Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

Is microfluidics the "assembly line" for CRISPR-Cas9 gene-editing?

Acclaimed as one of the biggest scientific breakthroughs, the technology of CRISPR has brought significant improvement in the biotechnological spectrum-from editing genetic defects in diseases for gene therapy to modifying organisms for the production of biofuels. Since its inception, the CRISPR-Cas9 system has become easier and more versatile to use. Many variants have been found, giving the CRISPR toolkit a great range that includes the activation and repression of genes aside from the previously known knockout and knockin of genes. Here, in this Perspective, we describe efforts on automating the gene-editing workflow, with particular emphasis given on the use of microfluidic technology. We discuss how automation can address the limitations of gene-editing and how the marriage between microfluidics and gene-editing will expand the application space of CRISPR.

RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data

MOTIVATION

Single-cell sequencing (SCS) data provide unprecedented insights into intratumoral heterogeneity. With SCS, we can better characterize clonal genotypes and reconstruct phylogenetic relationships of tumor cells/clones. However, SCS data are often error-prone, making their computational analysis challenging.

RESULTS

To infer the clonal evolution in tumor from the error-prone SCS data, we developed an efficient computational framework, termed RobustClone. It recovers the true genotypes of subclones based on the extended robust principal component analysis, a low-rank matrix decomposition method, and reconstructs the subclonal evolutionary tree. RobustClone is a model-free method, which can be applied to both single-cell single nucleotide variation (scSNV) and single-cell copy-number variation (scCNV) data. It is efficient and scalable to large-scale datasets. We conducted a set of systematic evaluations on simulated datasets and demonstrated that RobustClone outperforms state-of-the-art methods in large-scale data both in accuracy and efficiency. We further validated RobustClone on two scSNV and two scCNV datasets and demonstrated that RobustClone could recover genotype matrix and infer the subclonal evolution tree accurately under various scenarios. In particular, RobustClone revealed the spatial progression patterns of subclonal evolution on the large-scale 10X Genomics scCNV breast cancer dataset.

AVAILABILITY AND IMPLEMENTATION

RobustClone software is available at https://github.com/ucasdp/RobustClone.

CONTACT

lwan@amss.ac.cn or maliang@ioz.ac.cn.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Multi-step processing of single cells using semi-permeable capsules

Droplet microfluidics technology provides a powerful approach to isolate and process millions of single cells simultaneously. Despite many exciting applications that have emerged based on this technology, workflows based on multi-step operations, including molecular biology and cell-based phenotypic screening assays, cannot be easily adapted to droplet format. Here, we present a microfluidics-based technique to isolate single cells, or biological samples, into semi-permeable hydrogel capsules and perform multi-step biological workflows on thousands to millions of individual cells simultaneously. The biochemical reactions are performed by changing the aqueous buffer surrounding the capsules, without needing sophisticated equipment. The semi-permeable nature of the capsules' shell retains large encapsulated biomolecules (such as genome) while allowing smaller molecules (such as proteins) to passively diffuse. In contrast to conventional hydrogel bead assays, the approach presented here improves bacterial cell retention during multi-step procedures as well as the efficiency of biochemical reactions. We showcase two examples of capsule use for single genome amplification of bacteria, and expansion of individual clones into isogenic microcolonies for later screening for biodegradable plastic production.

