FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Animals : an open access journal from MDPI2025; 15(5); 758; doi: 10.3390/ani15050758

Gut Microbiota of Ruminants and Monogastric Livestock: An Overview.

Abstract: The diversity and composition of the gut microbiota are widely recognized as fundamental factors influencing the well-being and productivity of domestic animals. Advancements in sequencing technologies have revolutionized studies in this research field, allowing for deeper insights into the composition and functionality of microbiota in livestock. Ruminants and monogastric animals exhibit distinct digestive systems and microbiota characteristics: ruminants rely on fermentation, while monogastrics use enzymatic digestion, and monogastric animals have simpler stomach structures, except for horses and rabbits, where both processes coexist. Understanding the gut microbiota's impact and composition in both animal types is essential for optimizing production efficiency and promoting animal health. Following this perspective, the present manuscript review aims to provide a comprehensive overview of the gut microbiota in ruminants (such as cattle, sheep, and goats) and monogastric animals (including horses, pigs, rabbits, and chickens).
Get Full Text
Publication Date: 2025-03-06 PubMed ID: 40076043PubMed Central: PMC11899476DOI: 10.3390/ani15050758Google 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.
LinkedInCopy
  • Journal Article
  • Review

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.

Gut microbiota plays a crucial role in the health and productivity of livestock animals, with ruminants and monogastric species having different digestive systems and microbial communities. This research article reviews the composition and significance of gut microbiota in these two groups to improve animal health and production outcomes.

Introduction to Gut Microbiota in Livestock

  • The gut microbiota consists of diverse microorganisms living in the digestive tract of animals.
  • This microbial community influences digestion, nutrient absorption, immune function, and overall health.
  • Recent advances in sequencing technologies have enabled scientists to gain detailed insights into the microbiota’s composition and functionality.
  • Understanding the differences between ruminants and monogastric animals is important, as their digestive systems vary significantly.

Differences Between Ruminants and Monogastric Animals

  • Ruminants: Include animals like cattle, sheep, and goats.
  • Ruminants have a complex stomach with four compartments, facilitating fermentation by microbes.
  • Fermentation allows these animals to break down fibrous plant material efficiently.
  • The microbial population in ruminants is specialized to optimize fiber digestion and volatile fatty acid production.
  • Monogastric animals: Include species such as pigs, chickens, and rabbits.
  • Have simpler single-chambered stomachs primarily relying on enzymatic digestion rather than fermentation.
  • Exceptions like horses and rabbits utilize a hindgut fermentation process alongside enzymatic digestion.
  • Their gut microbiota is adapted to their digestion style and diet, often focusing on starch and protein breakdown.

Importance of Gut Microbiota in Livestock Health and Productivity

  • The composition of gut bacteria influences feed efficiency and nutrient utilization.
  • A balanced microbiota aids in protection against pathogens, reducing disease incidence.
  • Alterations or imbalances in microbial communities can negatively affect growth, milk production, and meat quality.
  • Microbiota manipulation via diet, probiotics, or other strategies offers potential to enhance animal well-being and production.

Aims of the Review Article

  • To provide a comprehensive summary of current knowledge about the gut microbiota in ruminants and monogastric livestock.
  • To highlight the distinctive microbiota features associated with each digestive system type.
  • To underscore the importance of gut microbial communities in animal health and production optimization.
  • To review recent technological advancements enabling these insights.

Conclusion

  • The gut microbiota is a pivotal factor influencing livestock health and productivity.
  • Recognizing digestive system differences between ruminants and monogastrics is vital for targeted strategies.
  • This review consolidates existing data on gut microbiota in key domestic species, providing a foundation for future research and applications.

Cite This Article

APA
Tardiolo G, La Fauci D, Riggio V, Daghio M, Di Salvo E, Zumbo A, Sutera AM. (2025). Gut Microbiota of Ruminants and Monogastric Livestock: An Overview. Animals (Basel), 15(5), 758. https://doi.org/10.3390/ani15050758

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 5
PII: 758

Researcher Affiliations

Tardiolo, Giuseppe
  • Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci 13, 98168 Messina, Italy.
La Fauci, Deborah
  • Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci 13, 98168 Messina, Italy.
Riggio, Valentina
  • The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK.
Daghio, Matteo
  • Department of Agriculture, Food, Environment and Forestry, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
Di Salvo, Eleonora
  • Department of Biomedical, Dental Sciences, Morphological and Functional Imaging, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy.
Zumbo, Alessandro
  • Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci 13, 98168 Messina, Italy.
Sutera, Anna Maria
  • Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy.

Conflict of Interest Statement

The authors declare no conflicts of interest.

