mBio
(Jun 2021)
Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil
Kimberley V. Sukhum,
Rhiannon C. Vargas,
Manish Boolchandani,
Alaric W. D’Souza,
Sanket Patel,
Akhil Kesaraju,
Gretchen Walljasper,
Harshad Hegde,
Zhan Ye,
Robert K. Valenzuela,
Paul Gunderson,
Casper Bendixsen,
Gautam Dantas,
Sanjay K. Shukla
Affiliations
Kimberley V. Sukhum
ORCiD The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Rhiannon C. Vargas
ORCiD The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Manish Boolchandani
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Alaric W. D’Souza
ORCiD The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Sanket Patel
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Akhil Kesaraju
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Gretchen Walljasper
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Harshad Hegde
Center for Oral Systemic Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
Zhan Ye
Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
Robert K. Valenzuela
Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
Paul Gunderson
Lake Region State College, Devils Lake, North Dakota, USA
Casper Bendixsen
National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
Gautam Dantas
ORCiD The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
Sanjay K. Shukla
Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
DOI
https://doi.org/10.1128/mBio.00798-21
Journal volume & issue
Vol. 12,
no. 3
Abstract
Read online
The addition of dairy cow manure—stored in manure pits—to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high.
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