Breast milk is known to provide many benefits to the newborn and developing infant.
According to 'Bioactive Proteins in Human Milk: Health, Nutrition, and Implications to Infant Formulas.’:
Several proteins in breast milk, including lactoferrin, α-lactalbumin, milk fat globule membrane proteins, and osteopontin, have been shown to have bioactivities that range from involvement in the protection against infection to the acquisition of nutrients from breast milk.
Research suggests that breastmilk can help re-establish a healthy balance of bacteria and antibodies even after the use of antibiotics. As stated in 'Early infant feeding and micro-ecology of the gut.':
Newborn infants are rapidly colonized by both aerobic and and anaerobic bacteria, initially with about 50% of each type. Several factors related both to the infant and its environment influence the composition of the intestinal microflora quantitatively as well as qualitatively. Major ecological disturbances are observed in newborn infants treated with antimicrobial agents. One way of minimizing the ecological disturbances, which may be seen in infants treated in neonatal intensive care units, is to provide them with fresh breast milk from their mothers and to use antimicrobial therapy only under strict clinical indications.
'Protective nutrients and bacterial colonization in the immature human gut.' describes the role breastfeeding has on infant intestinal microflora.
The normal human microflora is a complex ecosystem that is in part dependent on enteric nutrients for establishing colonization. The gut microbiota are important to the host with regard to metabolic functions and resistance to bacterial infections. At birth, bacterial colonization of a previously germ-free human gut begins. Diet and environmental conditions can influence this ecosystem. A breast-fed, full-term infant has a preferred intestine microbiota in which bifidobacteria predominate over potentially harmful bacteria, whereas in formula-fed infants, coliforms, enterococci, and bacteroides predominate. The pattern of bacterial colonization in the premature neonatal gut is different from that in the healthy, full-term infant gut. Those infants requiring intensive care acquire intestinal organisms slowly, and the establishment of bifidobacterial flora is retarded. A delayed bacterial colonization of the gut with a limited number of bacterial species tends to be virulent. Bacterial overgrowth is one of the major factors that promote bacterial translocation. The aberrant colonization of the premature infant may contribute to the development of necrotizing enterocolitis. Breastfeeding protects infants against infection. Oligo-saccharides and glycoconjugates, natural components in human milk, may prevent intestinal attachment of enteropathogens by acting as receptor homologues. Probiotics and prebiotics modulate the composition of the human intestinal microflora to the benefit of the host. These beneficial effects may result in the suppression of harmful microorganisms, the stimulation of bifidobacterial growth, or both. In the future, control and manipulation of the bacterial colonization in the neonatal gut may be a new approach to the prevention and treatment of intestinal infectious diseases of various etiologies.
While it is possible that the antibiotic your son is taking can impact his gut flora, it is also important to note that breast milk contains a host of factors that can assist in re-establishing a healthy balance.