In particular, we have previously shown that selection against a specific antigen is far more efficient when carried out against the individual antigen than when the antigen is present in a mixture of other antigens [59]. The situation is likely to be even more challenging for microbial communities, and may require selection in emulsions [60, 61], microfluidics [62–64] or against individual cells [65, 66] to ensure that individual bacteria are isolated from one another during the selection process. If the identity of the recognized bacteria in the microbiome is unimportant

– i.e. the goal is to catalog genome sequences present in a microbiome, whatever they are – the use of this method may be relatively straightforward. It is likely to be more challenging, find more however, if the goal is to select antibodies against particular species in a population, unless an alternative means of bacterial www.selleckchem.com/products/SB-202190.html isolation, such as fluorescent in situ hybridization [67], is available. One possible approach, which may be successful in microbiomes comprising few species, would be to select a panel

of positive antibodies against different species within the community, and then deconvolute species recognition using FACS and deep sequencing in a manner similar to that described here, after antibody selection and sorting. However, the number of bacteria that can be extracted from environmental samples easily exceeds the number MEK inhibitor review required for phage selection suggesting that this approach will be difficult for more complex populations. Since depletion is as feasible as enrichment using these scFvs with FACS, it may be possible to iterate the process using scFvs against high abundance species for their subtraction and, thus, enrich for the low abundance organisms. Even if antibodies cannot be raised to low abundance organisms, depletion of high abundance organisms in a mixture will concentrate the low abundance ones, and so lead to improved

Ribonucleotide reductase taxonomic identification and genome recovery. The described approach also has potential not only for the genome sequencing of novel and uncultivable organisms, but also in comparative genomics. In this regard, selection of antibodies against organisms initially grown in the lab then used on environmental and clinical samples holds great potential for medicine and epidemiology [68, 69]. For example, a recent study [46] reports the use of a commercially available IgG antibody for targeted enrichment using immunomagnetic separation (IMS) to fully sequence Chlamydia trachomatis directly from clinical isolates without culture. Our approach could extend on this work by adding a mechanism for the initial selection of suitable antibodies for studying pathogenic, probiotic, or other organisms. Near complete coverage, such as that provided by enrichment with phage-selected scFvs, is paramount for high resolution genomic comparisons.