Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Background: To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences. Results: Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55T, Herbinix luporum SD1DT, Clostridium bornimense M2/40T, Proteiniphilum saccharofermentans M3/6T, Fermentimonas caenicola ING2-E5BT, and Petrimonas mucosa ING2-E5AT. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis. Conclusions: Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members. © 2017 The Author(s)

Molecular Typing of Enterobacteriaceae from Pig Holdings in North-Western Germany Reveals Extended- Spectrum and AmpC β-Lactamases Producing but no Carbapenem Resistant Ones

The increase of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in humans and in food-producing animals is of public health concern. The latter could contribute to spreading of these bacteria or their resistance genes to humans. Several studies have reported the isolation of third generation cephalosporin resistant bacteria in livestock animals. However, the number of samples and the methodology used differ considerably between studies limiting comparability and prevalence assessment. In the present study, a total of 564 manure and dust samples were collected from 47 pig farms in Northern Germany and analysed to determine the prevalence of ESBL-E. Molecular typing and characterization of resistance genes was performed for all ESBL-E isolates. ESBL-E isolates were found in 55.3% of the farms. ESBL-Escherichia coli was found in 18.8% of the samples, ESBL-Klebsiella pneumoniae in 0.35%. The most prevalent ESBL genes among E. coli were CTX-M-1 like (68.9%), CTX-M-15 like (16%) and CTX-M-9 group (14.2%). In 20% of the latter two, also the OXA-1 like gene was found resulting in a combination of genes typical for isolates from humans. Genetic relation was found between isolates not only from the same, but also from different farms, with multilocus sequence type (ST) 10 being predominant among the E. coli isolates. In conclusion, we showed possible spread of ESBL-E between farms and the presence of resistance genes and STs previously shown to be associated with human isolates. Follow-up studies are required to monitor the extent and pathways of ESBL-E transmission between farms, animals and humans

Dünndarmschonung bei der IMRT des Rektumkarzinoms: Dosimetrische Studie zur Bauch- und Rückenlagerung

Background: This treatment planning study analyzes dose coverage and dose to organs at risk (OAR) in intensity-modulated radiotherapy (IMRT) of rectal cancer and compares prone vs. supine positioning as well as the effect of dose optimization for the small bowel (SB) by additional dose constraints in the inverse planning process. Patients and methods: Based on the CT datasets of ten male patients in both prone and supine position, a total of four different IMRT plans were created for each patient. OAR were defined as the SB, bladder, and femoral heads. In half of the plans, two additional SB cost functions were used in the inverse planning process. Results: There was a statistically significant dose reduction for the SB in prone position of up to 41% in the high and intermediate dose region, compared with the supine position. Furthermore, the femoral heads showed a significant dose reduction in prone position in the low dose region. Regarding the additional active SB constraints, the dose in the high dose region of the SB was significantly reduced by up to 14% with the additional cost functions. There were no significant differences in the dose distribution of the planning target volume (PTV) and the bladder. Conclusion: Prone positioning can significantly reduce dose to the SB in IMRT for rectal cancer and therefore should not only be used in 3D conformal radiotherapy but also in IMRT of rectal cancer. Further protection of the SB can be achieved by additional dose constraints in inverse planning without jeopardizing the homogeneity of the PTV

Development of an innovative 3D cell culture system to study tumour--stroma interactions in non-small cell lung cancer cells.

