repair mechanisms after ZVI-sand filtration. These data indicate an iron rich environment in the filter causing an oxidative stress response by the bacterial community present in the reclaimed water. Our findings demonstrate that ZVI-sand filtration effectively filters conventionally treated reclaimed water. Longer-term, field-based studies are needed to evaluate the effectiveness of the filter in agricultural settings and inform the development of future agricultural water reuse regulations.

The peritrophic matrix (PM) is an acellular membrane that covers the gut epithelium in arthropods and physically separates it from the lumen. The structure is thought to play an important role in tick biology. The PM is also known to impact the persistence of tick-borne pathogens like Borrelia burgdorferi, although limited information is available about its molecular constituents or their biological significance. Herein, we characterize a novel PM-associated gut protein in Ixodes scapularis ticks, annotated as Peritrophic Membrane Chitin Binding Protein (PM_CBP), for its role in the integrity and function of the matrix. The PM_CBP displays homology to the chitin deacetylase metalloenzyme, shows upregulation during tick feeding, and is localized at the luminal surface of the gut epithelium. The structural integrity of the PM was impaired both by the knock down of PM_CBP expression via RNA interference and by treatment with anti-PM_CBP antibodies, as revealed by its electron microscopic appearance. Additionally, the duration of tick engorgement on mice and the passage of experimentally-inoculated fluorescent dextran molecules across the PM are affected by the knock down of PM_CBP expression. The transfer of anti-PM_CBP antibodies into the tick gut impacted the overall composition of the resident microbiome, and also influenced Borrelia burgdorferi acquisition in ticks and its transmission to mice. Taken together, these data highlight the biological significance of the Ixodes PM and suggest that the targeting of its molecular constituents may contribute to the development of novel interventions against tick-borne infections. This article is protected by copyright. All rights reserved. WOS:000579839300001 33006213 Q2