The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology

Abstract

Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method. In the P method, mares were separated from foals at progressively increasing intervals every day, starting from five min during the fourth week prior to weaning and ending with 6 h during the last week before weaning. In the A method, mares and foals were never separated prior to weaning (0 d). Different host phenotypes and gut microbiota composition were studied across 6 age strata (days −30, 0, 3, 5, 7, and 30 after weaning) by 16S rRNA gene sequencing. Results revealed that the beneficial species belonging to Prevotella, Paraprevotella, and Ruminococcus were more abundant in the A group prior to weaning compared to the P group, suggesting that the gut microbiota in the A cohort was better adapted to weaning. Streptococcus, on the other hand, showed the opposite pattern after weaning. Fungal loads, which are thought to increase the capacity for fermenting the complex polysaccharides from diet, were higher in P relative to A. Beyond the effects of weaning methods, maternal separation at weaning markedly shifted the composition of the gut microbiota in all foals, which fell into three distinct community types at 3 days post-weaning. Most genera in community type 2 (i.e., Eubacterium, Coprococcus, Clostridium XI, and Blautia spp.) were negatively correlated with salivary cortisol levels, but positively correlated with telomere length and N-butyrate production. Average daily gain was also greater in the foals harboring a community type 2 microbiota. Therefore, community type 2 is likely to confer better stress response adaptation following weaning. This study identified potential microbial biomarkers that could predict the likelihood for physiological adaptations to weaning in horses, although causality remains to be addressed.

Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLAdd minipigs

“…The microbiota contributed to a similar, but slightly lower extent, while the role of CBCs was more limited. These findings were in agreement with those obtained by Mach and co-workers 31 and was possibly related to the number of variables of each dataset, which was highest in the case of transcriptome and lowest in the case of CBCs.…”

“…3). In agreement with the literature 22,31 , more than 95% of the sequences in both breeds were represented by the phyla Firmicutes and Bacteroidetes (Fig. 3A), followed by Proteobacteria, Actinobacteria and Spirochaetes.…”

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

“…However, there still are clear limitations when using NGS 16S rRNA based identification of bacteria beyond the family level [54], since current sequencing read lengths with Illumina technology only cover a region of around [173] bovis/equinus L-lactate producer [174] Lactobacillaceae Lactobacillus salivarius/ mucosae L-lactate producer, decarboxylating amino acids, vascoactive amines [174], [137] bulgaricus/ delbrueckii L-lactate producer [174] crispatus lactic acid bacteria [175] johnsonii lactic acid bacteria [175] reuteri lactic acid bacteria [175] equigenerosi lactic acid bacteria [176] hayakitensis lactic acid bacteria [176] buchneri lactic acid bacteria [176] vitulinus lactic acid bacteria [176] Acidaminococcaceae Mitsuokella jalaludinii D-lactate producer [174] Phascolarctobacterium spp. Fungi fiber degradation [178] Neocallimastigaceae Piromyces equi cellulose degradation [179] Protozoa hemicellulose, pectin degradation [99] Bacteriophages regulating bacterial species distribution [180] Archaea methanogens f [80], [81] 460 bp mostly from the V3 and V4 region while a fulllength or near full-length 16S rRNA sequence is needed for a confident taxonomic assignment of genus and species [50]. Since it is known that bacterial species differ with respect to their copy numbers of the 16S rRNA gene from one to 15 and more [55], amplification could lead to a bias considering semi quantitative proportions (relative abundances) in complex communities [56].…”

“…These bacteria are considerable residents in equine caecum, small colon, rectum and feces with relative abundance ranging from 10 to 23% [30]. Verrucomicrobia gained parasite egg burden decrease Bacteroides, Clostridium XIVa, Ruminococcus, unclassified Lachnospiraceae [178,183] parasite egg burden increase Clostridium IV, Coprococcus, Anaerovibrio, Agreia, Oscillibacter, Turicibacer, unclassified Cystobacteraceae, Campylobacter, Bacillus, Pseudomonas [178,183] laminitis increase Lactobacilli, Escherichia coli [138,184] increasing attention in obesity and metabolic disease research in humans [113,114]. Akkermansia, a mucindegrading genus within the phylum Verrucomicrobia helps to maintain the integrity of the mucin layer and decreases bowel inflammation [115].…”

Evaluation of DNA Extraction Methods of Mule Dung

“…Although most of the studies have used fecal DNA kits [5][6] , many have also used soil microbe DNA kits [7][8] or total DNA isolation kits 9 . The DNA extraction method is a critical step in microbial community profiling as apart from its effect on sequencing output and microbial community profiling 10 , it adversely affects the result comparison across studies, especially in physiological and pathological studies [11][12] . In addition to the differences in methods and protocols, the fecal samples also contain inhibitory compounds like humic acid, fulvic acid and proteins interfering with the PCR in amplicon generation before actual sequencing 13 .…”