High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

• Published in: Science (American Association for the Advancement of Science) Vol. 376; no. 6597; p. eabm1483
• Main Authors: Zheng, Wenshan, Zhao, Shijie, Yin, Yehang, Zhang, Huidan, Needham, David M., Evans, Ethan D., Dai, Chengzhen L., Lu, Peter J., Alm, Eric J., Weitz, David A.
• Format: Journal Article
• Language: English
• Published: United States The American Association for the Advancement of Science 03.06.2022; AAAS
• Subjects: Amplification; Antibiotic resistance; Antibiotics; Bacteria; Bacteria - genetics; Bacteriophages - genetics; Bacteroides - genetics; Bacteroides - virology; Bar codes; BASIC BIOLOGICAL SCIENCES; Biological research; Cell culture; Community Relations; Computer applications; Deoxyribonucleic acid; Digestive system; DNA; DNA, Bacterial - genetics; Droplets; Encapsulation; Feces; Gastrointestinal Microbiome - genetics; Gene transfer; Gene Transfer, Horizontal; Genome, Bacterial; Genomes; Genomics; Genomics - methods; Gut microbiota; High-Throughput Nucleotide Sequencing; Horizontal transfer; Human populations; Humans; Intestinal microflora; Metagenomics; Microbial activity; Microbial Interactions; Microbiomes; Microbiota; Microfluidics; Microorganisms; Nucleotide sequence; Phages; Single-Cell Analysis - methods; Species; Strain; Strains (organisms); Workflow
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.abm1483

Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus . Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution. Single-cell methods are the state of the art in biological research. Zheng et al . developed a high-throughput technique called Microbe-seq designed to analyze single bacterial cells from a microbiota. Microbe-seq uses microfluidics to separate individual bacterial cells within droplets and then extract, amplify, and barcode their DNA, which is then subject to pooled Illumina sequencing. The technique was tested by sequencing multiple human fecal samples to generate barcoded reads for thousands of single amplified genomes (SAGs) per sample. Pooling the SAGs corresponding to the same bacterial species allowed consensus assemblies of these genomes to provide insights into strain-level diversity and revealed a phage association and the limits on horizontal gene-transfer events between strains. —CA A microfluidic method was developed for high-throughput single-cell sequencing of human gut microbiota strains.