Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome

The poultry industry has traditionally relied on the use of antibiotic growth promoters (AGPs) to improve production efficiency and minimize infection. With the recent drive to eliminate the use of AGPs, novel alternatives are urgently required. Recently attention has turned to the use of synthetic communities that may be used to ‘seed’ the developing microbiome. The current challenge is identifying keystone taxa whose influences in the gut can be leveraged for probiotic development. To help define such taxa we present a meta-analysis of 16S rRNA surveys of 1572 cecal microbiomes generated from 19 studies. Accounting for experimental biases, consistent with previous studies, we find that AGP exposure can result in reduced microbiome diversity. Network community analysis defines groups of taxa that form stable clusters and further reveals Lactobacillus to elicit a polarizing effect on the cecal microbiome, exhibiting relatively equal numbers of positive and negative interactions with other taxa. Our identification of stable taxonomic associations provides a valuable framework for developing effective microbial consortia as alternatives to AGPs.