Ocular, Orbital, and Adnexal Toxicity With High-dose Volumetric Modulated Arc Radiation Therapy for Orbital Malignancies.

PURPOSE: Conventional modalities of external-beam radiation therapy (EBRT) are associated with high incidences of severe vision-threatening ocular and orbital toxicities when used to treat orbital malignancies. We investigate toxicities associated with high-dose volumetric modulated arc therapy (VMAT), a commonly used contemporary treatment modality for these tumors. METHODS: Retrospective analysis of malignant orbital tumors managed with adjuvant high-dose VMAT preceded by globe-salvaging surgical therapy (GST) or exenteration. Dosimetric quantitation of target volumes and critical structures was performed. Incidence and severity of ocular, orbital, and adnexal toxicities were evaluated and assessed with regard to conventional EBRT toxicities for orbital malignancies described in the literature. RESULTS: Eighty-four subjects (mean age = 65.9 ± 9.7 years) were included (N = 48 and N = 36 in GST and exenteration subgroups, respectively). Mean dose was 64.8 ± 2.1 Gy to the planning target volume. Dosing to critical structures typically did not surpass known tissue tolerance limits. Median follow up was 18.3 months. Visual acuity in the GST subgroup was not significantly different after VMAT (0.25 ± 0.06) compared with baseline (0.23 ± 0.02; P = 0.302). Whereas severe toxicities reported by major systematic analyses in the literature with older EBRT modalities were relatively common-for example, retinopathy (16-40%), optic neuropathy (16%), and corneal perforation (13%)-toxicities with VMAT were typically mild and less common. The most common toxicities with VMAT were mild dry eye (81.3%; 39/48), cataract (21.1%; 8/38 phakic eyes), and periocular dermatitis (15.5%; 13/84). Vision-threatening toxicities, including severe corneal pathologies, retinopathy, or optic neuropathy, were rare. There were no contralateral ocular or adnexal toxicities. CONCLUSIONS: High-dose VMAT for orbital malignancies demonstrated low incidence and severity of eye-related toxicity, in contradistinction to adverse events reported from conventional forms of radiotherapy.

A Digital Microscreen for the Enhanced Appearance of Ocular Prosthetic Motility (an American Ophthalmological Society Thesis).

PURPOSE: This study aims to improve the apparent motility of ocular prosthetic devices using technology. Prevailing ocular prostheses are acrylic shells with a static eye image rendered on the convex surface. A limited range of ocular prosthetic movement and lack of natural saccadic movements commonly causes the appearance of eye misalignment that may be disfiguring. Digital screens and computational systems may obviate current limitations in eye prosthetic motility and help prosthetic wearers feel less self-conscious about their appearance. METHODS: We applied convoluted neural networks (CNNs) to track pupil location in various conditions. These algorithms were coupled to a microscreen digital prosthetic eye (DPE) prototype to assess the ability of the system to capture full ocular ductions and saccadic movements in a miniaturized, portable, and wearable system. RESULTS: The CNNs captured pupil location with high accuracy. Pupil location data were transmitted to a miniature screen ocular prosthetic prototype that displayed a dynamic contralateral eye image. The transmission achieved a full range of ocular ductions and with grossly undetectable latency. Lack of iris and sclera color and detail, as well as constraints in luminosity, dimensionality and image stability limited the real eye appearance. Yet, the digitally rendered eye moved in the same amplitude and velocity as the native, tracked eye. CONCLUSIONS: Real-time image processing using CNNs coupled to microcameras and a miniscreen DPE may offer improvements in amplitude and velocity of apparent prosthetic eye movement. These developments, along with ocular image precision, may offer a next-generation eye prosthesis. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.

Opioid Use After Orbital, Eyelid, or Lacrimal Surgery.

