Systems analysis reveals differential expression of endocervical genes in African women randomized to DMPA-IM, LNG implant or cu-IUD.

Although effective contraceptives are crucial for preventing unintended pregnancies, evidence suggests that their use may perturb the female genital tract (FGT). A comparative analysis of the effects of the most common contraceptives on the FGT have not been evaluated in a randomized clinical trial setting. Here, we evaluated the effect of three long-acting contraceptive methods: depot medroxyprogesterone acetate(DMPA-IM), levonorgestrel(LNG) implant, and a copper intrauterine device (Cu-IUD), on the endocervical host transcriptome in 188 women from the Evidence for Contraceptive Options and HIV Outcomes Trial (ECHO) trial. Cu-IUD usage showed the most extensive transcriptomic changes, and was associated with inflammatory and anti-viral host responses. DMPA-IM usage was enriched for pathways associated with T cell responses. LNG implant had the mildest effect on endocervical gene expression, and was associated with growth factor signaling. These data provide a mechanistic basis for the diverse influence that varying contraceptives have on the FGT.

Initiating Intramuscular Depot Medroxyprogesterone Acetate Increases Frequencies of Th17-like Human Immunodeficiency Virus Target Cells in the Genital Tract of Women in South Africa: A Randomized Trial.

BACKGROUND: Cervicovaginal CD4+ T cells are preferential targets for human immunodeficiency virus (HIV) infection and have consequently been used as a proxy measure for HIV susceptibility. The ECHO randomized trial offered a unique opportunity to consider the association between contraceptives and Th17-like cells within a trial designed to evaluate HIV risk. In a mucosal substudy of the ECHO trial, we compared the impact of initiating intramuscular depot medroxyprogesterone acetate (DMPA-IM), copper-IUD, and the levonorgestrel (LNG) implant on cervical T cells. METHODS: Cervical cytobrushes from 58 women enrolled in the ECHO trial were collected at baseline and 1 month after contraceptive initiation. We phenotyped cervical T cells using multiparameter flow cytometry, characterized the vaginal microbiome using 16s sequencing, and determined proteomic signatures associated with Th17-like cells using mass spectrometry. RESULTS: Unlike the LNG implant or copper-IUD, DMPA-IM was associated with higher frequencies of cervical Th17-like cells within 1 month of initiation (P = .012), including a highly susceptible, activated population co-expressing CD38, CCR5, and α4ß7 (P = .003). After 1 month, women using DMPA-IM also had more Th17-like cells than women using the Cu-IUD (P = .0002) or LNG implant (P = .04). Importantly, in women using DMPA-IM, proteomic signatures signifying enhanced mucosal barrier function were associated with the increased abundance of Th17-like cells. We also found that a non-Lactobacillus-dominant microbiome at baseline was associated with more Th17-like cells post-DMPA-IM (P = .03), although this did not influence barrier function. CONCLUSIONS: Our data suggest that DMPA-IM-driven accumulation of HIV-susceptible Th17-like cells might be counteracted by their role in maintaining mucosal barrier integrity. CLINICAL TRIALS REGISTRATION: NCT02550067.

Anthropomorphic Character Animations Versus Digital Chalk Talks in a Resident Diabetes Pharmacotherapy Curriculum: a Randomized Controlled Trial.

BACKGROUND: Animation in medical education has boomed over the past two decades, and demand for distance learning technologies will likely continue in the context of the COVID-19 pandemic. However, experimental data guiding best practices for animation in medical education are scarce. OBJECTIVE: To compare the efficacy of two animated video styles in a diabetes pharmacotherapy curriculum for internal medicine residents. DESIGN: Learners were randomized to receive one of two versions of the same multimodal didactic curriculum. They received identical lectures, group activities, and quizzes, but were randomized to either digital chalk talk (DCT) videos or Sugar-Coated Science (SCS). SCS is an animated series using anthropomorphic characters, stories, and mnemonics to communicate knowledge. PARTICIPANTS: Ninety-two internal medicine residents at a single academic medical center received the curriculum within ambulatory medicine didactics. MAIN MEASURES: Knowledge was measured at multiple time points, as was residents' self-reported comfort using each medication class covered. Surveys assessed video acceptability and telepresence. Key themes were identified from open-ended feedback. KEY RESULTS: Baseline knowledge was low, consistent with prior needs assessments. On immediate posttest, mean scores were higher with SCS than DCT (74.8% versus 68.4%), but the difference was not statistically significant, p = 0.10. Subgroup analyses revealed increased knowledge in the SCS group for specific medication classes. Delayed posttest showed significant knowledge gains averaging 17.6% across all participants (p < 0.05); these gains were similar between animation types. SCS achieved significantly higher telepresence, entertainment, and acceptability scores than DCT. Qualitative data suggested that residents prioritize well-designed, multimodal curricula over specific animation characteristics. CONCLUSION: SCS and DCTs both led to learning within a multimodal curriculum, but SCS significantly enhanced learner experience. Animation techniques exemplified by both SCS and DCTs have roles in the medical educator toolkit. Selection between them should incorporate context, learner factors, and production resources.

