Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand

Fernandes, Karlette A.; Gee, Erica K.; Rogers, Chris W.; Kittelmann, Sandra; Biggs, Patrick J.; Bermingham, Emma N.; Bolwell, Charlotte F.; Thomas, David G.

doi:10.3390/ani11082300

Cited by 9 publications

(29 citation statements)

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“…As described previously [ 33 ], nucleic acids were extracted from 100 mg of each faecal sample ( n = 377) using a combined bead-beating, phenol-chloroform and column purification protocol and QIAquick 96 PCR purification kit (Qiagen, Hilden, Germany), and eluted in 80 μL elution buffer. After quantification and quality assessment, all ( n = 377) gDNA samples were normalised to 5 ng/μL gDNA per sample and bacterial 16S rRNA gene libraries were constructed using the Illumina single-step PCR library preparation method (Illumina, San Diago, CA, USA, ).…”

Section: Methodsmentioning

confidence: 99%

“…Seven blank samples containing water, were included as internal controls across the four plates (total 96 × 4 plates; n = 384 samples). Further details on the PCR protocol and the primer pair used to target the V3–V4 hypervariable region of the 16S rRNA gene are described previously [ 33 ], and the unique 8 bp dual-index barcode sequences (Nextera DNA library preparation kit, Illumina) used for individual sample identification are given in Table S1 . Following validation of the purified sequence libraries using a DNA 1000 labchip on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), the 16S amplicon libraries ( n = 384) were pooled in equimolar concentrations into two pools with 192 libraries each.…”

Section: Methodsmentioning

confidence: 99%

“…Quality control analysis was performed on the original sequences using three processes: SolexaQA++ ( , accessed on 30 November 2015), FastQC ( , accessed on 5 December 2015) and FastQscreen ( , accessed on 1 February 2015), which are described in detail previously [ 33 , 38 ]. Briefly, the raw sequence reads obtained from the Illumina MiSeq runs were aligned against the PhiX genome using BWA ( , accessed on 5 December 2015), and the PhiX sequences detected were removed, leaving the unaligned sequences that were included in further downstream analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Beta diversity was evaluated on a genus level using the QIIME pipeline [ 40 ], using bacterial taxa that represented ≥1% of the total community, in at least one sample, and differences between bacterial communities were determined using the Bray-Curtis dissimilarity metric. Clustering of samples was visualised by principal coordinate analysis (PCoA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) using various software tools [ 47 , 48 ], as described previously [ 33 ].…”

Section: Methodsmentioning

confidence: 99%

“…Previous studies in New Zealand showed that the faecal bacterial community in horses was diet-specific, and the diversity and community structure changed within four days following an abrupt dietary transition from an ensiled chopped forage diet (fed in stables) to grazing on pasture [ 15 ]. In healthy horses grazing on pasture, the diversity and community structure of the faecal bacteria also fluctuated with seasonal changes in the pasture composition [ 33 ], indicating that changes in dietary substrate affect the microbiota populations in the hindgut. A subsequent study showed that the transit time of forage diets through the GI tract varied between diets depending on the moisture content of the forage, and the feeding behaviour and the dry matter intake of horses consuming the diets [ 34 ].…”

Section: Introductionmentioning

confidence: 99%

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Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets

Fernandes

Rogers

Gee

et al. 2021

Animals

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The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota. In the present study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities; (1) responded to dietary change, and (2) stabilised following abrupt dietary transition. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (weeks 1, 3 and 5), before being abruptly transitioned to conserved forage-based diets, both offered ad libitum. Intestinal markers were administered to measure digesta transit time immediately before each diet change. The conserved forage-based diets were fed according to a 3 × 3 Latin square design (weeks 2, 4 and 6), and comprised a chopped ensiled forage fed exclusively (Diet FE) or with whole oats (Diet FE + O), and perennial ryegrass hay fed with whole oats (Diet H + O). Faecal samples were collected at regular intervals from each horse following the diet changes. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in alpha diversity across diets (p < 0.001), and a significant effect of diet on the beta diversity (ANOSIM, p = 0.001), with clustering of samples observed by diet group. There were differences in the bacterial phyla across diets (p < 0.003), with the highest relative abundances observed for Firmicutes (62–64%) in the two diets containing chopped ensiled forage, Bacteroidetes (32–38%) in the pasture diets, and Spirochaetes (17%) in the diet containing hay. Major changes in relative abundances of faecal bacteria appeared to correspond with the cumulative percentage of intestinal markers retrieved in the faeces as the increasing amounts of digesta from each new diet transited the animals. A stable faecal microbiota profile was observed in the samples from 96 h after abrupt transition to the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need to have modern horse feeding management that reflects the ecological niche, particularly by incorporating large proportions of forage into equine diets.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%