Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle

Table 1 Metagenomic sequencing metrics from cattle fecal DNA.

Feature	Mean	p-value*
Feature	Mean	Lactation Phase	Temperature	Treatment	Time post-treatment	Lactation Phase: Temperature: Treatment
*Reads*
Raw reads (150 bp)	5,735,481	0.94	0.70	0.84	0.40	0.61
Non-host reads (150 bp)	4,507,080	0.79	0.72	0.73	0.36	0.42
Proportion of host reads (Bos Taurus %)	21.417576	< 0.0001	0.60	0.83	0.78	0.46
*Proportion in non-host reads*
Bacteria (%)	11.027	< 0.0001	0.12	0.92	0.05	0.70
Archaea (%)	0.746	< 0.0001	0.89	0.53	0.08
Eukaryota (%)	0.170
Viruses (%)	0.004	0.45	0.94	0.33	0.65	0.31
Genome equivalents (Nº)	239.930	0.06	0.47	0.77	0.51	0.10
Average genome size (bp)	2,754,869	< 0.0001	0.97	0.33	< 0.0001	0.73
*Contig assemblies*
Contigs (Nº)	341430.855	1.00	0.62	0.99	0.09	0.31
Reads mapping contigs (%)	36.011	0.01	0.69	0.37	< 0.0001	0.02
N50 (Kbp)	0.764	0.98	0.35	0.87	0.88	0.23
L50 (Kbp)	5.703	0.92	0.81	0.63	0.01	0.12
Largest contig (Kbp)	38.065	0.15	0.35	0.75	0.02	0.38
Length (Mbp)	14.887	0.87	0.72	0.56	0.01	0.29

*P-values were calculated with ANOVA using mixed effects models including differences in lactation phase, ambient temperature (ºC), treatment group, time post-treatment, and diet while controlling by cow ID. It should be noted that the factor of diet did not contribute significantly to the model due to the correlation between diet variation and each specific lactation phase. Significant p-values are in bold. The analysis could not incorporate the factor of Eukaryota as it was not detected consistently across all samples

ISSN: 2524-4671