PURPOSE: Opioids may be indicated to mitigate pain after oculofacial surgery. The opioid crisis prompted attention to how these medications are dispensed and disposed. This study aims to characterize opioid usage and handling of patients undergoing oculofacial plastic surgery. METHODS: Eighty-nine adult patients were surveyed on their opioid usage after undergoing orbital, lacrimal, or eyelid (including esthetic) surgery at a tertiary oculofacial plastic surgery practice. Each patient was prescribed 10 tablets of hydrocodone/acetaminophen 5 mg/325 mg; one tablet taken orally as needed every 6 hours for pain not relieved by acetaminophen. Subset analysis was performed for type of surgery, age, and gender. RESULTS: Patients consumed an average of 3 ± 0.4 tablets. In the subsets, the averages were 2.1 ± 0.5 (n = 38) tablets after eyelid surgery, 1.6 ± 0.6 (n = 24) after lacrimal surgery, and 5.6 ± 0.9 (n = 27) after orbital surgery. Greater opioid usage was observed after orbital versus eyelid surgery (p = 0.0007) and orbital versus lacrimal surgery (p = 0.0005) but not eyelid versus lacrimal surgery (p = 0.8604). Forty-six patients (51.7%) used no opioids. Over half (57.3%; n = 51) filled their prescription. Thirty-three patients (37.1%) had unused medications, of which 21 patients did not properly dispose of their medications. The mean age of patients who used opioids was less than the mean age of those who needed no opioids (p = 0.024). There were no gender differences in opioid usage use versus not (p = 0.62). CONCLUSIONS: Opioid needs after oculofacial plastic surgeries, especially eyelid and lacrimal, were minimal in this cohort. For most patients, the prescription exceeded needs. Younger age but not gender was associated with opioid use versus not. Most did not properly discard these medications. Quality improvement in both the dispensing and disposal of opioids in oculofacial surgical practice may be warranted.

Corneal Neurotization: A Review of Pathophysiology and Outcomes.

PURPOSE: The objective of this study is to provide a systematic review of the clinical outcomes of corneal neurotization and present the pathophysiology of corneal wound healing, neurotrophic keratopathy, and corneal neurotization. METHODS: A literature review of published articles and meeting abstracts between December 2008 and February 2019 in the English language with the terms "corneal neurotization," "corneal neurotisation," "corneal reinnervation," and "neurotrophic keratopathy" was performed. Reported clinical data before and after corneal neurotization, and surgical techniques, were collected and analyzed. RESULTS: A total of 54 eyes that underwent corneal neurotization were identified. Final Logarithm of the Minimum Angle of Resolution (logMAR) best-corrected visual acuity improved to 0.85 (standard deviation [SD] = 0.65) from 1.25 (SD = 0.71) with a mean improvement of 0.41 (SD = 0.55; p < 0.0001). Central corneal sensation measured using Cochet-Bonnet esthesiometer improved from 2.18 mm (SD = 0.4) to 40.10 mm (SD = 18.66) with a mean filament length change of 38.00 mm (SD = 18.95; p < 0.0001). The median time to the reported maximal sensation return was 8 months (interquartile range 6-10). The most common reported limitation to visual recovery was corneal scarring (31.5%). Children (ages 0-17 years) as compared with adults (ages 18-82 years) had significantly greater final central corneal sensation esthesiometry readings, central corneal sensation return, and improvement in the logMAR best-corrected visual acuity (p < 0.011). CONCLUSIONS: Neurotrophic keratopathy disturbs the homeostatic balance of trophic factors and trigeminal nerve reflexes needed to support ocular surface health and corneal healing. Corneal neurotization can significantly improve corneal sensation and visual acuity and should be considered for the treatment of refractory neurotrophic keratopathy, especially in pediatric populations.

Diversity in the American Society of Ophthalmic Plastic and Reconstructive Surgery.

