Digging into How Bacteria and Viruses Change in Pig Manure Digests

Key Findings

• Anaerobic digestion (AD) alone cuts the total amount of antibiotic‑resistance genes (ARGs) and narrows their diversity.
• Adding metal‑organic frameworks (MOFs) amplifies this effect, especially on the most dangerous ARGs used in medicine.
• The bulk of ARG reduction stems from core genes shared across many bacteria; loss of rare ARGs mainly drives the drop in diversity.
• Viruses in the digester are highly diverse, with many new species. The largest group is Drexlerviridae.
• Viruses preferentially infect specific bacteria: ~47 % target Actinobacteria, 13 % target Atribacterota.
• Only a few viruses carry ARGs, so they contribute little to resistance spread. Instead, they often harbor helper genes that boost host bacterial metabolism.

Mechanisms of Action

• AD reshapes the viral community, influencing whether viruses are intracellular or extracellular and altering the helper genes they carry.
• It reduces co‑occurrence of ARGs with plasmids—mobile DNA elements that facilitate gene transfer—thereby slowing resistance spread.
• By decreasing both the connections between ARGs and plasmids and the number of bacterial hosts carrying ARGs, AD mitigates the environmental dissemination of resistance.

Implications

These insights equip farmers and scientists with strategies to optimize anaerobic digestion processes, curbing the release of antibiotic resistance into surrounding ecosystems.