SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level

One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering–two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.

With the rapid advances in both genotyping and phenotyping of single cells, bridging genotype and phenotype at the single-cell level is becoming a new frontier of science (1). Methods have been developed to shed light on the genotype–metabolism relationship of individual cells in a complex environment (2, 3), which is especially relevant for an in-depth understanding of complex microbial communities in the environment and host-associated microbiomes. For functional analyses of microbial communities, single-cell isotope probing is often performed in combination with nanoscale secondary ion mass spectrometry (NanoSIMS) (4–7), microautoradiography (MAR) (8, 9), or spontaneous Raman microspectroscopy (10–12) to visualize and quantify the incorporation of isotopes from labeled substrates. These methods can be combined with fluorescence in situ hybridization (FISH) using ribosomal ribonucleic acid (rRNA)-targeted probes (13), enabling a direct link between metabolism and identity of the organisms. In addition, Raman-activated cell sorting has been recently developed using either optical tweezers or cell ejection for downstream sequencing of the sorted cells (14–16). While these approaches have expanded the possibilities for functional analyses of microbiome members (17), all of the aforementioned methods suffer from extremely limited throughput. Consequently, only relatively few samples and cells per sample are typically analyzed in single-cell stable isotope probing studies, hampering a comprehensive understanding of the function of microbes in their natural environment.To overcome the limited throughput of Raman spectroscopy, coherent Raman scattering microscopy based on coherent anti-Stokes Raman scattering (CARS) or stimulated Raman scattering (SRS) has been developed (18, 19). Compared with CARS, the SRS signal is free of the electronic resonance response (20) and is linear to molecular concentration, thus permitting quantitative mapping of biomolecules (21, 22). Both CARS and SRS microscopy have successfully been applied for studying single-cell metabolism in eukaryotes (23–26). In a label-free manner, SRS imaging has led to the discovery of an aberrant cholesteryl ester storage in aggressive cancers (27, 28), lipid-rich protrusions in cancer cells under starvation (29), and fatty acid unsaturation in ovarian cancer stem cells (30) and more recently, in melanoma (31, 32). CARS and SRS have also been harnessed to explore lipid metabolism in live Caenorhabditis elegans (33–36). Combined with stable isotope probing, SRS microscopy has allowed the tracing of glucose metabolism in eukaryotic cells (37, 38) and the visualization of metabolic dynamics in living animals (25). Recently, SRS was successfully applied to infer antibiotic resistance patterns of bacterial pure cultures and heavy water (D2O) metabolism (39). Yet, SRS microscopy has not been adapted for studying functional properties of members of microbiomes as SRS itself lacks the capability of identifying cells in a complex community.Here, we present an integrative platform that exploits the advantages of SRS for single-cell stable isotope probing together with two-photon FISH for the identification of cells in a high-throughput manner. To deal with the challenges in detecting low concentrations of metabolites inside small cells with diameters around 1 µm, we have developed a protocol that maximizes the isotope label content in cells and exploits the intense SRS signal from the Raman band used for isotope detection.Conventionally, FISH is performed separately by one-photon excited fluorescence microscopy (40). To enhance efficiency, we developed a system that implements highly sensitive SRS metabolic imaging with two-photon FISH using the same laser source. These efforts collectively led to a high-throughput platform that enables correlative imaging of cell identity and metabolism at a speed of 10 to 100 ms per cell. In comparison, it takes about 20 s to record a Raman spectrum from a single cell in a conventional spontaneous Raman FISH experiment (41, 42).Our technology enabled high-throughput analysis of single-cell metabolism in the human gut microbiome. In the human body, microbes have been shown to modulate the host’s health (43, 44). Analytical techniques looking into their activities and specific physiologies (i.e., phenotype) as a result of both genotype and the environment provide key information on how microbes function, interact with, and shape their host. As a proof of principle, we used stimulated Raman scattering–two-photon fluorescence in situ hybridization (SRS-FISH) to track the incorporation of deuterium (D) from D2O into a mixture of two distinct gut microbiota taxa. Incorporation of D from D2O into newly synthesized cellular components of active cells, such as lipids and proteins, occurs analogously to incorporation of hydrogen from water during the reductive steps of biosynthesis of various cellular molecules (10, 45, 46). Importantly, D incorporation from D2O has been shown to be reliable to track metabolic activity of individual cells within complex microbial communities in response to the addition of external substrates (10, 17, 47). When microbial communities are incubated in the presence of D2O under nutrient-limiting conditions, individual cells display only minimal activity and only minor D incorporation (11, 17, 47). In contrary, when cells are stimulated by the addition of an external nutrient, cells that can metabolize this compound become active and incorporate D into macromolecules, which lead to the presence of C-D bonds into the cell’s biomass. Consequently, D incorporation from D2O can be combined with techniques able to detect C-D signals, such as Raman-based approaches, and to track metabolic activity at the single-cell level in response to a variety of compounds. Here, we show that SRS-FISH enables fast and sensitive determination of the D content of individual cells while simultaneously unveiling their phylogenetic identity. We applied this technique to complex microbial communities by tracking in situ the metabolic responses of two major phylogenetic groups of microbes in the human gut (Bacteroidales and Clostridia spp.) and of a particular species within each group to supplemented host-derived nutrients. Our study revealed that 1) Clostridia spp. can actually outperform Bacteroidales spp. at foraging on the mucosal sugar fucose and shows 2) a significant interindividual variability of responses of these major microbiome taxa toward mucosal sugars. Together, our results demonstrate the capability of SRS-FISH to unveil the metabolism of particular microbes in complex communities at a throughput that is two to three orders of magnitude higher than other metabolism identity bridging tools, therefore providing a valuable multimodal platform to the field of single-cell analysis.