Analyze Diet
Frontiers in veterinary science2024; 11; 1386135; doi: 10.3389/fvets.2024.1386135

Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet.

Abstract: Diet is one of the main factors influencing the intestinal microbiota in horses, yet a systematic characterization of the microbiota along the length of the digestive tract in clinically healthy horses, homogenous for age and breed and receiving a specific diet is lacking. Unassigned: The study used 16S rRNA amplicon sequencing to characterize the microbiota of the intestinal tracts of 19 healthy Bardigiano horses of 14.3  ±  0.7  months of age fed one of two diets. Nine horses received a high-starch diet (HS), and ten horses received a high-fiber diet (HF). After 129  days, the horses were slaughtered, and samples were collected from the different intestinal tract compartments. Unassigned: The microbiota alpha diversity indices were lower in the caecum, pelvic flexure and right dorsal colon of the horses fed the HS diet (False Discovery Rate, FDR  <  0.05). The values of beta diversity indicated significant compositional differences between the studied intestinal tract compartments according to the diet received (FDR  <  0.05). At the lower taxonomic level (genus or family), the HS diet was associated with a higher relative frequency of within the small intestine (jejunum and duodenum) (FDR  <  0.05). Within the hindgut (caecum and sternal flexure), the HS diet was associated with lower relative frequencies (i.e., a smaller core community) of bacteria belonging to and (FDR  <  0.05). Moreover, horses fed the HS diet displayed a higher relative abundance of in the caecum (FDR  <  0.05) and in the sternal flexure (FDR  <  0.05), both of which are pathogenic bacteria responsible for inflammation diseases. Samples collected from the pelvic flexure and rectum of horses fed the HS diet showed significantly higher relative frequencies of (FDR  <  0.05) - amylolytic bacteria associated with acidosis. The relative frequencies of the and were lower in the feces collected from the rectum of horses receiving the HS diet vs. HF diet, indicating smaller core communities of these bacteria (FDR  <  0.05). Fibrous diets should be promoted to prevent dysbiosis of the microbiota associated with high-starch diet.
Publication Date: 2024-05-14 PubMed ID: 38807937PubMed Central: PMC11130486DOI: 10.3389/fvets.2024.1386135Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study investigates the impact of a high-starch diet versus a high-fiber diet on the microbiota throughout the horse’s digestive tract, revealing that a high-starch diet is associated with lower diversity and potentially harmful alterations in the microbiota.

Research Methods and Participants

  • The study involved 19 healthy Bardigiano horses, all roughly the same age (14.3  ±  0.7  months).
  • The horses were divided into two dietary groups. Nine horses received a high-starch (HS) diet, while ten horses received a high-fiber (HF) diet.
  • After 129  days on these diets, the horses were euthanized, and samples were collected from various parts of their digestive tracts.
  • The researchers used a process called 16S rRNA amplicon sequencing to characterize the microbiota in these samples.

Impact of Diet on the Microbiota

  • Measured by alpha diversity indices, the HS diet was associated with reduced microbiota diversity in the caecum, pelvic flexure and right dorsal colon compared to the HF diet.
  • Beta diversity values revealed significant differences in the composition of the microbiota between different parts of the digestive tract, based on the diet received.

The High-Starch Diet’s Effects

  • In the small intestine, the HS diet led to a higher relative frequency of certain unnamed bacteria.
  • In the hindgut, the HS diet resulted in lower relative frequencies or a smaller core community of two other types of unnamed bacteria.
  • The HS diet was also associated with greater abundance of two sorts of pathogenic bacteria in the caecum and the sternal flexure, which are known to cause inflammatory diseases.
  • Furthermore, the HS diet caused higher relative frequencies of amylolytic bacteria (associated with acidosis) in the samples collected from the pelvic flexure and rectum.
  • In the feces from the rectum, the HS diet led to a smaller core community of two more unnamed types of bacteria.

Conclusion

The researchers concluded from this study that fibrous diets should be preferred over starch-heavy diets as they help to prevent dysbiosis of the microbiota associated with high-starch diet.