Safety and efficacy of an injectable nerve-specific hydrogel in a rodent crush injury model.

INTRODUCTION/AIMS: While the peripheral nervous system has the inherent ability to recover following injury, results are often unsatisfactory, resulting in permanent functional deficits and disability. Therefore, methods that enhance regeneration are of significant interest. The present study investigates an injectable nerve-tissue-specific hydrogel as a biomaterial for nerve regeneration in a rat nerve crush model. METHODS: Nerve-specific hydrogels were injected into the subepineurial space in both uninjured and crushed sciatic nerves of rats to assess safety and efficacy, respectively. The animals were followed longitudinally for 12 wk using sciatic functional index and kinematic measures. At 12 wk, electrophysiologic examination was also performed, followed by nerve and muscle histologic assessment. RESULTS: When the hydrogel was injected into an uninjured nerve, no differences in sciatic functional index, kinematic function, or axon counts were observed. A slight reduction in muscle fiber diameter was observed in the hydrogel-injected animals, but overall muscle area and kinematic function were not affected. Hydrogel injection following nerve crush injury resulted in multiple modest improvements in sciatic functional index and kinematic function with an earlier return to normal function observed in the hydrogel treated animals as compared to untreated controls. While no improvements in supramaximal compound motor action potential were observed in hydrogel treated animals, increased axon counts were observed on histologic assessment. DISCUSSION: These improvements in functional and histologic outcomes in a rapidly and fully recovering model suggest that injection of a nerve-specific hydrogel is safe and has the potential to improve outcomes following nerve injury.

Structure and impact of longitudinal Graduate Medical Education curricula designed to prepare future clinician-educators: A systematic scoping review: BEME Guide No. 74.

BACKGROUND: Many Graduate Medical Education (GME) programs offer clinician-educator curricula. The specific instructional methods employed and current best practices for clinician-educator curricula are unknown. We aimed to characterize the structure, curriculum content, instructional methods, and outcomes of longitudinal GME clinician-educator curricula. METHODS: We conducted a scoping review, registered with BEME, by comprehensively searching health science databases and related grey literature from January 2008 to January 2021 for studies involving longitudinal GME curricula aimed to train future clinician-educators. RESULTS: From 9437 articles, 36 unique curricula were included in our review. Most curricula were designed for residents (n = 26) but were heterogeneous in structure, instructional methods, and content. Several curricular themes emerged, including: 1) duration ≥ 12 months, 2) application of theory-based didactics with experiential activities, 3) independent projects, 4) exposure to faculty mentorship and educator communities, 5) strengthening competencies beyond teaching and scholarship, and 6) protected time and funding. Most outcomes were positive and focused on learner satisfaction or behavior change related to scholarly output and career tracking. CONCLUSIONS: Curricula in our review included important skills including experiential teaching, scholarly projects, and exposure to educator communities. Future curricula should build on these competencies and include more assessment of learner and program outcomes.

Inflammation and Ectopic Fat Deposition in the Aging Murine Liver Is Influenced by CCR2.