Host-Microbiome Interactions in the Era of Single-Cell Biology

Microbes are the most prevalent form of life yet also the least well-understood in terms of their diversity. Due to a greater appreciation of their role in modulating host physiology, microbes have come to the forefront of biological investigation of human health and disease. Despite this, capturing the heterogeneity of microbes, and that of the host responses they induce, has been challenging due to the bulk methods of nucleic acid and cellular analysis. One of the greatest recent advancements in our understanding of complex organisms has happened in the field of single-cell analysis through genomics, transcriptomics, and spatial resolution. While significantly advancing our understanding of host biology, these techniques have only recently been applied to microbial systems to shed light on their diversity as well as interactions with host cells in both commensal and pathogenic contexts. In this review, we highlight emerging technologies that are poised to provide key insights into understanding how microbe heterogeneity can be studied. We then take a detailed look into how host single-cell analysis has uncovered the impact of microbes on host heterogeneity and the effect of host biology on microorganisms. Most of these insights would have been challenging, and in some cases impossible, without the advent of single-cell analysis, suggesting the importance of the single-cell paradigm for progressing the microbiology field forward through a host-microbiome perspective and applying these insights to better understand and treat human disease.

Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants

The development of genomics and epigenomics has allowed rapid advances in our understanding of plant biology. However, conventional bulk analysis dilutes cell-specific information by providing only average information, thereby limiting the resolution of genomic and functional genomic studies. Recent advances in single-cell sequencing technology concerning genomics and epigenomics open new avenues to dissect cell heterogeneity in multiple biological processes. Recent applications of these approaches to plants have provided exciting insights into diverse biological questions. We highlight the methodologies underlying the current techniques of single-cell genomics and epigenomics before covering their recent applications, potential significance, and future perspectives in plant biology.

Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS

In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput screening via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying sizes and morphologies as well as a heterogeneous cell mixture of a whole dissociated flatworm (5-25 μm in diameter) within highly monodisperse double emulsions (35 μm in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS screening of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional phenotyping.

Droplet Microfluidics for Microbial Biotechnology

Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.

Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions

Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C₁₇) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C₂₁-C₃₀) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.

Experimental approaches to tracking mobile genetic elements in microbial communities

Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.

Microbial single-cell omics: the crux of the matter

Abstract

Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.

Key points

• Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways.

• Disadvantages of metagenome-assembled genomes are overcome by single-cell omics.

• Functional analysis of single cells explores the heterogeneity of gene expression.

• Technical challenges still limit this field, thus prompting new method developments.

A scalable microfluidic chamber array for sample-loss-free and bubble-proof sample compartmentalization by simple pipetting

Sample compartmentalization is a pivotal technique in many bioanalytical applications, such as multiplex polymerase chain reaction (PCR) and digital PCR (dPCR). In this study, we successfully developed a novel self-compartmentalization device containing an array of microchambers, each of which is connected to a main microchannel with three capillary burst valves (CBVs) for fluid switching and partitioning. As these CBVs can be automatically opened in a predefined sequence, an incoming solution can be spontaneously directed into the chamber and held in place without further mixing. After that, either air or oil can be loaded into the main channel to isolate each chamber completely. By optimizing the relative burst pressures of the CBVs, a 100% sample utilization rate can be achieved even using a manual pipette and air bubbles in the sample cannot interfere with the loading. In addition, the number of the microchambers in an array can be easily scaled from a few to tens of thousands. To verify the feasibility of this self-compartmentalization method, we successfully conducted mock multiplex loop-mediated isothermal amplifications (LAMP) in an array that contains 144 microchambers, proving that our design method will provide a robust and versatile platform for various sample discretization purposes in the future.

One Cell, One Drop, One Click: Hybrid Microfluidics for Mammalian Single Cell Isolation

Generating a stable knockout cell line is a complex process that can take several months to complete. In this work, a microfluidic method that is capable of isolating single cells in droplets, selecting successful edited clones, and expansion of these isoclones is introduced. Using a hybrid microfluidics method, droplets in channels can be individually addressed using a co-planar electrode system. In the hybrid microfluidics device, it is shown that single cells can be trapped and subsequently encapsulate them on demand into pL-sized droplets. Furthermore, droplets containing single cells are either released, kept in the traps, or merged with other droplets by the application of an electric potential to the electrodes that is actuated through an in-house user interface. This high precision control is used to successfully sort and recover single isoclones to establish monoclonal cell lines, which is demonstrated with a heterozygous NCI-H1299 lung squamous cell population resulting from loss-of-function eGFP and RAF1 gene knockout transfections.

