| Summary: | Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene <i>ermB</i> and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine <i>(aphA3)</i>, while the second decreased the tetracycline resistance gene <i>tetL</i>, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase <i>lnuB</i>, the cephalosporinase <i>cepA</i>, and the tetracycline resistance genes <i>tetG</i> and <i>tetM</i>, as well as microbes that never co-exist with the tetracycline resistance gene <i>tetQ</i>, the erythromycin resistance gene <i>ermG</i> and <i>aphA3</i>. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.
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