PURPOSE: To assess the epidemiology of women and underrepresented minorities (URMs; Hispanic, African American, and Native American) in the American Society of Ophthalmic Plastic and Reconstructive Surgery (ASOPRS). METHODS: An observational retrospective study of living ASOPRS members was identified through the ASOPRS member directory, search engine-driven informatics, and direct communication. Members were profiled for gender, race, geographic location, and academic rank (or not). The percentage of women and URMs in the society over time was also assessed. RESULTS: The authors identified 617 living ASOPRS members as of June 2017. Of these, 109 (17.7%) were female and 58 (9.4%) were URMs. Surgeons completed fellowships from 1961 (male) or 1973 (female) until 2015. Women members significantly increased from 7 (4.9% of the total) before 1986 to 24 (30.4%) between 2011 and 2015 (last 5 years). URMs significantly increased over time, with 0 female and 5 (3.4%) male minorities before 1985 to 5 (6.3%) females and 13 (16.5%) males within the last 5 years (p < 0.05). With only 1 female and 3 male members, African American representation was sparse. ASOPRS members were not found in 5 states and were most represented in California, New York, Florida, and Texas. Among ASOPRS members in full-time academic positions, women tended to have lower rank compared to men; however, after controlling for number of years post-fellowship, this finding was narrowly not statistically significant (p = 0.0624). There were no academic differences with URMs and nonminority groups. CONCLUSIONS: Women and URMs have increased steadily in ASOPRS, especially in recent years. Similar to the rest of ophthalmology and general medicine, there remain opportunities for ASOPRS to increase diversity.

Opioid Prescribing Patterns Among American Society of Ophthalmic Plastic and Reconstructive Surgery Members in the Medicare Part D Database.

PURPOSE: To assess opioid prescribing patterns among American Society of Ophthalmic Plastic and Reconstructive Surgery (ASOPRS) members. METHODS: An observational, retrospective, cohort study of ASOPRS members' prescribing patterns in the 2013-2016 Medicare Part D Prescriber database. These prescribers were stratified by years in practice, sex, and geography. The ASOPRS member cohort was compared with all ophthalmologists, as a group, and other surgeons. RESULTS: The authors identified 617 surgeons in the 2017 ASOPRS directory. Members wrote an average of 45 opioid prescriptions/year. Almost half (45%) wrote <10 prescriptions. Those with >10 prescriptions averaged 78 annually. A minority wrote >100 prescriptions per year (14.8%). Overall, opioids comprised 16.5% of all prescriptions written by ASOPRS members. Despite seeing a similar number of beneficiaries (p = 0.20), male members prescribed a greater number (p < 0.05) and a higher rate (p < 0.05) of opioids than female members. Older members had a lower opioid prescription rate (p < 0.0001). Many heavy opioid prescribers practiced in states with high opioid overdose deaths. CONCLUSIONS: American Society of Ophthalmic Plastic and Reconstructive Surgery members prescribe moderate amounts of opioids at a rate (16.5%) higher than all of ophthalmology (4%), above the national mean (6.8%), but lower than other surgical services (36.5%). Male gender, younger age, and practice in states with high opioid-related deaths were correlated to number of prescriptions. Prescribing patterns may naturally relate to the type of surgical intervention and population. Further research is warranted to understand opioid prescriptions and their role in the opioid epidemic.

Natural History of the Central Structural Abnormalities in Choroideremia: A Prospective Cross-Sectional Study.