Facile Production of Large-Area Cell Arrays Using Surface-Assembled Microdroplets

Techniques that enable the spatial arrangement of living cells into defined patterns are broadly applicable to tissue engineering, drug screening, and cell-cell investigations. Achieving large-scale patterning with single-cell resolution while minimizing cell stress/damage is, however, technically challenging using existing methods. Here, a facile and highly scalable technique for the rational design of reconfigurable arrays of cells is reported. Specifically, microdroplets of cell suspensions are assembled using stretchable surface-chemical patterns which, following incubation, yield ordered arrays of cells. The microdroplets are generated using a microfluidic-based aerosol spray nozzle that enables control of the volume/size of the droplets delivered to the surface. Assembly of the cell-loaded microdroplets is achieved via mechanically induced coalescence using substrates with engineered surface-wettability patterns based on extracellular matrices. Robust cell proliferation inside the patterned areas is demonstrated using standard culture techniques. By combining the scalability of aerosol-based delivery and microdroplet surface assembly with user-defined chemical patterns of controlled functionality, the technique reported here provides an innovative methodology for the scalable generation of large-area cell arrays with flexible geometries and tunable resolution.

A brief guide for the measurement and interpretation of microbial functional diversity

The importance of functional diversity for the functioning and behaviour of microbial communities is clear, yet the widespread incorporation of functional diversity measurements into environmental microbiology study designs remains surprisingly limited. This may, at least to some extent, be a consequence of the unique conceptual and methodological challenges to measuring functional diversity in microbial communities. To facilitate the increased incorporation of functional diversity measurements into environmental microbiology study designs, we review here the process and some key caveats for measuring functional diversity and provide specific examples. We highlight three main decision points and provide guidance to making these decisions based on the underlying mechanisms for how functional diversity relates to an ecosystem process or property of interest. We discuss the selection of an appropriate type of functional trait, selection of the specificity at which functional diversity will be measured, and selection of an appropriate metric for estimating functional diversity from quantitative measures of those traits. We further discuss decisions regarding the use of one- or multi-dimensional measures of functional diversity and how advances in the field of trait-based community ecology could be applied or adapted to address questions in environmental microbiology.

Double-Sided Microwells with a Stepped Through-Hole Membrane for High-Throughput Microbial Assays

To improve the throughput of microwell arrays for identifying immense cellular diversities even at a single-bacteria level, further miniaturization or densification of the microwells has been an obvious breakthrough. However, controlling millions of nanoliter samples or more at the microscale remains technologically difficult and has been spatially restricted to a single open side of the microwells. Here we employed a stepped through-hole membrane to utilize the bottom as well as top side of a high-density nanoliter microwell array, thus improving spatial efficiency. The stepped structure shows additional effectiveness for handling several millions of nanoliter bacterial samples in the overall perspectives of controllability, throughput, simplicity, versatility, and automation by using novel methods for three representative procedures in bacterial assays: partitioning cells, manipulating the chemical environment, and extracting selected cells. As a potential application, we show proof-of-concept isolation of rare cells in a mixed ratio of 1 to around 10⁶ using a single chip. Our device can be further applied to various biological studies pertaining to synthetic biology, drug screening, mutagenesis, and single-cell heterogeneity.

Microfluidic particle zipper enables controlled loading of droplets with distinct particle types

Current encapsulation approaches control the number of particles encapsulated per droplet, but not the particle types; consequently, they are unable to generate droplets containing combinations of distinct particle types, limiting the reactions that can be performed. We describe a microfluidic particle zipper that allows the number and types of particles encapsulated in every droplet to be controlled. The approach exploits self-ordering to generate repeating particle patterns that allow controlled encapsulation in droplets. We use the method to combine barcode particles with gel encapsulated cells to profile multiple disease relevant genomic loci with single cell sequencing. Particle zippers can operate in series to generate complex particle compositions in droplets.

