Effects of lactic acid bacteria as putative probiotics and host genetic profile on rumen microbial ecology of two South African goat breeds.

Abstract

Over a decade ago, the use of antibiotics as feed additives has been banned in most European Union countries because of the following risks: development of antibiotic resistance in pathogenic microbiota, release of unmanageable antibiotics into the environment and antibiotic or chemical residues in animal products. Due to consumer’s pressure and worries towards harmful effects of antibiotics as growth promoters, there was a need to think of alternatives to antibiotics. In recent years, probiotics have been preferred as a superior alternative to antibiotics because they no harmful attributes associated with antibiotics and also have the ability to stabilize the microbial diversity in the digestive tract, and promotes animal yield while preserving consumer’s health. Probiotics have also been observed to improve the functions of rumen microflora, fermentation processes and improve digestion in ruminants. The study therefore aimed to evaluate the effect of supplementation of putative probiotics- Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination for two South African goat breeds. The first objective of the study was to determine the effects of probiotics on feed intake and growth performance of Boer and Speckled goats. To achieve the first objective, a total of 18 Speckled and 18 Boer randomly selected goats were separated into five treatment groups according to gender and breed. The trial lasted for 30 days. The goats were fed with pellets. Also, fresh water and hay were provided ad libitum. The treatment groups were as follows: (T1) basal diet + Lactobacillus rhamnosus SCH; (T2) basal diet + Enterococcus faecalis 25a; T3 basal diet + probiotic Lactobacillus rhamnosus SCH and Enterococcus faecalis 25a; T4 (positive control) basal diet + antibiotic; and T5 (negative control) basal diet with no antibiotics and no probiotics. The animals were weighed before and after the trial to determine their growth performance. Ruminal contents were collected before and after trial to examine the changes in the ruminal pH. All the data collected were processed and analyzed using one-way analysis of variance (ANOVA) procedure of Statistical Analysis System (SAS, version 9.4). The efficiency of oral administration of putative probiotics on growth performance of South African goats showed the best performance in weight gain, final body weight and feed conversion ratios. Gender and breed affected weight gain and body weight, showing that male (18.4 kg) goats were heavier than females (15.3 kg) and that Boer goat had a faster percentage growth rate of 24% than Specked (18%). This indicates that Boer goats will reach the market weight faster; this is due to the effect of probiotics. Supplementation of probiotics had no effect on feed intake. The pH across all treatment groups decreased averagely from 7.01 to 6.18. The lowest pH of 6.18 was observed in treatment group 3 (combination of probiotics). The findings in this study suggest that probiotics may have beneficial effects in goats’ nutrition by increasing weight gain and lowering pH. The second aim of the study was to determine the effect of host genetic profile on rumen ecology and performance characteristics of two South African goat breeds. Gut microbiota compositions were determined by sequencing the V3-V4 region of the 16S rRNA gene from ruminal contents of 36 goats. A total of 1,260 operational taxonomic units were obtained and grouped in 19 Phyla and 97 Genera. Bacteroidetes, Firmicutes, Proteobacteria and Fibrobacters were the most dominant Phyla in all the treatment groups, while Prevotella and Anaerofustis were the most abundant Genera. Archaeal genus Vadin CA11, decreased in Treatment 1, 2, 3 and 5, while an increase was observed only in treatment 5. The presence of this genus has potential to allow the microbiome to adapt quickly to environmental stress like diet changes. However, the abundance of this genus must be controlled because it can produce additional ammonium through methanogenesis. The presence of Chlamydiae was observed only in Treatment 5 showing that probiotics and antibiotics eliminate obligate pathogens. Our result indicates that probiotics promote microbial diversity. The final objective was to examine the alterations triggered by the probiotics on the rumen microbial profiles of Boer and Speckled goats using the 50K SNP bead chip. Genome-wide association study was explored between genotype and the rumen microbiome composition. A total of 44 single-nucleotide polymorphisms dispersed across the goat genome were associated with the relative abundance of six microbial Genera: BF311, Clostridium, Fibrobacter, Methanobrevibacter, Prevotella, and Ruminococcus. A total of 47 candidate genes were identified within 1-Mb windows of the goat genome; CPT1A, STC2, AGPAT3 and ACSF3 genes were associated with fatty acid metabolism, while GH, BMP, MSTN, GHR and STMN1 were associated with regulation of developmental growth. Our results suggest that 47 candidate genes may positively shape the microbiome and elucidate the association between gastrointestinal (GI) microbiome and the host genome in two South African goat breeds used for this study.