Synthetic ecology of the human gut microbiota

Despite recent advances in sequencing and culturing, a deep knowledge of the wiring and functioning of the human gut ecosystem and its microbiota as a community is still missing. A holistic mechanistic understanding will require study of the gut microbiota as an interactive and spatially organized biological system, which is difficult to do in complex natural communities. Synthetic gut microbial ecosystems can function as model systems to further current understanding of the composition, stability and functional activities of the microbiota. In this Review, we provide an overview of the current synthetic ecology strategies that can be used towards a more comprehensive understanding of the human gut ecosystem. Such approaches that integrate in vitro experiments using cultured isolates with mathematical modelling will enable the ultimate goal: translating mechanistic and ecological knowledge into novel and effective therapies.status: publishe

Characterisation of the discrepancy between PCR and virus isolation in relation to classical swine fever virus detection

&lt;p&gt;In order to confirm and characterise further the discrepancies observed between diagnostic RT-nPCR and virus isolation results for the detection of classical swine fever virus (CSFV), a test panel of three new RT-PCRs was designed, amplifying parts of the NS2, NS3 and NS5A regions. Screening of negative samples by virus isolation with the new panel not only confirmed the discrepancies previously observed but also indicated that these were not associated with a specific genomic region. However, none of the PCR-positive samples were positive on all the different PCRs and preferential amplification was not obtained even when a more sensitive real-time RT-PCR was used. Furthermore, the primer-dependent amplification, most likely caused by the presence of viral fragments, demonstrates the necessity of confirming a single positive PCR result, certainly in the presence of contradictory virus isolation results. The new PCR panel, in combination with sequencing, can be used as a tool to provide additional information on the nature of the viral RNA present in the sample.&lt;/p&gt;</p

Molecular assemblies built with the artificial protein Pizza

Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric β-propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domainsstatus: Published onlin

Design of synthetic microbial consortia for gut microbiota modulation

The use of and interest in probiotics to modulate the human intestinal microbiota have strongly increased in recent years. However, most of the current probiotic products have been limited to single-strain formulations of easily culturable food-grade microorganisms and often resulted in mixed results or limited effects on host health. Therefore, a revision of current probiotic strategies by using synthetic human-derived microbial multispecies consortia is necessary. In light of this ongoing evolution of the field, novel approaches are needed to design and assemble bacterial cocktails targeted to restore dysbiotic states in microbiota-associated diseases. This review discusses the steps in the process for identifying effective targets, predicting putative multistrain communities, assembling ecosystems in silico and in vitro and monitoring stability and outputs before in vivo trials.status: publishe

Process development for hydrometallurgical recovery of valuable metals from sulfide-rich residue generated in a secondary lead smelter

Two routes were investigated to selectively recover lead and minor metals (Cu, Ni, Zn) from a sulfide-rich lead smelter residue, matte. The first route comprises a two-step leaching process that combines Fe(III)-HNO3 leaching with roasting, followed by water leaching. In the first step, the efficiency of Pb leaching was 90% at the optimum condition (L/S ratio 8, 0.5 mol ⋅ L− 1 HNO3, 0.15 mol ⋅ L− 1 Fe(III), 25 °C). In the second step, roasting at 600 °C followed by water leaching at 50 °C selectively leached Ni, Cu, and Zn while fully converting iron sulfides to oxides. One-step oxidative pressure leaching in HNO3 was investigated as an alternative to simultaneously leach Pb, Cu, Ni and Zn. At the optimal conditions (130 °C, 60 min, 0.3 mol ⋅ L− 1 HNO3, 0.07 mol ⋅ L− 1 Fe(III), L/S ratio 20), Pb, Cu, Zn and Ni leaching were 92, 60, 70 and 66%, respectively, while Fe leaching remained low (2%). The leachates obtained from both leaching routes were treated by ion-exchange adsorption with diethylenetriaminepentaacetic acid (DTPA) functionalized chitosan-silica hybrid materials to investigate the selective recovery of Cu, Zn and Ni. The adsorption order appeared to be in the same order as the corresponding stability constants for complexes between the respective metal ions and free DTPA: Ca(II) < Zn(II) < Pb(II) ≈ Ni(II) < Cu(II). This allows not only to selectively recover Cu, Zn and Ni from the leachates, but also to mutually separate them by using the functionalized resin as a stationary phase in column chromatography. To avoid adsorbent contamination, Fe(III) and Pb(II) may be removed from the leachates in a pre-treatment step. Based on these results, the investigated methods can be combined as process steps of two possible routes for the selective recovery of valuable metals from the studied secondary lead smelting residue. The two-step leaching process seems to be superior since a more concentrated solution of Cu, Ni, and Zn is produced in the 2nd leaching step with low capital cost.status: publishe