Cite This Article

APA
Raspa F, Chessa S, Bergero D, Sacchi P, Ferrocino I, Cocolin L, Corvaglia MR, Moretti R, Cavallini D, Valle E. (2024). Microbiota characterization throughout the digestive tract of horses fed a high-fiber vs. a high-starch diet. Front Vet Sci, 11, 1386135. https://doi.org/10.3389/fvets.2024.1386135

Publication

ISSN: 2297-1769
NlmUniqueID: 101666658
Country: Switzerland
Language: English
Volume: 11
Pages: 1386135
PII: 1386135

Researcher Affiliations

Raspa, Federica
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Chessa, Stefania
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Bergero, Domenico
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Sacchi, Paola
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Ferrocino, Ilario
  • Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy.
Cocolin, Luca
  • Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy.
Corvaglia, Maria Rita
  • Department of Agricultural, Forestry and Food Science, University of Turin, Grugliasco, Italy.
Moretti, Riccardo
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Cavallini, Damiano
  • Department of Veterinary Sciences, University of Bologna, Bologna, Italy.
Valle, Emanuela
  • Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

References

This article includes 46 references
  1. Stewart AS, Pratt-Phillips S, Gonzalez LM. Alterations in intestinal permeability: the role of the “leaky gut” in health and disease.. J Equine Vet (2017) 52:10–22.
    doi: 10.1016/j.jevs.2017.02.009pmc: PMC6467570pubmed: 31000910google scholar: lookup
  2. Valle E, Giusto G, Penazzi L, Giribaldi M, Bergero D, Fradinho MJ. Preliminary results on the association with feeding and recovery length in equine colic patients after laparotomy.. J Anim Physiol Anim Nutr (2019) 103:1233–41.
    doi: 10.1111/jpn.13102pubmed: 31025443google scholar: lookup
  3. Daly K, Proudman CJ, Duncan SH, Flint HJ, Dyer J, Shirazi-Beechey SP. Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease.. Br J Nutr (2012) 107:989–95.
    doi: 10.1017/S0007114511003825pubmed: 21816118google scholar: lookup
  4. Lorenzo-Figueras M, Morisset SM, Morisset J, Lainé J, Merrit AM. Digestive enzyme concentrations and activities in healthy pancreatic tissue of horses.. Am J Vet Res (2007) 68:1070–2.
    doi: 10.2460/ajvr.68.10.1070pubmed: 17916012google scholar: lookup
  5. Merritt AM, Julliand V. Gastrointestinal physiology. In: Saunders WB, editor. Equine applied and clinical nutrition. Amsterdam: Elsevier Ltd; (2013). 3–32.
  6. Bulmer LS, Murray JA, Burns NM, Garber A, Wemelsfelder F, McEwan NR. High-starch diets alter equine faecal microbiota and increase behavioural reactivity.. Sci Rep (2019) 9:1–11.
    doi: 10.1038/s41598-019-54039-8pmc: PMC6901590pubmed: 31819069google scholar: lookup
  7. Coenen M, Kienzle E, Vervuert I, Zeyner A. Recent German developments in the formulation of energy and nutrient requirements in horses and the resulting feeding recommendations.. J Equine Vet (2011) 31:219–29.
  8. Harris P, Shepherd M. What would be good for all veterinarians to know about equine nutrition.. Vet Clin North Am (2021) 37:1–20.
    doi: 10.1016/j.cveq.2020.11.001pubmed: 33820603google scholar: lookup
  9. Vervuert I, Voigt K, Hollands T, Cí·¯ord D, Coenen M. Effect of feeding increasing quantities of starch on glycaemic and insulinaemic responses in healthy horses.. Vet J (2009) 182:67–72.
    doi: 10.1016/j.tvjl.2008.04.011pubmed: 18558504google scholar: lookup
  10. Hoffman CJ, Costa LR, Freeman LM. Survey of feeding practices, supplement use, and knowledge of equine nutrition among a subpopulation of horse owners in New England.. J Equine Vet (2009) 29:719–26.
  11. Murray J-AMD, Bloxham C, Kulifay J, Stevenson A, Roberts J. Equine nutrition: a survey of perceptions and practices of horse owners undertaking a massive open online course in equine nutrition.. J Equine Vet (2015) 35:510–7.
  12. Raspa F, Tarantola M, Bergero D, Bellino C, Mastrazzo CM, Visconti A. Stocking density affects welfare indicators in horses reared for meat production.. Animals (2020) 10:1103.
    doi: 10.3390/ani10061103pmc: PMC7341190pubmed: 32604808google scholar: lookup
  13. Julliand V, de Fombelle A, Drogoul C, Jacoto E. Feeding and microbial disorders in horses: part 3- effects of three hay: grain ratios on microbial profile and activities.. J Equine Vet (2001) 21:543–6.
  14. Davis JL, Blikslager AT, Catto K, Jones SL. A retrospective analysis of hepatic injury in horses with proximal enteritis (1984-2002).. J Vet Intern Med (2003) 17:896–901.
  15. Raspa F, Dinardo FR, Vervuert I, Bergero D, Bottero MT, Pattono D. A fibre-vs. cereal grain-based diet: which is better for horse welfare? Effects on intestinal permeability, muscle characteristics and oxidative status in horses reared for meat production.. J Anim Physiol Anim Nutr (2021) 106:313–26.
    doi: 10.1111/jpn.13643pmc: PMC9292821pubmed: 34553422google scholar: lookup
  16. Raspa F, Vervuert I, Capucchio MT, Colombino E, Bergero D, Forte C. A high-starch vs. high-fibre diet: effects on the gut environment of the different intestinal compartments of the horse digestive tract.. BMC Vet Res (2022) 18:1–11.
    doi: 10.1186/s12917-022-03289-2pmc: PMC9118577pubmed: 35590319google scholar: lookup
  17. Ang L, Vinderola G, Endo A, Kantanen J, Jingfeng C, Binetti A. Gut microbiome characteristics in feral and domesticated horses from different geographic locations.. Commun Biol (2022) 5:1–10.
    doi: 10.1038/s42003-022-03116-2pmc: PMC8881449pubmed: 35217713google scholar: lookup
  18. Costa MC, Silva G, Ramos RV, Staempfli HR, Arroyo LG, Kim P. Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses.. Vet J (2015) 205:74–80.
    doi: 10.1016/j.tvjl.2015.03.018pubmed: 25975855google scholar: lookup
  19. Kauter A, Epping L, Semmler T, Antao E-M, Kannapin D, Stoeckle SD. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives.. Anim Microbiome (2019) 1:1–14.
    doi: 10.1186/s42523-019-0013-3pmc: PMC7807895pubmed: 33499951google scholar: lookup
  20. De Fombelle A, Varloud M, Goachet AG, Jacotot E, Philippeau C, Drogoul C. Characterization of the microbial and biochemical profile of the different segments of the digestive tract in horses given two distinct diets.. Anim Sci (2003) 77:293–304.
    doi: 10.1017/S1357729800059038google scholar: lookup
  21. Panek M, Paljetak HČ, Barešić A, Perić M, Matijašić M, Lojkić I. Methodology challenges in studying human gut microbiota-effects of collection, storage, DNA extraction and next generation sequencing technologies OPEN.. Sci Rep (2018) 8:5143.
    doi: 10.1038/s41598-018-23296-4pmc: PMC5865204pubmed: 29572539google scholar: lookup
  22. Dougal K, Harris PA, Edwards A, Pachebat JA, Blackmore TM, Worgan HJ. A comparison of the microbiome and the metabolome of different regions of the equine hindgut.. FEMS Microbiol Ecol (2012) 82:642–52.
  23. Costa MC, Weese JS. The equine intestinal microbiome.. Anim Health Res Rev (2012) 13:121–8.
    doi: 10.1017/S1466252312000035pubmed: 22626511google scholar: lookup
  24. Dougal K, De La Fuente G, Harris PA, Girdwood SE, Pinloche E, Newbold CJ. Identification of a Core bacterial community within the large intestine of the horse.. PLoS One (2013) 8:e77660.
  25. Colombino E, Raspa F, Perotti M, Bergero D, Vervuert I, Valle E. Gut health of horses: effects of high fibre vs high starch diet on histological and morphometrical parameters.. BMC Vet Res (2022) 18:1–9.
    doi: 10.1186/s12917-022-03433-ypmc: PMC9454146pubmed: 36076239google scholar: lookup
  26. Raspa F, Tarantola M, Muca E, Bergero D, Soglia D, Cavallini D. Does feeding management make a difference to behavioural activities and welfare of horses reared for meat production?. Animals (2022) 12:1740.
    doi: 10.3390/ani12141740pmc: PMC9311627pubmed: 35883287google scholar: lookup
  27. Martin-rosset W. Equine nutrition: INRA nutrient requirements, recommended allowances and feed tables.. Acad Publ (2015).
    doi: 10.3920/978-90-8686-855-1google scholar: lookup
  28. Klindworth A, Pruesse E, Schweer T, Rg Peplies J, Quast C, Horn M. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.. Nucleic Acids Res (2013) 41:e1.