Aging is associated with inflammation and metabolic syndrome, which manifests in the liver as nonalcoholic fatty liver disease (NAFLD). NAFLD can range in severity from steatosis to fibrotic steatohepatitis and is a major cause of hepatic morbidity. However, the pathogenesis of NAFLD in naturally aged animals is unclear. Herein, we performed a comprehensive study of lipid content and inflammatory signature of livers in 19-month-old aged female mice. These animals exhibited increased body and liver weight, hepatic triglycerides, and inflammatory gene expression compared with 3-month-old young controls. The aged mice also had a significant increase in F4/80+ hepatic macrophages, which coexpressed CD11b, suggesting a circulating monocyte origin. A global knockout of the receptor for monocyte chemoattractant protein (CCR2) prevented excess steatosis and inflammation in aging livers but did not reduce the number of CD11b+ macrophages, suggesting changes in macrophage accumulation precede or are independent from chemokine (C-C motif) ligand-CCR2 signaling in the development of age-related NAFLD. RNA sequencing further elucidated complex changes in inflammatory and metabolic gene expression in the aging liver. In conclusion, we report a previously unknown accumulation of CD11b+ macrophages in aged livers with robust inflammatory and metabolic transcriptomic changes. A better understanding of the hallmarks of aging in the liver will be crucial in the development of preventive measures and treatments for end-stage liver disease in elderly patients.

Vaccine completion and infectious diseases screening in a cohort of adult refugees following resettlement in the U.S.: 2013-2015.

BACKGROUND: Refugees are frequently not immune to vaccine-preventable infections. Adherence to consensus guidelines on vaccination and infectious diseases screening among refugees resettling in the U.S. is unknown. We sought to determine rates of vaccine completion and infectious diseases screening in refugees following resettlement. METHODS: We conducted a retrospective cohort study of refugees resettling in a region in the U.S. using medical data from June 2013-April 2015. We determined the proportion of vaccine-eligible refugees vaccinated with measles-mumps-rubella (MMR), hepatitis A/B, tetanus, diphtheria, and acellular pertussis (Tdap), and human papillomavirus (HPV) following resettlement. We also determined the proportion of refugees who completed HIV and hepatitis C (HCV) screening. RESULTS: One hundred and eleven subjects were included, primarily from Iraq (53%), Afghanistan (19%), and Eritrea (11%). Of the 84 subjects who were vaccine-eligible, 78 (93%) initiated and 42 (50%) completed vaccinations within one year of resettlement. Odds of completing vaccination were higher for men (OR: 2.38; 95%CI:1.02-5.71) and for subjects with English proficiency (OR: 3.70; 95%CI:1.04-17.49). Of the 78 subjects (70%) completing HIV screening, two (3%) were diagnosed with HIV. Nearly all subjects completed screening for HCV, and one had active infection. CONCLUSION: While most refugees initiate vaccinations, only 50% completed vaccinations and 70% completed HIV screening within 1 year of resettlement. There is a need to emphasize vaccine completion and HIV screening in refugee patients following resettlement.

Decellularization techniques and their applications for the repair and regeneration of the nervous system.

A variety of surgical and non-surgical approaches have been used to address the impacts of nervous system injuries, which can lead to either impairment or a complete loss of function for affected patients. The inherent ability of nervous tissues to repair and/or regenerate is dampened due to irreversible changes that occur within the tissue remodeling microenvironment following injury. Specifically, dysregulation of the extracellular matrix (i.e., scarring) has been suggested as one of the major factors that can directly impair normal cell function and could significantly alter the regenerative potential of these tissues. A number of tissue engineering and regenerative medicine-based approaches have been suggested to intervene in the process of remodeling which occurs following injury. Decellularization has become an increasingly popular technique used to obtain acellular scaffolds, and their derivatives (hydrogels, etc.), which retain tissue-specific components, including critical structural and functional proteins. These advantageous characteristics make this approach an intriguing option for creating materials capable of stimulating the sensitive repair mechanisms associated with nervous system injuries. Over the past decade, several diverse decellularization methods have been implemented specifically for nervous system applications in an attempt to carefully remove cellular content while preserving tissue morphology and composition. Each application-based decellularized ECM product requires carefully designed treatments that preserve the unique biochemical signatures associated within each tissue type to stimulate the repair of brain, spinal cord, and peripheral nerve tissues. Herein, we review the decellularization techniques that have been applied to create biomaterials with the potential to promote the repair and regeneration of tissues within the central and peripheral nervous system.

Effects of age-related shifts in cellular function and local microenvironment upon the innate immune response to implants.

