The Evolution of Ecological Diversity in Acidobacteria

Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success

Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation.

The study of biliary disease has been constrained by a lack of primary human cholangiocytes. Here we present an efficient, serum-free protocol for directed differentiation of human induced pluripotent stem cells into cholangiocyte-like cells (CLCs). CLCs show functional characteristics of cholangiocytes, including bile acids transfer, alkaline phosphatase activity, γ-glutamyl-transpeptidase activity and physiological responses to secretin, somatostatin and vascular endothelial growth factor. We use CLCs to model in vitro key features of Alagille syndrome, polycystic liver disease and cystic fibrosis (CF)-associated cholangiopathy. Furthermore, we use CLCs generated from healthy individuals and patients with polycystic liver disease to reproduce the effects of the drugs verapamil and octreotide, and we show that the experimental CF drug VX809 rescues the disease phenotype of CF cholangiopathy in vitro. Our differentiation protocol will facilitate the study of biological mechanisms controlling biliary development, as well as disease modeling and drug screening.This work was funded by ERC starting grant Relieve IMDs (L.V., N.H.), the Cambridge Hospitals National Institute for Health Research Biomedical Research Center (L.V., N.H., F.S.), the Evelyn trust (N.H.) and the EU Fp7 grant TissuGEN (M.CDB.). FS has been supported by an Addenbrooke’s Charitable Trust Clinical Research Training Fellowship and a joint MRC-Sparks Clinical Research Training Fellowship.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nbt.327

Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis

Objective Primary sclerosing cholangitis (PSC) is a genetically complex, inflammatory bile duct disease of largely unknown aetiology often leading to liver transplantation or death. Little is known about the genetic contribution to the severity and progression of PSC. The aim of this study is to identify genetic variants associated with PSC disease progression and development of complications. Design We collected standardised PSC subphenotypes in a large cohort of 3402 patients with PSC. After quality control, we combined 130 422 single nucleotide polymorphisms of all patients-obtained using the Illumina immunochip-with their disease subphenotypes. Using logistic regression and Cox proportional hazards models, we identified genetic variants associated with binary and time-to-event PSC subphenotypes. Results We identified genetic variant rs853974 to be associated with liver transplant-free survival (p=6.07x10(-9)). Kaplan-Meier survival analysis showed a 50.9% (95% CI 41.5% to 59.5%) transplant-free survival for homozygous AA allele carriers of rs853974 compared with 72.8% (95% CI 69.6% to 75.7%) for GG carriers at 10 years after PSC diagnosis. For the candidate gene in the region, RSPO3, we demonstrated expression in key liver-resident effector cells, such as human and murine cholangiocytes and human hepatic stellate cells. Conclusion We present a large international PSC cohort, and report genetic loci associated with PSC disease progression. For liver transplant-free survival, we identified a genome-wide significant signal and demonstrated expression of the candidate gene RSPO3 in key liver-resident effector cells. This warrants further assessments of the role of this potential key PSC modifier gene.Peer reviewe

Storcellet granulær lymfocytt-leukemi

Large granular lymphocytic leukaemia S Michalsen E Schrumpf K Beiske A Tierens V Stenberg G E Tjønnfjord Abstract Background. Large granular lymphocytic leukaemia (LGL-leukaemia) is a rare disease. Knowledge of the disease may contribute to targeted and quick diagnosis and effective treatment of those affected. Material and methods. We identified patients who had been diagnosed with LGL-leukaemia at Oslo University Hospital, Rikshospitalet in the period 01.10.2001–31.12.2007. Their medical records were assessed retrospectively. Results. During the study period, LGL-leukaemia was diagnosed in 52 patients (26 women and 26 men), median age of 59 (26–86) years. The leukaemia displayed NK-cell phenotype in one patient and T-cell phenotype in the remaining 51 patients. Slightly more than one third of the patients were asymptomatic. Cytopenia, usually granulocytopenia, was the most common cause for the clinical phenotype in symptomatic patients. Concomitant disease with immune pathogenesis was common, and we also found a high prevalence of clonal B-cell disease (17 %). Interpretation. Our patients with LGL-leukaemia are representative for presentations of the disease in the literature. The condition should be suspected when patients present with unexplained cytopenias. An early diagnosis may prevent an extensive and unnecessary diagnostic work-up and ensure that patients are offered a simple and effective treatment

I Semmelweis' fotspor : Implementering av eksisterende retningslinje for rengjøring av stetoskop på en indremedisinsk avdeling på Ahus - en ledelsesutfordring.

