Abstract:The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health. While they are both diverse groups, they share a common role as active plant degraders. By comparing the genomes of the Lachnospiraceae and Ruminococcaceae with the Clostridiaceae, a more commonly free-living group, we identify key carbohydrate-active enzymes, sugar transport mechanisms, and metabolic pathways that distinguish these two commensal groups as specialists for the degradation of complex plant material.

Due to modern management practices and the availability of energy dense feeds, obesity is a serious and increasingly common health problem for horses. Equine obesity is linked to insulin resistance and exacerbation of inflammatory issues such as osteoarthritis and laminitis. While the gut microbiome is thought to play a part in metabolic status in horses, bacterial communities associated with obesity have yet to be described. Here we report differences in metabolic factors in the blood of obese, normal and lean horses correlated with differences in gut microbiome composition. We report that obese horses had higher levels of leptin, triglycerides, glucose, and cortisol in their blood, and more diverse gut microbiome communities with higher relative abundance of Firmicutes, and lower numbers of Bacteroidetes and Actinobacteria. Network analyses of correlations between body condition, blood analytes, and microbial composition at the genus level revealed a more nuanced picture of microbe-host interactions, pointing to specific bacterial species and assemblages that may be signatures of obesity and leanness in the horse gut. In particular, bacteria groups positively associated with two blood analytes and obesity included Butyrivibrio spp., Prevotellaceae, Blautia spp., two members of Erysipelotrichaceae, and a Lachnospiraceae taxa. These results are an important first step in unraveling the metabolic differences between obese and lean horse gut communities, and designing targeted strategies for microbial intervention.

Laminitis is a chronic, crippling disease triggered by the sudden influx of dietary starch. Starch reaches the hindgut resulting in enrichment of lactic acid bacteria, lactate accumulation, and acidification of the gut contents. Bacterial products enter the bloodstream and precipitate systemic inflammation. Hindgut lactate levels are normally low because specific bacterial groups convert lactate to short chain fatty acids. Why this mechanism fails when lactate levels rapidly rise, and why some hindgut communities can recover is unknown. Fecal samples from three adult horses eating identical diets provided bacterial communities for this in vitro study. Triplicate microcosms of fecal slurries were enriched with lactate and/or starch. Metabolic products (short chain fatty acids, headspace gases, and hydrogen sulfide) were measured and microbial community compositions determined using Illumina 16S rRNA sequencing over 12-hour intervals. We report that patterns of change in short chain fatty acid levels and pH in our in vitro system are similar to those seen in in vivo laminitis induction models. Community differences between microcosms with disparate abilities to clear excess lactate suggest profiles conferring resistance of starch-induction conditions. Where lactate levels recover following starch induction conditions, propionate and acetate levels rise correspondingly and taxa related to Megasphaera elsdenii reach levels exceeding 70% relative abundance. In lactate and control cultures, taxa related to Veillonella montpellierensis are enriched as lactate levels fall. Understanding these community differences and factors promoting the growth of specific lactate utilizing taxa may be useful to prevent acidosis under starch-induction conditions.

Exercise has a significant effect on different physiological systems in the body of human and animals. Only limited numbers of published studies in laboratory animals or humans have shown the effect of exercise on the gut microbiota, and no studies have shown this effect in horses. In this study, 8 horses (4 mares, 4 geldings) were exercise trained for 12 weeks, and 4 additional mares were used as a parallel seasonal control. To identify bacterial community changes over time for both groups, rectal faecal samples were collected, DNA was extracted, and the 16S rRNA gene (V3-V4) was sequenced using the Illumina Miseq platform. One-way ANOVA, Shannon diversity index, and Principal Coordinate Analysis (PCoA) were used to identify differences between and among samples. The exercise training group showed significant changes in the levels of Bacteroidetes, Proteobacteria, and Spirochaetes phyla (P<0.05), while there were no changes in the gut microbiota of the seasonal control group through the three months of the study (P>0.05). Moreover, with training two genera significantly changed in their relative abundance over time, namely Clostridium and Dysgonomonas (P<0.05). Dysgonomonas spp. was significantly changed in abundance during the exercise training period (P<0.05). Also Treponema spp. showed significant changes during the exercise training period (P<0.05). Shannon diversity index was decreased (P<0.05) in the exercise group at the beginning of the study, but then returned to pre-training levels. PCoA showed significant separation between time points of the exercise training group as far as the levels of genera and species (P<0.05) represented. Our results show that exercise training influences the gut microbiota, especially at the beginning of training.

Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.