The host macrophage response is now well recognized as a predictor of the success or failure of biomaterial implants following placement. More specifically, shifts from an "M1" pro-inflammatory towards a more "M2-like" anti-inflammatory macrophage polarization profile have been shown to result in enhanced material integration and/or tissue regeneration downstream. As a result, a number of biomaterials-based approaches to controlling macrophage polarization have been developed. However, the ability to promote such activity is predicated upon an in-depth, context-dependent understanding of the host response to biomaterials. Recent work has shown the impacts of both tissue location and tissue status (i.e. underlying pathology) upon the host innate immune response to implants, representing a departure from a focus upon implant material composition and form. Thus, the ideas of "biocompatibility," the host macrophage reaction, and ideal material requirements and modification strategies may need to be revisited on a patient, tissue, and disease basis. Immunosenescence, dysregulation of macrophage function, and delayed resolution of immune responses in aged individuals have all been demonstrated, suggesting that the host response to biomaterials in aged individuals should differ from that in younger individuals. However, despite the increasing usage of implantable medical devices in aged patients, few studies examining the effects of aging upon the host response to biomaterials and the implications of this response for long-term integration and function have been performed. The objective of the present manuscript is to review the putative effects of aging upon the host response to implanted materials and to advance the hypothesis that age-related changes in the local microenvrionement, with emphasis on the extracellular matrix, play a previously unrecognized role in determining the host response to implants.

Macrophage phenotype in response to ECM bioscaffolds.

Macrophage presence and phenotype are critical determinants of the healing response following injury. Downregulation of the pro-inflammatory macrophage phenotype has been associated with the therapeutic use of bioscaffolds composed of extracellular matrix (ECM), but phenotypic characterization of macrophages has typically been limited to small number of non-specific cell surface markers or expressed proteins. The present study determined the response of both primary murine bone marrow derived macrophages (BMDM) and a transformed human mononuclear cell line (THP-1 cells) to degradation products of two different, commonly used ECM bioscaffolds; urinary bladder matrix (UBM-ECM) and small intestinal submucosa (SIS-ECM). Quantified cell responses included gene expression, protein expression, commonly used cell surface markers, and functional assays. Results showed that the phenotype elicited by ECM exposure (MECM) is distinct from both the classically activated IFNγ+LPS phenotype and the alternatively activated IL-4 phenotype. Furthermore, the BMDM and THP-1 macrophages responded differently to identical stimuli, and UBM-ECM and SIS-ECM bioscaffolds induced similar, yet distinct phenotypic profiles. The results of this study not only characterized an MECM phenotype that has anti-inflammatory traits but also showed the risks and challenges of making conclusions about the role of macrophage mediated events without consideration of the source of macrophages and the limitations of individual cell markers.

Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model.

Both maternal microbiota and helminth infection may alter offspring immunity but the relationship between these is underexplored. We hypothesized that maternal helminth exposure prior to pregnancy has lasting consequences on offspring intestinal microbiota and consequent immunity. Female BALB/c adult mice were infected with 500L3 Nippostrongylus brasiliensis (N brasiliensis). Infection was cleared by ivermectin treatment, and mice were mated 3 weeks post-infection (NbM). Control mice were not infected but were exposed to ivermectin (NvM). We analysed maternal gut microbiota during pregnancy, breastmilk microbiota and offspring faecal microbiota and immunity 2 weeks after delivery. During pregnancy, NbM (Mothers previously infected with Nippostrongylus brasiliensis) displayed significantly altered stool bacterial communities (R2  = .242; P = .001), with increased abundance of Enterococcaceae versus NvM (Naive mothers). Similarly, we observed a profound impact on breastmilk microbiota in NbM vs NvM. Moreover, NbM pups showed significantly altered gut microbial communities at 14 days of age versus those born to NvM with increased relative abundance of Coriobacteriaceae and Micrococcaceae. These changes were associated with alterations in pup immunity including increased frequencies and numbers of activated CD4 T cells (CD4 + CD44hi) in NbM offspring spleens. Taken together, we show that preconception helminth infections impact offspring immunity possibly through alteration of maternal and offspring microbiota.

Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae.

BACKGROUND: Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes. RESULTS: Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways. More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution. CONCLUSIONS: Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter.

Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants.