Nanoliter-Scale Droplet-Droplet Microfluidic Microextraction Coupled with MALDI-TOF Mass Spectrometry for Metabolite Analysis of Cell Droplets

The further miniaturization of liquid-phase microextraction (LPME) systems has important significance and major challenges for microscale sample analysis. Herein, we developed a rapid and flexible droplet-droplet microfluidic microextraction approach to perform nanoliter-scale miniaturized sample pretreatment, by combining droplet-based microfluidics, robotic liquid handling, and LPME techniques. Differing from the previous microextraction methods, both the extractant and sample volumes were decreased from the microliter scale or even milliliter scale to the nanoliter scale. We utilized the ability of a liquid-handling robot to manipulate nanoliter-scale droplets and micrometer-scale positioning to overcome the scaling effect difficulties in performing liquid-liquid extraction of nanoliter-volume samples in microsystems. Two microextraction modes, droplet-in-droplet microfluidic microextraction and droplet-on-droplet microfluidic microextraction, were developed according to the different solubility properties of the extractants. Various factors affecting the microextraction process were investigated, including the extraction time, recovery method of the extractant droplet, static and dynamic extraction mode, and cross-contamination. To demonstrate the validity and adaptability of the pretreatment and analysis of droplet samples with complex matrices, the present microextraction system coupled with MALDI-TOF mass spectrometry (MS) detection was applied to the quantitative determination of 7-ethyl-10-hydroxylcamptothecin (SN-38), an active metabolite of the anticancer drug irinotecan, in 800-nL droplets containing HepG2 cells. A linear relationship (y = 0.0305x + 0.376, R² = 0.984) was obtained in the range of 4-100 ng/mL, with the limits of detection and quantitation being 2.2 and 4.5 ng/mL for SN-38, respectively.

Phenome-Genome Profiling of Single Bacterial Cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing

The small size and low DNA amount of bacterial cells have hindered establishing phenome-genome links in a precisely indexed, one-cell-per-reaction manner. Here, Raman-Activated Gravity-driven single-cell Encapsulation and Sequencing (RAGE-Seq) is presented, where individual cells are phenotypically screened via single-cell Raman spectra (SCRS) in an aquatic, vitality-preserving environment, then the cell with targeted SCRS is precisely packaged in a picoliter microdroplet and readily exported in a precisely indexed, "one-cell-one-tube" manner. Such integration of microdroplet encapsulation to Raman-activated sorting ensures high-coverage one-cell genome sequencing or cultivation that is directly linked to metabolic phenotype. For clinical Escherichia coli isolates, genome assemblies derived from precisely one cell via RAGE-Seq consistently reach >95% coverage. Moreover, directly from a urine sample of urogenital tract infection, metabolic-activity-based antimicrobial susceptibility phenotypes and genome sequence of 99.5% coverage are obtained simultaneously from precisely one cell. This single-cell global mutation map corroborates resistance phenotype and genotype, and unveils epidemiological features with high specificity and sensitivity. The ability to profile and correlate bacterial metabolic phenome and high-quality genome sequences at one-cell resolution suggests broad application of RAGE-Seq.

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet

Whole genome amplification (WGA) is crucial for whole genome sequencing to investigate complex genomic alteration at the single-cell or even single-molecule level. Multiple displacement amplification (MDA) and multiple annealing and looping based amplification cycles (MALBAC) are two most widely applied WGA methods, which have different advantages and disadvantages, dependent on research objectives. Herein, we compared the MDA and MALBAC to provide more information on their performance in droplets and tubes. We observed that the droplet method could dramatically reduce the amplification bias and retain the high accuracy of replication than the conventional tube method. Furthermore, the droplet method exhibited higher efficiency and sensitivity for both homozygous and heterozygous single nucleotide variants (SNVs) at the low sequencing depth. In addition, we also found that MALBAC offered a greater uniformity and reproducibility and MDA showed a better efficiency of genomic coverage and SNV detection. Our results provided insights that will allow future decision making.

