Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.

In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and ß-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. IMPORTANCE: Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the ß-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane.

Genomic, proteomic and biochemical analysis of the chitinolytic machinery of Serratia marcescens BJL200.

The chitinolytic machinery of Serratia marcescens BJL200 has been studied in detail over the last couple of decades, however, the proteome secreted by this Gram-negative bacterium during growth on chitin has not been studied in depth. In addition, the genome of this most studied chitinolytic Serratia strain has until now, not been sequenced. We report a draft genome sequence for S. marcescens BJL200. Using label-free quantification (LFQ) proteomics and a recently developed plate-method for assessing secretomes during growth on solid substrates, we find that, as expected, the chitin-active enzymes (ChiA, B, C, and CBP21) are produced in high amounts when the bacterium grows on chitin. Other proteins produced in high amounts after bacterial growth on chitin provide interesting targets for further exploration of the proteins involved in degradation of chitin-rich biomasses. The genome encodes a fourth chitinase (ChiD), which is produced in low amounts during growth on chitin. Studies of chitin degradation with mixtures of recombinantly produced chitin-degrading enzymes showed that ChiD does not contribute to the overall efficiency of the process. ChiD is capable of converting N,N'-diacetyl chitobiose to N-acetyl glucosamine, but is less efficient than another enzyme produced for this purpose, the Chitobiase. Thus, the role of ChiD in chitin degradation, if any, remains unclear.

The glass is half full: evidence for efficacy of alcohol-wise at one university but not the other.

This research extends the growing literature about online alcohol prevention programs for first-year college students. Two independent randomized control studies, conducted at separate universities, evaluated the short-term effectiveness of Alcohol-Wise, an online alcohol prevention program not previously studied. It was hypothesized the prevention program would increase alcohol knowledge and reduce alcohol consumption, including high-risk alcohol-related behaviors, among first-year college students. At both universities, the intervention significantly increased alcohol-related knowledge. At one university, the prevention program also significantly reduced alcohol consumption and high-risk drinking behaviors, such as playing drinking games, heavy drinking, and extreme ritualistic alcohol consumption. Implications for the use of online alcohol prevention programs and student affairs are discussed.

Anterior cruciate ligament injuries in the skeletally immature athlete: diagnosis and management.

Intrasubstance anterior cruciate ligament (ACL) injuries in children and adolescents were once considered rare occurrences, with tibial eminence avulsion fractures generally regarded as the pediatric ACL injury equivalent. However, with increased single-sport focus, less free play, and year-round training at younger ages, intrasubstance ACL injuries in children and adolescents are being diagnosed with increased frequency. As in the adult, a knee devoid of ligamentous stability predisposes the pediatric patient to meniscal and chondral injuries and early degenerative changes. Management of ACL injuries in skeletally immature patients includes physeal-sparing, partial transphyseal, and complete transphyseal ACL reconstruction. Complications include iatrogenic growth disturbance resulting from physeal violation.

Hip pathology in the adolescent athlete.

Hip injuries in young athletes are being diagnosed with increasing frequency. Improvements in diagnostic imaging and surgical technologies have helped facilitate the diagnosis of intra- and extra-articular derangements that were previously untreated in this age group. Athletic injuries of the hip in the young athlete encompass both osseous and soft-tissue etiologies, which can be the result of a single traumatic event or repetitive microtrauma or may be associated with an underlying pediatric hip disorder. Without accurate diagnosis and management, these injuries may result in debilitating consequences. This article will review the more common causes of hip and groin pain in the adolescent athlete, as well as advances in diagnostic and therapeutic interventions.

Correlation between the Child Health Questionnaire and the International Knee Documentation Committee score in pediatric and adolescent patients with an anterior cruciate ligament tear.