    doi: 10.1093/nar/gks808pmc: PMC3592464pubmed: 22933715google scholar: lookup
  29. Bolyen E, Ram Rideout J, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.. Nat Biotechnol (2019) 37:852–7.
    doi: 10.1038/s41587-019-0209-9pmc: PMC7015180pubmed: 31341288google scholar: lookup
  30. Callahan BJ, Mcmurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from illumina amplicon data.. Nat Methods (2016) 13:581–3.
    doi: 10.1038/nmeth.3869pmc: PMC4927377pubmed: 27214047google scholar: lookup
  31. Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin.. Microbiome (2018) 6:1–17.
    doi: 10.1186/s40168-018-0470-zpmc: PMC5956843pubmed: 29773078google scholar: lookup
  32. Culhane AC, Thioulouse J, Perrière G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data.. Bioinformatics (2005) 21:2789–90.
    doi: 10.1093/bioinformatics/bti394pubmed: 15797915google scholar: lookup
  33. Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM. PICRUSt2 for prediction of metagenome functions.. Nat Biotechnol (2020) 386:685–8.
    doi: 10.1038/s41587-020-0548-6pmc: PMC7365738pubmed: 32483366google scholar: lookup
  34. Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. GAGE: generally applicable gene set enrichment for pathway analysis.. BMC Bioinformatics (2009) 10:1–17.
    doi: 10.1186/1471-2105-10-161pmc: PMC2696452pubmed: 19473525google scholar: lookup
  35. Al Jassim RAM, Andrews FM. The bacterial Community of the Horse Gastrointestinal Tract and its Relation to fermentative acidosis, laminitis, colic, and stomach ulcers.. Vet Clin North Am (2009) 25:199–215.
    doi: 10.1016/j.cveq.2009.04.005pubmed: 19580934google scholar: lookup
  36. Carrillo Heredero AM, Sabbioni A, Asti V, Ablondi M, Summer A, Bertini S. Fecal microbiota characterization of an Italian local horse breed.. Front Vet Sci (2024) 11:1236476.
    doi: 10.3389/fvets.2024.1236476pmc: PMC10902133pubmed: 38425839google scholar: lookup
  37. Ericsson AC, Johnson PJ, Lopes MA, Perry SC, Lanter HR. A microbiological map of the healthy equine gastrointestinal tract.. PLoS One (2016) 11:1–17.
  38. Biasato I, Ferrocino I, Biasibetti E, Grego E, Dabbou S, Sereno A. Modulation of intestinal microbiota, morphology and mucin composition by dietary insect meal inclusion in free-range chickens.. BMC Vet Res (2018) 14:1–15.
    doi: 10.1186/s12917-018-1690-ypmc: PMC6278000pubmed: 30514391google scholar: lookup
  39. Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, Geor RJ. Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing.. PLoS One (2014) 9:e87424.
  40. Steelman SM, Chowdhary BP, Dowd S, Suchodolski J, Janečka JE. Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis.. BMC Vet Res (2012) 8:1–11.
    doi: 10.1186/1746-6148-8-231pmc: PMC3538718pubmed: 23186268google scholar: lookup
  41. Costa MC, Arroyo LG, Allen-Vercoe E, Stämpfli HR, Kim PT, Sturgeon A. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16s rRNA gene.. PLoS One (2012) 7:e41484.
  42. Daly K, Stewart CS, Flint HJ, Shirazi-Beechey SP. Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes.. FEMS Microbiol Ecol (2001) 38:141–51.
  43. Julliand V, Grimm P. Horse species symposium: the microbiome of the horse hindgut: history and current knowledge.. J Anim Sci (2016) 94:2262–74.
    doi: 10.2527/jas.2015-0198pubmed: 27285903google scholar: lookup
  44. Rodriguez C, Taminiau B, Brévers B, Avesani V, Van Broeck J, Leroux A. Faecal microbiota characterisation of horses using 16 rDNA barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission.. BMC Microbiol (2015) 15:181.
    doi: 10.1186/s12866-015-0514-5pmc: PMC4573688pubmed: 26377067google scholar: lookup
  45. Harlow BE, Lawrence LM, Hayes SH, Crum A, Flythe MD. Effect of dietary starch source and concentration on equine fecal microbiota.. PLoS One (2016) 11:e0154037.
  46. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity.. Proc Natl Acad Sci USA (2013) 110:9066–71.
    doi: 10.1073/pnas.1219451110pmc: PMC3670398pubmed: 23671105google scholar: lookup

