Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.

IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces.

Hospitalization throws the preterm gut microbiome off-key.

Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host & Microbe, Thänert et al. characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.

Hadza require diet-derived microbiota-accessible carbohydrates to persist in mice.

Industrialization has transformed the gut microbiota, reducing the prevalence of relative to . Here, we isolate and strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of . We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of but not .

Milk to mucus: How B. fragilis colonizes the gut.

Human milk oligosaccharide (HMO) consumption by the infant microbiota is positively associated with immune health. In this issue of Cell Host & Microbe, Buzun et al. report a mechanism for HMO digestion by Bacteroides fragilis and demonstrate how the same pathway works on intestinal mucus to establish long-term gut residency.

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition.

The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses.

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.

IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are targeted by IgA and why. Here, we develop a new technique, Metagenomic Immunoglobulin Sequencing (MIG-Seq), and use it to determine IgA coating levels for thousands of gut microbiome strains in healthy humans.

Outcomes of Endoscopic Sinus Surgery for Chronic Rhinosinusitis in Adults with Primary Ciliary Dyskinesia.

 Primary ciliary dyskinesia (PCD) is a rare inherited disease associated with impairment of mucociliary transport and, consequently, with a high incidence of chronic rhinosinusitis. For patients with chronic rhinosinusitis who remain symptomatic despite medical treatment, endoscopic sinus surgery is a safe and effective therapeutic option. However, to date, no studies have been found evaluating the effect of surgery on the quality of life associated with the effect on olfaction and nasal endoscopy findings of patients with primary ciliary dyskinesia and chronic rhinosinusitis.

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.

The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California.

Hadza Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice.

Industrialization has transformed the gut microbiota, reducing the prevalence of relative to . Here, we isolate and strains from the microbiota of Hadza hunter-gatherers of Tanzania, a population with high levels of . We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of but not .

Using strain-resolved analysis to identify contamination in metagenomics data.

Background: Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.

Results: Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets.

Computed Tomography Evaluation of the Paranasal Sinuses in Adults with Primary Ciliary Dyskinesia.

 Primary ciliary dyskinesia is a rare inherited disease that results in a malfunction of mucociliary clearance and sinonasal complaints. Aplasia/hypoplasia of the frontal and sphenoid sinuses has been described as more frequent in this population. However, to date, no studies have provided a detailed description of computed tomography findings in adult patients with a diagnosis of this condition.

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.

Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species.

[Experiences with Regional Medical Coordinators in Ambulatory Care in the Early COVID-19 Phase 2020 in Bavaria: Survey of Regional Ambulatory Coordinators and General Practitioners].

Background: During the state of emergency in Bavaria in the early Corona phase 2020, some physicians in ambulatory care were appointed as regional medical coordinators (RMCs). The aim of the present study was to evaluate this newly introduced but temporary position.

Methods: In November 2020, a paper-based questionnaire was sent out to all 85 RMCs who could be identified through an internet research and to all 197 teaching practices of the Institute of General Practice and Health Services Research at the Technical University of Munich.

[The importance of the learning environment and reduction of burnout in clinical training: an analysis of the Competence Centre for Residency Training in Family Medicine Bavaria (CCRTB)].

Background: The Competence Centre for Residency Training in Family Medicine Bavaria (CCRTB) was established to improve the quality of postgraduate medical training by offering additional seminars and mentoring programmes as well as regular 'train-the-trainer' courses for educating physicians. In addition, residents have the opportunity to participate in a regional training network.

Objective: The aim was to assess the burden of burnout and the importance of the learning environment in the clinical training phase.

Reporting guidelines for human microbiome research: the STORMS checklist.

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies.

Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition.

Gut microbiome succession affects infant development. However, it remains unclear what factors promote persistence of initial bacterial colonizers in the developing gut. Here, we perform strain-resolved analyses to compare gut colonization of preterm and full-term infants throughout the first year of life and evaluate associations between strain persistence and strain origin as well as genetic potential.

Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.

The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome-resolved metagenomic analyses of benthic Microcoleus-dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.

Increased professionalization and lower burnout scores were associated with structured residency training program: results of a cross sectional survey.

The competence centre for Residency Training in Family Medicine Bavaria (CCRTB) was established to improve the quality of postgraduate medical education by offering training and mentoring programmes for residents, and by providing train-the-trainer and mentoring courses for supervisors. Beyond that, regional Residency Training Networks (RTN) on avoluntary basis were developed to facilitate structured and efficient clinical rotation programs. Primary aim was to investigate the burden of burnout and the development of professionalism among CCRTB-residencies within a cross-sectional study.

Ambulatory specialist costs and morbidity of coordinated and uncoordinated patients before and after abolition of copayment: A cohort analysis.

To strengthen the coordinating function of general practitioners (GPs) in the German healthcare system, a copayment of €10 was introduced in 2004. Due to a perceived lack of efficacy and a high administrative burden, it was abolished in 2012. The present cohort study investigates characteristics and differences of GP-coordinated and uncoordinated patients in Bavaria, Germany, concerning morbidity and ambulatory specialist costs and whether these differences have changed after the abolition of the copayment.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.

Background: Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.

Background: Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.

Results: We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado.