Next-generation sequencing has fostered an explosion of microbiome research. Due to the role our microbiota play in health, there is growing interest in cultivating beneficial bacterial strains for ‘next-generation probiotics’. However, many important species are difficult to cultivate. Faecalibacterium prausnitzii is associated with healthy gut microbiota but is extremely oxygen sensitive, and Christensenella minuta is a health-associated keystone species that is under-represented in the microbial community. A previously described cell sorter modified for anaerobic sorting conditions could be used to isolate sensitive strains of bacteria like this. First, researchers established that reference strains of F. prausnitzii and C. minuta had only minor viability loss during sorting and culture in this system. Then. they generated polyclonal antibodies against _F. prausnitzii _and C. minuta. After confirming antibody specificity, they used these antibodies along with anaerobic sorting and staining to isolate new bacterial strains from fecal samples. While this study generated antibodies from previously cultivated reference strains and many gut-residing bacteria remain uncultured, this proof-of-concept study demonstrated that targeted cell sorting under anaerobic conditions is a promising tool for fecal microbiota research.