Comparison of Clinical Features and Serum Parameters of Culture-Positive Children with Culture-Negative Children in Septic Arthritis and Acute Osteomyelitis.

PURPOSE OF THE STUDY The aim of this study was to investigate the culture results of children undergoing debridement for suspected septic arthritis or acute osteomyelitis and to compare the laboratory parameters and clinical characteristics of culture-positive and culture-negative patients. MATERIAL AND METHODS Patients who underwent surgery in our hospital for septic arthritis and acute osteomyelitis between 2011 and 2019 were retrospectively analyzed. Seventy-two of 96 patients were included in the study. The patients had documented joint swelling, redness, pain with joint movement and weight-bearing failure. Fever was assessed preoperatively. Sedimentation rate, C-reactive protein level, white blood cell count and the leukocyte count in aspiration material as well as complications were evaluated preoperatively and 3 months postoperatively. RESULTS Twenty patients underwent surgery of the hip; 39 of the knee; 7 of the foot, ankle and distal tibia; 1 of the elbow; and 1 of the distal radius. Additionally, 4 patients had septic arthritis and acute osteomyelitis of the femur. The mean age of the patients was 7.8 years (1-16). The mean follow-up period was 16.2 months (3-42). Preoperative aspiration was performed in 44 of 72 patients. Thirty of 72 patients had positive cultures. No statistically significant difference in age, preoperative duration, C-reactive protein, sedimentation, white blood cell count, preoperative fever or complications was found when compared between patients with culture growth and those without reproduction (p > 0.05). There was a significant difference between the leukocyte count in the aspiration material (p < 0.05). CONCLUSIONS Prediagnosis of septic arthritis or acute osteomyelitis in pediatric patients is important in terms of future joint health and sepsis. According to our findings an inability to obtain bacteria does not exclude septic arthritis as a diagnosis. Empirical antibiotic therapy with a wide postoperative spectrum is important for joint health in these patients. Preoperative serum parameters cannot predict the agent needed for treatment. Key words: septic arthritis, osteomyelitis, pediatric septic arthritis, pediatric joint infection, pediatric infection.

Hemoglobin A1c-related histologic characteristics of symptomatic carotid plaques.

BACKGROUND: The aims of our study were to compare the histomorphological characteristics of carotid plaques and glycosylated hemoglobin (HbA1c), which are risk factors for ischemic stroke, in patients who underwent carotid endarterectomy for carotid artery stenosis. Moreover, we aimed to identify the structures that were histologically affected by symptomatic carotid plaques in cases with elevated HbA1c. MATERIALS AND METHODS: A total of 64 patients who presented with ischemic stroke and had not previously been diagnosed with diabetes were retrospectively evaluated. All stroke risk factors were reviewed. Carotid plaques were graded separately by two different pathologists through microscopic assessment of the following parameters: plaque rupture, lipid core, fibrous cup thickness, inflammation, intraplaque hemorrhage, thrombus, calcification, necrotic core, and neovascularization. An HbA1c value <6.3% was accepted as normal or indicative of prediabetes (group 1), whereas patients with values ranging between 6.3-7.4%, 7.5-8.4%, and >8.4% were categorized into the effectively controlled (group 2), less effectively controlled (group 3), and uncontrolled (group 4) groups, respectively. RESULTS: The mean age of the patients was 73.0 ± 4.5 years in group 1, 69.7 ± 2.3 years in group 2, 66.0 ± 8.5 years in group 3, and 62.7 ± 7.1 years in group 4. A negative correlation was present between age and HbA1c. Smoking, hypertension, low-density lipoprotein cholesterol levels, and triglyceride levels were not significantly different among the four groups. According to the HbA1c classifications, the fibrous cup thickness was 2.64 ± 0.3 mm in group 1, 1.85 ± 0.4 mm in group 2, 1.68 ± 0.5 mm in group 3, and 1.45 ± 0.6 mm in group 4. The fibrous cup became thinner as the HbA1c value increased. Other parameters of unstable carotid plaques did not differ among the HbA1c groups. CONCLUSIONS: Increased HbA1c values seem to contribute to plaque instability through the formation of a thin fibrous cup. Thus, of the carotid artery plaque parameters including fibrous cup thickness, plaque rupture, lipid core, inflammation, intraplaque hemorrhage, thrombus, calcification, necrotic core, and neovascularization, fibrous cup thickness is the only histomorphological feature that affected by HbA1c.