BAKGRUNN: I lys av de siste årenes fokus på pasientsikkerhet, har smittevern fremkommet som en sentral faktor i forebygging av uheldige hendelser. Smittekilder som enkelt kan elimineres, selv om det ikke finnes dokumentasjon på at de direkte forårsaker sykehusinfeksjoner, har fått økt oppmerksomhet og har ført til økt bruk av hansker, munnbind og annet beskyttelsesutstyr. Stetoskop kan også være en slik potensiell smittevektor, ved at det legges på pasienters hud og er i kontakt med legens hender fra en pasient til den neste. Som studenter har vi sjelden observert leger som desinfiserer sine stetoskop. Vi ønsket å finne ut av om stetoskop er en reell smittevektor, og om den kan elimineres som ledd i generell sykehushygiene. KUNNSKAPSGRUNNLAG: Litteratursøk i PubMed og Cochranedatabasen viser at det er dyrket frem patogene bakterier fra stetoskopmembraner, blant annet MRSA og gram-negative kokker, samt at desinfisering med sprit reduserer bakteriefloraen på stetoskopmembranene med over 90 %. I følge intervjuer av avdelingsoverleger og EpiGen-senteret på Ahus anses stetoskopet som en smittekilde. Retningslinje 2712 på Ahus anbefaler regelmessig rengjøring av stetoskop, men denne er ikke implementert på avdelingene. En liten spørreundersøkelse vi utførte viser at avdelingsleger på Ahus ikke desinfiserer stetoskop regelmessig. TILTAK OG IMPLEMENTERING: Vi valgte tiltaket ”innføring av eksisterende retningslinje for rengjøring av stetoskop på en indremedisinsk avdeling på Ahus, ” bestående av to deler: Én anbefaling om innkjøp av egne desinfiseringsservietter til stetoskop (swabs) på pasient-rommene, og én ledelsesdel der Kotters 8 punkter konkret kan være til hjelp i prosessen med å skulle innføre et tiltak som kan møte motstand fordi det ikke har dokumentert effekt. Avdelingsoverlegen og smittevernsansvarlig sykepleier samarbeider med de ansatte på sin avdeling samt mikrobiologisk avdeling for å få dette gjennomført i en to-månedersperiode. På morgenvisitten registrerer sykepleierne på et eget indikatorskjema hvorvidt legen husket å desinfisere stetoskopet med swabs før neste pasient. Dette presenteres som to-ukersstatistikker for å holde fokus, og evalueres etter to måneder. Kotters 8 punkter kan anvendes. EVALUERING: Ved hjelp av prosessindikatoren ”andel leger som desinfiserer stetoskopet per aktuelle pasient” vil man kunne vurdere i hvilken grad tiltaket gjennomføres. Hvert ledd av tiltaket evalueres for å se om noe kan forbedres (egen sjekkliste). Dersom det etter to-månedersevalueringen viser seg å være realistisk gjennomførbart, kan man vurdere å innføre dette på andre sykehusavdelinger som et ledd i generell sykehushygiene

The role of natural killer T cells in a mouse model with spontaneous bile duct inflammation

Abstract Natural killer T (NKT) cells are activated by lipid antigens presented by CD1d molecules and represent a major lymphocyte subset of the liver. NOD.c3c4 mice spontaneously develop biliary inflammation in extra‐ and intrahepatic bile ducts. We demonstrated by flow cytometry that invariant NKT (iNKT) cells were more abundant in the thymus, spleen, and liver of NOD.c3c4 mice compared to NOD mice. iNKT cells in NOD.c3c4 mice displayed an activated phenotype. Further, NOD and NOD.Cd1d ‐/‐ mice were irradiated and injected with NOD.c3c4 bone marrow, and injection of NOD.c3c4 bone marrow resulted in biliary infiltrates independently of CD1d expression in recipient mice. Activation or blocking of NKT cells with α‐galactosylceramide or anti‐CD1d antibody injections did not affect the biliary phenotype of NOD.c3c4 mice. NOD.c3c4.Cd1d ‐/‐ mice were generated by crossing NOD.Cd1d ‐/‐ mice onto a NOD.c3c4 background. NOD.c3c4.Cd1d ‐/‐ and NOD.c3c4 mice developed the same extent of biliary disease. This study demonstrates that iNKT cells are more abundant and activated in the NOD.c3c4 model. The portal inflammation of NOD.c3c4 mice can be transferred to irradiated recipients, which suggests an immune‐driven disease. Our findings imply that NKT cells can potentially participate in the biliary inflammation, but are not the primary drivers of disease in NOD.c3c4 mice

The gut microbiota contributes to a mouse model of spontaneous bile duct inflammation

