Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.

Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.

Revealing thermodynamics of DNA origami folding via affine transformations.

Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.

Perspectives for Consideration in the Development of Microbial Cell Reference Materials.

Microbiome measurement and analyses benefit greatly from incorporation of reference materials as controls. However, there are many points to consider in defining an ideal whole-cell reference material standard. Such a standard would embody all the diversity and measurement challenges present in real samples, would be completely characterized to provide "ground truth" data, and would be inexpensive and widely available. This ideal is, unfortunately, not readily attainable because of the diverse nature of different sequencing projects. Some applications may benefit most from highly complex reference materials, while others will value characterization or low expense more highly. The selection of appropriate microbial whole-cell reference materials to benchmark and validate microbial measurements should be considered carefully and may vary among specific applications. In this article, we describe a perspective on the development of whole-cell microbial reference materials for use in metagenomics analyses.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.

Automation of antimicrobial activity screening.

Manual and automated methods were compared for routine screening of compounds for antimicrobial activity. Automation generally accelerated assays and required less user intervention while producing comparable results. Automated protocols were validated for planktonic, biofilm, and agar cultures of the oral microbe Streptococcus mutans that is commonly associated with tooth decay. Toxicity assays for the known antimicrobial compound cetylpyridinium chloride (CPC) were validated against planktonic, biofilm forming, and 24 h biofilm culture conditions, and several commonly reported toxicity/antimicrobial activity measures were evaluated: the 50 % inhibitory concentration (IC50), the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC). Using automated methods, three halide salts of cetylpyridinium (CPC, CPB, CPI) were rapidly screened with no detectable effect of the counter ion on antimicrobial activity.

Theoretical analysis of a magnetophoresis-diffusion T-sensor immunoassay.

We present the analytical investigation of a microfluidic homogeneous competitive immunoassay that incorporates antibody-conjugated superparamagnetic nanoparticles and magnetophoretic transport to enhance the limits of detection and dynamic range. The analytical model considers the advective, diffusive, and magnetophoretic transport of the antibody-coated nanoparticles relative to the labeled and sample antigens of interest in a T-sensor configuration. The magnetophoresis-diffusion immunoassay identified clear improvements to the assay response and reductions to the limit of detection for increased magnetophoretic velocities and larger nanoparticles. The externally applied magnetophoretic transport enriched the antibody-antigen accumulation region, while larger nanoparticles led to decreased diffusive peak broadening. The integration of nanoparticles to the diffusion immunoassay (NP-DIA) demonstrated an approximately 3-fold improvement to the limit of detection of the basic antibody/antigen system, while the integration of superparamagnetic nanoparticles and magnetophoretic transport (MIA) established an order of magnitude improvement in sensitivity as well as means to greatly reduce response time. The implementation of an external magnetic force enabled the detectable antigen size spectrum to extend from small molecules i.e., 10's Da to 100's Da, up to large proteins and macromolecules, i.e., 50 kDa to 150 kDa, for a single class of binding species, i.e., superparamagnetic nanoparticle. This investigation provides guidelines for the design and development of a magnetophoresis-diffusion T-sensor immunoassay, and clearly identifies the regimes for optimal operation.

Capturing rare cells from blood using a packed bed of custom-synthesized chitosan microparticles.

We describe batch generation of uniform multifunctional chitosan microparticles for isolation of rare cells, such as circulating tumor cells (CTCs), from a sample of whole blood. The chitosan microparticles were produced in large numbers using a simple and inexpensive microtubing arrangement. The particles were functionalized through encapsulation of carbon black, to control autofluorescence, and surface attachment of streptavidin, to enable interactions with biotinylated antibodies. These large custom modified microparticles (≈164 µm diameter) were then packed into a microfluidic channel to demonstrate their utility in rare cell capture. Blood spiked with breast cancer (MCF-7) cells was first treated with a biotinylated antibody (anti-EpCAM, which is selective for cancer cells like MCF-7) and then pumped through the device. In the process, the cancer cells were selectively bound to the microparticles through non-covalent streptavidin-biotin interactions. The number density of captured cells was determined by fluorescence microscopy at physiologically relevant levels. Selective capture of the MCF-7 cells was characterized, and compared favorably with previous approaches. The overall approach using custom synthesized microparticles is versatile, and can allow researchers more flexibility for rare cell capture through simpler and cheaper methods than are currently employed.

