380 The Sow Milk Microbiome and Resistome

• Published in: Journal of animal science 2023-11, Vol.101 (Supplement_3), p.313-314
• Main Authors: Holman, Devin B, Gzyl, Katherine E, Kommadath, Arun
• Format: Article
• Language: English
• Subjects: Antimicrobial agents; Antimicrobial resistance; Bacteria; Colostrum; Culture media; Drug resistance; E coli; Gene sequencing; Genes; Genomes; Hogs; Immunoglobulins; Klebsiella; Lactic acid; Lactobacilli; Lipids; Metagenomics; Microbiomes; Milk; Nucleotide sequence; Nucleotides; Nutrients; Oligosaccharides; Probiotics; rRNA 16S; Staphylococcus; Strains (organisms); Suckling behavior; Swine; Vitamins; Whole genome sequencing
• ISSN: 0021-8812; 1525-3163
• DOI: 10.1093/jas/skad281.373

Abstract In addition to oligosaccharides, proteins (e.g., immunoglobulins), lipids, vitamins, and other nutrients vital for piglet health, sow’s milk contains bacteria believed to be important in gut health. Therefore, certain sow milk isolates with potentially beneficial properties may be of interest for use as probiotic strains. Furthermore, given the relatively large reservoir of antimicrobial-resistant bacteria carried by commercial pigs even in the absence of direct antimicrobial exposure, it is possible that sow’s milk may also transfer antimicrobial-resistant bacteria to their piglets. The objective of this study was to characterize the bacterial microbiome of sow’s milk using both culturing and shotgun metagenomics. To do this, colostrum (within 24 h of farrowing) and milk samples (n = 42) were collected from 14 sows at d 0, 7, and 21 during the suckling phase. We recovered 323 isolates on four different culture media, and 135 of these were chosen for whole-genome sequencing based on their 16S rRNA gene sequence identity to maximize isolate diversity. The majority (n = 90) of the sequenced isolates belonged to either the Staphylococcus or Streptococcus genera. Twelve isolates (Lactiplantibacillus plantarum, Lactobacillus amylovorus, Ligilactobacillus salivarius, Limosilactobacillus reuteri, and Weissella paramesenteroides) were members of lactic acid-producing bacterial species noted for their beneficial properties in mammals. Several potentially pathogenic bacterial species were also isolated including Clostridium perfringens, Escherichia coli, Klebsiella pneumonia, Streptococcus dysgalactiae, Staphylococcus hyicus, and Streptococcus suis. In addition, seven isolates could not be assigned to a specific species (< 95% average nucleotide identity) and thus may represent potentially novel bacterial species. We also mapped the shotgun metagenomic reads back to the sequenced isolate genomes and found Rothia spp. and L. amylovorus to be relatively most abundant ( > 0.25%). Nearly all of the isolates (n = 130) carried at least one antimicrobial resistance gene and many strains, including S. suis and S. dysgalactiae isolates, encoded genes conferring resistance to more than three antimicrobial classes. The tetracycline resistance genes tet(W), tet(Q), tet(W/N/W), tet(K), and tet(O) were the relatively most abundant antimicrobial resistance genes in the colostrum and milk metagenomes. These results show that sow’s milk may be a source of both beneficial an