BACKGROUND: The modified International Knee Documentation Committee (Pedi-IKDC) Subjective Knee Evaluation Form has recently been shown to be valid, reliable, and responsive in a pediatric and adolescent population. The correlations between the Pedi-IKDC and quality-of-life-related health measures have not been studied in depth to determine how a knee injury affects patients in this age group. The purpose of this study was to examine the association between the Pedi-IKDC score and the Child Health Questionnaire (CHQ) in a group of pediatric patients with an anterior cruciate ligament (ACL) injury. METHODS: A prospectively collected registry of patients with ACL injuries was searched to indentify all patients who had completed both the Pedi-IKDC and CHQ (CHQ-CF87) questionnaires. These were analyzed to determine significant correlations between domains of the CHQ and the Pedi-IKDC. RESULTS: A total of 135 patients were included (80 male, 55 female) with a median age of 15.3 years (range, 13.1 to 17.2 y). The cohort included patients treated both operatively (120) and nonoperatively (15). The total Pedi-IKDC score was found to correlate with the majority of the CHQ including expected domains such as physical function (correlation coefficient = 0.64), bodily pain (0.7), and family activities (0.41), in addition to emotional role (0.45), mental health (0.46), self-esteem (0.45), and social limitations--physical (0.38) (P < 0.001 for all correlations). CONCLUSIONS: Seven of the 12 domains on the CHQ are significantly correlated with the IKDC in adolescent patients with an ACL tear. Self-esteem, mental health, emotional role, and social limitations categories are significantly correlated with knee function suggesting that quality-of-life in this population is affected in domains outside of physical function and pain. A greater understanding of the psychosocial impact of injury may be of utility in these patients. STUDY DESIGN: Level III cross-sectional study.

Endorsement of a Personal Responsibility to Adhere to the Minimum Drinking Age Law Predicts Consumption, Risky Behaviors, and Alcohol-Related Harms.

Despite minimum drinking age laws, underage college students engage in high levels of risky drinking and reach peak lifetime levels of alcohol dependence. A group of presidents of universities and colleges has argued that these laws promote disrespect for laws in general, and do not prevent drinking or related negative consequences. However, no study has investigated the policy-relevant question of whether students who endorse a personal responsibility to obey drinking laws, regardless of their opinions about the laws, are less likely to drink or to experience negative consequences. Therefore, we compared endorsers to non-endorsers, controlling for race, gender, and baseline outcomes, at two universities (Ns = 2007 and 2027). Neither sample yielded a majority (49% and 38% endorsement), but for both universities, all 17 outcome measures were significantly associated with endorsement across all types of analyses. Endorsers were less likely to drink, drank less, engaged in less high-risk behavior (e.g., heavy/binge drinking), and experienced fewer harms (e.g., physical injury), even when controlling for covariates. Racial/ethnic minority groups were more likely to endorse, compared to White students. By isolating a small window of time between high school and college that produces large changes in drinking behavior, and controlling for covariates, we can begin to hone in on factors that might explain relations among laws, risky behaviors, and harms. Internalization of a social norm to adhere to drinking laws could offer benefits to students and society, but subsequent research is needed to pin down causation and causal mechanisms.

Do Differences Exist in Impact Test Domains between Youth Athletes with and without an Anterior Cruciate Ligament Injury?

Poor baseline reaction time, as measured via the Immediate Post-Concussion Assessment and Cognitive Test (ImPACT), has been associated with anterior cruciate ligament (ACL) injury risk in adult athletes. Our study sought to determine whether the reaction time and impulse control ImPACT test domains differed between ACL injured and uninjured pediatric athletes. A total of 140 high-school aged athletes comprising 70 athletes who went on to sustain an ACL injury between 2012 and 2018 and 70 age- and sex-matched uninjured controls were included in the study. Mean reaction times were similar for the injured (0.67 s) and uninjured (0.66 s) athletes (p = 0.432), and the impulse control scores were also similar for those with (5.67) and without (6.07) an ACL injury (p = 0.611). Therefore, neurocognitive risk factors for sustaining an ACL injury in adults cannot necessarily be extrapolated to adolescent athletes. Further research is needed to understand why differences exist between injury risk in youth and adult athletes.

Age, Sex, and BMI Differences Related to Repairable Meniscal Tears in Pediatric and Adolescent Patients.

