Chaston Blog
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11 Sep 2020
Behavioral evidence for contextual olfactory-mediated avoidance of the ubiquitous phytopathogen Botrytis cinerea by Drosophila suzukii. The flies avoid feeding on raspberries if the raspberries are inoculated with a fly 'pathogen', but not if nearby strawberry leaves are inoculated with the pathogen. Important demonstration of a fly 'self-medication'-style response (though they're avoiding, not medicating).
Oxalate-Degrading Bacillus subtilis Mitigates Urolithiasis in a Drosophila melanogaster Model. Very cool demonstration that B. subtilis, presumably through oxalate degradation, reduces 'kidney stone' burden in a fruit fly model.
Older papers but saw recently:
The genetic basis for variation in olfactory behavior in Drosophila melanogaster. Impressive effort, measuring responses of 186 fly lines to 14 different odorants and followup mutant analysis. We're looking at the role of microbes in the diets on fly feeding preferences, and some of these genes may play a role.
The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.
Oxalate-Degrading Bacillus subtilis Mitigates Urolithiasis in a Drosophila melanogaster Model. Very cool demonstration that B. subtilis, presumably through oxalate degradation, reduces 'kidney stone' burden in a fruit fly model.
Older papers but saw recently:
The genetic basis for variation in olfactory behavior in Drosophila melanogaster. Impressive effort, measuring responses of 186 fly lines to 14 different odorants and followup mutant analysis. We're looking at the role of microbes in the diets on fly feeding preferences, and some of these genes may play a role.
The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.
7 Sep 2020
The quest for absolute abundance: the use of internal standards for DNA-based community ecology. Article on using internal standards to approximate absolute abundances.
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. Disrupting circadian rhythms can leads to Crohn's-like disease.
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. Maybe not surprising - maternal BMI, delivery mode, and antibiotics all influenced these. Fancy way of saying, "No detectable signal except for things we already know?"
1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding. Shotgun sequencing, small number of samples (24 samples from 6 individuals) - but nice depth. Focus is that these animals are usually subject to sub-optimal feeding; what insight can be gleaned?
The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly. A surprising (to me) finding has been that adult lepidoptera don't appear to have a robust associated microbiota; I've been skeptical but it seems to be consistent with emerging findings. This paper looks at how changes in the microbiota may affect the animals' life history, adn they conclude the microbiota does not affect the life history of the animal. One caveat is that antibiotic treatment also clearly influenced the traits (controls show this). It would be nice to see what happens without antibiotic treatments (bleach dechorionation), but again - appears to support that the adult lepidopteran microbiota seems not to to be that important. Maybe just in a lab setting? Why not?
Antipredatory Responses of Mosquito Pupae to Non-Lethal Predation Threat-Behavioral Plasticity Across Life-History Stages. Cool differences between larval and pupal movement directions (but not activity) when exposed to predator cues.
A hypothesis is a liability. Great idea for a study - if students don't just plot the data they'll never find the gorilla. Take home message is clear: look at the data. Still, I can't help but wonder if the title overstates - what would they get if they gave this to a graduate student or PI instead of undergrads. Still, a fascinating reminder!
A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas. Increased diversification of H. pylori in American versus other populations possibly linked to increased rates of cancer?
Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Awesome paper. Need to think about it as we work out how host feeding preferences may vary between animals.
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Awesome MGWA paper relating to keystone taxa.
Keystone taxa indispensable for microbiome recovery. And more on keystone taxa.
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. Disrupting circadian rhythms can leads to Crohn's-like disease.
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. Maybe not surprising - maternal BMI, delivery mode, and antibiotics all influenced these. Fancy way of saying, "No detectable signal except for things we already know?"
1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding. Shotgun sequencing, small number of samples (24 samples from 6 individuals) - but nice depth. Focus is that these animals are usually subject to sub-optimal feeding; what insight can be gleaned?
The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly. A surprising (to me) finding has been that adult lepidoptera don't appear to have a robust associated microbiota; I've been skeptical but it seems to be consistent with emerging findings. This paper looks at how changes in the microbiota may affect the animals' life history, adn they conclude the microbiota does not affect the life history of the animal. One caveat is that antibiotic treatment also clearly influenced the traits (controls show this). It would be nice to see what happens without antibiotic treatments (bleach dechorionation), but again - appears to support that the adult lepidopteran microbiota seems not to to be that important. Maybe just in a lab setting? Why not?
Antipredatory Responses of Mosquito Pupae to Non-Lethal Predation Threat-Behavioral Plasticity Across Life-History Stages. Cool differences between larval and pupal movement directions (but not activity) when exposed to predator cues.
A hypothesis is a liability. Great idea for a study - if students don't just plot the data they'll never find the gorilla. Take home message is clear: look at the data. Still, I can't help but wonder if the title overstates - what would they get if they gave this to a graduate student or PI instead of undergrads. Still, a fascinating reminder!
