Colonic Microbial Abundances Predict Adenoma Formers.

OBJECTIVE: We aimed to examine associations between the oral, fecal, and mucosal microbiome communities and adenoma formation. SUMMARY BACKGROUND DATA: Data are limited regarding the relationships between microbiota and preneoplastic colorectal lesions. METHODS: Individuals undergoing screening colonoscopy were prospectively enrolled and divided into adenoma and nonadenoma formers. Oral, fecal, nonadenoma and adenoma-adjacent mucosa were collected along with clinical and dietary information. 16S rRNA gene libraries were generated using V4 primers. DADA2 processed sequence reads and custom R-scripts quantified microbial diversity. Linear regression identified differential taxonomy and diversity in microbial communities and machine learning identified adenoma former microbial signatures. RESULTS: One hundred four subjects were included, 46% with adenomas. Mucosal and fecal samples were dominated by Firmicutes and Bacteroidetes whereas Firmicutes and Proteobacteria were most abundant in oral communities. Mucosal communities harbored significant microbial diversity that was not observed in fecal or oral communities. Random forest classifiers predicted adenoma formation using fecal, oral, and mucosal amplicon sequence variant (ASV) abundances. The mucosal classifier reliably diagnosed adenoma formation with an area under the curve (AUC) = 0.993 and an out-of-bag (OOB) error of 3.2%. Mucosal classifier accuracy was strongly influenced by five taxa associated with the family Lachnospiraceae, genera Bacteroides and Marvinbryantia, and Blautia obeum. In contrast, classifiers built using fecal and oral samples manifested high OOB error rates (47.3% and 51.1%, respectively) and poor diagnostic abilities (fecal and oral AUC = 0.53). CONCLUSION: Normal mucosa microbial abundances of adenoma formers manifest unique patterns of microbial diversity that may be predictive of adenoma formation.

Optical Properties of Secondary Organic Aerosol Produced by Photooxidation of Naphthalene under NOx Condition.

Secondary organic aerosols (SOAs) affect incoming solar radiation by interacting with light at ultraviolet and visible wavelength ranges. However, the relationship between the chemical composition and optical properties of SOA is still not well understood. In this study, the complex refractive index (RI) of SOA produced from OH oxidation of naphthalene in the presence of nitrogen oxides (NOx) was retrieved online in the wavelength range of 315-650 nm and the bulk chemical composition of the SOA was characterized by an online high-resolution time-of-flight mass spectrometer. In addition, the molecular-level composition of brown carbon chromophores was determined using high-performance liquid chromatography coupled to a photodiode array detector and a high-resolution mass spectrometer. The real part of the RI of the SOA increases with both the NOx/naphthalene ratio and aging time, likely due to the increased mean polarizability and decreased molecular weight due to fragmentation. Highly absorbing nitroaromatics (e.g., C6H5NO4, C7H7NO4, C7H5NO5, C8H5NO5) produced under higher NOx conditions contribute significantly to the light absorption of the SOA. The imaginary part of the RI linearly increases with the NOx/VOCs ratio due to the formation of nitroaromatic compounds. As a function of aging, the imaginary RI increases with the O/C ratio (slope = 0.024), mainly attributed to the achieved higher NOx/VOCs ratio, which favors the formation of light-absorbing nitroaromatics. The light-absorbing enhancement is not as significant with extensive aging as it is under a lower aging time due to the opening of aromatic rings by reactions.

Molecular Analysis of Secondary Brown Carbon Produced from the Photooxidation of Naphthalene.