A simple packed bed device for antibody labelled rare cell capture from whole blood.

We have developed a system to isolate rare cells from whole blood using commercially available components and simple microfluidics. We characterized the capture of MCF-7 cells spiked into whole human blood using this system to demonstrate that enrichment and enumeration studies give results similar to in situ surface-modified devices while reducing fabrication and operation complexity.

Measurement and validation of cell-based assays with microfluidics at the National Institute of Standards and Technology.

The National Institute of Standards and Technology (NIST) is the National Metrology Institute for the USA. Our mission is to advance measurement science, standards and technology in ways that enhance economic security and improve quality of life in the USA. Due to the increased need for technologies that advance biological research and the many new and exciting innovations in microfluidics, our projects are aimed at engineering well-controlled microenvironments for quantitative measurements of cell behavior in microfluidic systems. Cell-based microfluidics at NIST is a highly multidisciplinary activity and is greatly influenced by NIST programs in biochemical sciences, materials science, engineering and information technology. Although there are many microfluidic-related activities ongoing at NIST, we will focus on projects related to cell-based measurements in this article.

Microfluidic magnetophoretic separations of immunomagnetically labeled rare mammalian cells.

Immunomagnetic isolation and magnetophoresis in microfluidics have emerged as viable techniques for the separation, fractionation, and enrichment of rare cells. Here we present the development and characterization of a microfluidic system that incorporates an angled permanent magnet for the lateral magnetophoresis of superparamagnetic beads and labeled cell-bead complexes. A numerical model, based on the relevant transport processes, is developed as a design tool for the demonstration and prediction of magnetophoretic displacement. We employ a dimensionless magnetophoresis parameter to efficiently investigate the design space, gain insight into the physics of the system, and compare results across the vast spectrum of magnetophoretic microfluidic systems. The numerical model and theoretical analysis are experimentally validated by the lateral magnetophoretic deflection of superparamagnetic beads and magnetically labeled breast adenocarcinoma MCF-7 cells in a microfluidic device that incorporates a permanent magnet angled relative to the flow. Through the dimensionless magnetophoresis parameter, the transition between regimes of magnetophoretic action, from hydrodynamically dominated (magnetic deflection) to magnetically dominated (magnetic capture), is experimentally identified. This powerful tool and theoretical framework enables efficient device and experiment design of biologically relevant systems, taking into account their inherent variability and labeling distributions. This analysis identifies the necessary beads, magnet configuration (orientation), magnet type (permanent, ferromagnetic, electromagnet), flow rate, channel geometry, and buffer to achieve the desired level of magnetophoretic deflection or capture.

Regulating oxygen levels in a microfluidic device.

Microfluidic devices made from poly(dimethylsiloxane) (PDMS) are gas permeable and have been used to provide accurate on-chip oxygen regulation. However, pervaporation in PDMS devices can rapidly lead to dramatic changes in solution osmotic pressure. In the present study, we demonstrate a new method for on-chip oxygen control using pre-equilibrated aqueous solutions in gas-control channels to regulate the oxygen content in stagnant microfluidic test chambers. An off-chip gas exchanger is used to equilibrate each control solution prior to entering the chip. Using this strategy, problems due to pervaporation are considerably reduced. An integrated PDMS-based oxygen sensor allows accurate real-time measurements of the oxygen within the microfluidic chamber. The measurements were found to be consistent with predictions from finite-element modeling.

On-chip CO2 control for microfluidic cell culture.

Carbon dioxide partial pressure (P(CO(2))) was controlled on-chip by flowing pre-equilibrated aqueous solutions through control channels across the device. Elevated P(CO(2)) (e.g. 0.05 atm) was modulated in neighboring stagnant channels via equilibration through the highly gas permeable substrate, poly(dimethylsiloxane) (PDMS). Stable gradients in P(CO(2)) were demonstrated with a pair of control lines in a source-sink configuration. P(CO(2)) equilibration was found to be sufficiently rapid (minutes) and stable (days) to enable long-term microfluidic culture of mammalian cells. The aqueous solutions flowing through the device also mitigated pervaporative losses at sustained elevated temperatures (e.g. 37 C), as compared to flowing humidified gas through the control lines to control P(CO(2)). Since pervaporation (and the associated increase in osmolality) was minimized, stopped-flow cell culture became possible, wherein cell secretions can accumulate within the confined environment of the microfluidic culture system. This strategy was utilized to demonstrate long-term (> 7 days) microfluidic culture of mouse fibroblasts under stopped-flow conditions without requiring the microfluidic system to be placed inside a cell culture incubator.