PURPOSE: To describe in detail the central retinal structure of a large group of patients with choroideremia (CHM). DESIGN: A prospective, cross-sectional, descriptive study. PARTICIPANTS: Patients (n = 97, age 6-71 years) with CHM and subjects with normal vision (n = 44; ages 10-50 years) were included. METHODS: Subjects were examined with spectral-domain optical coherence tomography (SD OCT) and near-infrared reflectance imaging. Visual acuity (VA) was measured during their encounter or obtained from recent ophthalmic examinations. Visual thresholds were measured in a subset of patients (n = 24) with automated static perimetry within the central regions (±15°) examined with SD OCT. MAIN OUTCOME MEASURES: Visual acuity and visual thresholds; total nuclear layer, inner nuclear layer (INL), and outer nuclear layer (ONL) thicknesses; and horizontal extent of the ONL and the photoreceptor outer segment (POS) interdigitation zone (IZ). RESULTS: Earliest abnormalities in regions with normally appearing retinal pigment epithelium (RPE) were the loss of the POS and ellipsoid zone associated with rod dysfunction. Transition zones (TZs) from relatively preserved retina to severe ONL thinning and inner retinal thickening moved centripetally with age. Most patients (88%) retained VAs better than 20/40 until their fifth decade of life. The VA decline coincided with migration of the TZ near the foveal center. There were outer retinal tubulations in degenerated, nonatrophic retina in the majority (69%) of patients. In general, RPE abnormalities paralleled photoreceptor degeneration, although there were regions with detectable but abnormally thin ONL co-localizing with severe RPE depigmentation and choroidal thinning. CONCLUSIONS: Abnormalities of the POS and rod dysfunction are the earliest central abnormalities observed in CHM. Foveal function is relatively preserved until the fifth decade of life. Migration of the TZs to the foveal center with foveal thinning and structural disorganization heralded central VA loss. The relationships established may help outline the eligibility criteria and outcome measures for clinical trials for CHM.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

RATIONALE: Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES: We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS: Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS: Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS: The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.

The primary open-angle african american glaucoma genetics study: baseline demographics.

PURPOSE: To describe the baseline characteristics of the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study cohort, the largest African American population with primary open-angle glaucoma (POAG) recruited at a single institution (University of Pennsylvania [UPenn], Department of Ophthalmology, Scheie Eye Institute) to date. DESIGN: Population-based, cross-sectional, case-control study. PARTICIPANTS: A total of 2520 African American subjects aged 35 years or more who were recruited from the greater Philadelphia, Pennsylvania area. METHODS: Each subject underwent a detailed interview and eye examination. The interview assessed demographic, behavioral, medical, and ocular risk factors. Current ZIP codes surrounding UPenn were recorded and US census data were queried to infer socioeconomic status. The eye examination included measurement of visual acuity (VA) and intraocular pressure, and a detailed anterior and posterior segment examination, including gonioscopy, dilated fundus and optic disc examination, visual fields, stereo disc photography, optical coherence tomography, and measurement of central corneal thickness. MAIN OUTCOME MEASURES: The baseline characteristics of gender, age, and glaucoma diagnosis were collected. Body mass index (BMI), hypertension, diabetes, alcohol and tobacco use, ocular conditions (including blindness, cataract, nonproliferative diabetic retinopathy, and age-related macular degeneration), and use of ocular medication and surgery were examined. Median population density, income, education level, and other socioeconomic measures were determined for the study cohort. RESULTS: Of the 2520 African Americans recruited to the POAAGG study to date, 2067 (82.0%), including 807 controls and 1260 POAG cases, met all inclusion criteria and completed the detailed clinical ocular examination. Cases were more likely to have a lower BMI (P < 0.01) and report a history of blindness (VA of ≤20/200; P < 0.001), whereas controls were more likely to have diabetes (P < 0.001), have nonproliferative diabetic retinopathy (P = 0.02), and be female (P < 0.001). Study participants were drawn largely from predominantly African American neighborhoods of low income, high unemployment, and lower education surrounding UPenn. CONCLUSIONS: The POAAGG study has currently recruited more than 2000 African Americans eligible for a POAG genetics study. Blindness and low BMI were significantly associated with POAG. This population was predominantly recruited from neighborhoods whose population income exists at or near the federal poverty level.

Obstructive sleep apnea and central serous chorioretinopathy.

