Biology subjects

Hayase, E.

Publications and source records attributed to Hayase, E..

3 recordsLinked to original sources

bioRxiv2024

Sugar-rich foods exacerbate antibiotic-induced microbiome injury

Intestinal microbiota composition is implicated in several diseases; understanding the factors that influence it are key to elucidating host-commensal interactions and to designing microbiome-targeted therapies. We quantified how diet influences microbiome dynamics in hospitalized patients. We recorded 9,419 meals consumed by 173 patients undergoing hematopoietic cell transplantation and profiled the microbiome in 1,009 longitudinally collected stool samples from 158 of them. Caloric intake was correlated with fecal microbiota diversity. Bayesian inference revealed associations between intake of sweets or sugars during antibiotic exposure with microbiome disruption, as assessed by low diversity or expansion of the pathobiont Enterococcus. We validated this observation experimentally, finding that sucrose exacerbated antibiotic-induced Enterococcus expansion in mice. Taken together, our results suggest that avoiding sugar-rich foods during antibiotic treatment may reduce microbiome injury. One Sentence SummaryAnalyses of hematopoietic cell transplant patients and of mice uncover links between foods and microbiome disruption.

microbiology↗

bioRxiv2024

Accurate quantitation of 16S gene copies in low biomass samples post-antibiotic treatment through deep sequencing with a balanced nucleotide synthetic spike-in approach

The microbiota significantly impacts health and treatment outcomes. While 16S rRNA gene sequencing reveals relative bacterial abundances, it does not provide absolute quantification. We developed a cost-effective solution incorporating synthetic DNA standards designed to ensure balanced nucleotide representation at each position. These standards are spiked into samples before DNA extraction, enabling simultaneous quantification of both relative and absolute bacterial abundances. We applied this method to samples collected from mice and patients, both before and after antibiotic treatment. Our approach showed a reduction in total bacterial density in mice and patients post-antibiotic treatment. This spike-in standard method can be adapted to samples with varying bacterial densities, allowing quantification of absolute taxonomical abundances without the need for an additional quantitative PCR assessment. Our approach also improves sequencing quality scores for low biomass samples.

microbiology↗

bioRxiv2021

Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment

Not all cancer patients with severe neutropenia develop fever, and the fecal microbiome may play a role. In neutropenic hematopoietic cell transplant patients (n=119), 63 (53%) developed a subsequent fever and had increased fecal Akkermansia muciniphila, a mucus-degrading bacteria (p=0.006, corrected for multiple comparisons). In mouse models, two therapies, irradiation and melphalan, similarly expanded A. muciniphila. Dietary restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Azithromycin treatment depleted A. muciniphila and preserved colonic mucus. Dietary restriction raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila with lower pH and increased propionate prevented utilization of mucin. Treating irradiated mice with azithromycin or propionate preserved the mucus layer, lessened hypothermia, and reduced inflammatory cytokines in the colon. These results suggest that diet, metabolites and colonic mucus link the microbiome to neutropenic fever, and could guide future microbiome-based preventive strategies.

microbiology↗