Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate possession of open genomes rich in orthologous accessory genes with an abundance of carbohydrate-active enzyme isoforms

BackgroundButyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting energy from the diet. Within these genera, 5 rumen species have been classified (B. fibrisolvens, B. hungatei, B. proteoclasticus, P. ruminis and P. xylanivorans); nonetheless, the phylogeny and evolution of these genera is still unclear. Given the recent increase in available genomes, a re-investigation of the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio is timely.ResultsWe show, using both a 16S rDNA and 40 gene marker phylogenetic tree, that 6 species, namely 1. P. ruminis, 2. P. xylanivorans, 3. B. fibrisolvens, 4. Butyrivibrio sp., 5. B. hungatei, and 6. B. proteclasticus likely exist. Pangenome analysis at 100% core definition showed a high abundance of accessory genes (91.50 to 99.34%) compared with core genes (0.66 to 8.50%), illustrating possession of very open genomes. Across the 71 genomes, 870 COGs (clusters of orthologous genes) were shared by all taxa, suggesting evolution through speciation from a common ancestor. Further analysis of Carbohydrate-Active Enzymes (CAZymes) genes show that most are within the accessory genome and orthologous in descent with numerous within-family CAZyme isoforms apparent, CAZyme family tree lineages show that these isoforms largely group according to the 6 species, suggesting extensive horizontal gene transfer within these families.ConclusionsWe show the extensive genomic variation found within Butyrivibrio, and to a lesser extent, Pseudobutyrivibrio. and demonstrate the existence of a new Butyrivibrio species. The Butyrivibrio and Pseudobutyrivibrio genomes are very open with very low % core genomes and high % accessory genomes., and possess a number of GH isoforms that we hypothesise facilitate metabolic plasticity and resilience under dietary perturbations. This study utilizes all currently available genomes and consequently provides a major advancement in our understanding of these important anaerobic bacteria.

Challenges in Detecting the Abuse of Growth Hormone in Sport

Background: Growth hormone (GH) is reputed to be in widespread use in the sporting arena as a performance-enhancing agent and is on the list of banned substances published by the World Anti-Doping Agency. The detection of GH abuse poses many challenges. Unlike many substances of abuse, such as synthetic anabolic steroids, GH is a naturally occurring substance; therefore, demonstration of exogenous administration must rely on detecting concentrations in excess of an established reference interval. The purpose of this review is to discuss the methodologies being developed to detect GH abuse. Methods: We undertook a comprehensive search using multiple electronic databases and hand searches of reference lists of articles. The data for this review reflect our academic interests and experience through work on the GH-2000 and GH-2004 projects. Results: Two approaches have been taken to detect GH abuse. The first is based on assessment of the effect of exogenous GH on pituitary GH isoforms, and the second is based on measurement of markers of GH action. The advantages of each approach and the difficulties encountered with each technique, as well as future concepts in detection, are discussed. Conclusion: Although there are substantial challenges for the detection of GH, methodologies now exist to detect GH abuse with reasonable sensitivity and specificity.