Results of one-stage surgical treatment in children with Tönnis grade 4 developmental dysplasia of the hip: is it worse when it is bilateral?

This retrospective study compared the results of one-stage surgery of unilateral and bilateral Tönnis grade 4 hips (high dislocation in developmental hip dysplasia, DDH) : 41 hips, 30 patients. Mean follow-up was 56 months. Pelvic radiographs were evaluated at three time points. Acetabular inclination angle improved significantly in both groups. Results were satisfactory (Severin classes I-II) in 13 hips (68.5%) (unilateral group) and 21 hips (89.5%) (bilateral group). Functional evaluation (McKay classification) at final follow-up revealed satisfactory results in 94.8% (unilateral group) and 63.6% (bilateral group). One-stage surgery is a reliable method for treating children with unilateral or bilateral DDH.

The relationship between gastro-oesophageal reflux disease and asthma during childhood.

BACKGROUND: The relationship between GERD and asthma is complex. It is not yet clear whether GERD is an accompanying finding or a cause of asthma, or even if it is an aggravating factor. The aim of this study was to determine the frequency of asthma and allergic diseases in patients who underwent 24-h pH monitoring for a suspicion of GERD, including a comparison between subjects with and without GERD. METHOD: Subjects who were evaluated by 24h ambulatory intraoesophageal pH monitoring were investigated for the presence of asthma and allergic disorders. All participants were subjected to a skin prick test and a complete blood count and serum levels of specific IgE. RESULTS: A total of 204 subjects (49.5% male) with a mean age of 7.8±4.3 years were enrolled. A diagnosis of GERD was made in 78 (38.2%) subjects after 24h pH monitoring. The frequency of asthma in subjects with GERD was 20.5% compared to 25.4% in subjects without GERD (p=0.424). Subjects with GERD presenting with respiratory symptoms have higher incidence of asthma compared to subjects with GERD presenting with gastrointestinal symptoms (35.3% and 5.3% respectively; p=0.001). CONCLUSION: Although, patients with and without GERD had comparable frequencies of asthma, our findings suggest that subjects who present with respiratory symptoms suggestive of GERD should also be evaluated for the presence of an underlying asthma.

Medial malleolar screw hemiepiphysiodesis for ankle valgus in children with spina bifida.

Medial malleolar screw hemiepiphysiodesis has been shown to be an effective procedure for the treatment of ankle valgus in children with spina bifida. The purpose of this study was to highlight the guided growth technique and discuss its efficacy. We retrospectively reviewed 10 spina bifida patients with 18 ankle valgus deformities treated with medial malleolar screw hemiepiphysiodesis. Medical reports were obtained to document age at surgery, gender, concurrent operative procedures and postoperative early and late complications. Anteroposterior and lateral weight bearing radiographs of both ankles were evaluated using the tibiotalar angle, pre and postoperatively. The average age at operation was 10.05 years. Average follow up was 15.33 months (11-21 months). During follow-up, the average preoperative distal tibiotalar angle of 16.27 degrees improved to an average of 2.88 degrees with statistical significance (p < 0.05). No major complications were detected. In conclusion, hemiepiphysiodesis is a safe and sufficient method to correct ankle valgus deformity in children with spina bifida, with a low incidence.

Composite Restoration Design Effect During Curing and Chewing.

PURPOSE: The purpose of this work is to observe the effect of the cavity design of the direct composite restoration on a real case of the patient's tooth structures after applying his mandibular kinematics with finite element analysis. MATERIALS AND METHODS: Four complex maxillomandibular models of teeth 17 and 47 were constructed from the patient's cone-beam acquisition and the patient's kinematic data recorded with Modjaw® were added. Different shapes and sizes of mesio-occluso-distal (M.O.D.) composite restorations were simulated, including the polymerization shrinkage of this material. Finite element analyses were used to observe the Von Mises stresses occurring during polymerization and mastication. RESULTS: The stresses were observed at the cavity margin and the amplitude of the stresses was higher when the enamel volume was lower. The reduction in occlusal enamel volume with the open-angle vestibular and palatal walls resulted in a greater increase in stresses observed on the structures. CONCLUSIONS: The occlusal enamel is the area that bears the maximum masticatory stress, the loss of this enamel volume generates a much greater concentration of stress on the underlying structures. It is important to preserve as much enamel tissue as possible when designing a cavity for a direct composite restoration.

