Probiotic biogeography and sepsis prevention in the neonatal intestine

Neonatal infection is one of the leading causes of neonatal morbidity and mortality worldwide, particularly in those born prematurely or with low birth weight. Probiotic bacteria have been demonstrated to protect against the development of neonatal intestinal dysbiosis and are widely used in peri- and post-natal clinical settings. However, formulations and efficacy are highly variable, highlighting a critical gap in the current understanding of the mechanistic underpinnings of successful probiotic interventions in this population. Furthermore, current studies on probiotic efficacy largely rely on indirect or relative readouts of intestinal bacterial burden. Herein, we directly mapped the biogeography of intestinal colonization and quantify the probiotic effects of Escherichia coli Nissle 1917 (EcN) and Ligilactobacillus murinus strain V10 against Klebsiella pneumoniae dysbiosis across the span of the neonatal murine intestine. Despite substantial differences in biogeography within the intestine, both EcN and L. murinus V10 significantly reduced K. pneumoniae colonization and mortality from K. pneumoniae sepsis, with EcN doing so much more robustly. EcN's probiotic effect was partially dependent on its ability to respire oxygen. Contrary to the dominant paradigm and practice in the probiotic field, combining multiple probiotic strains did not necessarily increase efficacy. Simultaneous treatment with EcN and L. murinus V10 was less effective than EcN treatment alone at preventing death from sepsis. These results highlight important variables which must be taken into account in the design of effective future probiotic intervention strategies.