Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

We've all been there – the seminar speaker is done, and your brain goes 'Should I ask something? But what?? I got nothing 😫 ' … Here's a thing I wrote on how to get better at asking questions 💡 #PhDchat @AcademicChatter https://t.co/TeQjcaaKg5

— Elisa Granato (@Prokaryota) July 14, 2021

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

@Elinav_Lab @Elinav_DKFZ are happy to share our new @NatureMicrobiol paper on probiotics and antimicrobial resistance, led by @LabMihar, @rvaldesmas, @SuezLab. We show in mice and humans that the gut antimicrobial ‘resistome' is

https://t.co/LJ1efUaiNI

— ElinavLab (@Elinav_Lab) July 5, 2021

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Had a lot of fun in #drawing this one! 🎨
Imagining all these little #bacteria with these signs going around our #gut! 💭🦠#sciart https://t.co/A6yBV0RCfY

— enigrox (@enigrox) June 28, 2021

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

2 months until our first MVIF meeting ft. keynote Prof @RuthLeyMicro!

Have you submitted your abstract yet?

We have prizes for best Selected Talk and Research Highlight 🏆🗨️

Deadline the 3rd of Augusthttps://t.co/PHH4kULBJH pic.twitter.com/Djq9xp3Iaj

— Microbiome Virtual International Forum (@MicrobiomeVIF) July 14, 2021