P50 sensory gating in hypoxemic chronic obstructive pulmonary disease patients.

PURPOSE: Chronic obstructive pulmonary disease (COPD) is a condition characterized by progressive airway obstruction and recurrent attacks. Multisystem involvement with extrapulmonary manifestations has been seen in COPD patients. Numerous neurological involvement like cerebrovascular diseases, polyneuropathies, motor neuron diseases and cognitive impairement has been reported in COPD patients. Cognitive dysfunction is usually associated with hypoxia or hypercapnia in COPD patients. To our knowledge there is no study about sensory gating in COPD patients. We performed p50 test to COPD patients and we investigate sensory gating in COPD patients. PATIENTS AND METHODS: 25 male patients with COPD and 17 healthy male subjects for controls included to this study. The patients were diagnosed with COPD according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria. p50 amplitude and latency, percentage of P50 suppression, N100 amplitude and latency and the N100 suppression percentage of the COPD patients and controls presented were measured and compared. RESULTS: We found that the conditioning amplitudes (S1) did not differ between COPD patients and controls (p > 0.05) but (S2) amplitude was significantly increased in COPD patients (p < 0.05). COPD patients showed significantly lower P50 and N100 suppression percentage than controls (p < 0.05). CONCLUSIONS: COPD patients showed a disturbance cognitive function such as attention with p50 suppression rate decrease. P50 sensory gating test can be useful to analyze the pre-attention period of cognitive impairment in the early phase of COPD patients.

Knowledge and attitudes of primary care physicians regarding food allergy and anaphylaxis in Turkey.

BACKGROUND: Food allergy, which becomes an important public health problem, can lead to important morbidity and mortality. Patients with food allergies are more likely to first present to their primary care physicians. We aimed to determine the knowledge of primary care physicians with regard to management of food allergies and anaphylaxis. METHODS: Primary care physicians were surveyed via a questionnaire aimed to document their knowledge and attitudes about food allergy and anaphylaxis management. RESULTS: A total of 297 participants completed questionnaires, 55.6% of which were female. Participating physicians had a mean of 17.0 ± 6.1 years of experience. Participants answered 47.2% of knowledge-based items correctly. Overall, participants fared poorly with regard to their knowledge on the treatment of food allergies and anaphylaxis. For example while 60.7% knew that a child can die from the milk allergy reaction, only 37.5% were aware that a child with IgE mediated milk allergies cannot eat yoghourts/cheese with milk. Besides, 53.1% of them chose epinephrine as their first treatment of choice in case of anaphylaxis, yet only 16.6% gave the correct answer about its dosage. Nearly a third of participants (36.7%) felt they were knowledgeable enough regarding the management of patients with food allergies, while 98.2% extended their request for future periodic educational meetings on allergic disorders. CONCLUSION: Knowledge of food allergy and anaphylaxis among primary care physicians was unsatisfactory. Provision or periodic educational programmes should be aimed at improving the standard of practice as acknowledged by the participants.

The effect of oral contraceptives on current wheezing in young women.

BACKGROUND: Emerging evidence suggests that sex steroid hormones may influence respiratory symptoms. The existing literature about the role of oral contraceptive pill (OCP) on respiratory disease is scarce and conflicting especially during the adolescent period. In this study, we aimed to investigate the effect of OCPs on current wheezing among adolescents and young adults. METHODS: A questionnaire was administered face-to-face to adolescents and young women by a physician. The questionnaire included ISAAC survey-comprised questions on ever wheezing, current wheezing, allergic diseases, smoking history (active or passive), and family history of allergic diseases and questions on OCP usage status. The effect of OCPs on wheezing was evaluated by logistic regression analysis. RESULTS: A total of 487 subjects aged between 11.3 and 25.6years participated in the study and 196 (40.2%) reported that they had used OCPs. 7.4% of the participants had physician-diagnosed asthma and 10.3% of them were active smokers. It was detected that OCPs were associated with increased risk for current wheezing (odds ratio, 2.36; 95% CI, 1.25-4.47 adjusted for asthma and current smoker) and this risk was related with the usage during the past year. CONCLUSION: Young women taking oral contraceptives had a higher rate of current wheezing, suggesting that sex steroids may be of importance for respiratory health.