Characterization of collagen fibrils films formed on polydimethylsiloxane surfaces for microfluidic applications.

Type I collagen fibrillar thin films have been prepared on hydrophobic recovered poly(dimethylsiloxane) (PDMS) surfaces and inside of irreversibly sealed PDMS microfluidic devices. Fibrillar films prepared on PDMS surfaces have been characterized with optical microscopy and atomic force microscopy and compared with films prepared using more traditional bulk methods on thiol-coated gold substrates. Collagen fibril films formed after 18 h of incubation on PDMS surfaces were observed to have similar underlying film thicknesses (15 nm), fibril size (67 nm), fibril coverage (45%), and physiologically supermolecular structure when compared to films on gold substrates. Collagen fibrils formed within devices were also determined to be usable across physiologically relevant cell perfusion rates. To validate the utility of these collagen fibril thin films for cell culture applications, vascular smooth muscle cells are shown to attach to collagen fibrils and exhibit cell spread areas equivalent to those seen on collagen fibrils created via bulk cell culture methods on thiol-coated gold substrates. These results extend the use and benefits of collagen fibril thin films into microfluidic-based cellular studies.

Dynamics and mechanisms of quantum dot nanoparticle cellular uptake.

BACKGROUND: The rapid growth of the nanotechnology industry and the wide application of various nanomaterials have raised concerns over their impact on the environment and human health. Yet little is known about the mechanism of cellular uptake and cytotoxicity of nanoparticles. An array of nanomaterials has recently been introduced into cancer research promising for remarkable improvements in diagnosis and treatment of the disease. Among them, quantum dots (QDs) distinguish themselves in offering many intrinsic photophysical properties that are desirable for targeted imaging and drug delivery. RESULTS: We explored the kinetics and mechanism of cellular uptake of QDs with different surface coatings in two human mammary cells. Using fluorescence microscopy and laser scanning cytometry (LSC), we found that both MCF-7 and MCF-10A cells internalized large amount of QD655-COOH, but the percentage of endocytosing cells is slightly higher in MCF-7 cell line than in MCF-10A cell line. Live cell fluorescent imaging showed that QD cellular uptake increases with time over 40 h of incubation. Staining cells with dyes specific to various intracellular organelles indicated that QDs were localized in lysosomes. Transmission electron microscopy (TEM) images suggested a potential pathway for QD cellular uptake mechanism involving three major stages: endocytosis, sequestration in early endosomes, and translocation to later endosomes or lysosomes. No cytotoxicity was observed in cells incubated with 0.8 nM of QDs for a period of 72 h. CONCLUSIONS: The findings presented here provide information on the mechanism of QD endocytosis that could be exploited to reduce non-specific targeting, thereby improving specific targeting of QDs in cancer diagnosis and treatment applications. These findings are also important in understanding the cytotoxicity of nanomaterials and in emphasizing the importance of strict environmental control of nanoparticles.

A noninvasive thin film sensor for monitoring oxygen tension during in vitro cell culture.

Oxygen tension in mammalian cell culture can profoundly affect cellular differentiation, viability, and proliferation. However, precise measurement of dissolved oxygen in real time remains difficult. We report a new noninvasive sensor that can accurately measure oxygen concentration during cell culture while being compatible with live-cell imaging techniques such as fluorescence and phase contrast microscopy. The sensor is prepared by integrating the porphyrin dye, Pt(II) meso-tetrakis(pentafluorophenyl)porphine (PtTFPP) into polydimethylsiloxane (PDMS) thin films. Response of the sensor in the presence of oxygen can be characterized by the linear Stern-Volmer relationship with high sensitivity (K(SV) = 584 +/- 71 atm(-1)). A multilayer sensor design, created by sandwiching the PtTFPP-PDMS with a layer of Teflon AF followed by a second PDMS layer, effectively mitigates against dye cytotoxicity while providing a substrate for cell attachment. Using this sensor, changes in oxygen tension could be monitored in real-time as attached cells proliferated. The oxygen tension was found to decrease due to oxygen consumption by the cells, and the data could be analyzed using Fick's law to obtain the per-cell oxygen consumption rate. This sensor is likely to enable new studies on the effects of dissolved oxygen on cellular behavior.