References

This article includes 220 references
  1. Wang W, Dong Y, Guo W, Zhang X, Degen AA, Bi S, Ding L, Chen X, Long R. Linkages between Rumen Microbiome, Host, and Environment in Yaks, and Their Implications for Understanding Animal Production and Management.. Front. Microbiol. 2024;15:1301258.
    doi: 10.3389/fmicb.2024.1301258pmc: PMC10860762pubmed: 38348184google scholar: lookup
  2. Guo CY, Ji SK, Yan H, Wang YJ, Liu JJ, Cao ZJ, Yang HJ, Zhang WJ, Li SL. Dynamic Change of the Gastrointestinal Bacterial Ecology in Cows from Birth to Adulthood.. MicrobiologyOpen 2020;9:e1119.
    doi: 10.1002/mbo3.1119pmc: PMC7658451pubmed: 33034165google scholar: lookup
  3. Arshad MA, Hassan F, Rehman MS, Huws SA, Cheng Y, Din AU. Gut Microbiome Colonization and Development in Neonatal Ruminants: Strategies, Prospects, and Opportunities.. Anim. Nutr. 2021;7:883–895.
    doi: 10.1016/j.aninu.2021.03.004pmc: PMC8484983pubmed: 34632119google scholar: lookup
  4. Wegener Parfrey L, Walters WA, Knight R. Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions.. Front. Microbiol. 2011;2.
    doi: 10.3389/fmicb.2011.00153pmc: PMC3135866pubmed: 21808637google scholar: lookup
  5. Gresse R, Chaucheyras Durand F, Dunière L, Blanquet-Diot S, Forano E. Microbiota Composition and Functional Profiling throughout the Gastrointestinal Tract of Commercial Weaning Piglets.. Microorganisms 2019;7:343.
    doi: 10.3390/microorganisms7090343pmc: PMC6780805pubmed: 31547478google scholar: lookup
  6. Shkoporov AN, Hill C. Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome.. Cell Host Microbe 2019;25:195–209.
    doi: 10.1016/j.chom.2019.01.017pubmed: 30763534google scholar: lookup
  7. Lin Y, Zhou B, Zhu W. Pathogenic Escherichia Coli-Specific Bacteriophages and Polyvalent Bacteriophages in Piglet Guts with Increasing Coliphage Numbers after Weaning.. Appl. Environ. Microbiol. 2021;87:e00966-21.
    doi: 10.1128/AEM.00966-21pmc: PMC8357296pubmed: 34160270google scholar: lookup
  8. Loc-Carrillo C, Abedon ST. Pros and Cons of Phage Therapy.. Bacteriophage 2011;1:111–114.
    doi: 10.4161/bact.1.2.14590pmc: PMC3278648pubmed: 22334867google scholar: lookup
  9. Hartinger T, Zebeli Q. The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition.. J. Fungi 2021;7:200.
    doi: 10.3390/jof7030200pmc: PMC8000393pubmed: 33802104google scholar: lookup
  10. Król B, Słupczyńska M, Wilk M, Asghar M, Cwynar P. Anaerobic Rumen Fungi and Fungal Direct-Fed Microbials in Ruminant Feeding.. J. Anim. Feed Sci. 2023;32:3–16.
    doi: 10.22358/jafs/153961/2022google scholar: lookup
  11. Jyothi C, Muwel N, Nayak S, Khare A, Sharma R, Keshri A, Singour S, Mishra R, Tiwari S. Anaerobic Rumen Fungi as a Feed Additive in Ruminants: A Review.. J. Livest. Sci. 2024;15:78–85.
    doi: 10.33259/JLivestSci.2024.78-85google scholar: lookup
  12. Hess M, Paul SS, Puniya AK, Van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future.. Front. Microbiol. 2020;11:584893.
    doi: 10.3389/fmicb.2020.584893pmc: PMC7609409pubmed: 33193229google scholar: lookup
  13. Iliev ID, Underhill DM. Striking a Balance: Fungal Commensalism versus Pathogenesis.. Curr. Opin. Microbiol. 2013;16:366–373.
    doi: 10.1016/j.mib.2013.05.004pmc: PMC3742553pubmed: 23756050google scholar: lookup
  14. Donaldson GP, Lee SM, Mazmanian SK. Gut Biogeography of the Bacterial Microbiota.. Nat. Rev. Microbiol. 2016;14:20–32.
    doi: 10.1038/nrmicro3552pmc: PMC4837114pubmed: 26499895google scholar: lookup
  15. Bickhart DM, McClure JC, Schnabel RD, Rosen BD, Medrano JF, Smith TPL. Symposium Review: Advances in Sequencing Technology Herald a New Frontier in Cattle Genomics and Genome-Enabled Selection.. J. Dairy Sci. 2020;103:5278–5290.
    doi: 10.3168/jds.2019-17693pubmed: 32331872google scholar: lookup
  16. Russell JB, Rychlik JL. Factors That Alter Rumen Microbial Ecology. Science 2001;292:1119–1122.
    doi: 10.1126/science.1058830pubmed: 11352069google scholar: lookup
  17. Tugnoli B, Giovagnoni G, Piva A, Grilli E. From Acidifiers to Intestinal Health Enhancers: How Organic Acids Can Improve Growth Efficiency of Pigs. Animals 2020;10:134.
    doi: 10.3390/ani10010134pmc: PMC7022919pubmed: 31947627google scholar: lookup
  18. McCallum G, Tropini C. The Gut Microbiota and Its Biogeography. Nat. Rev. Microbiol. 2024;22:105–118.
    doi: 10.1038/s41579-023-00969-0pubmed: 37740073google scholar: lookup
  19. Malmuthuge N, Li M, Goonewardene LA, Oba M, Guan LL. Effect of Calf Starter Feeding on Gut Microbial Diversity and Expression of Genes Involved in Host Immune Responses and Tight Junctions in Dairy Calves during Weaning Transition. J. Dairy. Sci. 2013;96:3189–3200.
    doi: 10.3168/jds.2012-6200pubmed: 23498024google scholar: lookup
  20. Shin N-R, Whon TW, Bae J-W. Proteobacteria: Microbial Signature of Dysbiosis in Gut Microbiota. Trends Biotechnol. 2015;33:496–503.
    doi: 10.1016/j.tibtech.2015.06.011pubmed: 26210164google scholar: lookup
  21. Amos GCA, Logan A, Anwar S, Fritzsche M, Mate R, Bleazard T, Rijpkema S. Developing Standards for the Microbiome Field. Microbiome 2020;8:98.
    doi: 10.1186/s40168-020-00856-3pmc: PMC7320585pubmed: 32591016google scholar: lookup
  22. Wegl G, Grabner N, Köstelbauer A, Klose V, Ghanbari M. Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. Front. Microbiol. 2021;12:627539.
    doi: 10.3389/fmicb.2021.627539pmc: PMC7940207pubmed: 33708184google scholar: lookup
  23. Malmuthuge N, Guan LL. Gut Microbiome and Omics: A New Definition to Ruminant Production and Health. Anim. Front. 2016;6:8–12.
    doi: 10.2527/af.2016-0017google scholar: lookup
  24. Alexander TW, Plaizier JC. From the Editors: The Importance of Microbiota in Ruminant Production. Anim. Front. 2016;6:4–7.
    doi: 10.2527/af.2016-0016google scholar: lookup
  25. Cholewińska P, Czyż K, Nowakowski P, Wyrostek A. The Microbiome of the Digestive System of Ruminants—A Review. Anim. Health Res. Rev. 2020;21:3–14.
    doi: 10.1017/S1466252319000069pubmed: 31918781google scholar: lookup
  26. Alexandratos N, Bruinsma J. World Agriculture Towards 2030/2050: The 2012 Revision. FAO; Rome, Italy: 2012. ESA Working Papers 12-03.
  27. Chen B, Li D, Leng D, Kui H, Bai X, Wang T. Gut Microbiota and Meat Quality. Front. Microbiol. 2022;13:951726.
    doi: 10.3389/fmicb.2022.951726pmc: PMC9445620pubmed: 36081790google scholar: lookup
  28. Celi P, Cowieson AJ, Fru-Nji F, Steinert RE, Kluenter A-M, Verlhac V. Gastrointestinal Functionality in Animal Nutrition and Health: New Opportunities for Sustainable Animal Production. Anim. Feed Sci. Technol. 2017;234:88–100.
    doi: 10.1016/j.anifeedsci.2017.09.012google scholar: lookup
  29. Denman SE, Morgavi DP, McSweeney CS. Review: The Application of Omics to Rumen Microbiota Function. Animal 2018;12:s233–s245.
    doi: 10.1017/S175173111800229Xpubmed: 30261940google scholar: lookup
  30. Li B, Zhang K, Li C, Wang X, Chen Y, Yang Y. Characterization and Comparison of Microbiota in the Gastrointestinal Tracts of the Goat (Capra Hircus) During Preweaning Development. Front. Microbiol. 2019;10:2125.
    doi: 10.3389/fmicb.2019.02125pmc: PMC6753876pubmed: 31572331google scholar: lookup
  31. Vántus V.B., Kovács M., Zsolnai A.. The Rabbit Caecal Microbiota: Development, Composition and Its Role in the Prevention of Digestive Diseases–a Review on Recent Literature in the Light of Molecular Genetic Methods. Acta Agrar. Kaposváriensis 2014;18:55–65.
  32. Henderson G., Cox F., Ganesh S., Jonker A., Young W., Janssen P.H.. Rumen Microbial Community Composition Varies with Diet and Host, but a Core Microbiome Is Found across a Wide Geographical Range. Sci. Rep. 2015;5:14567.
    doi: 10.1038/srep14567pmc: PMC4598811pubmed: 26449758google scholar: lookup
  33. Xiao L., Estellé J., Kiilerich P., Ramayo-Caldas Y., Xia Z., Feng Q., Liang S., Pedersen A.Ø., Kjeldsen N.J., Liu C.. A Reference Gene Catalogue of the Pig Gut Microbiome. Nat. Microbiol. 2016;1:16161.
    doi: 10.1038/nmicrobiol.2016.161pubmed: 27643971google scholar: lookup
  34. Reece W.O., Rowe E.W.. Functional Anatomy and Physiology of Domestic Animals. .
  35. Bagwan W.A., Durgawale P., Jadhav M.A.V., Vidyapeeth K.V.. Exploring the Gut Microbiota of Ruminants and Its Impact on Digestive Efficiency and Methane Emissions in Livestock Production Systems. Afr. J. Biol. Sci. 2024;6:2226–2236.
  36. Na S.W., Guan L.L.. Understanding the Role of Rumen Epithelial Host-Microbe Interactions in Cattle Feed Efficiency. Anim. Nutr. 2022;10:41–53.
    doi: 10.1016/j.aninu.2022.04.002pmc: PMC9117530pubmed: 35647325google scholar: lookup
  37. Palumbo F., Squartini A., Barcaccia G., Macolino S., Pornaro C., Pindo M., Sturaro E., Ramanzin M.. A Multi-Kingdom Metabarcoding Study on Cattle Grazing Alpine Pastures Discloses Intra-Seasonal Shifts in Plant Selection and Faecal Microbiota. Sci. Rep. 2021;11:889.
    doi: 10.1038/s41598-020-79474-wpmc: PMC7806629pubmed: 33441587google scholar: lookup
  38. Mao S., Zhang M., Liu J., Zhu W.. Characterising the Bacterial Microbiota across the Gastrointestinal Tracts of Dairy Cattle: Membership and Potential Function. Sci. Rep. 2015;5:16116.
    doi: 10.1038/srep16116pmc: PMC4630781pubmed: 26527325google scholar: lookup
  39. McGovern E., Kenny D.A., McCabe M.S., Fitzsimons C., McGee M., Kelly A.K., Waters S.M.. 16S rRNA Sequencing Reveals Relationship Between Potent Cellulolytic Genera and Feed Efficiency in the Rumen of Bulls. Front. Microbiol. 2018;9:01842.
    doi: 10.3389/fmicb.2018.01842pmc: PMC6097346pubmed: 30147683google scholar: lookup
  40. Daghio M., Ciucci F., Buccioni A., Cappucci A., Casarosa L., Serra A., Conte G., Viti C., McAmmond B.M., Van Hamme J.D.. Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions. Front. Microbiol. 2021;12:652031.
    doi: 10.3389/fmicb.2021.652031pmc: PMC8117017pubmed: 33995309google scholar: lookup
  41. Plaizier J.C., Li S., Tun H.M., Khafipour E.. Nutritional Models of Experimentally-Induced Subacute Ruminal Acidosis (SARA) Differ in Their Impact on Rumen and Hindgut Bacterial Communities in Dairy Cows. Front. Microbiol. 2017;7:02128.
    doi: 10.3389/fmicb.2016.02128pmc: PMC5265141pubmed: 28179895google scholar: lookup