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.

Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.

The effect of a structured empathy course on the students of a medical and a nursing school.

AIM: The study aims to determine the effect of an empathy course for medical and nursing school students in one university in Turkey. Being able to relate to others empathetically is important for health professionals who need to develop therapeutic relationships with people who are sick, weak, sensitive and vulnerable. Professionals need empathic communication skills and professionalism not only for patients and their families but also for colleagues and other members of the health team. METHOD: All first year students (257) from a medical and a nursing school in one Turkish university in 2008-2009 and 2009-2010 were enrolled to the study. The course included 10 h of lectures on empathy and communication skills given through five consecutive weeks with 2 h in a week in the first year of both schools. Data were collected by using the Empathic Communication Skills Scale (ECSS), and the Empathic Tendency Scale (ETS) before and after the course. There were 143 medical students and 83 nursing students (total: 226, 88%) who completed the ECSS and ETS in a pre-/post-test study. FINDINGS: Results demonstrated that all students received significantly higher scores for the final application than for initial scores on both scales. This implied that the targeted educational programme could have a positive effect on learning empathy and gaining empathy skills and tendency. CONCLUSION: Effective educational programmes might facilitate and improve empathic skills and empathic tendency of medical and nursing students, and both male and female students benefitted from the empathy course.

The effect of growth hormone addition protocols to poor ovarian responders in in vitro fertilization cycles.

OBJECTIVE: In vitro fertilization failure (IVF) is high in women with poor ovarian response or non-responder. For this reason, the addition of adjuvant treatments to IVF protocols has come to the fore. We assessed to investigate the effects of adjuvant GH therapy initiated in the mid-luteal phase on IVF success in poor ovarian response or non-responder women. PATIENTS AND METHODS: A retrospective study was performed in 93 poor ovarian response or non-responder women from a single center. GH treatment was added (GH-plus group) in the mid-luteal phase of the previous menstrual cycle to 47 of the women who underwent controlled ovarian stimulation with the flexible antagonist protocol. 46 women, as another group, were applied to a flexible antagonist-only protocol (GH-free group). The IVF outcome results were evaluated and compared within the groups. RESULTS: The number of retrieved oocytes was statistically significantly higher in the GH-plus group (2.28±1.975) than in the GH-free group (1.24±1.728) (p=0.01). Although statistically insignificant (p=0.55), the clinical pregnancy rate was higher in the GH-plus group [(8/47), 17%] than in the GH-free group [(5/46, 11%]. The cancellation rate was statistically significantly higher in the GH-free group (65.2%) than in the GH-plus group (44.7%) (p=0.04). No oocyte retrieved cycle rate was higher in the GH-free group (56%) than in the GH-plus group (25%) (p=0.002). CONCLUSIONS: Adjuvant GH therapy administration to IVF protocol in the mid-luteal phase gives poor ovarian response or non-responder women a chance to have a baby.

Relationships of total leukocyte, neutrophil and lymphocyte levels with the menstrual cycle in patients receiving fingolimod treatment.

