Ortiz de Ora, L. | Search bioRxiv

bioRxiv2024

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.

microbiology↗

bioRxiv2022

Discovery of a Gut Bacterial Metabolic Pathway that Drives α-Synuclein Aggregation and Neurodegeneration

Parkinsons disease (PD) etiology is associated with aggregation and accumulation of -synuclein (- syn) proteins in midbrain dopaminergic neurons. Emerging evidence suggests that in certain subtypes of PD, -syn aggregates originate in the gut and subsequently spread to the brain. However, the mechanisms that instigate -syn aggregation in the gut have remained elusive. In the brain, the aggregation of -syn is induced by oxidized dopamine. Such a mechanism has not been explored in the gastrointestinal (GI) tract, a niche harboring 46% of the bodys dopamine reservoirs. Here, we report that gut bacteria Enterobacteriaceae induce -syn aggregation. More specifically, our in vitro data indicate that respiration of nitrate by Escherichia coli K-12 yields nitrite, a potent oxidizing agent that creates an oxidizing redox potential in the bacterial environment. In these conditions, Fe2+ was oxidized to Fe3+, enabling formation of dopamine-derived quinones and -syn aggregates. Exposing nitrite, but not nitrate, to enteroendocrine STC-1 cells induced aggregation of -syn that is natively expressed in these cells, which line the intestinal tract. Finally, we examined the in vivo relevance of bacterial nitrate respiration to the formation of -syn aggregates using Caenorhabditis elegans models of PD. We discovered that nematodes exposed to nitrate-reducing E. coli K-12 displayed significantly enhanced neurodegeneration as compared to an E. coli K-12 mutant that could not respire nitrate. This neurodegenerative effect was absent when -syn was mutated to prevent interactions with dopamine-derived quinones. Taken together, our findings indicate that gut bacterial nitrate reduction may be critical to initiating intestinal - syn aggregation. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/495350v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@258b2org.highwire.dtl.DTLVardef@d3b42org.highwire.dtl.DTLVardef@ad6b1borg.highwire.dtl.DTLVardef@152d39b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