Background: Exclusive breastfeeding reduces the rate of postnatal human immunodeficiency virus (HIV) transmission compared to nonexclusive breastfeeding; however, the mechanisms of this protection are unknown. Our study aimed to interrogate the mechanisms underlying the protective effect of exclusive breastfeeding. Methods: We performed a prospective, longitudinal study of infants from a high-HIV-prevalence, low-income setting in South Africa. We evaluated the role of any non-breast milk feeds, excluding prescribed medicines on stool microbial communities via 16S rRNA gene sequencing, peripheral T-cell activation via flow cytometry, and buccal mucosal gene expression via quantitative polymerase chain reaction assay. Results: A total of 155 infants were recruited at birth with mean gestational age of 38.9 weeks and mean birth weight of 3.2 kg. All infants were exclusively breastfed (EBF) at birth, but only 43.5% and 20% remained EBF at 6 or 14 weeks of age, respectively. We observed lower stool microbial diversity and distinct microbial composition in exclusively breastfed infants. These microbial communities, and the relative abundance of key taxa, were correlated with peripheral CD4+ T-cell activation, which was lower in EBF infants. In the oral mucosa, gene expression of chemokine and chemokine receptors involved in recruitment of HIV target cells to tissues, as well as epithelial cytoskeletal proteins, was lower in EBF infants. Conclusions: These data suggest that nonexclusive breastfeeding alters the gut microbiota, increasing T-cell activation and, potentially, mucosal recruitment of HIV target cells. Study findings highlight a biologically plausible mechanistic explanation for the reduced postnatal HIV transmission observed in EBF infants.

Species Pool Functional Diversity Plays a Hidden Role in Generating ß-Diversity.

Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drives the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive ß-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity to ß-diversity. We interpret the results to mean that functional diversity can play an important role in driving ß-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mesocosms to enhance our understanding of the role that functional variation plays in generating spatial biodiversity patterns.

Properties of the Temporomandibular Joint in Growing Pigs.

A subset of temporomandibular joint (TMJ) disorders is attributed to joint degeneration. The pig has been considered the preferred in vivo model for the evaluation of potential therapies for TMJ disorders, and practical considerations such as cost and husbandry issues have favored the use of young, skeletally immature animals. However, the effect of growth on the biochemical and biomechanical properties of the TMJ disk and articulating cartilage has not been examined. The present study investigates the effect of age on the biochemical and biomechanical properties of healthy porcine TMJs at 3, 6, and 9 months of age. DNA, hydroxyproline, and glycosaminoglycan (GAG) content were determined and the disks and condyles were tested in uniaxial unconfined stress relaxation compression from 10% to 30% strain. TMJ disks were further assessed with a tensile test to failure technique, which included the ability to test multiple samples from the same region of an individual disk to minimize the intraspecimen variation. No differences in biochemical properties for the disk or compressive properties at 30% stress relaxation in the disk and condylar cartilage were found. In tension, no differences were observed for peak stress and tensile modulus. The collagen content of the condyle was higher at 9 months than 3 months (p < 0.05), and the GAG content was higher at 9 months than 6 months (p < 0.05). There was a trend of increased compressive instantaneous modulus with age. As such, age-matched controls for growing pigs are probably appropriate for most parameters measured.

Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration.

An often-cited benefit of river restoration is an increase in biodiversity or shift in composition to more desirable taxa. Yet, hard manipulations of habitat structure often fail to elicit a significant response in terms of biodiversity patterns. In contrast to conventional wisdom, the dispersal of organisms may have as large an influence on biodiversity patterns as environmental conditions. This influence of dispersal may be particularly influential in river networks that are linear branching, or dendritic, and thus constrain most dispersal to the river corridor. As such, some locations in river networks, such as isolated headwaters, are expected to respond less to environmental factors and less by dispersal than more well-connected downstream reaches. We applied this metacommunity framework to study how restoration drives biodiversity patterns in river networks. By comparing assemblage structure in headwater vs. more well-connected mainstem sites, we learned that headwater restoration efforts supported higher biodiversity and exhibited more stable ecological communities compared with adjacent, unrestored reaches. Such differences were not evident in mainstem reaches. Consistent with theory and mounting empirical evidence, we attribute this finding to a relatively higher influence of dispersal-driven factors on assemblage structure in more well-connected, higher order reaches. An implication of this work is that, if biodiversity is to be a goal of restoration activity, such local manipulations of habitat should elicit a more profound response in small, isolated streams than in larger downstream reaches. These results offer another significant finding supporting the notion that restoration activity cannot proceed in isolation of larger-scale, catchment-level degradation.