For the Greater (Bacterial) Good: Heterogeneous Expression of Energetically Costly Virulence Factors

Bacterial populations are phenotypically heterogeneous, which allows subsets of cells to survive and thrive following changes in environmental conditions. For bacterial pathogens, changes within the host environment occur over the course of the immune response to infection and can result in exposure to host-derived, secreted antimicrobials or force direct interactions with immune cells. Many recent studies have shown host cell interactions promote virulence factor expression, forcing subsets of bacterial cells to battle the host response, while other bacteria reap the benefits of this pacification. It still remains unclear whether virulence factor expression is truly energetically costly within host tissues and whether expression is sufficient to impact the growth kinetics of virulence factor-expressing cells. However, it is clear that slow-growing subsets of bacteria emerge during infection and that these subsets are particularly difficult to eliminate with antibiotics. This minireview will focus on our current understanding of heterogenous virulence factor expression and discuss the evidence that supports or refutes the hypothesis that virulence factor expression is linked to slowed growth and antibiotic tolerance.

Single-Cell Genomics and the Oral Microbiome

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

Advancing Cancer Research and Medicine with Single-Cell Genomics

Single-cell sequencing (SCS) has impacted many areas of cancer research and improved our understanding of intratumor heterogeneity, the tumor microenvironment, metastasis, and therapeutic resistance. The development and refinement of SCS technologies has led to massive reductions in costs, increased cell throughput, and improved reproducibility, paving the way for clinical applications. However, before translational applications can be realized, there are a number of logistical and technical challenges that must be overcome. This review discusses past cancer research studies, emerging technologies, and future clinical applications that are bound to transform cancer medicine.

Dissolvable Polyacrylamide Beads for High-Throughput Droplet DNA Barcoding

Droplet-based single cell sequencing technologies, such as inDrop, Drop-seq, and 10X Genomics, are catalyzing a revolution in the understanding of biology. Barcoding beads are key components for these technologies. What is limiting today are barcoding beads that are easy to fabricate, can efficiently deliver primers into drops, and thus achieve high detection efficiency. Here, this work reports an approach to fabricate dissolvable polyacrylamide beads, by crosslinking acrylamide with disulfide bridges that can be cleaved with dithiothreitol. The beads can be rapidly dissolved in drops and release DNA barcode primers. The dissolvable beads are easy to synthesize, and the primer cost for the beads is significantly lower than that for the previous barcoding beads. Furthermore, the dissolvable beads can be loaded into drops with >95% loading efficiency of a single bead per drop and the dissolution of beads does not influence reverse transcription or the polymerase chain reaction (PCR) in drops. Based on this approach, the dissolvable beads are used for single cell RNA and protein analysis.

A facile technology for the high-throughput sequencing of the paired VH:VL and TCRβ:TCRα repertoires

Natively paired sequencing (NPS) of B cell receptors [variable heavy (VH) and light (VL)] and T cell receptors (TCRb and TCRa) is essential for the understanding of adaptive immunity in health and disease. Despite many recent technical advances, determining the VH:VL or TCRb:a repertoire with high accuracy and throughput remains challenging. We discovered that the recently engineered xenopolymerase, RTX, is exceptionally resistant to cell lysate inhibition in single-cell emulsion droplets. We capitalized on the characteristics of this enzyme to develop a simple, rapid, and inexpensive in-droplet overlap extension reverse transcription polymerase chain reaction method for NPS not requiring microfluidics or other specialized equipment. Using this technique, we obtained high yields (5000 to >20,000 per sample) of paired VH:VL or TCRb:a clonotypes at low cost. As a demonstration, we performed NPS on peripheral blood plasmablasts and T follicular helper cells following seasonal influenza vaccination and discovered high-affinity influenza-specific antibodies and TCRb:a.