Background & Aims A strong association between human inflammatory biliary diseases and gut inflammation has led to the hypothesis that gut microbes and lymphocytes activated in the intestine play a role in biliary inflammation. The NOD.c3c4 mouse model develops spontaneous biliary inflammation in extra- and intra-hepatic bile ducts. We aimed to clarify the role of the gut microbiota in the biliary disease of NOD.c3c4 mice. Methods We sampled cecal content and mucosa from conventionally raised (CONV-R) NOD.c3c4 and NOD control mice, extracted DNA and performed 16S rRNA sequencing. NOD.c3c4 mice were rederived into a germ free (GF) facility and compared with CONV-R NOD.c3c4 mice. NOD.c3c4 mice were also co-housed with NOD mice and received antibiotics from weaning. Results The gut microbial profiles of mice with and without biliary disease were different both before and after rederivation (unweighted UniFrac-distance). GF NOD.c3c4 mice had less distended extra-hepatic bile ducts than CONV-R NOD.c3c4 mice, while antibiotic treated mice showed reduction of biliary infarcts. GF animals also showed a reduction in liver weight compared with CONV-R NOD.c3c4 mice, and this was also observed in antibiotic treated NOD.c3c4 mice. Co-housing of NOD and NOD.c3c4 mice indicated that the biliary phenotype was neither transmissible nor treatable by co-housing with healthy mice. Conclusions NOD.c3c4 and NOD control mice show marked differences in the gut microbiota. Germ free NOD.c3c4 mice develop a milder biliary affection compared with conventionally raised NOD.c3c4 mice. Our findings suggest that the intestinal microbiota contributes to disease in this murine model of biliary inflammation. Lay Summary Mice with liver disease have a gut microflora (microbiota) that differs substantially from normal mice. When these mice, that under normal circumstances spontaneously develops disease in their bile ducts, are raised in an environment devoid of bacteria, the disease in the bile ducts diminishes. Overall this clearly indicates that the bacteria in the gut (the gut microbiota) influences the liver disease in these mice

The role of soil chemical properties, land use and plant diversity for microbial phosphorus in forest and grassland soils

Management intensity modifies soil properties, e.g., organic carbon (Corg) concentrations and soil pH with potential feedbacks on plant diversity. These changes might influence microbial P concentrations (Pmic) in soil representing an important component of the P cycle. Our objectives were to elucidate whether abiotic and biotic variables controlling Pmic concentrations in soil are the same for forests and grasslands, and to assess the effect of region and management on Pmic concentrations in forest and grassland soils as mediated by the controlling variables. In three regions of Germany, Schwäbische Alb, Hanich-Dün, and Schorfheide-Chorin, we studied forest and grassland plots (each n = 150) differing in plant diversity and land-use intensity. In contrast to controls of microbial biomass carbon (Cmic), Pmic was strongly influenced by soil pH, which in turn affected phosphorus (P) availability and thus microbial P uptake in forest and grassland soils. Furthermore, Pmic concentrations in forest and grassland soils increased with increasing plant diversity. Using structural equation models, we could show that soil Corg is the profound driver of plant diversity effects on Pmic in grasslands. For both forest and grassland, we found regional differences in Pmic attributable to differing environmental conditions (pH, soil moisture). Forest management and tree species showed no effect on Pmic due to a lack of effects on controlling variables (e.g., Corg). We also did not find management effects in grassland soils which might be caused by either compensation of differently directed effects across sites or by legacy effects of former fertilization constraining the relevance of actual practices. We conclude that variables controlling Pmic or Cmic in soil differ in part and that regional differences in controlling variables are more important for Pmic in soil than those induced by management

Plant functional trait shifts explain concurrent changes in the structure and function of grassland soil microbial communities

Land‐use intensification drives changes in microbial communities and the soil functions they regulate, but the mechanisms underlying these changes are poorly understood as land use can affect soil communities both directly (e.g. via changes in soil fertility) and indirectly (e.g. via changes in plant inputs). The speed of microbial responses is also poorly understood. For instance, whether it is long‐term legacies or short‐term changes in land‐use intensity that drive changes in microbial communities. To address these topics, we measured multiple microbial functions, bacterial and fungal biomass and abiotic soil properties at two time intervals 3 years apart. This was performed in 150 grassland sites differing greatly in management intensity across three German regions. Observed changes in microbial soil properties were related to both long‐term means and short‐term changes in: abiotic soil properties, land‐use intensity, community abundance‐weighted means of plant functional traits and plant biomass properties in regression and structural equation models. Plant traits, particularly leaf phosphorus, and soil pH were the best predictors of change in soil microbial function, as well as fungal and bacterial biomass, while land‐use intensity showed weaker effects. Indirect legacy effects, in which microbial change was explained by the effects of long‐term land‐use intensity on plant traits, were important, thus indicating a time lag between plant community and microbial change. Whenever the effects of short‐term changes in land‐use intensity were present, they acted directly on soil microorganisms. Synthesis. The results provide new evidence that soil communities and their functioning respond to short‐term changes in land‐use intensity, but that both rapid and longer time‐scale responses to changes in plant functional traits are at least of equal importance. This suggests that management which shapes plant communities may be an effective means of managing soil communities and the functions and services they provide