Manipulation of local environment produces different diversity outcomes depending on location within a river network.

Ecologists have long been interested in mechanisms governing community composition and assembly. Spatial connectivity is one potential mechanism that can have a large influence on community processes. In accordance with network metrics such as closeness and betweenness, headwater streams are more isolated than mainstem streams. Theory and observational studies predict that community structure in isolated locations of dispersal networks should respond more strongly to manipulations of local conditions, whereas well-connected communities subject to high levels of dispersal should not respond strongly to local manipulations. We experimentally investigated this prediction by manipulating habitat complexity in headwaters and mainstem streams while monitoring macroinvertebrate communities through time. As predicted, the manipulation of local habitat had a stronger influence in headwaters than mainstreams. Both taxon richness and community similarity showed strong responses to alterations in habitat complexity in headwaters, but not in mainstem streams. These findings support the hypothesis that location within a dispersal network affects the relative importance of local and regional factors in structuring the local communities within a spatially structured metacommunity. In addition, our results suggest that conservation strategies need to account for the possibility that the relative importance of local and regional drivers of community composition and assembly can vary spatially.

Making sense of metacommunities: dispelling the mythology of a metacommunity typology.

Metacommunity ecology has rapidly become a dominant framework through which ecologists understand the natural world. Unfortunately, persistent misunderstandings regarding metacommunity theory and the methods for evaluating hypotheses based on the theory are common in the ecological literature. Since its beginnings, four major paradigms-species sorting, mass effects, neutrality, and patch dynamics-have been associated with metacommunity ecology. The Big 4 have been misconstrued to represent the complete set of metacommunity dynamics. As a result, many investigators attempt to evaluate community assembly processes as strictly belonging to one of the Big 4 types, rather than embracing the full scope of metacommunity theory. The Big 4 were never intended to represent the entire spectrum of metacommunity dynamics and were rather examples of historical paradigms that fit within the new framework. We argue that perpetuation of the Big 4 typology hurts community ecology and we encourage researchers to embrace the full inference space of metacommunity theory. A related, but distinct issue is that the technique of variation partitioning is often used to evaluate the dynamics of metacommunities. This methodology has produced its own set of misunderstandings, some of which are directly a product of the Big 4 typology and others which are simply the product of poor study design or statistical artefacts. However, variation partitioning is a potentially powerful technique when used appropriately and we identify several strategies for successful utilization of variation partitioning.

Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants.

BACKGROUND: Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these relationships are significantly influenced by a variety of factors, including niche localization, interaction potential, and symbiont transmission mode. In eusocial insect hosts, socially transmitted gut microbiota may represent an intermediate point between free living or environmentally acquired bacteria and those with strict host association and maternal transmission. RESULTS: We characterized the bacterial communities associated with an abundant ant species, Camponotus chromaiodes. While many bacteria had sporadic distributions, some taxa were abundant and persistent within and across ant colonies. Specially, two Acetobacteraceae operational taxonomic units (OTUs; referred to as AAB1 and AAB2) were abundant and widespread across host samples. Dissection experiments confirmed that AAB1 and AAB2 occur in C. chromaiodes gut tracts. We explored the distribution and evolution of these Acetobacteraceae OTUs in more depth. We found that Camponotus hosts representing different species and geographical regions possess close relatives of the Acetobacteraceae OTUs detected in C. chromaiodes. Phylogenetic analysis revealed that AAB1 and AAB2 join other ant associates in a monophyletic clade. This clade consists of Acetobacteraceae from three ant tribes, including a third, basal lineage associated with Attine ants. This ant-specific AAB clade exhibits a significant acceleration of substitution rates at the 16S rDNA gene and elevated AT content. Substitutions along 16S rRNA in AAB1 and AAB2 result in ~10 % reduction in the predicted rRNA stability. CONCLUSIONS: Combined, these patterns in Camponotus-associated Acetobacteraceae resemble those found in cospeciating gut associates that are both socially and maternally transmitted. These associates may represent an intermediate point along an evolutionary trajectory manifest most extremely in symbionts with strict maternal transmission. Collectively, these results suggest that Acetobacteraceae may be a frequent and persistent gut associate in Camponotus species and perhaps other ant groups, and that its evolution is strongly impacted by this host association.