BACKGROUND: The incidence of meniscus tears and ACL tears in pediatric patients continues to rise, bringing to question the risk factors associated with these injuries. As meniscus tears are commonly repaired in pediatric populations, the epidemiology of repairable meniscus tears is an important for consideration for surgeons evaluating treatment options. PURPOSE: To describe meniscal tear patterns in pediatric and adolescent patients who underwent meniscal repair across multiple institutions and surgeons, as well as to evaluate the relationship between age, sex, and body mass index (BMI) and their effect on the prevalence, type, and displacement of repaired pediatric meniscal tears. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: Data within a prospective multicenter cohort registry for quality improvement, Sport Cohort Outcome Registry (SCORE), were reviewed to describe repaired meniscal tear patterns. All consecutive arthroscopic meniscal repairs from participating surgeons in patients aged <19 years were analyzed. Tear pattern, location, and displacement were evaluated by patient age, sex, and BMI. A subanalysis was also performed to investigate whether meniscal tear patterns differed between those occurring in isolation or those occurring with a concomitant anterior cruciate ligament (ACL) injury. Analysis of variance was used to generate a multivariate analysis of specified variables. Sex, age, and BMI results were compared across the cohort. RESULTS: There were 1185 total meniscal repairs evaluated in as many patients, which included 656 (55.4%) male and 529 (44.6%) female patients. Patients underwent surgery at a mean age of 15.3 years (range, 5-19 years), with a mean BMI of 24.9 (range, 12.3-46.42). Of the 1185 patients, 816 (68.9%) had ACL + meniscal repair and 369 (31.1%) had isolated meniscal repair. The male patients underwent more lateral tear repairs than the female patients (54.3% to 40.9%; P < .001) and had a lower incidence of medial tear repair (32.1% vs 41.4%; P < .001). Patients with repaired lateral tears had a mean age of 15.0 years, compared with a mean age of 15.4 years for patients with repaired medial or bilateral tears (P = .001). Higher BMI was associated with "complex" and "radial" tear repairs of the lateral meniscus (P < .001) but was variable with regard to medial tear repairs. CONCLUSION: In pediatric and adolescent populations, the data suggest that the surgical team treating knees with potential meniscal injury should be prepared to encounter more complex meniscal tears, commonly indicated in those with higher BMI, while higher rates of lateral meniscal tears were seen in male and younger patients. Future studies should analyze correlates for meniscal repair survival and outcomes in this pediatric cohort undergoing knee surgery.

Relationship Between Age and Pathology With Treatment of Pediatric and Adolescent Discoid Lateral Meniscus: A Report From the SCORE Multicenter Database.

BACKGROUND: Surgical treatment options of discoid lateral meniscus in pediatric patients consist of saucerization with or without meniscal repair, meniscocapular stabilization, and, less often, subtotal meniscectomy. PURPOSE: To describe a large, prospectively collected multicenter cohort of discoid menisci undergoing surgical intervention, and further investigate corresponding treatment of discoid menisci. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: A multicenter quality improvement registry (16 institutions, 26 surgeons), Sports Cohort Outcomes Registry, was queried. Patient characteristics, discoid type, presence and type of intrasubstance meniscal tear, peripheral rim instability, repair technique, and partial meniscectomy/debridement beyond saucerization were reviewed. Discoid meniscus characteristics were compared between age groups (<14 and >14 years old), based on receiver operating characteristic curve, and discoid morphology (complete and incomplete). RESULTS: In total, 274 patients were identified (mean age, 12.4 years; range, 3-18 years), of whom 55.6% had complete discoid. Meniscal repairs were performed in 55.1% of patients. Overall, 48.5% of patients had rim instability and 36.8% had >1 location of peripheral rim instability. Of the patients, 21.5% underwent meniscal debridement beyond saucerization, with 8.4% undergoing a subtotal meniscectomy. Patients <14 years of age were more likely to have a complete discoid meniscus (P < .001), peripheral rim instability (P = .005), and longitudinal tears (P = .015) and require a meniscal repair (P < .001). Patients ≥14 years of age were more likely to have a radial/oblique tear (P = .015) and require additional debridement beyond the physiologic rim (P = .003). Overall, 70% of patients <14 years of age were found to have a complete discoid meniscus necessitating saucerization, and >50% in this young age group required peripheral stabilization/repair. CONCLUSION: To preserve physiological "normal" meniscus, a repair may be indicated in >50% of patients <14 years of age but occurred in <50% of those >14 years. Additional resection beyond the physiological rim may be needed in 15% of younger patients and 30% of those aged >14 years.

Intra-abdominal fluid extravasation during hip arthroscopy: a survey of the MAHORN group.

PURPOSE: The purpose of this study was to survey experts in the field of hip arthroscopy from the Multicenter Arthroscopy of the Hip Outcomes Research Network (MAHORN) group to determine the frequency of symptomatic intra-abdominal fluid extravasation (IAFE) after arthroscopic hip procedures, identify potential risk factors, and develop preventative measures and treatment strategies in the event of symptomatic IAFE. METHODS: A survey was sent to all members of the MAHORN group. Surveys collected data on general hip arthroscopy settings, including pump pressure and frequency of different hip arthroscopies performed, as well as details on cases of symptomatic IAFE. Responses to the survey were documented and analyzed. RESULTS: Fifteen hip arthroscopists from the MAHORN group were surveyed. A total of 25,648 hip arthroscopies between 1984 and 2010 were reviewed. Arthroscopic procedures included capsulotomies, labral reattachment after acetabuloplasty, peripheral compartment arthroscopy, and osteoplasty of the femoral head-neck junction. Of the arthroscopists, 7 (47%) had 1 or more cases of IAFE (40 cases reported). The prevalence of IAFE in this study was 0.16% (40 of 25,650). Significant risk factors associated with IAFE were higher arthroscopic fluid pump pressure (P = .004) and concomitant iliopsoas tenotomy (P < .001). In all 40 cases, the condition was successfully treated without long-term sequelae. Treatment options included observation, intravenous furosemide, and Foley catheter placement, as well as 1 case of laparotomy. CONCLUSIONS: Symptomatic IAFE after hip arthroscopy is a rare occurrence, with an approximate prevalence of 0.16%. Prevention of IAFE should include close intraoperative and postoperative monitoring of abdominal distention, core body temperature, and hemodynamic stability. Concomitant iliopsoas tenotomy and high pump pressures may be risk factors leading to symptomatic IAFE. LEVEL OF EVIDENCE: Level IV, therapeutic case series.

Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies.

The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. The genomes of strains REY15A and HVE10/4 are 2.5 and 2.7 Mb, respectively, and each genome carries a variable region of 0.5 to 0.7 Mb where major differences in gene content and gene order occur. These include gene clusters involved in specific metabolic pathways, multiple copies of VapBC antitoxin-toxin gene pairs, and in strain HVE10/4, a 50-kb region rich in glycosyl transferase genes. The variable region also contains most of the insertion sequence (IS) elements and high proportions of the orphan orfB elements and SMN1 miniature inverted-repeat transposable elements (MITEs), as well as the clustered regular interspaced short palindromic repeat (CRISPR)-based immune systems, which are complex and diverse in both strains, consistent with them having been mobilized both intra- and intercellularly. In contrast, the remainder of the genomes are highly conserved in their protein and RNA gene syntenies, closely resembling those of other S. islandicus and Sulfolobus solfataricus strains, and they exhibit only minor remnants of a few genetic elements, mainly conjugative plasmids, which have integrated at a few tRNA genes lacking introns. This provides a possible rationale for the presence of the introns.

Quantitative metagenomic analyses based on average genome size normalization.

Over the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (the Cyanobacteria); anaerobic, photosynthetic carbon fixers (the Chlorobi); and anaerobic, nonphotosynthetic carbon fixers (the Desulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.

Differences between the normal vaginal bacterial community of baboons and that of humans.

Humans and baboons (Papio spp.) share considerable anatomical and physiological similarities in their reproductive tracts. Given the similarities, it is reasonable to expect that the normal vaginal microbial composition (microbiota) of baboons would be similar to that of humans. We have used a 16S rRNA phylogenetic approach to assess the composition of the baboon vaginal microbiota in a set of nine animals from a captive facility and six from the wild. Results show that although Gram-positive bacteria dominate in baboons as they do in humans, there are major differences between the vaginal microbiota of baboons and that of humans. In contrast to humans, the species of Gram-positive bacteria (Firmicutes) were taxa other than Lactobacillus species. In addition, some groups of Gram-negative bacteria that are not normally abundant in humans were found in the baboon samples. A further level of difference was also seen even within the same bacterial phylogenetic group, as baboon strains tended to be more phylogenetically distinct from human strains than human strains were with each other. Finally, results of our analysis suggests that co-evolution of microbes and their hosts cannot account for the major differences between the microbiota of baboons and that of humans because divergences between the major bacterial genera were too ancient to have occurred since primates evolved. Instead, the primate vaginal tracts appear to have acquired discrete subsets of bacteria from the vast diversity of bacteria available in the environment and established a community responsive to and compatible with host species physiology.

Complications of hip arthroscopy in children and adolescents.

BACKGROUND: Hip arthroscopy has become an established procedure for certain hip disorders. Complications of hip arthroscopy have been characterized in adult populations, but complications in children and adolescents have not been well described. The purpose of this study was to characterize complications of hip arthroscopy in children and adolescents. METHODS: The study design was a retrospective review of 218 hip arthroscopies in 175 patients aged 18 years old and younger over a 9-year period by a single surgeon at a tertiary-care children's hospital. Patient demographics, indications for surgery, and complications after surgery were recorded. Indications for surgery included: isolated labral tear (n=131), labral tear with concomitant hip disorder (n=37), Perthes disease (n=10), hip dysplasia (n=5), juvenile rheumatoid arthritis (n=3), loose bodies (n=3), osteochondral fracture (n=3), synovitis (n=2), avascular necrosis (n=1), chondral lesion (n=1), iliopsoas tendinitis (n=1), and slipped capital femoral epiphysis (n=1). RESULTS: The overall complication rate in the study population was 1.8%. Complications of arthroscopy included: transient pudendal nerve palsy (n=2), instrument breakage (n=1), and suture abscess (n=1). No cases of proximal femoral physeal separation, osteonecrosis, or growth disturbance were noted. CONCLUSIONS: Hip arthroscopy in children and adolescents seems to be a safe procedure with a low complication rate similar to adults. LEVEL OF EVIDENCE: IV (case series).

Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation.

Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.

Acute, avulsion fractures of the medial epicondyle while throwing in youth baseball players: a variant of Little League elbow.

HYPOTHESIS: The young throwing athlete is susceptible to medial elbow injury due to valgus overload. We hypothesized that this injury can occur during the throwing motion with an acute episode of medial elbow pain resulting in an inability to effectively participate in throwing activities. In addition, appropriate treatment of acute, medial epicondyle avulsion fractures in baseball players can result in an asymptomatic elbow with subsequent return to play within a year of injury. MATERIALS AND METHODS: A case series of all youth baseball players with medial epicondyle avulsion fractures that occurred while throwing were identified. We studied several variables, including demographics, adherence to USA Baseball youth pitching recommendations, clinical history, radiographic findings, treatment, and outcome. RESULTS: Eight skeletally immature baseball players, who were a mean age of 13 years (range, 11-15 years), presented with medial epicondyle fractures that occurred while throwing. All 8 players experienced sudden pain during throwing, and all 5 players with appropriate age and position qualifications did not conform to the USA Baseball youth pitching recommendations. Anteroposterior radiographs documented average fracture displacement of 5.1 mm (range, 2.5-10 mm). Five of 8 players had 5 mm or less of displacement and were selected for nonoperative treatment. Three of 8 players had more than 5 mm of displacement and underwent open reduction and internal fixation. All players were able to return to play at an average of 7.6 months (range, 4-10 months). DISCUSSION: Medial epicondyle avulsion fractures can occur with a characteristic acute presentation while throwing in youth baseball players. Prevention may be possible when conforming to established USA Baseball youth pitching recommendations. Once an acute medial epicondyle avulsion fracture occurs, these injuries may be managed using published treatment algorithms, with successful return to play in less than 1 year.

Heterogeneity of vaginal microbial communities within individuals.

Recent culture-independent studies have revealed that a healthy vaginal ecosystem harbors a surprisingly complex assemblage of microorganisms. However, the spatial distribution and composition of vaginal microbial populations have not been investigated using molecular methods. Here, we evaluated site-specific microbial composition within the vaginal ecosystem and examined the influence of sampling technique in detection of the vaginal microbiota. 16S rRNA gene clone libraries were prepared from samples obtained from different locations (cervix, fornix, outer vaginal canal) and by different methods (swabbing, scraping, lavaging) from the vaginal tracts of eight clinically healthy, asymptomatic women. The data reveal that the vaginal microbiota is not homogenous throughout the vaginal tract but differs significantly within an individual with regard to anatomical site and sampling method used. Thus, this study illuminates the complex structure of the vaginal ecosystem and calls for the consideration of microenvironments when sampling vaginal microbiota as a clinical predictor of vaginal health.

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.

rRNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an analysis and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives by using linear amplification-providing an assessment that is independent of a reverse primer-and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.

The number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from a genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities. Furthermore, it suggests protein families associated with the presence of particular phenotypes. Our method uses L1-regularized L2-loss support vector machines for phenotype assignments based on phyletic patterns of protein families and their evolutionary histories across a diverse set of microbial species. We demonstrate reliable phenotype assignment for Traitar to bacterial genomes from 572 species of eight phyla, also based on incomplete single-cell genomes and simulated draft genomes. We also showcase its application in metagenomics by verifying and complementing a manual metabolic reconstruction of two novel Clostridiales species based on draft genomes recovered from commercial biogas reactors. Traitar is available at https://github.com/hzi-bifo/traitar. IMPORTANCE Bacteria are ubiquitous in our ecosystem and have a major impact on human health, e.g., by supporting digestion in the human gut. Bacterial communities can also aid in biotechnological processes such as wastewater treatment or decontamination of polluted soils. Diverse bacteria contribute with their unique capabilities to the functioning of such ecosystems, but lab experiments to investigate those capabilities are labor-intensive. Major advances in sequencing techniques open up the opportunity to study bacteria by their genome sequences. For this purpose, we have developed Traitar, software that predicts traits of bacteria on the basis of their genomes. It is applicable to studies with tens or hundreds of bacterial genomes. Traitar may help researchers in microbiology to pinpoint the traits of interest, reducing the amount of wet lab work required.