“…In cattle, genomic approaches (both culture and nonculture-based) have mostly focused on the rumen (Pitta et al , 2016 ; Seshadri et al , 2018 ; Stewart et al , 2018 ; Bickhart et al , 2019 ). Despite the clear role of the large intestine in many aspects of health, nutrition, and the spread of zoonotic pathogens and AMR, the knowledge of its microbiota is mainly limited to: - descriptive 16S/18S rRNA targeted sequencing (Holman and Gzyl, 2019 ),
- single bacterial species (i.e., Escherichia and Salmonella ) and their antagonists that pose a threat to the cattle host or human consumers (Wang et al , 2017 ; Holschbach and Peek, 2018 ), and
- the occurrence and distribution of AMR genes in the feces (Noelle Noyes et al , 2016a , b ; Doster et al , 2018 ; Zaheer et al, 2018 , 2019 ; Keijser et al , 2019 ; Liu et al , 2019 ; Rovira et al , 2019 ; Weinroth et al , 2019 ; Gaeta et al , 2020 ; Haley et al , 2020 ; Lim et al , 2020 ; Salaheen et al , 2020 ; Duarte et al , 2021 ) (see also ).
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