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi

Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.

Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir.

IMPORTANCE Current understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider than previously anticipated.

Deep learning guided image-based droplet sorting for on-demand selection and analysis of single cells and 3D cell cultures

Uncovering the heterogeneity of cellular populations and multicellular constructs is a long-standing goal in fields ranging from antimicrobial resistance to cancer research. Emerging technology platforms such as droplet microfluidics hold the promise to decipher such heterogeneities at ultra-high-throughput. However, there is a lack of methods able to rapidly identify and isolate single cells or 3D cell cultures. Here we demonstrate that deep neural networks can accurately classify single droplet images in real-time based on the presence and number of micro-objects including single mammalian cells and multicellular spheroids. This approach also enables the identification of specific objects within mixtures of objects of different types and sizes. The training sets for the neural networks consisted of a few hundred images manually picked and augmented to up to thousands of images per training class. Training required less than 10 minutes using a single GPU, and yielded accuracies of over 90% for single mammalian cell identification. Crucially, the same model could be used to classify different types of objects such as polystyrene spheres, polyacrylamide beads and MCF-7 cells. We applied the developed method for the selection of 3D cell cultures generated with Hek293FT cells encapsulated in agarose gel beads, highlighting the potential of the technology for the selection of objects with a high diversity of visual appearances. The real-time sorting of single droplets was in-line with droplet generation and occurred at rates up to 40 per second independently of image size up to 480 × 480 pixels. The presented microfluidic device also enabled storage of sorted droplets to allow for downstream analyses.

On-Demand Droplet Collection for Capturing Single Cells

Droplet-based microfluidic techniques are extensively used in efficient manipulation and genome-wide analysis of individual cells, probing the heterogeneity among populations of individuals. However, the extraction and isolation of single cells from individual droplets remains difficult due to the inevitable sample loss during processing. Herein, an automated system for accurate collection of defined numbers of droplets containing single cells is presented. Based on alternate sorting and dispensing in three branch channels, the droplet number can be precisely controlled down to single-droplet resolution. While encapsulating single cells and reserving one branch as a waste channel, sorting can be seamlessly integrated to enable on-demand collection of single cells. Combined with a lossless recovery strategy, this technique achieves capture and culture of individual cells with a harvest rate of over 95%. The on-demand droplet collection technique has great potential to realize quantitative processing and analysis of single cells for elucidating the role of cell-to-cell variations.

Microfluidic Single-Cell Omics Analysis

The commonly existing cellular heterogeneity plays a critical role in biological processes such as embryonic development, cell differentiation, and disease progress. Single-cell omics-based heterogeneous studies have great significance for identifying different cell populations, discovering new cell types, revealing informative cell features, and uncovering significant interrelationships between cells. Recently, microfluidics has evolved to be a powerful technology for single-cell omics analysis due to its merits of throughput, sensitivity, and accuracy. Herein, the recent advances of microfluidic single-cell omics analysis, including different microfluidic platform designs, lysis strategies, and omics analysis techniques, are reviewed. Representative applications of microfluidic single-cell omics analysis in complex biological studies are then summarized. Finally, a few perspectives on the future challenges and development trends of microfluidic-assisted single-cell omics analysis are discussed.

Microfluidics as an Enabling Technology for Personalized Cancer Therapy

Tailoring patient-specific treatments for cancer is necessary in order to achieve optimal results but requires new diagnostic approaches at affordable prices. Microfluidics has immense potential to provide solutions for this, as it enables the processing of samples that are not available in large quantities (e.g., cells from patient biopsies), is cost efficient, provides a high level of automation, and allows the set-up of complex models for cancer studies. In this review, individual solutions in the fields of genetics, circulating tumor cell monitoring, biomarker analysis, phenotypic drug sensitivity tests, and systems providing controlled environments for disease modeling are discussed. An overview on how these early stage achievements can be combined or developed further is showcased, and the required translational steps before microfluidics becomes a routine tool for clinical applications are critically discussed.