Citations

This article has been cited 12 times.
  1. Wang M, Qu Y, Ma X, Fan Y, Zhang C, Li J, Liu X, Wang Z, Li J, Wang Y, Zhang T, Chu D, Liu J, Li Y. Temporal dynamics of the fecal microbiome in wintering seagulls: a One Health perspective. BMC Genomics 2026 Feb 12;27(1):191.
    doi: 10.1186/s12864-026-12629-7pubmed: 41680605google scholar: lookup
  2. Wei L, Wei J, Liu X, Chen W, Wang C, Khan MZ, Zhang Z. Effects of Feeding Strategies on Gut Microbial Communities in Donkeys: A Comprehensive Narrative Review. Vet Sci 2025 Dec 20;13(1).
    doi: 10.3390/vetsci13010007pubmed: 41600662google scholar: lookup
  3. Sun M, Yao H, Wang R, Zhang Z, Wu H, Zhao D. How Habitat Micromodification Influences Gut Microbiota and Diet Composition of Reintroduced Species: Evidence from Endangered Père David's Deer. Microorganisms 2026 Jan 10;14(1).
  4. François AC, Taminiau B, Renaud B, Gonza-Quito IE, Massey C, Hyde C, Piercy RJ, Douny C, Scippo ML, Daube G, Gustin P, Delcenserie V, Votion DM. In Vitro Investigation of Equine Gut Microbiota Alterations During Hypoglycin A Exposure. Animals (Basel) 2025 Nov 19;15(22).
    doi: 10.3390/ani15223343pubmed: 41302050google scholar: lookup
  5. Austin MMP, Ivey JLZ, Shepherd EA, Myer PR. Methodologies to Identify Metabolic Pathway Differences Between Emaciated and Moderately Conditioned Horses: A Review of Multiple Gene Expression Techniques. Animals (Basel) 2025 Oct 10;15(20).
    doi: 10.3390/ani15202933pubmed: 41153862google scholar: lookup
  6. Li F, Kong X, Khan MZ, Wei L, Wei J, Zhu M, Liu G, Huang B, Wang C, Zhang Z. Gut microbiome regulation in equine animals: current understanding and future perspectives. Front Microbiol 2025;16:1602258.
    doi: 10.3389/fmicb.2025.1602258pubmed: 41070119google scholar: lookup
  7. Brands L, Ullrich C, Wilke V, Visscher C, Kamphues J, Abd El-Wahab A. Effects of Poultry By-Product Composition and Processing on Nutrient Digestibility and Fecal Characteristics of High-Protein Dry Dog Food. Animals (Basel) 2025 Sep 15;15(18).
    doi: 10.3390/ani15182693pubmed: 41007938google scholar: lookup
  8. Irving J, Pineau V, Shultz S, Ter Woort F, Julien F, Lambey S, van Erck-Westergren E. Impact of Low-Starch Dietary Modifications on Faecal Microbiota Composition and Gastric Disease Scores in Performance Horses. Animals (Basel) 2025 Jun 28;15(13).
    doi: 10.3390/ani15131908pubmed: 40646806google scholar: lookup
  9. Fusaro I, Parrillo S, Buonaiuto G, Prasinou P, Gramenzi A, Bucci R, Cavallini D, Carosi A, Carluccio A, De Amicis I. Effects of hemp-based polyunsaturated fatty acid supplementation on membrane lipid profiles and reproductive performance in Martina Franca jacks. Front Vet Sci 2025;12:1553218.
    doi: 10.3389/fvets.2025.1553218pubmed: 40308695google scholar: lookup
  10. Cross K, Beckman N, Jahnes B, Sabree ZL. Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy. Appl Environ Microbiol 2025 Feb 19;91(2):e0236824.
    doi: 10.1128/aem.02368-24pubmed: 39882875google scholar: lookup
  11. Brandi LA, Nunes AT, Faleiros CA, Poleti MD, Oliveira ECM, Schmidt NT, Sousa RLM, Fukumasu H, Balieiro JCC, Brandi RA. Dietary Energy Sources Affect Cecal and Fecal Microbiota of Healthy Horses. Animals (Basel) 2024 Dec 3;14(23).
    doi: 10.3390/ani14233494pubmed: 39682460google scholar: lookup
  12. Bishop RC, Kemper AM, Clark LV, Wilkins PA, McCoy AM. Stability of Gastric Fluid and Fecal Microbial Populations in Healthy Horses under Pasture and Stable Conditions. Animals (Basel) 2024 Oct 16;14(20).
    doi: 10.3390/ani14202979pubmed: 39457909google scholar: lookup