OBJECTIVE: Multiple sclerosis (MS) is a demyelinating, chronic, and progressive autoimmune disease of the central nervous system that causes the loss of axons and grey matter, and has a high prevalence in young female patients. Fingolimod is an oral treatment agent that acts by blocking the passage of the T lymphocytes responsible for the pathogenesis of MS from lymphoid tissue into the peripheral blood. We aimed to research the effects of menstrual cycles on leukocytes and lymphocyte levels in RRMS (relapsing-remitting MS) patients who received fingolimod treatment. PATIENTS AND METHODS: This study was performed to determine the most suitable phase of the menstrual cycle in patients with RRMS for follow-up assessment of lymphopaenia levels after fingolimod treatment. The study population consisted of 41 RRMS patients receiving fingolimod therapy and 33 healthy women of reproductive age. Complete blood counts were performed in three different phases of the menstrual cycle, and the two groups were compared. Variability in the total leukocyte, lymphocyte, and neutrophil immune cell numbers between cycles was examined. RESULTS: The results indicated that total leukocyte, neutrophil, and lymphocyte levels were decreased in RRMS patients receiving fingolimod treatment, but these changes were not related to the phase of the menstrual cycle. In our study, leukocyte levels in healthy individuals were significantly lower in the proliferative phase than in other phases. CONCLUSIONS: The results indicated that lymphocyte monitoring in RRMS patients receiving fingolimod treatment can be performed at any stage of the menstrual cycle.

Radial shortening osteotomy vs partial capitate shortening osteotomy in Kienböck's disease: Medium-term radiological and clinical results.

This study aimed to compare medium-term results for partial capitate shortening (PCS) and radial shortening (RS) osteotomies on lunate bone revascularization and disease progression in patients with stage II or IIIA Kienböck's disease. Patients who underwent surgery for Kienböck's disease between March 2010 and July 2020 were retrospectively evaluated. Clinical evaluation included assessment of pain, joint range of motion, strength, DASH, visual analog scale (VAS) for pain, Modified Mayo Wrist Score (MMWS), satisfaction and time to return to work, with comparison as appropriate to the contralateral side. Preoperative and postoperative plain radiographs and magnetic resonance imaging (MRI) were used for radiological evaluation. Lichtman staging and signal changes in the lunate were evaluated using MRI. Group 1 (PCS) included 14 patients and Group 2 (RS) 14. Mean follow-up was 57.8 months (range 24-102) in Group 1 and 49.4 months (range 36-73) in Group 2. Clinical evaluation included pain on VAS, DASH score, MMWS, range of motion, and grip, palmar and key pinch strength. Regarding lunate bone vascularization, increased signal on final follow-up MRI was observed in 10 of the 14 patients in Group 1 and 7 of the 14 patients in Group 2. There was a positive correlation between revascularization and final follow-up MMWS (p = 0.006). The present study thus showed that functional scores were improved by revascularization in Kienböck's disease. Both osteotomies had clinically and radiologically satisfactory results. However, we believe that PCS osteotomy is preferable, as it leads to higher revascularization rates without increasing ulnolunate load.

Surgery in patients with haemophilia and high responding inhibitors: Izmir experience.

This report evaluates the haemostatic efficacy of recombinant factor VIIa (rFVIIa) and activated prothrombin complex concentrate (APCC) in patients with haemophilia and high responding inhibitors who underwent major and minor surgery. Data pertaining to surgeries from 2001 to 2009 at a single centre were retrospectively analysed. During this period, 53 surgical procedures were performed in 30 haemophiliacs with high responding inhibitors. Mean age was 16.2±9.4 years. Eleven major surgeries in 4 patients, 41 radioisotope synovectomies (RS) and one circumcision classified as minor surgery in 28 patients were performed. Among the major surgery procedures, four were treated with rFVIIa, five with APCC and two with sequential use of APCC and rFVIIa. We used rFVIIa at the dosage of 80-120 µg kg(-1) every 2 h and APCC 100 IU kg(-1) every 12 h for the major surgery. When performing RS, we used rFVIIa in 18 patients with 26 target joints and APCC in 9 patients with 15 target joints. Three consecutive doses of rFVIIa (90 µg kg(-1) ) were used at 2-h intervals followed by additional three doses at 6-h intervals. The initial dose of APCC was 75 IU kg(-1) followed by a second and third dose of 50 IU kg(-1) at 12-h intervals. APCC and rFVIIa demonstrated excellent efficacy in our major and minor surgical interventions [100% (22/22) and 94% (31/33), respectively]. We had only two bleeding complications with rFVIIa. There were no thromboembolic complications. APCC and rFVIIa provide an effective and safe first line haemostatic therapy for inhibitor-positive haemophiliacs, allowing both major and minor surgery to be successfully performed.

Empathy: the effects of undergraduate nursing education in Turkey.