PURPOSE: The purpose of this study was to determine if there is an association between obstructive sleep apnea (OSA) and central serous chorioretinopathy (CSCR). METHODS: Patients with CSCR without a history of steroid use or secondary retinal disease were matched based on age/gender/body mass index with control patients and administered the Berlin Questionnaire to assess for OSA risk. Patients were scored "OSA+" if they were at "high risk" on the Berlin Questionnaire or reported a previous OSA diagnosis. Rates of OSA+ were compared between the 2 groups, odds ratio and its 95% confidence interval was calculated using exact conditional logistic regression. RESULTS: Forty-eight qualifying patients with CSCR were identified. There were no statistically significant differences between the CSCR and control groups by age (mean = 55 years), gender (79% male), body mass index (mean = 28.2), history of diabetes, or hypertension. Within the CSCR group, 22 patients (45.8%) were OSA+ versus 21 control patients (43.8%) (difference = 2.1%; 95% confidence interval, -18.2% to 22.2%; exact odds ratio = 1.08, 95% confidence interval, 0.47-2.49; P = 1.00). CONCLUSION: When compared with matched controls, patients with CSCR did not have statistically significant higher rates of OSA risk or previous diagnosis. This finding contrasts with previous work showing a strong association between the diseases. The divergence is likely due to our matching controls for body mass index, a significant risk factor for OSA.

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.

BACKGROUND: Fungi are important pathogens but challenging to enumerate using next-generation sequencing because of low absolute abundance in many samples and high levels of fungal DNA from contaminating sources. RESULTS: Here, we analyze fungal lineages present in the human airway using an improved method for contamination filtering. We use DNA quantification data, which are routinely acquired during DNA library preparation, to annotate output sequence data, and improve the identification and filtering of contaminants. We compare fungal communities and bacterial communities from healthy subjects, HIV+ subjects, and lung transplant recipients, providing a gradient of increasing lung impairment for comparison. We use deep sequencing to characterize ribosomal rRNA gene segments from fungi and bacteria in DNA extracted from bronchiolar lavage samples and oropharyngeal wash. Comparison to clinical culture data documents improved detection after applying the filtering procedure. CONCLUSIONS: We find increased representation of medically relevant organisms, including Candida, Cryptococcus, and Aspergillus, in subjects with increasingly severe pulmonary and immunologic deficits. We analyze covariation of fungal and bacterial taxa, and find that oropharyngeal communities rich in Candida are also rich in mitis group Streptococci,a community pattern associated with pathogenic polymicrobial biofilms. Thus, using this approach, it is possible to characterize fungal communities in the human respiratory tract more accurately and explore their interactions with bacterial communities in health and disease.

The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report.

Study of the human lung microbiome in the context of pulmonary health and disease is an area of emerging research interest that is being driven by several contributing factors. These factors include increased recognition of the diversity of human-associated microbiota, their roles in health and in diseases associated with chronic inflammation, and advancements in technologies and tools that have facilitated such discoveries about the microbiota in organ systems outside of the lung. Therefore, the overarching goals of lung microbiome research are: to identify and characterize microbial populations associated with the respiratory tract and lungs; to understand their roles in lung health and disease; and, we hope, to allow the development of improved approaches for diagnosing and treating chronic respiratory diseases in which the microbiome has a role. Recent studies of the lung microbiome have yielded a number of interesting findings but also highlighted questions and challenges for researchers and clinicians. In December 2011, the National Heart, Lung, and Blood Institute convened a workshop to identify key issues and areas for further attention or development to advance research on the lung microbiome. Current knowledge and the state of research on the lung and related areas of human microbiome investigation were reviewed and discussed.

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

RATIONALE: Lung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV. OBJECTIVES: To determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota. METHODS: We used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects. MEASUREMENTS AND MAIN RESULTS: Sequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease. CONCLUSIONS: Asymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.