  42. Rudi K., Moen B., Sekelja M., Frisli T., Lee M.R.. An Eight-Year Investigation of Bovine Livestock Fecal Microbiota. Vet. Microbiol. 2012;160:369–377.
    doi: 10.1016/j.vetmic.2012.06.003pubmed: 22749759google scholar: lookup
  43. Jami E., Mizrahi I.. Composition and Similarity of Bovine Rumen Microbiota across Individual Animals. PLoS ONE 2012;7:e33306.
    doi: 10.1371/journal.pone.0033306pmc: PMC3303817pubmed: 22432013google scholar: lookup
  44. Li R.W., Connor E.E., Li C., Baldwin R.L., VI, Sparks M.E.. Characterization of the Rumen Microbiota of Pre-Ruminant Calves Using Metagenomic Tools. Environ. Microbiol. 2012;14:129–139.
    doi: 10.1111/j.1462-2920.2011.02543.xpubmed: 21906219google scholar: lookup
  45. Hagey J.V., Bhatnagar S., Heguy J.M., Karle B.M., Price P.L., Meyer D., Maga E.A.. Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows. Front. Microbiol. 2019;10:1093.
    doi: 10.3389/fmicb.2019.01093pmc: PMC6532609pubmed: 31156599google scholar: lookup
  46. Xue M, Sun H, Wu X, Guan L.L, Liu J. Assessment of Rumen Microbiota from a Large Dairy Cattle Cohort Reveals the Pan and Core Bacteriomes Contributing to Varied Phenotypes. Appl. Environ. Microbiol. 2018;84:e00970-18.
    doi: 10.1128/AEM.00970-18pmc: PMC6146982pubmed: 30054362google scholar: lookup
  47. Taxis T.M, Wolff S, Gregg S.J, Minton N.O, Zhang C, Dai J, Schnabel R.D, Taylor J.F, Kerley M.S, Pires J.C. The Players May Change but the Game Remains: Network Analyses of Ruminal Microbiomes Suggest Taxonomic Differences Mask Functional Similarity. Nucleic Acids Res. 2015;43:9600–9612.
    doi: 10.1093/nar/gkv973pmc: PMC4787786pubmed: 26420832google scholar: lookup
  48. Forcina G, Pérez-Pardal L, Carvalheira J, Beja-Pereira A. Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals 2022;12:3375.
    doi: 10.3390/ani12233375pmc: PMC9736591pubmed: 36496896google scholar: lookup
  49. Rawal S, Kaur H, Bhathan S, Mittal D, Kaur G, Ali S.A. Ruminant Gut Microbiota: Interplay, Implications, and Innovations for Sustainable Livestock Production. Sustainable Agriculture Reviews: Animal Biotechnology for Livestock Production 2024;4:205–228.
  50. Wallace R.J, Sasson G, Garnsworthy P.C, Tapio I, Gregson E, Bani P, Huhtanen P, Bayat A.R, Strozzi F, Biscarini F. A Heritable Subset of the Core Rumen Microbiome Dictates Dairy Cow Productivity and Emissions. Sci. Adv. 2019;5:eaav8391.
    doi: 10.1126/sciadv.aav8391pmc: PMC6609165pubmed: 31281883google scholar: lookup
  51. Stewart R.D, Auffret M.D, Warr A, Walker A.W, Roehe R, Watson M. Compendium of 4,941 Rumen Metagenome-Assembled Genomes for Rumen Microbiome Biology and Enzyme Discovery. Nat. Biotechnol. 2019;37:953–961.
    doi: 10.1038/s41587-019-0202-3pmc: PMC6785717pubmed: 31375809google scholar: lookup
  52. Xue M.-Y, Sun H.-Z, Wu X.-H, Liu J.-X, Guan L.L. Multi-Omics Reveals That the Rumen Microbiome and Its Metabolome Together with the Host Metabolome Contribute to Individualized Dairy Cow Performance. Microbiome 2020;8:64.
    doi: 10.1186/s40168-020-00819-8pmc: PMC7218573pubmed: 32398126google scholar: lookup
  53. Scicutella F, Cucu M.A, Mannelli F, Pastorelli R, Daghio M, Paoli P, Pazzagli L, Turini L, Mantino A, Luti S. Rumen Microbial Community and Milk Quality in Holstein Lactating Cows Fed Olive Oil Pomace as Part in a Sustainable Feeding Strategy. Animal 2023;17:100815.
    doi: 10.1016/j.animal.2023.100815pubmed: 37167820google scholar: lookup
  54. Song Y.C, Holland S.I, Lee M, Chen G, Zaugg J, Löffler F.E, Manefield M.J, Hugenholtz P, Kappler U. Corrigendum: ‘A Comparative Genome Analysis of the Bacillota (Firmicutes) Class Dehalobacteriia’. Microb. Genom. 2023;9:001092.
    doi: 10.1099/mgen.0.001092pmc: PMC10483425pubmed: 37555754google scholar: lookup
  55. Jami E, Israel A, Kotser A, Mizrahi I. Exploring the Bovine Rumen Bacterial Community from Birth to Adulthood. ISME J. 2013;7:1069–1079.
    doi: 10.1038/ismej.2013.2pmc: PMC3660679pubmed: 23426008google scholar: lookup
  56. Kim Y.-H, Nagata R, Ohkubo A, Ohtani N, Kushibiki S, Ichijo T, Sato S. Changes in Ruminal and Reticular pH and Bacterial Communities in Holstein Cattle Fed a High-Grain Diet. BMC Vet. Res. 2018;14:310.
    doi: 10.1186/s12917-018-1637-3pmc: PMC6186129pubmed: 30314483google scholar: lookup
  57. Myer P.R, Freetly H.C, Wells J.E, Smith T.P.L, Kuehn L.A. Analysis of the Gut Bacterial Communities in Beef Cattle and Their Association with Feed Intake, Growth, and Efficiency. J. Anim. Sci. 2017;95:3215–3224.
    doi: 10.2527/jas2016.1059pubmed: 28727105google scholar: lookup
  58. Danielsson R, Dicksved J, Sun L, Gonda H, Müller B, Schnürer A, Bertilsson J. Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure. Front. Microbiol. 2017;8:226.
    doi: 10.3389/fmicb.2017.00226pmc: PMC5313486pubmed: 28261182google scholar: lookup
  59. Danielsson R, Schnürer A, Arthurson V, Bertilsson J. Methanogenic Population and CH4 Production in Swedish Dairy Cows Fed Different Levels of Forage. Appl. Environ. Microbiol. 2012;78:6172–6179.
    doi: 10.1128/AEM.00675-12pmc: PMC3416586pubmed: 22752163google scholar: lookup
  60. Janssen P.H, Kirs M. Structure of the Archaeal Community of the Rumen. Appl. Environ. Microbiol. 2008;74:3619–3625.
    doi: 10.1128/AEM.02812-07pmc: PMC2446570pubmed: 18424540google scholar: lookup
  61. Toyber I, Kumar R, Jami E. Rumen Protozoa Are a Hub for Diverse Hydrogenotrophic Functions.. Environ. Microbiol. Rep. 2024;16:e13298.
    doi: 10.1111/1758-2229.13298pmc: PMC11222294pubmed: 38961629google scholar: lookup
  62. Morgavi DP, Forano E, Martin C, Newbold CJ. Microbial Ecosystem and Methanogenesis in Ruminants.. Animal 2010;4:1024–1036.
    doi: 10.1017/S1751731110000546pubmed: 22444607google scholar: lookup
  63. Foggi G, Terranova M, Daghio M, Amelchanka SL, Conte G, Ineichen S, Agnolucci M, Viti C, Mantino A, Buccioni A. Evaluation of Ruminal Methane and Ammonia Formation and Microbiota Composition as Affected by Supplements Based on Mixtures of Tannins and Essential Oils Using Rusitec.. J. Anim. Sci. Biotechnol. 2024;15:48.
    doi: 10.1186/s40104-024-01005-8pmc: PMC10986001pubmed: 38561832google scholar: lookup
  64. Palangi V, Taghizadeh A, Abachi S, Lackner M. Strategies to Mitigate Enteric Methane Emissions in Ruminants: A Review.. Sustainability 2022;14:13229.
    doi: 10.3390/su142013229google scholar: lookup
  65. Popova M, McGovern E, McCabe MS, Martin C, Doreau M, Arbre M, Meale SJ, Morgavi DP, Waters SM. The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate.. Front. Microbiol. 2017;8:937.
    doi: 10.3389/fmicb.2017.00937pmc: PMC5442214pubmed: 28596764google scholar: lookup
  66. Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA. Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge.. PLoS ONE 2013;8:e83424.
    doi: 10.1371/journal.pone.0083424pmc: PMC3877040pubmed: 24391765google scholar: lookup
  67. Zhang Z, Yang L, He Y, Luo X, Zhao S, Jia X. Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle.. Animals 2021;11:3167.
    doi: 10.3390/ani11113167pmc: PMC8614352pubmed: 34827898google scholar: lookup
  68. Cui X, Wang Z, Guo P, Li F, Chang S, Yan T, Zheng H, Hou F. Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis Aries) To Adapt to the Cold Season.. Microbiol. Spectr. 2023;11:e02816-22.
    doi: 10.1128/spectrum.02816-22pmc: PMC10100778pubmed: 36809032google scholar: lookup
  69. Wang J, Fan H, Han Y, Zhao J, Zhou Z. Characterization of the Microbial Communities along the Gastrointestinal Tract of Sheep by 454 Pyrosequencing Analysis.. Asian-Australas J. Anim. Sci. 2017;30:100–110.
    doi: 10.5713/ajas.16.0166pmc: PMC5205584pubmed: 27383798google scholar: lookup
  70. Wang X, Hu L, Liu H, Xu T, Zhao N, Zhang X, Geng Y, Kang S, Xu S. Characterization of the Bacterial Microbiota across the Different Intestinal Segments of the Qinghai Semi-Fine Wool Sheep on the Qinghai-Tibetan Plateau.. Anim. Biosci. 2021;34:1921–1929.
    doi: 10.5713/ab.20.0809pmc: PMC8563230pubmed: 34237935google scholar: lookup
  71. Cortés A, Wills J, Su X, Hewitt RE, Robertson J, Scotti R, Price DRG, Bartley Y, McNeilly TN, Krause L. Infection with the Sheep Gastrointestinal Nematode Teladorsagia Circumcincta Increases Luminal Pathobionts.. Microbiome 2020;8:60.
    doi: 10.1186/s40168-020-00818-9pmc: PMC7193420pubmed: 32354347google scholar: lookup
  72. McLoughlin S, Spillane C, Claffey N, Smith PE, O’Rourke T, Diskin MG, Waters SM. Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency.. Front. Microbiol. 2020;11:1981.
    doi: 10.3389/fmicb.2020.01981pmc: PMC7477290pubmed: 32983009google scholar: lookup
  73. Chang J, Yao X, Zuo C, Qi Y, Chen D, Ma W. The Gut Bacterial Diversity of Sheep Associated with Different Breeds in Qinghai Province.. BMC Vet. Res. 2020;16:254.
    doi: 10.1186/s12917-020-02477-2pmc: PMC7376942pubmed: 32703277google scholar: lookup
  74. Minozzi G, Biscarini F, Dalla Costa E, Chincarini M, Ferri N, Palestrini C, Minero M, Mazzola S, Piccinini R, Vignola G. Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions.. Animals 2020;11:4.
    doi: 10.3390/ani11010004pmc: PMC7822195pubmed: 33375098google scholar: lookup
  75. Zhang YK, Zhang XX, Li FD, Li C, Li GZ, Zhang DY, Song QZ, Li XL, Zhao Y, Wang WM. Characterization of the Rumen Microbiota and Its Relationship with Residual Feed Intake in Sheep.. Animal 2021;15:100161.
    doi: 10.1016/j.animal.2020.100161pubmed: 33785185google scholar: lookup
  76. Jewell KA, McCormick CA, Odt CL, Weimer PJ, Suen G. Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency. Appl. Environ. Microbiol. 2015;81:4697–4710.
    doi: 10.1128/AEM.00720-15pmc: PMC4551193pubmed: 25934629google scholar: lookup
  77. Shabat SKB, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, White BA, Shterzer N, Mizrahi I. Specific Microbiome-Dependent Mechanisms Underlie the Energy Harvest Efficiency of Ruminants. ISME J. 2016;10:2958–2972.
    doi: 10.1038/ismej.2016.62pmc: PMC5148187pubmed: 27152936google scholar: lookup
  78. Zeng Y, Zeng D, Ni X, Zhu H, Jian P, Zhou Y, Xu S, Lin Y, Li Y, Yin Z. Microbial Community Compositions in the Gastrointestinal Tract of Chinese Mongolian Sheep Using Illumina MiSeq Sequencing Revealed High Microbial Diversity. AMB Express 2017;7:75.
    doi: 10.1186/s13568-017-0378-1pmc: PMC5380569pubmed: 28378284google scholar: lookup
  79. Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, Wang X, Yang C, Li Q, Yan X. An Integrated Gene Catalog and over 10,000 Metagenome-Assembled Genomes from the Gastrointestinal Microbiome of Ruminants. Microbiome 2021;9:137.
    doi: 10.1186/s40168-021-01078-xpmc: PMC8199421pubmed: 34118976google scholar: lookup
  80. Mani S, Aiyegoro OA, Adeleke MA. Association between Host Genetics of Sheep and the Rumen Microbial Composition. Trop. Anim. Health Prod. 2022;54:109.
    doi: 10.1007/s11250-022-03057-2pubmed: 35192073google scholar: lookup
  81. Lv W, Liu X, Sha Y, Shi H, Wei H, Luo Y, Wang J, Li S, Hu J, Guo X. Rumen Fermentation—Microbiota—Host Gene Expression Interactions to Reveal the Adaptability of Tibetan Sheep in Different Periods. Animals 2021;11:3529.
    doi: 10.3390/ani11123529pmc: PMC8697948pubmed: 34944301google scholar: lookup
  82. Tanca A, Fraumene C, Manghina V, Palomba A, Abbondio M, Deligios M, Pagnozzi D, Addis MF, Uzzau S. Diversity and Functions of the Sheep Faecal Microbiota: A Multi-Omic Characterization. Microb. Biotechnol. 2017;10:541–554.
    doi: 10.1111/1751-7915.12462pmc: PMC5404191pubmed: 28165194google scholar: lookup
  83. Guo H, Cui J, Li Q, Liang X, Li J, Yang B, Kalds P, Chen Y, Yang Y. A Multi-Omic Assessment of the Mechanisms of Intestinal Microbes Used to Treat Diarrhea in Early-Weaned Lambs. Msystems 2024;9:e00953-23.
    doi: 10.1128/msystems.00953-23pmc: PMC10878098pubmed: 38193712google scholar: lookup
  84. Perea K, Perz K, Olivo SK, Williams A, Lachman M, Ishaq SL, Thomson J, Yeoman CJ. Feed Efficiency Phenotypes in Lambs Involve Changes in Ruminal, Colonic, and Small-Intestine-Located Microbiota. J. Anim. Sci. 2017;95:2585–2592.
    doi: 10.2527/jas2016.1222pubmed: 28727071google scholar: lookup
  85. Fu Z, Xu X, Zhang J, Zhang L. Effect of Different Feeding Methods on Rumen Microbes in Growing Chinese Tan Sheep. Rev. Bras. Zootec. 2020;49:e20190258.
    doi: 10.37496/rbz4920190258google scholar: lookup
  86. Wang L, Zhang K, Zhang C, Feng Y, Zhang X, Wang X, Wu G. Dynamics and Stabilization of the Rumen Microbiome in Yearling Tibetan Sheep. Sci. Rep. 2019;9:19620.
    doi: 10.1038/s41598-019-56206-3pmc: PMC6927978pubmed: 31873173google scholar: lookup
  87. Daghio M, Viti C, Mannelli F, Pauselli M, Natalello A, Luciano G, Valenti B, Buccioni A. A Diet Supplemented with Hazelnut Skin Changes the Microbial Community Composition and the Biohydrogenation Pattern of Linoleic Acid in the Rumen of Growing Lambs. Ital. J. Anim. Sci. 2021;20:1256–1263.
    doi: 10.1080/1828051X.2021.1955020google scholar: lookup
  88. Lima J, Ingabire W, Roehe R, Dewhurst RJ. Estimating Microbial Protein Synthesis in the Rumen—Can ‘Omics’ Methods Provide New Insights into a Long-Standing Question?. Vet. Sci. 2023;10:679.
    doi: 10.3390/vetsci10120679pmc: PMC10747152pubmed: 38133230google scholar: lookup
  89. Zhou G, Zhou X, He Y, Shao J, Hu Z, Liu R, Zhou H, Hosseinibai S. Grazing Intensity Significantly Affects Belowground Carbon and Nitrogen Cycling in Grassland Ecosystems: A Meta-Analysis. Glob. Change Biol. 2017;23:1167–1179.
    doi: 10.1111/gcb.13431pubmed: 27416555google scholar: lookup
  90. Liu X, Sha Y, Lv W, Cao G, Guo X, Pu X, Wang J, Li S, Hu J, Luo Y. Multi-Omics Reveals That the Rumen Transcriptome, Microbiome, and Its Metabolome Co-Regulate Cold Season Adaptability of Tibetan Sheep. Front. Microbiol. 2022;13:859601.
    doi: 10.3389/fmicb.2022.859601pmc: PMC9043902pubmed: 35495720google scholar: lookup
  91. Asanuma N, Yokoyama S, Hino T. Effects of Nitrate Addition to a Diet on Fermentation and Microbial Populations in the Rumen of Goats, with Special Reference to Elenomonas Ruminantium Having the Ability to Reduce Nitrate and Nitrite. Anim. Sci. J. 2015;86:378–384.
    doi: 10.1111/asj.12307pubmed: 25439583google scholar: lookup
  92. Cremonesi P, Conte G, Severgnini M, Turri F, Monni A, Capra E, Rapetti L, Colombini S, Chessa S, Battelli G. Evaluation of the Effects of Different Diets on Microbiome Diversity and Fatty Acid Composition of Rumen Liquor in Dairy Goat. Animal 2018;12:1856–1866.
    doi: 10.1017/S1751731117003433pubmed: 29306345google scholar: lookup
  93. Fliegerova K.O, Podmirseg S.M, Vinzelj J, Grilli D.J, Kvasnová S, Schierová D, Sechovcová H, Mrázek J, Siddi G, Arenas G.N. The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi. Microorganisms 2021;9:157.
    doi: 10.3390/microorganisms9010157pmc: PMC7827659pubmed: 33445538google scholar: lookup
  94. Peng X, Wilken S.E, Lankiewicz T.S, Gilmore S.P, Brown J.L, Henske J.K, Swift C.L, Salamov A, Barry K, Grigoriev I.V. Genomic and Functional Analyses of Fungal and Bacterial Consortia That Enable Lignocellulose Breakdown in Goat Gut Microbiomes. Nat. Microbiol. 2021;6:499–511.
    doi: 10.1038/s41564-020-00861-0pmc: PMC8007473pubmed: 33526884google scholar: lookup
  95. Min B.R, Solaiman S, Shange R, Eun J.-S. Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing. Int. J. Microbiol. 2014;2014:141909.
    doi: 10.1155/2014/141909pmc: PMC3941959pubmed: 24669219google scholar: lookup
  96. Zou X, Liu G, Meng F, Hong L, Li Y, Lian Z, Yang Z, Luo C, Liu D. Exploring the Rumen and Cecum Microbial Community from Fetus to Adulthood in Goat. Animals 2020;10:1639.
    doi: 10.3390/ani10091639pmc: PMC7552217pubmed: 32932976google scholar: lookup
  97. Zhang J, Cai K, Mishra R, Jha R. In Ovo Supplementation of Chitooligosaccharide and Chlorella Polysaccharide Affects Cecal Microbial Community, Metabolic Pathways, and Fermentation Metabolites in Broiler Chickens. Poult. Sci. 2020;99:4776–4785.
    doi: 10.1016/j.psj.2020.06.061pmc: PMC7598314pubmed: 32988512google scholar: lookup
  98. Palma-Hidalgo J.M, Jiménez E, Popova M, Morgavi D.P, Martín-García A.I, Yáñez-Ruiz D.R, Belanche A. Inoculation with Rumen Fluid in Early Life Accelerates the Rumen Microbial Development and Favours the Weaning Process in Goats. Anim. Microbiome 2021;3:11.
    doi: 10.1186/s42523-021-00073-9pmc: PMC7814744pubmed: 33499992google scholar: lookup
  99. Bu D, Zhang X, Ma L, Park T, Wang L, Wang M, Xu J, Yu Z. Repeated Inoculation of Young Calves With Rumen Microbiota Does Not Significantly Modulate the Rumen Prokaryotic Microbiota Consistently but Decreases Diarrhea. Front. Microbiol. 2020;11:1403.
    doi: 10.3389/fmicb.2020.01403pmc: PMC7326819pubmed: 32670244google scholar: lookup
  100. Mammeri M, Obregón D.A, Chevillot A, Polack B, Julien C, Pollet T, Cabezas-Cruz A, Adjou K.T. Cryptosporidium Parvum Infection Depletes Butyrate Producer Bacteria in Goat Kid Microbiome. Front. Microbiol. 2020;11:548737.
    doi: 10.3389/fmicb.2020.548737pmc: PMC7596689pubmed: 33178145google scholar: lookup
  101. Tong J, Ma W, Yang R, Wang T, Chen X, Zhang X, Tang X, Wen Y, Chang J, Chen D. Dysbiosis of the Gut Microbiota Maybe Exacerbate Orf Pathology by Promoting Inflammatory Immune Responses. Vet. Microbiol. 2020;251:108884.
    doi: 10.1016/j.vetmic.2020.108884pubmed: 33086176google scholar: lookup
  102. Jiang S, Huo D, You Z, Peng Q, Ma C, Chang H, Lin X, Wang L, Zhang J. The Distal Intestinal Microbiome of Hybrids of Hainan Black Goats and Saanen Goats. PLoS ONE 2020;15:e0228496.
    doi: 10.1371/journal.pone.0228496pmc: PMC6992168pubmed: 31999767google scholar: lookup
  103. Wang L, Shah A.M, Liu Y, Jin L, Wang Z, Xue B, Peng Q. Relationship between True Digestibility of Dietary Phosphorus and Gastrointestinal Bacteria of Goats. PLoS ONE 2020;15:e0225018.
    doi: 10.1371/journal.pone.0225018pmc: PMC7244181pubmed: 32442173google scholar: lookup
  104. Ren Z, Yao R, Liu Q, Deng Y, Shen L, Deng H, Zuo Z, Wang Y, Deng J, Cui H. Effects of Antibacterial Peptides on Rumen Fermentation Function and Rumen Microorganisms in Goats. PLoS ONE 2019;14:e0221815.
    doi: 10.1371/journal.pone.0221815pmc: PMC6716671pubmed: 31469857google scholar: lookup
  105. Shabana I, Bouqellah N.A, Albakri N.N. Comparative Metagenomic Analysis of Small Ruminants’ Fecal Microbiota. Res. Sq. 2020;10.
    doi: 10.21203/rs.2.21081/v1google scholar: lookup
  106. Wang Z, Yin L, Liu L, Lan X, He J, Wan F, Shen W, Tang S, Tan Z, Yang Y. Tannic Acid Reduced Apparent Protein Digestibility and Induced Oxidative Stress and Inflammatory Response without Altering Growth Performance and Ruminal Microbiota Diversity of Xiangdong Black Goats. Front. Vet. Sci. 2022;9:1004841.
    doi: 10.3389/fvets.2022.1004841pmc: PMC9516568pubmed: 36187804google scholar: lookup
  107. Cao Y, Feng T, Wu Y, Xu Y, Du L, Wang T, Luo Y, Wang Y, Li Z, Xuan Z. The Multi-Kingdom Microbiome of the Goat Gastrointestinal Tract. Microbiome 2023;11:219.
    doi: 10.1186/s40168-023-01651-6pmc: PMC10544373pubmed: 37779211google scholar: lookup
  108. Dal Pont G.C, Eyng C, Bortoluzzi C, Kogut M.H. Enzymes and Gut Health in Monogastric Animals: Effects Beyond Digestibility. .
  109. Zhao G, Xiang Y, Wang X, Dai B, Zhang X, Ma L, Yang H, Lyu W. Exploring the Possible Link between the Gut Microbiome and Fat Deposition in Pigs. Oxidative Med. Cell. Longev. 2022;2022:1098892.
    doi: 10.1155/2022/1098892pmc: PMC8800603pubmed: 35103093google scholar: lookup
  110. Williams A.R, Myhill L.J, Stolzenbach S, Nejsum P, Mejer H, Nielsen D.S, Thamsborg S.M. Emerging Interactions between Diet, Gastrointestinal Helminth Infection, and the Gut Microbiota in Livestock. BMC Vet. Res. 2021;17:62.
    doi: 10.1186/s12917-021-02752-wpmc: PMC7845040pubmed: 33514383google scholar: lookup
  111. Jha R, Berrocoso J.F.D. Dietary Fiber and Protein Fermentation in the Intestine of Swine and Their Interactive Effects on Gut Health and on the Environment: A Review. Anim. Feed Sci. Technol. 2016;212:18–26.
    doi: 10.1016/j.anifeedsci.2015.12.002google scholar: lookup
  112. Kauter A, Epping L, Semmler T, Antao E.-M, Kannapin D, Stoeckle S.D, Gehlen H, Lübke-Becker A, Günther S, Wieler L.H. The Gut Microbiome of Horses: Current Research on Equine Enteral Microbiota and Future Perspectives. Anim. Microbiome 2019;1:14.
    doi: 10.1186/s42523-019-0013-3pmc: PMC7807895pubmed: 33499951google scholar: lookup
  113. Pan D, Yu Z. Intestinal Microbiome of Poultry and Its Interaction with Host and Diet. Gut Microbes 2014;5:108–119.
    doi: 10.4161/gmic.26945pmc: PMC4049927pubmed: 24256702google scholar: lookup
  114. Metcalf J.L, Song S.J, Morton J.T, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A. Evaluating the Impact of Domestication and Captivity on the Horse Gut Microbiome. Sci. Rep. 2017;7:15497.
    doi: 10.1038/s41598-017-15375-9pmc: PMC5686199pubmed: 29138485google scholar: lookup
  115. Boucher L, Leduc L, Leclère M, Costa M.C. Current Understanding of Equine Gut Dysbiosis and Microbiota Manipulation Techniques: Comparison with Current Knowledge in Other Species. Animals 2024;14:758.
    doi: 10.3390/ani14050758pmc: PMC10931082pubmed: 38473143google scholar: lookup
  116. Lara F, Castro R, Thomson P. Changes in the Gut Microbiome and Colic in Horses: Are They Causes or Consequences?. Open Vet. J. 2022;12:242–249.
    doi: 10.5455/OVJ.2022.v12.i2.12pmc: PMC9109837pubmed: 35603065google scholar: lookup
  117. Garber A, Hastie P, Murray J.-A. Factors Influencing Equine Gut Microbiota: Current Knowledge. J. Equine Vet. Sci. 2020;88:102943.
    doi: 10.1016/j.jevs.2020.102943pubmed: 32303307google scholar: lookup
  118. Sorensen R.J, Drouillard J.S, Douthit T.L, Ran Q, Marthaler D.G, Kang Q, Vahl C.I, Lattimer J.M. Effect of Hay Type on Cecal and Fecal Microbiome and Fermentation Parameters in Horses. J. Anim. Sci. 2021;99:skaa407.
    doi: 10.1093/jas/skaa407pmc: PMC7846146pubmed: 33515482google scholar: lookup
  119. Ericsson A.C, Johnson P.J, Lopes M.A, Perry S.C, Lanter H.R. A Microbiological Map of the Healthy Equine Gastrointestinal Tract. PLoS ONE 2016;11:e0166523.
    doi: 10.1371/journal.pone.0166523pmc: PMC5112786pubmed: 27846295google scholar: lookup
  120. Mach N, Foury A, Kittelmann S, Reigner F, Moroldo M, Ballester M, Esquerré D, Rivière J, Sallé G, Gérard P. The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology. Front. Physiol. 2017;8:535.
    doi: 10.3389/fphys.2017.00535pmc: PMC5524898pubmed: 28790932google scholar: lookup
  121. Mura E, Edwards J, Kittelmann S, Kaerger K, Voigt K, Mrázek J, Moniello G, Fliegerova K. Anaerobic Fungal Communities Differ along the Horse Digestive Tract.. Fungal Biol. 2019;123:240–246.
    doi: 10.1016/j.funbio.2018.12.004pubmed: 30798879google scholar: lookup
  122. Costa MC, Silva G, Ramos RV, Staempfli HR, Arroyo LG, Kim P, Weese JS. 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
  123. McKinney CA, Oliveira BC, Bedenice D, Paradis M-R, Mazan M, Sage S, Sanchez A, Widmer G. The Fecal Microbiota of Healthy Donor Horses and Geriatric Recipients Undergoing Fecal Microbial Transplantation for the Treatment of Diarrhea.. PLoS ONE 2020;15:e0230148.
    doi: 10.1371/journal.pone.0230148pmc: PMC7064224pubmed: 32155205google scholar: lookup
  124. Chaucheyras-Durand F, Sacy A, Karges K, Apper E. Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens.. Microorganisms 2022;10:2517.
    doi: 10.3390/microorganisms10122517pmc: PMC9783266pubmed: 36557769google scholar: lookup
  125. Álvarez Narváez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S. Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.. Animals 2024;14:445.
    doi: 10.3390/ani14030445pmc: PMC10854943pubmed: 38338088google scholar: lookup
  126. Cooke CG, Gibb Z, Grupen CG, Schemann K, Deshpande N, Harnett JE. Effect of Probiotics and Prebiotics on the Composition of the Equine Fecal and Seminal Microbiomes and Sperm Quality: A Pilot Study.. J. Equine Vet. Sci. 2024;135:105032.
    doi: 10.1016/j.jevs.2024.105032pubmed: 38401778google scholar: lookup
  127. Dou S, Gadonna-Widehem P, Rome V, Hamoudi D, Rhazi L, Lakhal L, Larcher T, Bahi-Jaber N, Pinon-Quintana A, Guyonvarch A. Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea.. PLoS ONE 2017;12:e0169851.
    doi: 10.1371/journal.pone.0169851pmc: PMC5225014pubmed: 28072880google scholar: lookup
  128. Sutera AM, Arfuso F, Tardiolo G, Riggio V, Fazio F, Aiese Cigliano R, Paytuví A, Piccione G, Zumbo A. Effect of a Co-Feed Liquid Whey-Integrated Diet on Crossbred Pigs’ Fecal Microbiota.. Animals 2023;13:1750.
    doi: 10.3390/ani13111750pmc: PMC10252047pubmed: 37889679google scholar: lookup
  129. Tardiolo G, Romeo O, Zumbo A, Di Marsico M, Sutera AM, Cigliano RA, Paytuví A, D’Alessandro E. Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet.. Animals 2023;13:642.
    doi: 10.3390/ani13040642pmc: PMC9951753pubmed: 36830429google scholar: lookup
  130. De Rodas B, Youmans BP, Danzeisen JL, Tran H, Johnson TJ. Microbiome Profiling of Commercial Pigs from Farrow to Finish.. J. Anim. Sci. 2018;96:1778–1794.
    doi: 10.1093/jas/sky109pmc: PMC6140882pubmed: 29635455google scholar: lookup
  131. Motta V, Trevisi P, Bertolini F, Ribani A, Schiavo G, Fontanesi L, Bosi P. Exploring Gastric Bacterial Community in Young Pigs.. PLoS ONE 2017;12:e0173029.
    doi: 10.1371/journal.pone.0173029pmc: PMC5332105pubmed: 28249050google scholar: lookup
  132. Verbeek E, Keeling L, Landberg R, Lindberg JE, Dicksved J. The Gut Microbiota and Microbial Metabolites Are Associated with Tail Biting in Pigs.. Sci. Rep. 2021;11:20547.
    doi: 10.1038/s41598-021-99741-8pmc: PMC8521594pubmed: 34654857google scholar: lookup
  133. Borewicz KA, Kim HB, Singer RS, Gebhart CJ, Sreevatsan S, Johnson T, Isaacson RE. Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella Enterica and Lawsonia Intracellularis.. PLoS ONE 2015;10:e0139106.
    doi: 10.1371/journal.pone.0139106pmc: PMC4604083pubmed: 26461107google scholar: lookup
  134. Azziz G, Giménez M, Carballo C, Espino N, Barlocco N, Batista S. Characterization of the Fecal Microbiota of Pampa Rocha Pigs, a Genetic Resource Endemic to Eastern Uruguay.. Heliyon 2023;9:e16643.
    doi: 10.1016/j.heliyon.2023.e16643pmc: PMC10248110pubmed: 37303559google scholar: lookup
  135. Ma J, Chen J, Gan M, Chen L, Zhao Y, Zhu Y, Niu L, Zhang S, Zhu L, Shen L. Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages.. Animals 2022;12:1607.
    doi: 10.3390/ani12131607pmc: PMC9264831pubmed: 35804507google scholar: lookup
  136. Han G.G., Lee J.-Y., Jin G.-D., Park J., Choi Y.H., Chae B.J., Kim E.B., Choi Y.-J.. Evaluating the Association between Body Weight and the Intestinal Microbiota of Weaned Piglets via 16S rRNA Sequencing. Appl. Microbiol. Biotechnol. 2017;101:5903–5911.
    doi: 10.1007/s00253-017-8304-7pubmed: 28523395google scholar: lookup
  137. Holman D.B., Gzyl K.E., Mou K.T., Allen H.K.. Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome. Msystems 2021;6:e00682-21.
    doi: 10.1128/mSystems.00682-21pmc: PMC8609972pubmed: 34812652google scholar: lookup
  138. Gaio D., DeMaere M.Z., Anantanawat K., Chapman T.A., Djordjevic S.P., Darling A.E.. Post-Weaning Shifts in Microbiome Composition and Metabolism Revealed by over 25,000 Pig Gut Metagenome-Assembled Genomes. Microb. Genom. 2021;7:000501.
    pmc: PMC8549361pubmed: 34370660
  139. Guevarra R.B., Hong S.H., Cho J.H., Kim B.-R., Shin J., Lee J.H., Kang B.N., Kim Y.H., Wattanaphansak S., Isaacson R.E.. The Dynamics of the Piglet Gut Microbiome during the Weaning Transition in Association with Health and Nutrition. J. Anim. Sci. Biotechnol. 2018;9:54.
    doi: 10.1186/s40104-018-0269-6pmc: PMC6065057pubmed: 30069307google scholar: lookup
  140. Munk P., Andersen V.D., de Knegt L., Jensen M.S., Knudsen B.E., Lukjancenko O., Mordhorst H., Clasen J., Agersø Y., Folkesson A.. A Sampling and Metagenomic Sequencing-Based Methodology for Monitoring Antimicrobial Resistance in Swine Herds. J. Antimicrob. Chemother. 2017;72:385–392.
    doi: 10.1093/jac/dkw415pubmed: 28115502google scholar: lookup
  141. Gweon H.S., Shaw L.P., Swann J., De Maio N., AbuOun M., Niehus R., Hubbard A., Bowes M.J., Bailey M.J., Peto T.E.. The Impact of Sequencing Depth on the Inferred Taxonomic Composition and AMR Gene Content of Metagenomic Samples. Environ. Microbiome 2019;14:1–15.
    doi: 10.1186/s40793-019-0347-1pmc: PMC8204541pubmed: 33902704google scholar: lookup
  142. Fenske G.J., Ghimire S., Antony L., Christopher-Hennings J., Scaria J.. Integration of Culture-Dependent and Independent Methods Provides a More Coherent Picture of the Pig Gut Microbiome. FEMS Microbiol. Ecol. 2020;96:fiaa022.
    doi: 10.1093/femsec/fiaa022pubmed: 32031212google scholar: lookup
  143. Wylezich C., Belka A., Hanke D., Beer M., Blome S., Höper D.. Metagenomics for Broad and Improved Parasite Detection: A Proof-of-Concept Study Using Swine Faecal Samples. Int. J. Parasitol. 2019;49:769–777.
    doi: 10.1016/j.ijpara.2019.04.007pubmed: 31361998google scholar: lookup
  144. Ramayo-Caldas Y., Prenafeta-Boldú F., Zingaretti L.M., Gonzalez-Rodriguez O., Dalmau A., Quintanilla R., Ballester M.. Gut Eukaryotic Communities in Pigs: Diversity, Composition and Host Genetics Contribution. Anim. Microbiome 2020;2:18.
    doi: 10.1186/s42523-020-00038-4pmc: PMC7807704pubmed: 33499953google scholar: lookup
  145. Mann E., Schmitz-Esser S., Zebeli Q., Wagner M., Ritzmann M., Metzler-Zebeli B.U.. Mucosa-Associated Bacterial Microbiome of the Gastrointestinal Tract of Weaned Pigs and Dynamics Linked to Dietary Calcium-Phosphorus. PLoS ONE 2014;9:e86950.
    doi: 10.1371/journal.pone.0086950pmc: PMC3900689pubmed: 24466298google scholar: lookup
  146. Wang C., Wei S., Chen N., Xiang Y., Wang Y., Jin M.. Characteristics of Gut Microbiota in Pigs with Different Breeds, Growth Periods and Genders. Microb. Biotechnol. 2022;15:793–804.
    doi: 10.1111/1751-7915.13755pmc: PMC8913877pubmed: 33566446google scholar: lookup
  147. Combes S., Fortun-Lamothe L., Cauquil L., Gidenne T.. Engineering the Rabbit Digestive Ecosystem to Improve Digestive Health and Efficacy. Animal 2013;7:1429–1439.
    doi: 10.1017/S1751731113001079pubmed: 23769161google scholar: lookup
  148. Zeng B., Han S., Wang P., Wen B., Jian W., Guo W., Yu Z., Du D., Fu X., Kong F.. The Bacterial Communities Associated with Fecal Types and Body Weight of Rex Rabbits. Sci. Rep. 2015;5:9342.
    doi: 10.1038/srep09342pmc: PMC4366860pubmed: 25791609google scholar: lookup
  149. Velasco-Galilea M., Piles M., Viñas M., Rafel O., González-Rodríguez O., Guivernau M., Sánchez J.P.. Rabbit Microbiota Changes Throughout the Intestinal Tract. Front. Microbiol. 2018;9:2144.
    doi: 10.3389/fmicb.2018.02144pmc: PMC6146034pubmed: 30271392google scholar: lookup
  150. Ye D., Ding X., Pang S., Gan Y., Li Z., Gan Q., Fang S.. Seasonal Variations in Production Performance, Health Status, and Gut Microbiota of Meat Rabbit Reared in Semi-Confined Conditions. Animals 2023;14:113.
    doi: 10.3390/ani14010113pmc: PMC10778228pubmed: 38200844google scholar: lookup
  151. Clemente JC, Manasson J, Scher JU. The Role of the Gut Microbiome in Systemic Inflammatory Disease.. BMJ 2018;360:j5145.
    doi: 10.1136/bmj.j5145pmc: PMC6889978pubmed: 29311119google scholar: lookup
  152. Fang S, Chen X, Ye X, Zhou L, Xue S, Gan Q. Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits.. Front. Microbiol. 2020;11:1835.
    doi: 10.3389/fmicb.2020.01835pmc: PMC7431612pubmed: 32849435google scholar: lookup
  153. Wang Z, He H, Chen M, Ni M, Yuan D, Cai H, Chen Z, Li M, Xu H. Impact of Coprophagy Prevention on the Growth Performance, Serum Biochemistry, and Intestinal Microbiome of Rabbits.. BMC Microbiol. 2023;23:125.
    doi: 10.1186/s12866-023-02869-ypmc: PMC10170819pubmed: 37165350google scholar: lookup
  154. De Cesare A, Sirri F, Manfreda G, Moniaci P, Giardini A, Zampiga M, Meluzzi A. Effect of Dietary Supplementation with Lactobacillus Acidophilus D2/CSL (CECT 4529) on Caecum Microbioma and Productive Performance in Broiler Chickens.. PLoS ONE 2017;12:e0176309.
    doi: 10.1371/journal.pone.0176309pmc: PMC5417446pubmed: 28472118google scholar: lookup
  155. Durazzi F, Sala C, Castellani G, Manfreda G, Remondini D, De Cesare A. Comparison between 16S rRNA and Shotgun Sequencing Data for the Taxonomic Characterization of the Gut Microbiota.. Sci. Rep. 2021;11:3030.
    doi: 10.1038/s41598-021-82726-ypmc: PMC7862389pubmed: 33542369google scholar: lookup
  156. Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan N-F, Baker D, Gharbi K, Hall N, Watson M. Extensive Microbial Diversity within the Chicken Gut Microbiome Revealed by Metagenomics and Culture.. PeerJ 2021;9:e10941.
    doi: 10.7717/peerj.10941pmc: PMC8035907pubmed: 33868800google scholar: lookup
  157. Sun B, Hou L, Yang Y. The Development of the Gut Microbiota and Short-Chain Fatty Acids of Layer Chickens in Different Growth Periods.. Front. Vet. Sci. 2021;8:666535.
    doi: 10.3389/fvets.2021.666535pmc: PMC8284478pubmed: 34277754google scholar: lookup
  158. Ramírez GA, Richardson E, Clark J, Keshri J, Drechsler Y, Berrang ME, Meinersmann RJ, Cox NA, Oakley BB. Broiler Chickens and Early Life Programming: Microbiome Transplant-Induced Cecal Community Dynamics and Phenotypic Effects.. PLoS ONE 2020;15:e0242108.
    doi: 10.1371/journal.pone.0242108pmc: PMC7665843pubmed: 33186366google scholar: lookup
  159. Kabir MHB, Han Y, Lee S-H, Nugraha AB, Recuenco F, Murakoshi F, Xuan X, Kato K. Prevalence and Molecular Characterization of Cryptosporidium Species in Poultry in Bangladesh.. One Health 2020;9:100122.
    doi: 10.1016/j.onehlt.2020.100122pmc: PMC7184206pubmed: 32368610google scholar: lookup
  160. Lee S-J, Cho S, La T-M, Lee H-J, Lee J-B, Park S-Y, Song C-S, Choi I-S, Lee S-W. Comparison of Microbiota in the Cloaca, Colon, and Magnum of Layer Chicken.. PLoS ONE 2020;15:e0237108.
    doi: 10.1371/journal.pone.0237108pmc: PMC7402502pubmed: 32750076google scholar: lookup
  161. Wei S, Morrison M, Yu Z. Bacterial Census of Poultry Intestinal Microbiome.. Poult. Sci. 2013;92:671–683.
    doi: 10.3382/ps.2012-02822pubmed: 23436518google scholar: lookup
  162. Malmuthuge N, Guan LL. Understanding Host-Microbial Interactions in Rumen: Searching the Best Opportunity for Microbiota Manipulation.. J. Anim. Sci. Biotechnol. 2017;8:8.
    doi: 10.1186/s40104-016-0135-3pmc: PMC5244612pubmed: 28116074google scholar: lookup
  163. Liu K, Zhang Y, Yu Z, Xu Q, Zheng N, Zhao S, Huang G, Wang J. Ruminal Microbiota–Host Interaction and Its Effect on Nutrient Metabolism.. Anim. Nutr. 2021;7:49–55.
    doi: 10.1016/j.aninu.2020.12.001pmc: PMC8110878pubmed: 33997331google scholar: lookup
  164. Hernandez-Sanabria E, Goonewardene LA, Wang Z, Durunna ON, Moore SS, Guan LL. Impact of Feed Efficiency and Diet on Adaptive Variations in the Bacterial Community in the Rumen Fluid of Cattle.. Appl. Environ. Microbiol. 2012;78:1203–1214.
    doi: 10.1128/AEM.05114-11pmc: PMC3273029pubmed: 22156428google scholar: lookup
  165. de Assis Lage CF, Räisänen SE, Melgar A, Nedelkov K, Chen X, Oh J, Fetter ME, Indugu N, Bender JS, Vecchiarelli B. Comparison of Two Sampling Techniques for Evaluating Ruminal Fermentation and Microbiota in the Planktonic Phase of Rumen Digesta in Dairy Cows.. Front. Microbiol. 2020;11:618032.
    doi: 10.3389/fmicb.2020.618032pmc: PMC7785721pubmed: 33424820google scholar: lookup
  166. Amin N, Schwarzkopf S, Kinoshita A, Tröscher-Mußotter J, Dänicke S, Camarinha-Silva A, Huber K, Frahm J, Seifert J. Evolution of Rumen and Oral Microbiota in Calves Is Influenced by Age and Time of Weaning. Anim. Microbiome 2021;3:31.
    doi: 10.1186/s42523-021-00095-3pmc: PMC8059317pubmed: 33883031google scholar: lookup
  167. Hagey JV, Laabs M, Maga EA, DePeters EJ. Rumen Sampling Methods Bias Bacterial Communities Observed. PLoS ONE 2022;17:e0258176.
    doi: 10.1371/journal.pone.0258176pmc: PMC9070869pubmed: 35511785google scholar: lookup
  168. Xiang Q, Su Q, Li Q, Liu J, Du Y, Shi H, Li Z, Ma Y, Niu Y, Chen L. Microbial Community Analyses Provide a Differential Diagnosis for the Antemortem and Postmortem Injury of Decayed Cadaver: An Animal Model. J. Forensic Leg. Med. 2023;93:102473.
    doi: 10.1016/j.jflm.2022.102473pubmed: 36580880google scholar: lookup
  169. Yang F, Zhang X, Hu S, Nie H, Gui P, Zhong Z, Guo Y, Zhao X. Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation. Microorganisms 2023;11:2811.
    doi: 10.3390/microorganisms11112811pmc: PMC10672931pubmed: 38004822google scholar: lookup
  170. Hilal MG, Yu Q, Zhou R, Wang Y, Feng T, Li X, Li H. Exploring Microbial Communities, Assessment Methodologies and Applications of Animal’s Carcass Decomposition: A Review. FEMS Microbiol. Ecol. 2021;97:fiab098.
    doi: 10.1093/femsec/fiab098pubmed: 34185048google scholar: lookup
  171. Turner PV, Kloeze H, Dam A, Ward D, Leung N, Brown EEL, Whiteman A, Chiappetta ME, Hunter DB. Mass Depopulation of Laying Hens in Whole Barns with Liquid Carbon Dioxide: Evaluation of Welfare Impact. Poult. Sci. 2012;91:1558–1568.
    doi: 10.3382/ps.2012-02139pubmed: 22700499google scholar: lookup
  172. Kittelmann S, Kirk MR, Jonker A, McCulloch A, Janssen PH. Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen. Appl. Environ. Microbiol. 2015;81:7470–7483.
    doi: 10.1128/AEM.02385-15pmc: PMC4592876pubmed: 26276109google scholar: lookup
  173. Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PLoS ONE 2016;11:e0151220.
    doi: 10.1371/journal.pone.0151220pmc: PMC4795602pubmed: 26986467google scholar: lookup
  174. Young J, Skarlupka JH, Cox MS, Resende RT, Fischer A, Kalscheur KF, McClure JC, Cole JB, Suen G, Bickhart DM. Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach. Appl. Environ. Microbiol. 2020;86:e00861-20.
    doi: 10.1128/AEM.00861-20pmc: PMC7440797pubmed: 32591382google scholar: lookup
  175. Miura H, Takeda M, Yamaguchi M, Ohtani Y, Endo G, Masuda Y, Ito K, Nagura Y, Iwashita K, Mitani T. Application of MinION Amplicon Sequencing to Buccal SWAB Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis. Front. Microbiol. 2022;13:783058.
    doi: 10.3389/fmicb.2022.783058pmc: PMC8989143pubmed: 35401463google scholar: lookup
  176. Eisler MC, Lee MRF, Tarlton JF, Martin GB, Beddington J, Dungait JAJ, Greathead H, Liu J, Mathew S, Miller H. Agriculture: Steps to Sustainable Livestock. Nature 2014;507:32–34.
    doi: 10.1038/507032apubmed: 24605375google scholar: lookup
  177. Nkrumah JD, Okine EK, Mathison GW, Schmid K, Li C, Basarab JA, Price MA, Wang Z, Moore SS. Relationships of Feedlot Feed Efficiency, Performance, and Feeding Behavior with Metabolic Rate, Methane Production, and Energy Partitioning in Beef Cattle. J. Anim. Sci. 2006;84:145–153.
    doi: 10.2527/2006.841145xpubmed: 16361501google scholar: lookup
  178. Kumar S, Dagar SS, Puniya AK, Upadhyay RC. Changes in Methane Emission, Rumen Fermentation in Response to Diet and Microbial Interactions. Res. Vet. Sci. 2013;94:263–268.
    doi: 10.1016/j.rvsc.2012.09.007pubmed: 23046919google scholar: lookup
  179. Curtis H, Blaser MJ, Dirk G, Kota KC, Rob K, Liu B, Wang L, Sahar A, White JR, Badger JH. Structure, Function and Diversity of the Healthy Human Microbiome. Nature 2012;486:207–214.
    pmc: PMC3564958pubmed: 22699609
  180. Elolimy A, Alharthi A, Zeineldin M, Parys C, Loor JJ. Residual Feed Intake Divergence during the Preweaning Period Is Associated with Unique Hindgut Microbiome and Metabolome Profiles in Neonatal Holstein Heifer Calves. J. Anim. Sci. Biotechnol. 2020;11:13.
    doi: 10.1186/s40104-019-0406-xpmc: PMC6972010pubmed: 31988748google scholar: lookup
  181. Diaz J, Reese AT. Possibilities and Limits for Using the Gut Microbiome to Improve Captive Animal Health.. Anim. Microbiome 2021;3:89.
    doi: 10.1186/s42523-021-00155-8pmc: PMC8715647pubmed: 34965885google scholar: lookup
  182. Lourenco JM, Welch CB. Using Microbiome Information to Understand and Improve Animal Performance.. Ital. J. Anim. Sci. 2022;21:899–913.
    doi: 10.1080/1828051X.2022.2077147google scholar: lookup
  183. Du W, Wang X, Hu M, Hou J, Du Y, Si W, Yang L, Xu L, Xu Q. Modulating Gastrointestinal Microbiota to Alleviate Diarrhea in Calves.. Front. Microbiol. 2023;14:1181545.
    doi: 10.3389/fmicb.2023.1181545pmc: PMC10286795pubmed: 37362944google scholar: lookup
  184. Xiang Q, Wu X, Pan Y, Wang L, Guo Y, Cui C, Hu L, Zhu L, Peng J, Wei H. Early Intervention Using Fecal Microbiota Transplantation Combined with Probiotics Influence the Growth Performance, Diarrhea, and Intestinal Barrier Function of Piglets.. Appl. Sci. 2020;10:568.
    doi: 10.3390/app10020568google scholar: lookup
  185. Khalil A, Batool A, Arif S. Healthy Cattle Microbiome and Dysbiosis in Diseased Phenotypes.. Ruminants 2022;2:134–156.
    doi: 10.3390/ruminants2010009google scholar: lookup
  186. Clemmons BA, Voy BH, Myer PR. Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation.. Microb. Ecol. 2019;77:523–536.
    doi: 10.1007/s00248-018-1234-9pubmed: 30033500google scholar: lookup
  187. Yu S, Zhang G, Liu Z, Wu P, Yu Z, Wang J. Repeated Inoculation with Fresh Rumen Fluid before or during Weaning Modulates the Microbiota Composition and Co-Occurrence of the Rumen and Colon of Lambs.. BMC Microbiol. 2020;20:29.
    doi: 10.1186/s12866-020-1716-zpmc: PMC7006167pubmed: 32028889google scholar: lookup
  188. Cox A, Bomstein Z, Jayaraman A, Allred C. The Intestinal Microbiota as Mediators between Dietary Contaminants and Host Health.. Exp. Biol. Med. 2023;248:2131–2150.
    doi: 10.1177/15353702231208486pmc: PMC10800128pubmed: 37997859google scholar: lookup
  189. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes Database (CAZy): An Expert Resource for Glycogenomics.. Nucleic Acids Res. 2009;37:D233–D238.
    doi: 10.1093/nar/gkn663pmc: PMC2686590pubmed: 18838391google scholar: lookup
  190. Kaoutari AE, Armougom F, Gordon JI, Raoult D, Henrissat B. The Abundance and Variety of Carbohydrate-Active Enzymes in the Human Gut Microbiota.. Nat. Rev. Microbiol. 2013;11:497–504.
    doi: 10.1038/nrmicro3050pubmed: 23748339google scholar: lookup
  191. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial Degradation of Complex Carbohydrates in the Gut.. Gut Microbes 2012;3:289–306.
    doi: 10.4161/gmic.19897pmc: PMC3463488pubmed: 22572875google scholar: lookup
  192. Berlemont R, Martiny AC. Genomic Potential for Polysaccharide Deconstruction in Bacteria.. Appl. Environ. Microbiol. 2015;81:1513–1519.
    doi: 10.1128/AEM.03718-14pmc: PMC4309713pubmed: 25527556google scholar: lookup
  193. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The Carbohydrate-Active Enzymes Database (CAZy) in 2013.. Nucleic Acids Res. 2014;42:D490–D495.
    doi: 10.1093/nar/gkt1178pmc: PMC3965031pubmed: 24270786google scholar: lookup
  194. Dao T-K, Do T-H, Le N-G, Nguyen H-D, Nguyen T-Q, Le T-T-H, Truong N-H. Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing.. Animals 2021;11:3257.
    doi: 10.3390/ani11113257pmc: PMC8614338pubmed: 34827987google scholar: lookup
  195. Betancur-Murillo CL, Aguilar-Marín SB, Jovel J. Prevotella: A Key Player in Ruminal Metabolism.. Microorganisms 2022;11:1.
    doi: 10.3390/microorganisms11010001pmc: PMC9866204pubmed: 36677293google scholar: lookup
  196. Kou X, Ma Q, Liu Y, Khan MZ, Wu B, Chen W, Liu X, Wang C, Li Y. Exploring the Effect of Gastrointestinal Prevotella on Growth Performance Traits in Livestock Animals. Animals 2024;14:1965.
    doi: 10.3390/ani14131965pmc: PMC11240335pubmed: 38998077google scholar: lookup
  197. Solden L, Lloyd K, Wrighton K. The Bright Side of Microbial Dark Matter: Lessons Learned from the Uncultivated Majority. Curr. Opin. Microbiol. 2016;31:217–226.
    doi: 10.1016/j.mib.2016.04.020pubmed: 27196505google scholar: lookup
  198. Li J, Toyama H, Matsumoto T, Qasimi MI, Inoue R, Murase H, Yamamoto Y, Nagaoka K. Changes in Fecal Microbiota during Estrous Cycle in Healthy Thoroughbred Mares. J. Equine Vet. Sci. 2024;135:105034.
    doi: 10.1016/j.jevs.2024.105034pubmed: 38428754google scholar: lookup
  199. Diviccaro S, FitzGerald JA, Cioffi L, Falvo E, Crispie F, Cotter PD, O’Mahony SM, Giatti S, Caruso D, Melcangi RC. Gut Steroids and Microbiota: Effect of Gonadectomy and Sex. Biomolecules 2022;12:767.
    doi: 10.3390/biom12060767pmc: PMC9220917pubmed: 35740892google scholar: lookup
  200. Org E, Mehrabian M, Parks BW, Shipkova P, Liu X, Drake TA, Lusis AJ. Sex Differences and Hormonal Effects on Gut Microbiota Composition in Mice. Gut Microbes 2016;7:313–322.
    doi: 10.1080/19490976.2016.1203502pmc: PMC4988450pubmed: 27355107google scholar: lookup
  201. Sovijit WN, Sovijit WE, Pu S, Usuda K, Inoue R, Watanabe G, Yamaguchi H, Nagaoka K. Ovarian Progesterone Suppresses Depression and Anxiety-like Behaviors by Increasing the Lactobacillus Population of Gut Microbiota in Ovariectomized Mice. Neurosci. Res. 2021;168:76–82.
    doi: 10.1016/j.neures.2019.04.005pubmed: 31022413google scholar: lookup
  202. Gu X, Chen J, Li H, Song Z, Chang L, He X, Fan Z. Isomaltooligosaccharide and Bacillus Regulate the Duration of Farrowing and Weaning-Estrous Interval in Sows during the Perinatal Period by Changing the Gut Microbiota of Sows. Anim. Nutr. 2021;7:72–83.
    doi: 10.1016/j.aninu.2020.06.010pmc: PMC8110870pubmed: 33997334google scholar: lookup
  203. Diviccaro S, Giatti S, Borgo F, Falvo E, Caruso D, Garcia-Segura LM, Melcangi RC. Steroidogenic Machinery in the Adult Rat Colon. J. Steroid Biochem. Mol. Biol. 2020;203:105732.
    doi: 10.1016/j.jsbmb.2020.105732pubmed: 32777355google scholar: lookup
  204. Sand E, Bergvall M, Ekblad E, D’Amato M, Ohlsson B. Expression and Distribution of GnRH, LH, and FSH and Their Receptors in Gastrointestinal Tract of Man and Rat. Regul. Pept. 2013;187:24–28.
    doi: 10.1016/j.regpep.2013.09.002pubmed: 24103690google scholar: lookup
  205. Schieren A, Koch S, Pecht T, Simon M-C. Impact of Physiological Fluctuations of Sex Hormones during the Menstrual Cycle on Glucose Metabolism and the Gut Microbiota. Exp. Clin. Endocrinol. Diabetes 2024;132:267–278.
    doi: 10.1055/a-2273-5602pmc: PMC11093651pubmed: 38382644google scholar: lookup
  206. Mihajlovic J, Leutner M, Hausmann B, Kohl G, Schwarz J, Röver H, Stimakovits N, Wolf P, Maruszczak K, Bastian M. Combined Hormonal Contraceptives Are Associated with Minor Changes in Composition and Diversity in Gut Microbiota of Healthy Women. Environ. Microbiol. 2021;23:3037–3047.
    doi: 10.1111/1462-2920.15517pubmed: 33876556google scholar: lookup
  207. Wu D, Wang C, Simujide H, Liu B, Chen Z, Zhao P, Huangfu M, Liu J, Gao X, Wu Y. Reproductive Hormones Mediate Intestinal Microbiota Shifts during Estrus Synchronization in Grazing Simmental Cows. Animals 2022;12:1751.
    doi: 10.3390/ani12141751pmc: PMC9311722pubmed: 35883298google scholar: lookup
  208. Menon R, Watson SE, Thomas LN, Allred CD, Dabney A, Azcarate-Peril MA, Sturino JM. Diet Complexity and Estrogen Receptor β Status Affect the Composition of the Murine Intestinal Microbiota. Appl. Environ. Microbiol. 2013;79:5763–5773.
    doi: 10.1128/AEM.01182-13pmc: PMC3754184pubmed: 23872567google scholar: lookup
  209. Yoon K, Kim N. Roles of Sex Hormones and Gender in the Gut Microbiota. J. Neurogastroenterol. Motil. 2021;27:314–325.
    doi: 10.5056/jnm20208pmc: PMC8266488pubmed: 33762473google scholar: lookup
  210. Hussain T, Murtaza G, Kalhoro DH, Kalhoro MS, Metwally E, Chughtai MI, Mazhar MU, Khan SA. Relationship between Gut Microbiota and Host-Metabolism: Emphasis on Hormones Related to Reproductive Function. Anim. Nutr. 2021;7:1–10.
    doi: 10.1016/j.aninu.2020.11.005pmc: PMC8110851pubmed: 33997325google scholar: lookup
  211. Gancz N.N., Levinson J.A., Callaghan B.L. Sex and Gender as Critical and Distinct Contributors to the Human Brain-Gut-Microbiome Axis. Brain Res. Bull. 2023;199:110665. doi: 10.1016/j.brainresbull.2023.110665.
    doi: 10.1016/j.brainresbull.2023.110665pmc: PMC11149430pubmed: 37192716google scholar: lookup
  212. García-Gómez E., González-Pedrajo B., Camacho-Arroyo I. Role of Sex Steroid Hormones in Bacterial-Host Interactions. BioMed Res. Int. 2013;2013:928290. doi: 10.1155/2013/928290.
    doi: 10.1155/2013/928290pmc: PMC3591248pubmed: 23509808google scholar: lookup
  213. Santos-Marcos J.A., Mora-Ortiz M., Tena-Sempere M., Lopez-Miranda J., Camargo A. Interaction between Gut Microbiota and Sex Hormones and Their Relation to Sexual Dimorphism in Metabolic Diseases. Biol. Sex Differ. 2023;14:4. doi: 10.1186/s13293-023-00490-2.
    doi: 10.1186/s13293-023-00490-2pmc: PMC9903633pubmed: 36750874google scholar: lookup
  214. Liu M., Zhang J., Zhou Y., Xiong S., Zhou M., Wu L., Liu Q., Chen Z., Jiang H., Yang J., et al. Gut Microbiota Affects the Estrus Return of Sows by Regulating the Metabolism of Sex Steroid Hormones. J. Anim. Sci. Biotechnol. 2023;14:155. doi: 10.1186/s40104-023-00959-5.
    doi: 10.1186/s40104-023-00959-5pmc: PMC10731813pubmed: 38115159google scholar: lookup
  215. Xu H., Lu Y., Li D., Yan C., Jiang Y., Hu Z., Zhang Z., Du R., Zhao X., Zhang Y., et al. Probiotic Mediated Intestinal Microbiota and Improved Performance, Egg Quality and Ovarian Immune Function of Laying Hens at Different Laying Stage. Front. Microbiol. 2023;14:1041072. doi: 10.3389/fmicb.2023.1041072.
    doi: 10.3389/fmicb.2023.1041072pmc: PMC9902371pubmed: 36760506google scholar: lookup
  216. McCann J.C., Luan S., Cardoso F.C., Derakhshani H., Khafipour E., Loor J.J. Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium. Front. Microbiol. 2016;7:701. doi: 10.3389/fmicb.2016.00701.
    doi: 10.3389/fmicb.2016.00701pmc: PMC4870271pubmed: 27242724google scholar: lookup
  217. Ouwehand A.C., Salminen S., Isolauri E. Probiotics: An Overview of Beneficial Effects. In: Siezen R.J., Kok J., Abee T., Schasfsma G., editors. Lactic Acid Bacteria: Genetics, Metabolism and Applications: Proceedings of the Seventh Symposium on Lactic Acid Bacteria: Genetics, Metabolism and Applications, 1–5 September 2002, Egmond aan Zee, The Netherlands. Springer; Dordrecht, The Netherlands: 2002. pp. 279–289.
  218. Xu Y., Victor Curtasu M., Bendiks Z.L., Marco M., Nørskov N.P., Bach Knudsen K.E., Skou Hedemann M., Nygaard Lærke H. Effects of Dietary Fibre and Protein Content on Intestinal Fibre Degradation, Short-Chain Fatty Acid and Microbiota Composition in a High-Fat Fructose-Rich Diet Induced Obese Göttingen Minipig Model. Food Funct. 2020;11:10758–10773. doi: 10.1039/D0FO02252G.
    doi: 10.1039/D0FO02252Gpubmed: 33231591google scholar: lookup
  219. Kim S., Covington A., Pamer E.G. The Intestinal Microbiota: Antibiotics, Colonization Resistance, and Enteric Pathogens. Immunol. Rev. 2017;279:90–105. doi: 10.1111/imr.12563.
    doi: 10.1111/imr.12563pmc: PMC6026851pubmed: 28856737google scholar: lookup
  220. Deng Y., Jiang S., Duan H., Shao H., Duan Y. Bacteriophages and Their Potential for Treatment of Metabolic Diseases. J. Diabetes. 2024;16:e70024. doi: 10.1111/1753-0407.70024.
    doi: 10.1111/1753-0407.70024pmc: PMC11586638pubmed: 39582431google scholar: lookup

Citations

This article has been cited 12 times.
  1. Zhao Y, Wang Z, Fan D, Zhang J, Tu Y, Diao Q, Cui K. Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs.. J Anim Sci Biotechnol 2026 Apr 4;17(1).
    doi: 10.1186/s40104-026-01371-5pubmed: 41933424google scholar: lookup
  2. Benavides-Infante AP, Fresno-Rueda AM, Rodrigues LA, Socha MT, Fernandes T, St-Pierre B, Perez-Palencia JY, Levesque CL. Interactive effects of dietary protein and fiber levels on total tract and apparent ileal nutrient digestibility, microbiota profiling, and fermentation products in pigs fed a blend of branched-chain volatile fatty acids.. Front Vet Sci 2025;12:1731832.
    doi: 10.3389/fvets.2025.1731832pubmed: 41669238google scholar: lookup
  3. Ibiwoye DO, Oladejo OA, Akinsola OA, Adekiya AO, Alabi OM, Ayansina AD, Dahunsi SO. Methanogenic activities signatures in broilers fed black soldier fly (Hermetia illucens) larvae-based diets.. Biochem Biophys Rep 2026 Mar;45:102441.
    doi: 10.1016/j.bbrep.2026.102441pubmed: 41568060google scholar: lookup
  4. Guo P, Qin W, Song W, Chen H. Spatial Multi-Omics Analysis of the Qianqiu Goat Gut Microbiome and Metabolome.. Int J Mol Sci 2025 Dec 7;26(24).
    doi: 10.3390/ijms262411815pubmed: 41465245google scholar: lookup
  5. Jespersen SG, Lutz VT, Poulsen LL, Brøndsted L. The potential of using bacteriophages targeting Salmonella Dublin in cattle herds.. Front Microbiol 2025;16:1698141.
    doi: 10.3389/fmicb.2025.1698141pubmed: 41234745google scholar: lookup
  6. Su M, Du C, Zhang W, Liao J, Li T, Gan S, Ma J. Comparison of Bacterial Community in the Jejunum, Ileum and Cecum of Suckling Lambs During Different Growth Stages.. Microorganisms 2025 Aug 29;13(9).
    doi: 10.3390/microorganisms13092024pubmed: 41011354google scholar: lookup
  7. Mhalhel K, Cavallaro M, Pansera L, Ledesma LH, Levanti M, Germanà A, Sutera AM, Tardiolo G, Zumbo A, Aragona M, Montalbano G. Histological Assessment of Intestinal Changes Induced by Liquid Whey-Enriched Diets in Pigs.. Vet Sci 2025 Jul 30;12(8).
    doi: 10.3390/vetsci12080716pubmed: 40872668google scholar: lookup
  8. Niyazbekova Z, Kassen K, Jiang Y, Li D, Qi Y, Khussainov D, Batanova Z, Chen D, Ma W. Establishment and development of the gut microbiota in dairy goats during the early life.. BMC Vet Res 2025 Aug 26;21(1):523.
    doi: 10.1186/s12917-025-04958-8pubmed: 40859227google scholar: lookup
  9. Clemente-Suárez VJ, Redondo-Flórez L, Beltrán-Velasco AI, Yáñez-Sepúlveda R, Rubio-Zarapuz A, Martín-Rodríguez A, Navarro-Jimenez E, Tornero-Aguilera JF. Human Digestive Physiology and Evolutionary Diet: A Metabolomic Perspective on Carnivorous and Scavenger Adaptations.. Metabolites 2025 Jul 4;15(7).
    doi: 10.3390/metabo15070453pubmed: 40710552google scholar: lookup
  10. Song M, Tian K, Ren C, Liu Y, Ye X, Wang Y, Xie J, Zhao F. Impact of chemical composition on metabolizable energy and its prediction models in brewer's spent grains for broilers at different ages.. Poult Sci 2025 Aug;104(8):105323.
    doi: 10.1016/j.psj.2025.105323pubmed: 40446680google scholar: lookup
  11. Wang Y, Shi M, Wu J, Han X, Li M, Wu Y, Jiang Y, Zhang H, Liu S, Hu D. Variations in Intestinal Microbiota Among Three Species in the Cervidae Family Under the Same Feeding Conditions.. Vet Sci 2025 May 3;12(5).
    doi: 10.3390/vetsci12050438pubmed: 40431531google scholar: lookup
  12. Tardiolo G, Di Salvo E, Tringali S, Bartolomeo G, Genovese C, Furfaro ME, Sutera AM, Virga AN, Cicero N, Zumbo A. Ripening-Associated Changes in Fatty Acid Composition and Nutritional Indices in Caciocavallo Silano PDO Cheese.. Foods 2025 Apr 29;14(9).
    doi: 10.3390/foods14091566pubmed: 40361653google scholar: lookup
Subscribe to our newsletter
Join 100,127 horse owners like you who receive our email updates on horse health and nutrition.