Draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from the bovine rumen

Morphologically and biochemically diverse members of the Treponema genus are present in the gastrointestinal tract of ruminants, yet very little is understood about their functional importance to this microbiome. Here we describe the annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from a bovine rumen sample

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Diet and the microbiome

The gut microbiota provides a range of ecologic, metabolic, and immunomodulatory functions relevant to health and well-being. The gut microbiota not only responds quickly to changes in diet, but this dynamic equilibrium may be managed to prevent and/or treat acute and chronic diseases. This article provides a working definition of the term “microbiome” and uses two examples of dietary interventions for the treatment of large bowel conditions to emphasize the links between diet and microbiome. There remains a need to develop a better functional understanding of the microbiota, if its management for clinical utility is to be fully realized

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