Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning

Torre, Ubaldo De La; Henderson, John D.; Furtado, Kathleen L; Pedroja, Madeleine; Elenamarie, O'Malley; Mora, Anthony; Pechanec, Monica Y.; Maga, Elizabeth A.; Mienaltowski, Michael J.

doi:10.1371/journal.pone.0216211

Cited by 36 publications

(73 citation statements)

References 72 publications

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“…, but colonization is probably restricted by differences in diet and intestinal environment. Similar observations were recently reported by De La Torre et al: the foalmicrobiota was very different from the adults at day 7, and developing towards the adult composition at day 2823 . Their day 7 gut microbiota was similar with our observations at the family level.…”

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confidence: 91%

The composition of the perinatal intestinal microbiota in horse

Husso

Jalanka

Alipour

et al. 2019

Preprint

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The establishment of the intestinal microbiota is critical for the digestive and immune systems. We studied the early development of the microbiota in horse, a hindgut fermenter, from birth until 7 days of age, by qPCR and 16S rRNA gene amplicon sequencing. To evaluate initial sources of foal microbiota, we characterized dam fecal, vaginal and oral microbiotas. We utilised an amplicon sequence variant (ASV) based pipeline to maximize resolution and reproducibility. Stringent ASV filtering based on prevalence and abundance in samples and controls purged reagent contaminants while preserving intestinal taxa. The newborn rectum contained small amounts of diverse bacterial DNA, with a profile closer to mare feces and vagina than mouth. 24 hours after birth, the intestine was colonized by Firmicutes and Proteobacteria, some foals dominated by a single genus. At day 7, the phylum-level composition resembled adult feces but genera were different. The mare vaginal microbiota contributed to 24 h and 7 day microbiotas. It contained few lactobacilli, with Corynebacterium, Porphyromonas, Campylobacter and Helcococcus as the most abundant genera. In the oral mucosa, Gemella was extremely abundant. Our observations suggest that bacteria or bacterial components translocate to the equine fetus, but the intestinal microbiota changes rapidly after birth.

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confidence: 91%

The composition of the perinatal intestinal microbiota in horse

Husso

Jalanka

Alipour

et al. 2019

Preprint

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“…DNA concentration was determined using a NanoDrop UV spectrophotometer (ThermoFisher Scientific). Primers F515 (forward: 5′-GTGCCAGCMGCCGCGGTAA-3′) and R806 (5′-GGACTACHVGGGTWTCTAAT-3′) were used to amplify the V4 domain bacterial 16S rRNA genes, along with a unique barcode on each forward primer for each sample [ 20 – 22 ]. PCR, product purification, and agarose gel electrophoresis visualization were performed as previously described [ 20 ].…”

Section: Main Textmentioning

confidence: 99%

“…Primers F515 (forward: 5′-GTGCCAGCMGCCGCGGTAA-3′) and R806 (5′-GGACTACHVGGGTWTCTAAT-3′) were used to amplify the V4 domain bacterial 16S rRNA genes, along with a unique barcode on each forward primer for each sample [ 20 – 22 ]. PCR, product purification, and agarose gel electrophoresis visualization were performed as previously described [ 20 ]. Combined barcoded libraries were submitted to the University of California Davis Genome Center DNA Technologies Core for 250 bp paired-end sequencing using the Illumina MiSeq platform.…”

Section: Main Textmentioning

confidence: 99%

Psyllium supplementation is associated with changes in the fecal microbiota of horses

et al. 2020

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Objective Prophylactic supplementation of psyllium husk is recommended to enhance passage of ingested sand from the gastrointestinal tracts of horses. We hypothesized that psyllium supplementation would increase fecal sand passage and favorably alter bacterial populations in the hindgut. Six yearlings and six mature mares were fed a psyllium supplement in the diet daily for seven days. Voluntarily-voided feces were collected over the course of 29 days, prior, during, and after treatment. Feces were analyzed for acid detergent fiber (ADF) and acid detergent insoluble ash analyses. Microbial DNA was also isolated, and the V4 region of the 16S ribosomal RNA gene was PCR-amplified and sequenced using MiSeq technology. Results Fecal ADF concentration was greater in adults while silica concentration was greater in yearlings. Mature mare fecal ADF decreased during and just after supplementation but thereafter increased. No changes in silica levels were noted in either group over time. Fecal microbial population phylogenetic diversity was greatest mid-supplementation and lowest at 11 days post-supplementation. Functional profiles of the microbial communities presented some benefits for psyllium supplementation. These findings provide compelling evidence for further detailed studies of prophylactic psyllium supplementation.

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“…Enriched taxa were also analyzed using LEfSe (Linear Discriminant Analysis Effect Size) [38]. DCM and SFM foals were analyzed separately for each of their 6 age groups (Tables 3 and 4).…”

Section: Differences In Community Compositionmentioning

confidence: 99%

“…Enriched taxa by management group and time were identi ed using LEfSe [38]. Statistical analysis and visualization were completed using R [39].…”

Section: Dna Extraction and Sequencingmentioning

confidence: 99%

Development of the Equine Hindgut Microbiome in Semi-feral and Domestic Conventionally-Managed Foals

Tavenner

McDonnell

Biddle

2020

Preprint

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Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age.Conclusions: This study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

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Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning

Cited by 36 publications

References 72 publications

The composition of the perinatal intestinal microbiota in horse

The composition of the perinatal intestinal microbiota in horse

Psyllium supplementation is associated with changes in the fecal microbiota of horses

Development of the Equine Hindgut Microbiome in Semi-feral and Domestic Conventionally-Managed Foals

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