We investigate the chemical composition of organic light-absorbing components, also known as brown carbon (BrC) chromophores, formed in a proxy of anthropogenic secondary organic aerosol generated from the photooxidation of naphthalene (naph-SOA) in the absence and presence of NOx. High-performance liquid chromatography equipped with a photodiode array detector and electrospray ionization high-resolution mass spectrometer is employed to characterize naph-SOA and its BrC components. We provide molecular-level insights into the chemical composition and optical properties of individual naph-SOA components and investigate their BrC relevance. This work reveals the formation of strongly absorbing nitro-aromatic chromophores under high-NOx conditions and describes their degradation during atmospheric aging. NOx addition enhanced the light absorption of naph-SOA while reducing wavelength-dependence, as seen by the mass absorption coefficient (MAC) and absorption Ångström exponent (AAE). Optical parameters of naph-SOA generated under low- and high-NOx conditions showed a range of values from MACOM 405nm ∼ 0.12 m2 g-1 and AAE300-450nm ∼ 8.87 (low-NOx) to MACOM 405nm ∼ 0.19 m2 g-1 and AAE300-450nm ∼ 7.59 (high-NOx), consistent with "very weak" and "weak" BrC optical classes, respectively. The weak-BrC class is commonly attributed to biomass smoldering emissions, which appear to have optical properties comparable with the naph-SOA. Molecular chromophores contributing to naphthalene BrC absorption were identified with substantial nitro-aromatics, indicating that these species may be used as source-specific markers of BrC related to the anthropogenic emissions.

Dietary and lifestyle associations with microbiome diversity.

BACKGROUND: Microbial dysbiosis has been closely linked with colorectal cancer development. However, data is limited regarding the relationship of the mucosal microbiome, adenomatous polyps and dietary habits. Understanding these associations may elucidate pathways for risk stratification according to diet. RESULTS: Patients undergoing screening colonoscopy were included in our prospective, single center study and divided into adenoma or no adenoma cohorts. Oral, fecal, and mucosal samples were obtained. Microbial DNA was extracted, and amplicon libraries generated using primers for the 16S rRNA gene V4 region. Patient and dietary information was collected. Of 104 participants, 44% presented with polyps, which were predominantly tubular adenomas (87%). Adenoma formation and multiple patient dietary and lifestyle characteristics were associated with mucosal microbiome diversity. Lifestyle factors included age, body mass index, adenoma number, and dietary consumption of red meats, processed meats, vegetables, fruit, grain, fermented foods and alcohol. CONCLUSION: In this study we showed associations between dietary habits, adenoma formation and the mucosal microbiome. These early findings suggest that ongoing research into diet modification may help reduce adenoma formation and subsequently the development of CRC.

First experience in clinical application of hyperspectral endoscopy for evaluation of colonic polyps.

Early detection and resection of adenomatous polyps prevents their progression to colorectal cancer (CRC), significantly improving patient outcomes. Polyps are typically identified and removed during white-light colonoscopy. Unfortunately, the rate of interval cancers that arise between CRC screening events remains high, linked to poor visualization of polyps during screening and incomplete polyp removal. Here, we sought to evaluate the potential of a hyperspectral endoscope (HySE) to enhance polyp discrimination for detection and resection. We designed, built and tested a new compact HySE in a proof-of-concept clinical study. We successfully collected spectra from three tissue types in seven patients undergoing routine colonoscopy screening. The acquired spectral data from normal tissue and polyps, both pre- and post- resection, were subjected to quantitative analysis using spectral angle mapping and machine learning, which discriminated the data by tissue type, meriting further investigation of HySE as a clinical tool.

Daylight exposure modulates bacterial communities associated with household dust.

BACKGROUND: Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model "rooms" with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities. RESULTS: Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community. CONCLUSIONS: Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings.

Cleanliness in context: reconciling hygiene with a modern microbial perspective.

The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with sterilization. In reviewing studies across the hygiene literature (most often hand hygiene), we found that nearly all studies of hand hygiene utilize bulk reduction in bacterial load as a proxy for reduced transmission of pathogenic organisms. This treatment of hygiene may be insufficient in light of recent microbial ecology research, which has demonstrated that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota). The human skin is home to a diverse and specific community of microorganisms, which include members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as "those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease."