Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives

Microba has identified over 800 numerically abundant and prevalent gut bacteria associated with human health, which are underrepresented or absent in several disease states including inflammatory bowel disease (IBD), asthma, gastroesophageal reflux disease (GERD), irritable bowel syndrome (IBS), hypertension, anxiety and depression. These comprise a heterogenous group of diseases however several feature inflammation as a major pathology. Notably, the nuclear factor‐κB (NF‐κB) driven inflammatory response plays a central role in the pathogenesis of IBD, asthma and GERD, and it also plays a role in other diseases including metabolic disease, colorectal cancer (CRC), rheumatoid arthritis, multiple sclerosis, chronic obstructive pulmonary disorder (COPD) and atherosclerosis. Inflammation is the primary pathology in IBD and Microba researchers have demonstrated gut bacteria produce potent NF‐κB suppressive bioactives. Moreover, we have established methodologies relevant to IBD that could expedite the identification of precision Live Biotherapeutics (LBPs) and NF‐κB suppressive bioactives. These LBPs and/or their bioactives could potentially be exploited to prevent or treat IBD

Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives

Microba has identified over 800 numerically abundant and prevalent gut bacteria associated with human health, which are underrepresented or absent in several disease states including inflammatory bowel disease (IBD), asthma, gastroesophageal reflux disease (GERD), irritable bowel syndrome (IBS), hypertension, anxiety and depression. These comprise a heterogenous group of diseases however several feature inflammation as a major pathology. Notably, the nuclear factor‐κB (NF‐κB) driven inflammatory response plays a central role in the pathogenesis of IBD, asthma and GERD, and it also plays a role in other diseases including metabolic disease, colorectal cancer (CRC), rheumatoid arthritis, multiple sclerosis, chronic obstructive pulmonary disorder (COPD) and atherosclerosis. Inflammation is the primary pathology in IBD and Microba researchers have demonstrated gut bacteria produce potent NF‐κB suppressive bioactives. Moreover, we have established methodologies relevant to IBD that could expedite the identification of precision Live Biotherapeutics (LBPs) and NF‐κB suppressive bioactives. These LBPs and/or their bioactives could potentially be exploited to prevent or treat IBD

454 Sequencing for Gap Closure in Microbial Genome Assemblies

Most microbial genome finishing projects at the Joint Genome Institute require the use of a multitude of molecular techniques to achieve a finished genome. The majority of these techniques are applied to sequencing through gaps in the assembly. Traditional shotgun sequencing is known to have difficulty in both cloning of A/T rich regions and sequencing of G/C rich regions. To help alleviate this problem we have applied the 454 sequencing platform as another tool for gap closure. Although 454 Sequencing has been shown to have difficulty with homopolymer stretches of nucleotides, it does not have the same biases as shotgun sequencing. Therefore we feel these two approaches together can be complementary. We have developed a protocol in which gap-spanning fosmids are pooled together, from one or more projects. This DNA is sequenced with 454 and assemblied using the Newbler Assembler and the resulting contigs are added into their respective projects. One 60x60 picotiter chip can yield as much as 32 Mb, allowing for the pooling of 20-28 fosmids with and average read depth of 20-28X. We chose fosmids that spanned gaps in a single microbial genome assembly as well as gap spanning fosmids within a given scaffold of a metagenomic sequencing project. We are also applying 454 technology to whole genome shotgun sequencing to assist with poorly assembled projects from Sanger sequencing alone

454 Sequencing for Gap Closure in Microbial Genome Assemblies

Most microbial genome finishing projects at the Joint Genome Institute require the use of a multitude of molecular techniques to achieve a finished genome. The majority of these techniques are applied to sequencing through gaps in the assembly. Traditional shotgun sequencing is known to have difficulty in both cloning of A/T rich regions and sequencing of G/C rich regions. To help alleviate this problem we have applied the 454 sequencing platform as another tool for gap closure. Although 454 Sequencing has been shown to have difficulty with homopolymer stretches of nucleotides, it does not have the same biases as shotgun sequencing. Therefore we feel these two approaches together can be complementary. We have developed a protocol in which gap-spanning fosmids are pooled together, from one or more projects. This DNA is sequenced with 454 and assemblied using the Newbler Assembler and the resulting contigs are added into their respective projects. One 60x60 picotiter chip can yield as much as 32 Mb, allowing for the pooling of 20-28 fosmids with and average read depth of 20-28X. We chose fosmids that spanned gaps in a single microbial genome assembly as well as gap spanning fosmids within a given scaffold of a metagenomic sequencing project. We are also applying 454 technology to whole genome shotgun sequencing to assist with poorly assembled projects from Sanger sequencing alone