Microbes of the human respiratory tract are important in health and disease, but accurate sampling of the lung presents challenges. Lung microbes are commonly sampled by bronchoscopy, but to acquire samples the bronchoscope must pass through the upper respiratory tract, which is rich in microbes. Here we present methods to identify authentic lung microbiota in bronchoalveolar lavage (BAL) fluid that contains substantial oropharyngeal admixture. We studied clinical BAL samples from six selected subjects with potential heavy lung colonization. A single sample of BAL fluid was obtained from each subject along with contemporaneous oral wash (OW) to sample the oropharynx, and then DNA was extracted from three separate aliquots of each. Bacterial 16S rDNA sequences were amplified and products analyzed by 454 pyrosequencing. By comparing replicates, we were able to specify the depth of sequencing needed to reach a 95% chance of identifying a bacterial lineage of a given proportion--for example, at a depth of 5,000 tags, OTUs of proportion 0.3% or greater would be called with 95% confidence. We next constructed a single-sided outlier test that allowed lung-enriched organisms to be quantified against a background of oropharyngeal admixture, and assessed improvements available with replicate sequence analysis. This allowed identification of lineages enriched in lung in some BAL specimens. Finally, using samples from healthy volunteers collected at multiple sites in the upper respiratory tract, we show that OW provides a reasonable but not perfect surrogate for bacteria carried into to the lung by a bronchoscope. These methods allow identification of microbes that can replicate in the lung despite the background due to oropharyngeal microbes derived from aspiration and bronchoscopic carry-over.

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.

RATIONALE: Long-term survival after lung transplantation is limited by infectious complications and by bronchiolitis obliterans syndrome (BOS), a form of chronic rejection linked in part to microbial triggers. OBJECTIVES: To define microbial populations in the respiratory tract of transplant patients comprehensively using unbiased high-density sequencing. METHODS: Lung was sampled by bronchoalveolar lavage (BAL) and upper respiratory tract by oropharyngeal wash (OW). Bacterial 16S rDNA and fungal internal transcribed spacer sequencing was used to profile organisms present. Outlier analysis plots defining taxa enriched in lung relative to OW were used to identify bacteria enriched in lung against a background of oropharyngeal carryover. MEASUREMENTS AND MAIN RESULTS: Lung transplant recipients had higher bacterial burden in BAL than control subjects, frequent appearance of dominant organisms, greater distance between communities in BAL and OW indicating more distinct populations, and decreased respiratory tract microbial richness and diversity. Fungal populations were typically dominated by Candida in both sites or by Aspergillus in BAL but not OW. 16S outlier analysis identified lung-enriched taxa indicating bacteria replicating in the lower respiratory tract. In some cases this confirmed respiratory cultures but in others revealed enrichment by anaerobic organisms or mixed outgrowth of upper respiratory flora and provided quantitative data on relative abundances of bacteria found by culture. CONCLUSIONS: Respiratory tract microbial communities in lung transplant recipients differ in structure and composition from healthy subjects. Outlier analysis can identify specific bacteria replicating in lung. These findings provide novel approaches to address the relationship between microbial communities and transplant outcome and aid in assessing lung infections.

Associating microbiome composition with environmental covariates using generalized UniFrac distances.

MOTIVATION: The human microbiome plays an important role in human disease and health. Identification of factors that affect the microbiome composition can provide insights into disease mechanism as well as suggest ways to modulate the microbiome composition for therapeutical purposes. Distance-based statistical tests have been applied to test the association of microbiome composition with environmental or biological covariates. The unweighted and weighted UniFrac distances are the most widely used distance measures. However, these two measures assign too much weight either to rare lineages or to most abundant lineages, which can lead to loss of power when the important composition change occurs in moderately abundant lineages. RESULTS: We develop generalized UniFrac distances that extend the weighted and unweighted UniFrac distances for detecting a much wider range of biologically relevant changes. We evaluate the use of generalized UniFrac distances in associating microbiome composition with environmental covariates using extensive Monte Carlo simulations. Our results show that tests using the unweighted and weighted UniFrac distances are less powerful in detecting abundance change in moderately abundant lineages. In contrast, the generalized UniFrac distance is most powerful in detecting such changes, yet it retains nearly all its power for detecting rare and highly abundant lineages. The generalized UniFrac distance also has an overall better power than the joint use of unweighted/weighted UniFrac distances. Application to two real microbiome datasets has demonstrated gains in power in testing the associations between human microbiome and diet intakes and habitual smoking. AVAILABILITY: http://cran.r-project.org/web/packages/GUniFrac