Biology subjects

Kearney, S.

Publications and source records attributed to Kearney, S..

3 recordsLinked to original sources

bioRxiv2019

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Phototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts were dominated by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We found multiple uncultured phototrophic lineages and present metagenome-assembled genomes of two uncultured organisms within the Chlorobiales. Apparently, those Chlorobiales populations were affected by Microviridae viruses. We suggest a sulfur cycle within the bloom in which elemental sulfur produced by phototrophs is reduced to sulfide by Desulfuromonas sp. These findings improve our understanding of the ecology and ecophysiology of phototrophic blooms and their impact on biogeochemical cycles.

microbiology↗

bioRxiv2018

Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal

Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. While probiotic or prebiotic approaches typically lead to a transient pulse in an organisms abundance, persistent establishment of an introduced species may require alternative strategies. Here, we introduce the concept of orthogonal niche engineering in the gut, where we include a resource typically absent from the diet, seaweed, to establish a customized niche for an introduced organism. We show that in the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, B. plebeius DSM 17135, enables it to colonize at a median abundance of 1%, frequently increasing in abundance to 10 or more percent. We construct a mathematical model of the system to infer that B. plebeius competitively acquires endogenous resources. We provide evidence that it competes with native commensals to achieve its observed abundance. We observe a diet-dependent loss in seaweed responsiveness of B. plebeius in the long term and show the potential for IgA-mediated control of putative invaders by the immune system. These results point to the potential for diet-based intervention as a means to introduce target organisms, but also indicate potential modes for failure of this strategy in the long term.

microbiology↗

bioRxiv2017

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a hosts microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patients microbiota.

microbiology↗