A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas. Increased diversification of H. pylori in American versus other populations possibly linked to increased rates of cancer?
Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Awesome paper. Need to think about it as we work out how host feeding preferences may vary between animals.
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Awesome MGWA paper relating to keystone taxa.
Keystone taxa indispensable for microbiome recovery. And more on keystone taxa.
2 Jun 2020
Microbiome of the Queensland Fruit Fly Through Metamorphosis - in Bactrocera tryoni. Looked at pupal stage. Also looked at fungi. Sort of like Wong 2011.
The Human Tumor Microbiome Is Composed of Tumor Type-Specific Intracellular Bacteria - Tumor-specific microbiota! But can't access it yet. Very curious if they did any work to distinguish dead and living cells. Apparently bacteria are known to inhabit tumors, but i did not know this!
Longitudinal Analysis Reveals Transition Barriers Between Dominant Ecological States in the Gut Microbiome - Very cool to use paired and longitudinal microbiome and metabolome data. Hopefully future work can get us deeper than the Bacteroides / Prevotella divide. Interested if any wearable data are correlated with the microbiota, but this paper is just the serum metabolite and clinical chemistry profile. Nice to give the paper an ecological touch.
Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population - Human MGWA for rheumatoid arthritis implicates bacterial redox, fatty acid biosynthesis, glycosaminoglycan degradation genes.
Predictive Biology: Modelling, Understanding and Harnessing Microbial Complexity. Nature Reviews Microbiology, AJ Lopatkin and JJ Collins. No article access yet.
Ageing and genetic background influence anaesthetic effects in a D. melanogaster model of blunt trauma with brain injury - GWAS paper
Impact of the Gut Microbiota on Atorvastatin Mediated Effects on Blood Lipids - "The cholesterol lowering effect of atorvastatin was significantly attenuated in mice with depleted gut microbiota". Depletion was done with antibiotics, not a germ-free facility, so depletion may have really meant change. There was a difference in body weight but didn't see anything on a quick scan for tests confrming mic were bacteria free (they were not).
16S rRNA Gene Amplicon Sequence Data From Feces of Wild Deer (Cervus Nippon) in Japan - could be useful ref for deer paper.
The Human Tumor Microbiome Is Composed of Tumor Type-Specific Intracellular Bacteria - Tumor-specific microbiota! But can't access it yet. Very curious if they did any work to distinguish dead and living cells. Apparently bacteria are known to inhabit tumors, but i did not know this!
Longitudinal Analysis Reveals Transition Barriers Between Dominant Ecological States in the Gut Microbiome - Very cool to use paired and longitudinal microbiome and metabolome data. Hopefully future work can get us deeper than the Bacteroides / Prevotella divide. Interested if any wearable data are correlated with the microbiota, but this paper is just the serum metabolite and clinical chemistry profile. Nice to give the paper an ecological touch.
Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population - Human MGWA for rheumatoid arthritis implicates bacterial redox, fatty acid biosynthesis, glycosaminoglycan degradation genes.
Predictive Biology: Modelling, Understanding and Harnessing Microbial Complexity. Nature Reviews Microbiology, AJ Lopatkin and JJ Collins. No article access yet.
Ageing and genetic background influence anaesthetic effects in a D. melanogaster model of blunt trauma with brain injury - GWAS paper
Impact of the Gut Microbiota on Atorvastatin Mediated Effects on Blood Lipids - "The cholesterol lowering effect of atorvastatin was significantly attenuated in mice with depleted gut microbiota". Depletion was done with antibiotics, not a germ-free facility, so depletion may have really meant change. There was a difference in body weight but didn't see anything on a quick scan for tests confrming mic were bacteria free (they were not).
16S rRNA Gene Amplicon Sequence Data From Feces of Wild Deer (Cervus Nippon) in Japan - could be useful ref for deer paper.
28 May 2020
Peptidoglycan Production by an Insect-Bacterial Mosaic. Here we show that horizontally transferred genes on the mealybug genome work together with genes retained on the Moranella genome to produce a PG layer exclusively at the Moranella cell periphery. Mealybug with Moranella that live inside of Tremblaya. McCutcheon lab. Cell.
Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis. 3 invaginations > expansion to 3 pores > V. fischeri migration through three anatomically distinct regions to blind-ended crypts, with a dynamic bottleneck and spatial restriction in crypts. Bottlenecks maintain daily expulsion. Not influenced by known MAMPs and requires live cells. Vibrio-Squid. McFall-Ngai, Ruby, Goldman labs. mBio.
Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis. 3 invaginations > expansion to 3 pores > V. fischeri migration through three anatomically distinct regions to blind-ended crypts, with a dynamic bottleneck and spatial restriction in crypts. Bottlenecks maintain daily expulsion. Not influenced by known MAMPs and requires live cells. Vibrio-Squid. McFall-Ngai, Ruby, Goldman labs. mBio.
Discrete Fiber Structures Dictate Human Gut Bacteria Outcomes.
Clinical trial with prebiotics! Very cool.
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