Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
Humans ; Gastrointestinal Microbiome/genetics* ; Bacteriophages/physiology* ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA/methods* ; Bacteria/virology*

Humans ; Acute Disease ; Pancreatitis/diagnosis* ; Follow-Up Studies ; Patient Discharge ; Disease Progression

Objective To investigate the mechanism of hearing loss caused by tympanic membrane(TM)per-foration.Methods We constructed a full ear finite element model,and the personalized finite element model of TM perforation was constructed to simulate hearing loss caused by TM perforation.The difference between the displace-ment response of the basement membrane and the baseline was applied to simulate hearing loss,and the contribution of various components of the middle ear to hearing loss was analyzed to study the mechanism of hearing loss caused by TM perforation.Results If the coupling of the round window membrane and the middle ear air was removed,the hearing loss at the low frequency was about 40 dB,while the high-frequency was the same as the baseline.Re-moval of the coupling between the inner side of the eardrum and the middle ear cavity resulted in a reduction in par-tial low-frequency hearing and an increase in high-frequency hearing loss.The continuous disconnection between the air in the external auditory canal and the air in the middle ear cavity increased the low-frequency hearing loss.How-ever,after the removal of the coupling between the round window membrane and the middle ear air and the connec-tion between the middle ear air and the lateral side of the TM,the original hearing loss of 40 dB at low-frequency dropped to 10 dB.While the removal of the coupling between the middle ear cavity air and the ossicular chain had no significant impact on hearing loss.Conclusion TM perforation may cause hearing loss by both the reduction of sound transmission and the reduction of sound pressure difference between the two sides of TM.The round window membrane can counteract the influence of the hearing loss caused by TM perforation.