AIM: To evaluate the empathic skills and the empathetic tendency of nursing students throughout their years of undergraduate education. BACKGROUND: Empathy is a major component of the relationships between patients and nurses, and is an observable and teachable skill that nurses are claimed to possess. METHODS: A cross-sectional study was designed to determine the differences in the empathic skills and tendency of nursing students in the successive years of undergraduate nursing education. A longitudinal study was also designed to evaluate the changes between the beginning and the end of the nursing education in the same group. All the registered students were asked to participate in the study. The total population was 466 nursing students of whom 438 participated (94%) in the cross-sectional study and 81 in the longitudinal study. The Empathic Communication Skills Scale (ECSS) and the Empathic Tendency Scale (ETS) were used to collect data. FINDINGS: An increase in the ECSS and a decrease in the ETS were observed in both the cross-sectional and longitudinal studies. Comparing the years, fourth-year students have higher empathic skills level, whereas newly registered students have a higher empathic tendency score (P<0.05). CONCLUSIONS: The findings have shown that empathic skills developed during undergraduate nursing education. However, empathetic tendency has shown a decline during these educational years. The decrease in empathetic tendency during undergraduate education should be taken into account, and educators and researchers should consider possible reasons for this outcome. Further research is indicated.

Misinterpretation of ISO 4049 standard recommendations: Impact on Young's modulus and conversion degree of dental composites.

OBJECTIVES: The purpose of this study was to study the effects on Young's modulus and conversion degree of variations in polymerization conditions during the 3-point bending test of composite samples in accordance with the ISO 4049 standard. METHODS: Three nanocomposites were used in the 3-point bending test based on the conditions described in the ISO 4049 standard. Samples of 2 mm × 2 mm x 25 mm were fabricated and tested with a different number of irradiation points and irradiation time. Conversion degree of the samples were also measured by micro-Raman spectroscopy and correlated with the Young's modulus values obtained for each one. RESULTS: The variations in curing protocol during specimen's realization influenced the Young's modulus and degree of conversion of all composites. These two properties correlated well. The ISO 4049 standard defines the conditions for performing the properties tests of composites to allow reproducibility and comparison of different studies. Concerning the 3-point bending test, even a minimal change in the state causes differences in the results obtained. The standard should thus clarify the tools that can be used when producing samples in order to minimize discrepancies. SIGNIFICANCE: The influence of the parameters surrounding the design of the samples should be controlled and defined so as not to include bias in the studies carried out. This will allow literature studies to be compared with more accuracy.

FORENSIC: an Online Platform for Fecal Source Identification.

Sewage overflows, agricultural runoff, and stormwater discharges introduce fecal pollution into surface waters. Distinguishing these sources is critical for evaluating water quality and formulating remediation strategies. With the falling costs of sequencing, microbial community-based water quality assessment tools are under development. However, their application is limited by the need to build reference libraries, which requires extensive sampling of sources and bioinformatic expertise. Here, we introduce FORest Enteric Source IdentifiCation (FORENSIC; https://forensic.sfs.uwm.edu/), an online, library-independent source tracking platform based on random forest classification and 16S rRNA gene amplicon sequences to identify in environmental samples common fecal contamination sources, including humans, domestic pets, and agricultural animals. FORENSIC relies on a broad reference signature database of Bacteroidales and Clostridiales, two predominant bacterial groups that have coevolved with their hosts. As a result, these groups demonstrate cohesive and reliable assemblage patterns within mammalian species or among species sharing the same diet/physiology. We created a scalable and extensible platform that we tested for global applicability using samples collected in distant geographic locations. This Web application offers a fast and intuitive approach for fecal source identification, particularly in sewage-contaminated waters.IMPORTANCE FORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk in polluted waters. To test for fecal contamination sources, the platform only requires paired-end reads targeting the V4 or V6 regions of the 16S rRNA gene. We demonstrated that we could use V4V5 reads trimmed to the V4 positions to generate the reference signature. The systematic workflow we describe to create and validate the signatures could be applied to many disciplines. With the increasing gap between advancing technology and practical applications, this platform makes sequence-based water quality assessments accessible to the public health and water resource communities.

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.

INTRODUCTION: Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. RESULTS: Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. CONCLUSIONS: Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade.

Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions.