Dataset Information

Analysis of microbial communities from a methane-fed bio-reactor with metagenomes and metaproteomics

ABSTRACT: In this study, we analyzed the microbial communities from a methane-based bio-reactor with selenate as an electron accepter. Four biological replicates were analyzed by metagenomics, of which data can be found in the SRA database (Accession number: SRP136677, SRP136696, SRP136790 and SRP136859). Based on the metagenomic data, we detected the expressed proteins using metaproteomics. This data is also included in this submission.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Pseudoxanthomonas Sp. Methylocystis Sp. Meiothermus Sp.

TISSUE(S): Whole Body

SUBMITTER: xiaonan fu

LAB HEAD: Ling-Dong Shi

PROVIDER: PXD011889 | Pride | 2022-03-01

REPOSITORIES: Pride

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Project description:We sought to test whether vaccine-induced immune responses could protect rhesus macaques (RMs) against upfront heterologous challenges with an R5 simian-human immunodeficiency virus, SHIV-2873Nip. We immunized the RMs with recombinant Env proteins heterologous to the challenge virus. For induction of immune responses against Gag, Tat, and Nef, we explored a strategy of immunization with overlapping synthetic peptides (OSP). The immune responses against Gag and Tat were finally boosted with recombinant proteins. The vaccinees and a group of ten control animals were given five low-dose intrarectal (i.r.) challenges with SHIV-2873Nip. All controls and seven out of eight vaccinees became systemically infected; there was no significant difference in viremia levels of vaccinees vs. controls. Prevention of viremia was observed in one vaccinee which showed strong boosting of virus-specific cellular immunity during virus exposures. The protected animal showed no challenge virus-specific neutralizing antibodies in the TZM-bl or A3R5 cell-based assays and had low level ADCC activity after the virus exposures. Microarray data strongly supported a role for cellular immunity in the protected animal. Our study represents a case of protection against heterologous tier 2 SHIV-C by vaccine-induced, virus-specific cellular immune responses. For the protected RM, blood was collected before vaccination, on the day of first virus exposure and six weeks after last virus challenge. Lymph node and rectal pinch biopsies were performed before vaccination and six weeks after last virus challenge. Blood was collected in tempus tubes and processed immediately according to the manufacturer’s instructions and stored at -80C. The biopsy specimens were cut into small pieces and immediately placed into RNAlater solution (Qiagen, Valencia, CA) and also stored at -80C. Total RNA from blood, lymph node and rectal biopsies was extracted using RNAeasy extraction kits (Qiagen, Valencia, CA). cDNA labeling, hybridization, staining and scanning were performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) for rhesus gene expression arrays.

Dataset Information

Analysis of microbial communities from a methane-fed bio-reactor with metagenomes and metaproteomics

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