Project description:Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses.
Project description:Genome-scale metabolic model of recently isolated kefir-associated bacterial species Rothia kefirresidentii KRP. See also https://github.com/cdanielmachado/kefir_paper, https://journals.asm.org/doi/full/10.1128/genomeA.00869-17
Project description:5' RNASeq of mRNA from Shewanella amazonensis SB2B grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.
Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
Project description:5' RNASeq of mRNA from Shewanella putrefaciens CN-32 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.
Project description:5' RNASeq of mRNA from Shewanella sp ANA-3 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.
Project description:5' RNASeq of mRNA from Shewanella sp MR-7 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.
