Current Microbiology

, Volume 75, Issue 6, pp 651–657 | Cite as

Evaluating Protocols for Porcine Faecal Microbiome Recollection, Storage and DNA Extraction: from the Farm to the Lab

  • Anixa Muiños-Bühl
  • Oscar González-Recio
  • María Muñoz
  • Cristina Óvilo
  • Juan García-Casco
  • Ana I. FernándezEmail author


There is a growing interest in understanding the role of the gut microbiome on productive and meat quality-related traits in livestock species in order to develop new useful tools for improving pig production systems and industry. Faecal samples are analysed as a proxy of gut microbiota and here the selection of suitable protocols for faecal sampling and DNA isolation is a critical first step in order to obtain reliable results, even more to compare results obtained from different studies. The aim of the current study was to establish in a cost-effective way, using automated ribosomal intergenic spacer analysis technique, a protocol for porcine faecal sampling and storage at farm and slaughterhouse and to determine the most efficient microbiota DNA isolation kit among those most widely used. Operational Taxonomic Unit profiles were compared from Iberian pig faecal samples collected from rectum or ground, stored with liquid N2, room temperature or RNAlater, and processed with QIAamp DNA Stool (Qiagen), PowerFecal DNA Isolation (Mobio) or SpeedTools Tissue DNA extraction (Biotools) commercial kits. The results, focused on prokaryote sampling, based on DNA yield and quality, OTU number and Sørensen similarity Indexes, indicate that the recommended protocol for porcine faecal microbiome sampling at farm should include: the collection from porcine rectum to avoid contamination; the storage in liquid N2 or even at room temperature, but not in RNAlater; and the isolation of microbiota DNA using PowerFecal DNA Isolation kit. These conditions provide more reliable DNA samples for further microbiome analysis.



This work has received funding by Ministerio de Economía y Competitividad (MINECO) project AGL2014-56369-C2 and from project TREASURE (this project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 634476. The content of this paper reflects only the author’s view and the European Union Agency is not responsible for any use that may be made of the information it contains). We also wish to thank IBÉRICOS PUROS DE EXTREMADURA SL, MAZAFRA and Reproduction Department at INIA for helping us in faecal sampling.

Compliance with Ethical Standards

Conflict of interest

There is no conflict of interest.

Supplementary material

284_2017_1429_MOESM1_ESM.xlsx (37 kb)
Supplementary material 1 (XLSX 37 KB)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Anixa Muiños-Bühl
    • 1
  • Oscar González-Recio
    • 1
  • María Muñoz
    • 2
  • Cristina Óvilo
    • 1
  • Juan García-Casco
    • 2
  • Ana I. Fernández
    • 3
    Email author
  1. 1.Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
  2. 2.Departamento de Mejora Genética Animal, Centro I+D Cerdo Ibérico INIAZafraSpain
  3. 3.Department of CardiologyHospital General Universitario Gregorio Marañón, Translational ResearchMadridSpain

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