General microbiome and science, July 29

Bioinformatics tools, metabolomics, antibiotic resistance, biomeme hypothesis and the Kardashian index. Mine is still very low, so I’m good.


STAMP: Statistical analysis of taxonomic and functional profiles – Donovan H. Parks – Bioinformatics

“STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. It supports tests for comparing pairs of samples or samples organized into two or more treatment groups. “


Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence – Ran Blekhman – Scientific Reports

“we performed a comparative study using a combination of gene expression and metabolomic profiling in livers from humans, chimpanzees, and rhesus macaques. We show that dietary differences between species have a strong effect on metabolic concentrations”

Antibiotics and resistance

Emergence of quinolone resistance in the microbiota of hospitalized patients treated or not with a fluoroquinolone – Victoire de Lastours – Journal of Antimicrobial Chemotherapy

“FQs received during hospitalization account for high rates of emergence of resistance to FQs in clinically relevant bacteria from human microbiota, reflecting the important ecological impact of FQs. “

The expression of antibiotic resistance genes in antibiotic-producing bacteria
Stefanie Mak – Molecular Microbiology

“The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. “

Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater – Alex R. Hall – FEMS Microbiology Ecology

“These results suggest that antibiotics such as tetracycline may have important consequences for interactions among bacterial species, but in our experiments this was because species varied in their capacities for growth in the presence of tetracycline, rather than reduced competition at increasing tetracycline concentrations.”

Microbiology general

Please note that this one is just a hypothesis paper – there is no actual data to support this prediction. It’s very speculative, but discussed a lot on forums and Twitter.
Midichlorians – the biomeme hypothesis: is there a microbial component to religious rituals? – Alexander Y Panchin – Biology Direct

“We predict that next-generation microbiome sequencing of samples obtained from gut or brain tissues of control subjects and subjects with a history of voluntary active participation in certain religious rituals that promote microbial transmission will lead to the discovery of microbes, whose presence has a consistent and positive association with religious behavior. “

Science and publishing

Spotlight falls on top 1% in science – Chris Woolston – Nature

“News that a rarified group of scientists has claimed the lion’s share of publications has set off a social-media discussion about the fairness of the system”

Belongs to:

Estimates of the Continuously Publishing Core in the Scientific Workforce – John P. A. Ioannidis, Kevin W. Boyack, Richard Klavans – PLOS ONE

“However, only 150,608 (<1%) of them have published something in each and every year in this 16-year period (uninterrupted, continuous presence [UCP] in the literature).”

Academia’s seamier side: Lying, cheating and fraud – Fred Barbash – Washington Post

“The seamier side of academia, lying, cheating and occasionally stealing, this is the world revealed by a blog which, by all rights, should be dry and boring, like its name, “Retraction Watch.””

The Kardashian index: a measure of discrepant social media profile for scientists – Neil Hall – Genome Biology – Hat tip: Liz Costello

“if your K-index gets above 5, then it’s time to get off Twitter and write those papers”

 Dr. Bik’s Picks

The influence of emotional facial expressions on gaze-following in grouped and solitary pedestrians – Andrew C. Gallup – Nature Scientific Reports

“We found that pedestrians walking alone were not sensitive to this manipulation, while individuals traveling together in groups did reliably alter their response in relation to emotional cues. “

Timing of circadian genes in mammalian tissues – Anja Korenčič – Nature Scientific Reports

“To study the phase variability of CCGs in mammalian peripheral tissues, we develop a core clock model for mouse liver and adrenal gland based on expression profiles and known cis-regulatory sites.”

Footprint of Deepwater Horizon blowout impact to deep-water coral communities –
Charles R. Fisher – PNAS

“Here we show this was not an isolated incident; at least two other coral communities were also impacted by the spill. “



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