The red seaweed genus Asparagopsis is renowned for producing antimicrobial compounds that can be used in various applications (reducing methane emissions from cattle, cosmetic skin care and boosting the fish immune system) and that also benefits the seaweed itself by controlling its microbiome. However, it is unclear how any specific bacteria on the seaweed surface interact with the growth and health of Asparagopsis in culture. This study demonstrates that domesticated seaweed has very different microbiomes from wild samples. We subsequently explore the effects of manipulating the microbiome of the domesticated seaweed using different antibiotics, quantifying the change in the bacterial community and densities using fluorescence microscopy, and exploring any correlations to the growth rates of the seaweed. At the same time, we explore the impact of antibiotic treatments on the production of halogenated compounds, the key metabolites responsible for methane reduction and antimicrobial activity. These compounds include bromoform (CHBr3) as the most prevalent and another 5-10 major compounds. We then isolated various bacterial strains which can be reinoculated onto A. taxiformis. These results are discussed as the potential for use of isolated epiphytic bacteria as probiotics for seaweed culture.