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The authors thank Mr. Neil Macowan for revising the English version.

Analysis of institutional authors

Guitart-Matas, JudithAuthorGiler-Baquerizo, NoemiAuthorMigura-Garcia, LourdesCorresponding Author

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Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status

Publicated to:Bmc Veterinary Research. 21 (1): 246- - 2025-04-04 21(1), DOI: 10.1186/s12917-025-04693-0

Authors: Tort-Miro, Carla; Lorenzo-Rebenaque, Laura; Montoro-Dasi, Laura; Vega, Santiago; Rodriguez, Juan Carlos; Ventero, Maria-Paz; Perez-Gracia, Maria Teresa; Guitart-Matas, Judith; Giler-Baquerizo, Noemi; Marco-Fuertes, Ana; D'Auria, Giuseppe; Marin, Clara; Migura-Garcia, Lourdes

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Abstract

BackgroundAntibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore.ResultsOverall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005.ConclusionsThis study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.

Keywords

Animal husbandryAnimalsAntimicrobial resistanceBacteriaDiarrheaFarmsFemaleGastrointestinal microbiomeHealth statusIllumina sequencingIntestinal microbiomIntestinal microbiomeNanopore sequencingNanoporesPigsPost-weaning diarrhoeaRna, ribosomal, 16sSwineSwine diseases

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Bmc Veterinary Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 28/167, thus managing to position itself as a Q1 (Primer Cuartil), in the category Veterinary Sciences.

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-27:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 5.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 3 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 6.65.
  • The number of mentions on the social network X (formerly Twitter): 7 (Altmetric).

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Tort-Miro, Carla) and Last Author (MIGURA GARCIA, LOURDES).

the author responsible for correspondence tasks has been MIGURA GARCIA, LOURDES.