Biogeography of intestinal mucus-associated microbiome. Depletion of genus Pseudomonas is associated with depressive-like behaviors in female cynomolgus macaques
This is a summary of our May 16th, 2024 DalMUG journal club discussion, written by Monica Alvaro Fuss
Summary
This study characterized differences in microbial composition of the intestinal mucus layer in female cynomolgus macaques exhibiting depressive-like behaviours versus healthy controls. The authors collected samples from the mucosal surface of the duodenum, jejunum, ileum, cecum and colon and subjected them to shotgun metagenomic sequencing to generate both taxonomic and functional profiles. The authors find that alpha diversity could predict depressive-like behaviors along duodenum to colon. They also find that Pseudomonas spp. were positively associated with positive behaviors. The authors state that the genus Pseudomonas contributed to lipid metabolism pathways including PPAR signaling pathway, cholesterol metabolism, and fat digestion and absorption, which was found to be decreased in the depressive-like group.
Below are the key points that came up during our discussion.
Points of discussion
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We discussed the use of mucus-associated samples versus fecal samples.
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We noted that only three healthy individuals had high levels of Pseudomonas.
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We discussed the use of LEfSe analysis for differential abundance testing, as it often identifies high numbers of false positives.
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We discussed how co-occurrence network analyses can help collapse high-dimensional data for interpretation.
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We noted that gene expression cannot be inferred from DNA sequencing data.