Microfluidic single-cell analysis-Toward integration and total on-chip analysis

Various types of single-cell analyses are now extensively used to answer many biological questions, and with this growth in popularity, potential drawbacks to these methods are also becoming apparent. Depending on the specific application, workflows can be laborious, low throughput, and run the risk of contamination. Microfluidic designs, with their advantages of being high throughput, low in reaction volume, and compatible with bio-inert materials, have been widely used to improve single-cell workflows in all major stages of single-cell applications, from cell sorting to lysis, to sample processing and readout. Yet, designing an integrated microfluidic chip that encompasses the entire single-cell workflow from start to finish remains challenging. In this article, we review the current microfluidic approaches that cover different stages of processing in single-cell analysis and discuss the prospects and challenges of achieving a full integrated workflow to achieve total single-cell analysis in one device.

Interfacial Nanoinjection-Based Nanoliter Single-Cell Analysis

Single-cell analysis offers unprecedented resolution for the investigation of cellular heterogeneity and the capture of rare cells from large populations. Here, described is a simple method named interfacial nanoinjection (INJ), which can miniaturize various single-cell assays to be performed in nanoliter water-in-oil droplets on standard microwell plates. The INJ droplet handler can adjust droplet volumes for multistep reactions on demand with high precision and excellent monodispersity, and consequently enables a wide range of single-cell assays. Importantly, INJ can be coupled with fluorescence-activated cell sorting (FACS), which is currently the most effective and accurate single-cell sorting and isolation method. FACS-INJ pipelines for high-throughput plate well-based single-cell analyses, including single-cell proliferation, drug-resistance testing, polymerase chain reaction (PCR), reverse-transcription PCR, and whole-genome sequencing are introduced. This FACS-INJ pipeline is compatible with a wide range of samples and can be extended to various single-cell analysis applications in microbiology, cell biology, and biomedical diagnostics.

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance

One Health surveillance of antimicrobial resistance (AMR) depends on a harmonized method for detection of AMR. Metagenomics-based surveillance offers the possibility to compare resistomes within and between different target populations. Its potential to be embedded into policy in the future calls for a timely and integrated knowledge dissemination strategy. We developed a blended training (e-learning and a workshop) on the use of metagenomics in surveillance of pathogens and AMR. The objectives were to highlight the potential of metagenomics in the context of integrated surveillance, to demonstrate its applicability through hands-on training and to raise awareness to bias factors. The target participants included staff of competent authorities responsible for AMR monitoring and academic staff. The training was organized in modules covering the workflow, requirements, benefits and challenges of surveillance by metagenomics. The training had 41 participants. The face-to-face workshop was essential to understand the expectations of the participants about the transition to metagenomics-based surveillance. After revision of the e-learning, we released it as a Massive Open Online Course (MOOC), now available at https://www.coursera.org/learn/metagenomics. This course has run in more than 20 sessions, with more than 3,000 learners enrolled, from more than 120 countries. Blended learning and MOOCs are useful tools to deliver knowledge globally and across disciplines. The released MOOC can be a reference knowledge source for international players in the application of metagenomics in surveillance.

Next-generation physiology approaches to study microbiome function at single cell level

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities

This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities.

IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

Injection Molded Microfluidics for Establishing High-Density Single Cell Arrays in an Open Hydrogel Format

Here, we develop an injection molded microfluidic approach for single cell analysis by making use of (1) rapidly curing injectable hydrogels, (2) a high density microfluidic weir trap array, and (3) reversibly bonded PDMS lids that are strong enough to withstand the injection molding process, but which can be peeled off after the hydrogel sets. This approach allows for single cell patterns to be created with densities exceeding 40 cells per mm2, is amenable to high speed imaging, and creates microfluidic devices that enable efficient nutrient and gas exchange and the delivery of specific biological and chemical reagents to individual cells. We show that it is possible to organize up to 10 000 single cells in a few minutes on the device, and we developed an image analysis program to automatically analyze the single-cell capture efficiency. The results show single cell trapping rates were better than 80%. We also demonstrate that the genomic DNA of the single cells trapped in the hydrogel can be amplified via localized, multiple displacement amplification in a massively parallel format, which offers a promising strategy for analyzing single cell genomes. Finally, we show the ability to perform selective staining of individual cells with a commercial bioprinter, providing proof of concept of its ability to deliver tailored reagents to specific cells in an array for future downstream analysis. This injection molded microfluidic approach leverages the benefits of both closed and open microfluidics, allows multiday single cell cultures, direct access to the trapped cells for genotypic end point studies.

Ultracompact 3D microfluidics for time-resolved structural biology

To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

BACKGROUND

The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota.

RESULTS

Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production.

CONCLUSIONS

Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health. Video abstract.

Improving Single-Cell Encapsulation Efficiency and Reliability through Neutral Buoyancy of Suspension

Single-cell analysis is of critical importance in revealing cell-to-cell heterogeneity by characterizing individual cells and identifying minority sub-populations of interest. Droplet-based microfluidics has been widely used in the past decade to achieve high-throughput single-cell analysis. However, to maximize the proportion of single-cell emulsification is challenging due to cell sedimentation and aggregation. The purpose of this study was to investigate the influence of single-cell encapsulation and incubation through the use of neutral buoyancy. As a proof of concept, OptiPrep™ was used to create neutrally buoyant cell suspensions of THP-1, a human monocytic leukemia cell line, for single-cell encapsulation and incubation. We found that using a neutrally buoyant suspension greatly increased the efficiency of single-cell encapsulation in microdroplets and eliminated unnecessary cell loss. Moreover, the presence of OptiPrep™ was shown to not affect cellular viability. This method significantly improved the effectiveness of single-cell study in a non-toxic environment and is expected to broadly facilitate single-cell analysis.

Step emulsification in microfluidic droplet generation: mechanisms and structures

Step emulsification for micro- and nano-droplet generation is reviewed in brief, including the emulsion mechanisms and microfluidic devices.

Emerging aqueous two-phase systems: from fundamentals of interfaces to biomedical applications

This review summarizes recent advances of aqueous two-phase systems (ATPSs), particularly their interfaces, with a focus on biomedical applications.

Thermodynamic perspectives on liquid–liquid droplet reactors for biochemical applications

Liquid–liquid droplet reactors have garnered significant interest in biochemical applications by simulating thermodynamic systmes, ranging from closed systems, semi-closed/semi-open systems, to open systems.

Streamlined digital bioassays with a 3D printed sample changer

Off-chip sample changer device increase the sample throughput of droplet digital bioassays.

Active particles as mobile microelectrodes for selective bacteria electroporation and transport

Self-propelling micromotors are emerging as a promising micro- and nanoscale tool for single-cell analysis. We have recently shown that the field gradients necessary to manipulate matter via dielectrophoresis can be induced at the surface of a polarizable active ("self-propelling") metallodielectric Janus particle (JP) under an externally applied electric field, acting essentially as a mobile floating microelectrode. Here, we successfully demonstrated that the application of an external electric field can singularly trap and transport bacteria and can selectively electroporate the trapped bacteria. Selective electroporation, enabled by the local intensification of the electric field induced by the JP, was obtained under both continuous alternating current and pulsed signal conditions. This approach is generic and applicable to bacteria and JP, as well as a wide range of cell types and micromotor designs. Hence, it constitutes an important and novel experimental tool for single-cell analysis and targeted delivery.

Common principles and best practices for engineering microbiomes

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.

Single-Cell Analysis Using Droplet Microfluidics

Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.