INTRODUCTION: We describe a novel 3D co-culture model using non-small cell lung cancer (NSCLC) cell lines in combination with lung fibroblasts. This model allows the investigation of tumour-stroma interactions and addresses the importance of having a more in vivo like cell culture model. METHODS: Automation-compatible multi-well hanging drop microtiter plates were used for the production of 3D mono- and co-cultures. In these hanging drops the two NSCLC cell lines A549 and Colo699 were cultivated either alone or co-cultured with lung fibroblasts. The viability of tumour spheroids was confirmed after five and ten days by using Annexin V/Propidium Iodide staining for flow-cytometry. Tumour fibroblast spheroid formation was characterized by scanning electron microscope (SEM), semi-thin sections, fluorescence microscope and immunohistochemistry (IHC). In addition to conventional histology, protein expression of E-Cadherin, vimentin, Ki67, fibronectin, cytokeratin 7 and α-smooth muscle actin (α-SMA) was investigated by IHC. RESULTS: Lower viability was observed in A549 monocultures compared to co-cultures, whereas Colo699 monocultures showed better viability compared to co-cultures. Ki67 expression varied significantly between mono- and co-cultures in both tumour cell lines. An increase of vimentin and decreased E-Cadherin expression could be detected during the course of the cultivation suggesting a transition to a more mesenchymal phenotype. Furthermore, the fibroblast cell line showed an expression of α-SMA only in co-culture with the cancer cell line A549, thereby indicating a mesenchymal to mesenchymal shift to an even more myofibroblast phenotype. CONCLUSION: We demonstrate that our method is a promising tool for the generation of tumour spheroid co-cultures. Furthermore, these spheroids allow the investigation of tumour-stroma interactions and a better reflection of in vivo conditions of cancer cells in their microenvironment. Our method holds potential to contribute to the development of anti-cancer agents and support the search for biomarkers

Novel radiotherapy techniques for involved-field and involved-node treatment of mediastinal Hodgkin lymphoma: when should they be considered and which questions remain open?

PURPOSE Hodgkin lymphoma (HL) is a highly curable disease. Reducing late complications and second malignancies has become increasingly important. Radiotherapy target paradigms are currently changing and radiotherapy techniques are evolving rapidly. DESIGN This overview reports to what extent target volume reduction in involved-node (IN) and advanced radiotherapy techniques, such as intensity-modulated radiotherapy (IMRT) and proton therapy-compared with involved-field (IF) and 3D radiotherapy (3D-RT)- can reduce high doses to organs at risk (OAR) and examines the issues that still remain open. RESULTS Although no comparison of all available techniques on identical patient datasets exists, clear patterns emerge. Advanced dose-calculation algorithms (e.g., convolution-superposition/Monte Carlo) should be used in mediastinal HL. INRT consistently reduces treated volumes when compared with IFRT with the exact amount depending on the INRT definition. The number of patients that might significantly benefit from highly conformal techniques such as IMRT over 3D-RT regarding high-dose exposure to organs at risk (OAR) is smaller with INRT. The impact of larger volumes treated with low doses in advanced techniques is unclear. The type of IMRT used (static/rotational) is of minor importance. All advanced photon techniques result in similar potential benefits and disadvantages, therefore only the degree-of-modulation should be chosen based on individual treatment goals. Treatment in deep inspiration breath hold is being evaluated. Protons theoretically provide both excellent high-dose conformality and reduced integral dose. CONCLUSION Further reduction of treated volumes most effectively reduces OAR dose, most likely without disadvantages if the excellent control rates achieved currently are maintained. For both IFRT and INRT, the benefits of advanced radiotherapy techniques depend on the individual patient/target geometry. Their use should therefore be decided case by case with comparative treatment planning

Primary antibodies used for immunohistochemistry.

<p>Primary antibodies used for immunohistochemistry.</p

SV80 microtissue protein expression pattern.

<p>IHC slices of SV80 in monocultures after ten days (Bar in A: 100 μm); SV80 microtissue staining is only shown representatively after ten days because no difference in the staining pattern between five and ten days was detected. Microtissues were completely positive for vimentin and Ki67, whereas no E-Cadherin and α-SMA expression was observed.</p

Tumour microtissue formation.

<p>SEM pictures were taken after ten days: Monocultures of A549 and SV80 were seeded in a ratio of 2500 cells/40 μl, whereas Colo699 monocultures were cultured in form of 1250 cells/40 μl. All co-cultures were seeded in a carcinoma cell: fibroblast ratio of 1∶2/40 μl (A549 co-cultures: 2500 cancer cells +5000 fibroblasts / Colo699 co-cultures: 1250 cancer cells +2500 fibroblasts). (A/B) A549 monocultures, (C/D) A549 co-cultures; (E/F) Colo699 monocultures, (G/H) Colo699 co-cultures; (I/J) SV80 monocultures. All co-cultures displayed a more homogenous and rounder microtissue surface compared to monocultures.</p

Cytokeratin 7 expression pattern.

<p>IHC staining of A549, SV80 monocultures and A549 co-cultures after ten days (Bar in 1–3: 100 μm). Cytokeratin 7 staining could only be observed in cancer cells but not in SV80 cells.</p