Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

BACKGROUND

Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.

RESULTS

To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.

CONCLUSIONS

Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.

A bio-artificial renal epithelial cell system conveys survival advantage in a porcine model of septic shock

Renal cell therapy using the hollow fiber based renal assist device (RAD) improved survival time in an animal model of septic shock (SS) through the amelioration of cardiac and vascular dysfunction. Safety and ability of the RAD to improve clinical outcomes was demonstrated in a Phase II clinical trial, in which patients had high prevalence of sepsis. Even with these promising results, clinical delivery of cell therapy is hampered by manufacturing hurdles, including cell sourcing, large-scale device manufacture, storage and delivery. To address these limitations, the bioartificial renal epithelial cell system (BRECS) was developed. The BRECS contains human renal tubule epithelial cells derived from adult progenitor cells using enhanced propagation techniques. Cells were seeded onto trabeculated disks of niobium-coated carbon, held within cryopreservable, perfusable, injection-moulded polycarbonate housing. The study objective was to evaluate the BRECS in a porcine model of SS to establish conservation of efficacy after necessary cell sourcing and design modifications; a pre-clinical requirement to move back into clinical trials. SS was incited by peritoneal injection of E. coli simultaneous to insertion of BRECS (n=10) or control (n=15), into the ultrafiltrate biofeedback component of an extracorporeal circuit. Comparable to RAD, prolonged survival of the BRECS cohort was conveyed through stabilization of cardiac output and vascular leak. In conclusion, the demonstration of conserved efficacy with BRECS therapy in a porcine SS model represents a crucial step toward returning renal cell therapy to the clinical setting, initially targeting ICU patients with acute kidney injury requiring continuous renal replacement therapy. Copyright © 2014 John Wiley & Sons, Ltd.

Antimicrobial polyethylene with controlled copper release

Good antiinfection properties of medical polymers, especially those used in artificial organs, are crucial to the minimization of microbial attack in nosocomial treatments. However, medical polymers fabricated by conventional methods usually have unstable and short-lived antimicrobial effects because of unsteady out-diffusion of the antibacterial species from the organic matrix. Here, we introduce a dual plasma implantation process to enhance the properties. An inorganic antibacterial element, copper, is introduced into a medical polymer, polyethylene (PE), by means of copper plasma immersion ion implantation (PIII) and a subsequent nitrogen PIII process is used to regulate the release of the implanted Cu. X-ray photoelectron spectroscopy and transmission electron microscopy reveal that a relatively large amount of copper of about 11% is implanted into PE to a depth of several hundred nanometers. Chemical analyses confirm that the implanted Cu does not bond with the polymer matrix. However, the N(2) plasma treatment produces various functional bonds such as C=N, and C[triple bond]N which exert appreciable influence on regulating the out-diffusion rate of copper. The large amount of embedded Cu, coupled with controlled release of the element to the surface, gives rise to excellent and long-lasting surface antibacterial properties of the plasma-treated polymer. The capability of controlling the release and storing the antibacterial reagent in a buried layer leads to better antimicrobial polymeric materials for medicine.

Use of whey protein beads as a new carrier system for recombinant yeasts in human digestive tract

A new immobilizing protocol using whey protein isolates was developed to entrap recombinant Saccharomyces cerevisiae. The model yeast strain expresses the heterologous P45073A1 that converts trans-cinnamic acid into p-coumaric acid. Beads resulted from a cold-induced gelation of a whey protein solution (10%) containing yeasts (7.5 x 10(7)cells ml(-1)) into 0.1M CaCl(2). The viability and growth capability of yeasts were not altered by our entrapment process. The release and activity of immobilized yeasts were studied in simulated human gastric conditions. During the first 60 min of digestion, 2.2+/-0.9% (n=3) of initial entrapped yeasts were recovered in the gastric medium suggesting that beads should cross the gastric barrier in human. The P45073A1 activity of entrapped yeasts remained significantly higher (p<0.05) than that of free ones throughout digestion (trans-cinnamic acid conversion rate of 63.4+/-1.6% versus 51.5+/-1.8% (n=3) at 120 min). The protein matrix seemed to create a microenvironment favoring the activity of yeasts in the stringent gastric conditions. These results open up new opportunities for the development of drug delivery system using recombinant yeasts entrapped in whey protein beads. The main potential medical applications include biodetoxication or the correction of digestive enzyme deficiencies.

Reassessing artificial bowel sphincters

The artificial sphincter has now been used for the treatment of patients with faecal incontinence since 1996. Presently, results in the UK do not match those reported from the rest of Europe, with infection caused by methicillin-resistant Staphylococcus aureus being the most common cause of failure.