Aims:To determine the composition and temporal stability of the gut (faecal) microbiota of sheep (Ovis aries). Methods and Results: Microbial population dynamics was conducted using ARISA (28 sheep) and 16S rRNA sequencing (11 sheep). Firmicutes and Bacteroidetes were the predominant bacterial phyla, constituting~80% of the total population. The core faecal bacterial microbiota of sheep consisted of 67 of 136 detected families and 91 of 215 detected species. Predominant microbial taxa included Ruminococcaceae, unassigned families in Bacteroidales and Clostridiales, Verrucomicrobiaceae and Paraprevotellaceae. Diversity indices and core microbiota composition demonstrated the stability of the core microbiota over 2-4 weeks. The core microbiota remained similar over 5 months. Conclusions: Temporal stability of the sheep microbiota is high over 2-4 weeks in the absence of experimental variables. The core microbiota of Merino sheep shares taxa found in other breeds of sheep and other ruminants. Significance and Impact of the Study: Numerous studies seek to investigate the impact of experimental variables on gut microbiota composition. To do so, knowledge of the innate stability (or instability) of the microbiota over an experimental time course is required, independent of other variables. We have demonstrated high stability of the gut microbiota in sheep over 3-4 weeks, with moderate stability over~5 months.

Background: One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiota and its impact on health. Relatively little is known about interactions between the gut microbiota and gastrointestinal tract pathogens in sheep. Thus, this study was undertaken to investigate the link between the faecal microbiota of sheep, as a sample representing the gastrointestinal microbiota, and infection with H. contortus. Results: Sheep (n = 28) were experimentally inoculated with 14,000 H. contortus infective larvae. Faecal samples were collected 4 weeks prior to and 4 weeks after infection. Microbial analyses were conducted using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. A comparison of pre-infection microbiota to post-infection microbiota was conducted. A high parasite burden associated with a relatively large change in community composition, including significant (p ≤ 0.001) differences in the relative abundances of Firmicutes and Bacteroidetes following infection. In comparison, low parasite burden associated with a smaller change in community composition, with the relative abundances of the most abundant phyla remaining stable. Interestingly, differences were observed in pre-infection faecal microbiota in sheep that went on to develop a high burden of H. contortus infection (n = 5) to sheep that developed a low burden of infection (n = 5). Differences observed at the community level and also at the taxa level, where significant (p ≤ 0.001) in relative abundance of Bacteroidetes (higher in high parasite burden sheep) and Firmicutes (lower in high parasite burden sheep). Conclusions: This study reveals associations between faecal microbiota and high or low H. contortus infection in sheep. Further investigation is warranted to investigate causality and the impact of microbiome manipulation.

The production of high quality effluent from membrane bioreactors (MBRs) arguably requires less supervision than conventional activated sludge (CAS) processes. Nevertheless, the use of membranes brings additional issues of activated sludge filterability, cake layer formation and membrane fouling. From a practical standpoint, process engineers and operators require simple tools which offer timely information about the biological health and filterability of the mixed liquor as well as risks of membrane fouling. To this end, a range of analytical tools and biological assays are critically reviewed from this perspective. This review recommends that Capillary Suction Time (CST) analysis along with Total Suspended and Volatile Solids (TSS/VSS) analysis is used daily. For broad characterisation, total carbon and nitrogen analysis offer significant advantages over the commonly used chemical and biological oxygen demand (COD/BOD) analyses. Of the technologies for determining the vitality of the microbial biomass the most robust and reproducible, are the second generation adenosine-5'-triphosphate (ATP) test kits. Extracellular polymer concentrations are best monitored by measurement of turbidity after centrifugation. Taken collectively these tools can be used routinely to ensure timely intervention and smoother operation of MBR systems.