T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements.

We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilized on microfluidic packed beds down to single-cell quantities. The microfluidically amplified antisense-RNA (aRNA) was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes. For both benchtop and microfluidic assays, we measured the expression of approximately 4000 to 9000 genes for sample amounts ranging from 20 pg to 10 ng (2 to 1000 cell equivalents), corresponding to 41 to 93% of the absolute number of genes detected from a 100 ng total RNA control sample. Concordance of genes detected between methods (benchtop vs. microfluidic) and repeats (microfluidic vs. microfluidic) typically exceeded 90%. Validation of microarray by Real-time PCR of a panel of five genes suggests transcription of genes present is approximately six times more efficient with the microfluidic IVT compared with benchtop processing. Microfluidic IVT introduces no bias to the gene expression profile of the sample and provides more efficient transcription of mRNA sequences present at the single-cell level.

Dielectrophoretic capture of mammalian cells using transparent indium tin oxide electrodes in microfluidic systems.

Transparent indium tin oxide microelectrodes were fabricated and used to immobilize suspended NIH 3T3 fibroblast cells by positive dielectrophoresis. The indium tin oxide electrodes facilitated microscopic observation of immobilized cells compared with opaque metallized electrodes. Dielectrophoresis was used to capture arrays of individual cells and form small cell clusters within a microfluidic network. The extent of cellular immobilization (no-cell, single-cell, or multiple-cell capture) was correlated with the applied voltage and inversely with the flow velocity. Specific conditions yielding predominantly single-cell capture were identified. The viability of immobilized cells was confirmed using fluorescence microscopy.

Cellular immobilization within microfluidic microenvironments: dielectrophoresis with polyelectrolyte multilayers.

The development of biomimetic microenvironments will improve cell culture techniques by enabling in vitro cell cultures that mimic in vivo behavior; however, experimental control over attachment, cellular position, or intercellular distances within such microenvironments remains challenging. We report here the rapid and controllable immobilization of suspended mammalian cells within microfabricated environments using a combination of electronic (dielectrophoresis, DEP) and chemical (polyelectrolyte multilayers, PEMS) forces. While cellular position within the microsystem is rapidly patterned via intermittent DEP trapping, persistent adhesion after removal of electronic forces is enabled by surface treatment with PEMS that are amenable to cellular attachment. In contrast to DEP trapping alone, persistent adhesion enables the soluble microenvironment to be systematically varied, facilitating the use of soluble probes of cell state and enabling cellular characterization in response to various soluble stimuli.

Facilitating the culture of mammalian nerve cells with polyelectrolyte multilayers.

When neuron-like cells (NLCs) derived from pluripotent embryonal carcinoma cells (P19) are cultured on bare tissue culture substrates, they require a monolayer of fibroblast cells to exhibit normal neurite outgrowth, behavior typical of neuronal cultures. However, substrate treatment with polyelectrolyte multilayers (PEMs) composed of poly(allylamine hydrochloride) (PAH) and poly(styrenesulfonic acid) (PSS) significantly improved these cultures. Cell morphology was more spread, indicative of healthy cells, and direct attachment of neuronal cell bodies to the treated surface was observed. Neuronal outgrowth across the surface was not dependent on an underlying fibroblast monolayer with the PEMs surface treatment. Additionally, the PEMs surface treatment can be used to condition various surfaces, facilitating neuronal cultures on surfaces which are natively hydrophilic (tissue culture polystyrene) or hydrophobic (poly(dimethylsiloxane), PDMS). Microfluidic networks were used to micropattern the PEMs onto PDMS, resulting in confined regions of cellular attachment and directed neuronal outgrowth. The ability of PEMs to encourage NLC attachment without supporting cells to a variety of surfaces and surface geometries greatly simplifies neuronal culture methodology and enables neuronal investigations in new environments.