Probiotic biogeography and sepsis prevention in the neonatal intestine

Abstract

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. EcNs 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. IMPORTANCEIn this work we use a mouse model of late-onset neonatal sepsis (LOS) to rigorously test fundamental assumptions that underlie the current paradigm for understanding the impact of probiotics on intestinal disease. We demonstrate that two distantly related probiotic bacteria (Escherichia coli Nissle 1917 and Ligilactobacillus murinus V10) can each effectively reduce both intestinal colonization and death caused by the LOS pathobiont Klebsiella pneumoniae, acting by distinct ecological and molecular mechanisms. Our results provide new evidence that will be critical for designing and implementing safe and effective probiotic treatment regimens for LOS, a devastating and difficult to treat disease. More broadly, our results show that ecological principles are key to understanding how interventions that modulate the gut microbiome work, and that some of the assumptions underlying current interventions need to be reevaluated, especially when it comes to combining multiple probiotic strains and species.