Large-scale metagenomic assemblies have uncovered thousands of new species greatly expanding the known diversity of microbiomes in specific habitats. To investigate the roles of these uncultured species in human health or the environment, researchers need to incorporate their genome assemblies into a reference database for taxonomic classification. However, this procedure is hindered by the lack of a well-curated taxonomic tree for newly discovered species, which is required by current metagenomics tools. Here we report DeepMicrobes, a deep learning-based computational framework for taxonomic classification that allows researchers to bypass this limitation. We show the advantage of DeepMicrobes over state-of-the-art tools in species and genus identification and comparable accuracy in abundance estimation. We trained DeepMicrobes on genomes reconstructed from gut microbiomes and discovered potential novel signatures in inflammatory bowel diseases. DeepMicrobes facilitates effective investigations into the uncharacterized roles of metagenomic species.

Purpose: A growing body of evidence suggests that the microbiome of the ocular surface confers potent immunoregulatory functions and has a key role in the physiologic maintenance of healthy eyes and in the pathogenesis of ocular diseases. Although the microbiome is known to be affected by age and sex, the influence of these factors on ocular surface microbiota in healthy adults remains largely unknown. Methods: Ocular surface microbiome samples were obtained from the inferior bulbar conjunctiva of 48 young and 42 old adults at Zhongshan Ophthalmic Center. Using metagenomic shotgun sequencing, we characterized the sex- and age-differences in conjunctival microbiome profiles of healthy adults. Results: Male and female groups differed only in the β diversity of bacterial communities, while there were significant differences in bacterial composition, metabolic functions, and the abundance of antibiotic resistance genes between young and old adult groups. Conclusions: Our findings suggest that age and sex collectively shape the conjunctival microbiome, and may change the immune homeostasis of the ocular surface through alterations of its commensal microbiome.

T follicular helper (Tfh) cell is a unique T cell subset specialized in promoting humoral immunity. B-cell lymphoma 6 protein (Bcl6) has been identified as an obligatory transcription factor in Tfh cells; however, the molecular mechanism underlying Bcl6 function remains largely unknown. Here, we defined Bcl6 target genes in Tfh cells by analyzing genome-wide Bcl6 occupancy together with transcriptome profiling. With consensus sequences being different from those in Th9, B cells, and macrophages, Bcl6 binding in Tfh cell was closely associated with a decrease in 5-hydroxymethylcytosine (5hmC). Importantly, Bcl6 promoted Tfh cell differentiation through antagonizing IL-7R (CD127)/signal transducer and activator of transcription (STAT) 5 axis; deletion of the Bcl6 gene in T cells resulted in enhanced IL-7R-STAT5 signaling and substantial expansion of CD127(hi) non-Tfh cells. Thus, our study systemically examines Bcl6-controlled regulatory networks and provides important insights into Bcl6's biological functions in Tfh cells.

Significance: Recent success of T cell-based cancer immunotherapies highlights the importance of further understanding molecular mechanisms in the regulation of T cell responsiveness. Here, we performed a genome-wide CRISPR screen to identify genes that regulate T cell activation upon anti-T cell receptor (TCR) stimulation. Our screen confirmed many of the known regulators in proximal T cell signaling. Moreover, we identified a previously uncharacterized gene named FAM49B, which acts as a negative regulator in T cell activation. Our study suggests that genome-wide CRISPR screening is a powerful means to identify key regulators of TCR signaling. The same strategy could be applied to CD28-mediated costimulatory signaling or PD-1–mediated coinhibitory signaling. The unbiased approach presented here may allow us to identify new therapeutic targets for cancer immunotherapy.