Microbial Community Structure and Functionality in Ruminants Fed the Probiotic Bacillus amyloliquefaciens H57

Abstract

In the agricultural industry, farmers are continually searching for ways to improve animal production. Developing a more efficient digestive system is one such way that this can be achieved.In domesticated ruminants such as sheep and cattle, the feed material is initially digested in the largest and most prominent compartment of the alimentary canal: the rumen. The rumen is populated by a complex community of microorganisms that are capable of degrading the tough fibrous components of the plant cell wall, releasing fermentable and digestible carbohydrates, proteins, lipids and nucleic acids. Probiotics, defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host", have been used as a means to influence the rumen microbial community to improve the efficiency of feed digestion.In this study we cultivate the probiotic Bacillus amyloliquefaciens strain H57 as an inoculum, to be added to pelleted animal feed in concentrations of 10 9 cfu kg -1 (Chapter 2). To determine the genetic makeup of H57, its genome was sequenced (Chapter 3). The sequence analysis revealed a number of antimicrobial lipopeptides and polyketides, which if expressed in the rumen could significantly alter the rumen microbial community. Other genes of interest within the H57 genome include a number of carbohydrate degrading enzymes as well as those involved with nitrate reduction, which has been recognised as a potential alternative electron acceptor under anaerobic conditions such as the rumen.The H57 inoculum was administered in two animal feeding trials, one using pregnant Dorper ewes and the other using newborn dairy calves. In both instances a significant increase in weight gain was observed in the H57 fed animals compared to the control group. As a means to understand how H57 benefits these animals, the rumen microbial community was profiled by sequencing PCR amplicons of the 16S rRNA gene (Chapter 4). Analysis of the calf rumen microbiome did not reveal any significant differences between the control calves and those that were fed H57 for eight weeks. The only differences in the rumen community occurred between the initial sampling at four weeks and after weaning at eight weeks. In the sheep, however, there was a clear shift in microbial community structure between the control and H57 fed sheep. In both the control and H57 fed sheep the most abundant bacterial populations were Prevotella, although different species were dominant in each treatment group. The H57 fed sheep also had an abundance of Roseburia.Further analysis into the genetic potential and functionality of differentially abundant rumen microorganisms was performed on the sheep samples using metagenomic and metatranscriptomic sequencing. It was found that in the H57 fed sheep the rumen microbial community had an increased expression of hemicellulolytic enzymes, including β-glucosidase/β-galactosidase, α-galactosidase and L-arabinose isomerase. As hemicellulose contributes a significant portion of plant iii cell wall bio...

Pellets Inoculated with Bacillus amyloliquefaciens H57 Modulates Diet Preference and Rumen Factors Associated with Appetite Regulation in Steers

“…Although not measured directly, a higher ruminal NH 3 concentration due to the H57 supplementation recorded in this study may be associated with higher proteolytic and deamination activities by ruminal bacteria. Schofield [ 29 ] found that feeding H57 pellets to pregnant ewes caused an increase in Prevotella spp. populations, which are generally major contributors to protein and peptide degradation in the rumen [ 55 ].…”

“…The method used to prepare H57 inoculum for the cattle trial was as described by Schofield [ 29 ]. Briefly, the production of the H57 inoculum was performed in a series of batch cultures, then cultivated in a 100 L fermenter for the production of spores.…”

Volatile Organic Compound Profiles Associated with Microbial Development in Feedlot Pellets Inoculated with Bacillus amyloliquefaciens H57 Probiotic

“…The un-inoculated pellets were produced prior to the H57 inoculated pellets. The procedure used to prepare the H57 inoculum for this experiment was as described by Schofield [ 26 ]. Briefly, the H57 inoculum was prepared in a 100 L fermenter at the University of Queensland and the bacterial spores and vegetative cells were subsequently separated from the supernatant in a Sharples Centrifuge AS26 at 2500 g (Sharples Separator Works, West Chester, PA, USA).…”

Feed Preference Response of Weaner Bull Calves to Bacillus amyloliquefaciens H57 Probiotic and Associated Volatile Organic Compounds in High Concentrate Feed Pellets

“…The method used to prepare H57 inoculum for the cattle trial was as described by Reference [ 17 ]. Briefly, the production of the H57 inoculum was performed in a series of batch cultures, then cultivated in a 100 L fermenter for the production of spores.…”