High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.

Exploring the optimization of aerobic food waste digestion efficiency through the engineering of functional biofilm Bio-carriers

The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion.