Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

Overview

Journal J Vet Intern Med

Specialties General Medicine
Veterinary Medicine

Date 2017 Apr 9

PMID 28390070

Citations 93

Authors

D E Gomez

L G Arroyo

M C Costa

L Viel

J S Weese

Affiliations

Soon will be listed here.

Abstract

Background: Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea.

Objectives: To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.

Methods: Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).

Results: Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.

Clinical Relevance: The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Citing Articles

The Therapeutic Potential of Gut-Microbiota-Derived Metabolite 4-Phenylbutyric Acid in -Induced Colitis.

Wang K, Hu Y, Wu Y, Xu J, Zhao Y, Yang J Int J Mol Sci. 2025; 26(5).

PMID: 40076603 PMC: 11901052. DOI: 10.3390/ijms26051974.

Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.

Zhang H, Wang Y, Luo Z, Zhang B, Lan X, Xu L BMC Microbiol. 2025; 25(1):128.

PMID: 40069605 PMC: 11895240. DOI: 10.1186/s12866-025-03812-z.

Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.

Frazier A, Ferree L, Belk A, Al-Lakhen K, Cramer M, Metcalf J Animals (Basel). 2025; 15(3).

PMID: 39943131 PMC: 11816138. DOI: 10.3390/ani15030361.

16S rRNA and metabolomics reveal the key microbes and key metabolites that regulate diarrhea in Holstein male calves.

Cao P, Hu C, Li M, An Y, Feng X, Ma X Front Microbiol. 2025; 15:1521719.

PMID: 39881985 PMC: 11778179. DOI: 10.3389/fmicb.2024.1521719.

Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis.

Hares M, Griffiths B, Barningham L, Vamos E, Gregory R, Duncan J Anim Microbiome. 2025; 7(1):3.

PMID: 39762941 PMC: 11706078. DOI: 10.1186/s42523-024-00352-1.

References

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett W . Metagenomic biomarker discovery and explanation. Genome Biol. 2011; 12(6):R60. PMC: 3218848. DOI: 10.1186/gb-2011-12-6-r60. View

Furusawa Y, Obata Y, Fukuda S, Endo T, Nakato G, Takahashi D . Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013; 504(7480):446-50. DOI: 10.1038/nature12721. View

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

Dominguez-Bello M, Costello E, Contreras M, Magris M, Hidalgo G, Fierer N . Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010; 107(26):11971-5. PMC: 2900693. DOI: 10.1073/pnas.1002601107. View

Lievin V, Peiffer I, Hudault S, Rochat F, Brassart D, Neeser J . Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity. Gut. 2000; 47(5):646-52. PMC: 1728100. DOI: 10.1136/gut.47.5.646. View

Duffy L, Zielezny M, Riepenhoff-Talty M, Dryja D, Sayahtaheri-Altaie S, Griffiths E . Effectiveness of Bifidobacterium bifidum in mediating the clinical course of murine rotavirus diarrhea. Pediatr Res. 1994; 35(6):690-5. DOI: 10.1203/00006450-199406000-00014. View

Malmuthuge N, Li M, Goonewardene L, Oba M, Guan L . 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(5):3189-200. DOI: 10.3168/jds.2012-6200. View

Lukas F, Koppova I, Kudrna V, Kopecny J . Postnatal development of bacterial population in the gastrointestinal tract of calves. Folia Microbiol (Praha). 2007; 52(1):99-104. DOI: 10.1007/BF02932147. View

Pereira R, Lima S, Siler J, Foditsch C, Warnick L, Bicalho R . Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves. PLoS One. 2016; 11(1):e0147525. PMC: 4726667. DOI: 10.1371/journal.pone.0147525. View

10.

McGuirk S . Disease management of dairy calves and heifers. Vet Clin North Am Food Anim Pract. 2008; 24(1):139-53. PMC: 7135781. DOI: 10.1016/j.cvfa.2007.10.003. View

11.

Pereira R, Siler J, Ng J, Davis M, Warnick L . Effect of preweaned dairy calf housing system on antimicrobial resistance in commensal Escherichia coli. J Dairy Sci. 2014; 97(12):7633-43. PMC: 4351789. DOI: 10.3168/jds.2014-8588. View

12.

Klindworth A, Pruesse E, Schweer T, 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. 2012; 41(1):e1. PMC: 3592464. DOI: 10.1093/nar/gks808. View

13.

Smith H . The development of the flora of the alimentary tract in young animals. J Pathol Bacteriol. 1965; 90(2):495-513. View

14.

Macpherson A, Harris N . Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol. 2004; 4(6):478-85. DOI: 10.1038/nri1373. View

15.

Suchodolski J, Foster M, Sohail M, Leutenegger C, Queen E, Steiner J . The fecal microbiome in cats with diarrhea. PLoS One. 2015; 10(5):e0127378. PMC: 4437779. DOI: 10.1371/journal.pone.0127378. View

16.

Uyeno Y, Sekiguchi Y, Kamagata Y . rRNA-based analysis to monitor succession of faecal bacterial communities in Holstein calves. Lett Appl Microbiol. 2010; 51(5):570-7. DOI: 10.1111/j.1472-765X.2010.02937.x. View

17.

Malmuthuge N, Chen Y, Liang G, Goonewardene L, Guan L . Heat-treated colostrum feeding promotes beneficial bacteria colonization in the small intestine of neonatal calves. J Dairy Sci. 2015; 98(11):8044-53. DOI: 10.3168/jds.2015-9607. View

18.

Nelson M, Morrison H, Benjamino J, Grim S, Graf J . Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One. 2014; 9(4):e94249. PMC: 3983156. DOI: 10.1371/journal.pone.0094249. View

19.

Veiga P, Pons N, Agrawal A, Oozeer R, Guyonnet D, Brazeilles R . Changes of the human gut microbiome induced by a fermented milk product. Sci Rep. 2014; 4:6328. PMC: 4160712. DOI: 10.1038/srep06328. View

20.

Li R, Connor E, Li C, Baldwin Vi R, Sparks M . Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol. 2011; 14(1):129-39. DOI: 10.1111/j.1462-2920.2011.02543.x. View