Treatments of porcine fecal samples affect high-throughput virome sequencing results

Nantel-Fortier, Nicolas; Gauthier, Martin; L’Homme, Yvan; Fravalo, Philippe; Brassard, Julie

doi:10.1016/j.jviromet.2020.114045

Cited by 4 publications

(2 citation statements)

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“…Viruses are important pathogens of boilers, and we applied shotgun metagenome sequencing to examine viruses present in the MT within bioreactors, and in birds ± MT. We observed that although viruses were present within the bioreactor microbiota, and in birds administered the MT, the relative abundance of viruses was very low relative to other studies [29]. Importantly, bacteriophages are important regulators of bacterial community structures in intestines [30], and the degree to which propagation of a MT within bioreactors affects bacteriophages, as well as avian pathogenic viruses, warrants further examination.…”

Section: Bioreactor System To Generate the Microbiota Transplantmentioning

confidence: 65%

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Microbiota Transplantation in Day-Old Broiler Chickens Ameliorates Necrotic Enteritis via Modulation of the Intestinal Microbiota and Host Immune Responses

et al. 2022

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A microbiota transplant (MT) originating from mature adult chicken ceca and propagated in bioreactors was administered to day-old broiler chicks to ascertain the degree to which, and how, the MT affects Clostridium perfringens (Cp)-incited necrotic enteritis (NE). Using a stress predisposition model of NE, birds administered the MT and challenged with Cp showed fewer necrotic lesions, and exhibited a substantially higher α- and β-diversity of bacteria in their jejunum and ceca. Birds challenged with Cp and not administered the MT showed decreased Lactobacillus and increased Clostridium sensu strico 1 in the jejunum. In ceca, Megamonas, a genus containing butyrate-producing bacteria, was only present in birds administered the MT, and densities of this genus were increased in birds challenged with Cp. Metabolite profiles in cecal digesta were altered in birds administered the MT and challenged with the pathogen; 59 metabolites were differentially abundant following MT treatment, and the relative levels of short chain fatty acids, butyrate, valerate, and propionate, were decreased in birds with NE. Birds administered the MT and challenged with Cp showed evidence of enhanced restoration of intestinal barrier functions, including elevated mRNA of MUC2B, MUC13, and TJP1. Likewise, birds administered the MT exhibited higher mRNA of IL2, IL17A, and IL22 at 2-days post-inoculation with Cp, indicating that these birds were better immunologically equipped to respond to pathogen challenge. Collectively, study findings demonstrated that administering an MT containing a diverse mixture of microorganisms to day-old birds ameliorated NE in broilers by increasing bacterial diversity and promoting positive immune responses.

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Section: Bioreactor System To Generate the Microbiota Transplantmentioning

confidence: 65%

“…DNA and RNA viruses in fecal samples obtained from birds (2 g) and from MT bioreactors (2 mL) were examined using metagenome sequence analysis as described previously [29]. Viral abundance at a family level of resolution was calculated relative to total microbial read counts (i.e., eukaryotes, prokaryotes, and viruses).…”

Section: Characterization Of the Viromementioning

confidence: 99%