Joseph Nesme

Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes? sfamjournals.onlinelibrary.wiley.com/doi/abs/10.111…

Out in final form: "Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning" in @iscb journal Bioinformatics academic.oup.com/bioinformatics… (now fully open access)

@OlgaAnczukow @PacBio @jacksonlab @Magdoll @JBibliowicz76 @LEGO_Group I have no building steps leaflet in my box 😭

The role of plasmids in the gut microbiome during the first year of life biorxiv.org/cgi/content/sh… #biorxiv_micrbio

Copenhagen - the PacBio Discoveries Roadshow is back. Come along and hear our customers sharing their latest breakthroughs, and network with leading scientists on your doorstep. View full agenda: bit.ly/3lKfpbH

For all Cyano lovers and/or those who have children (4-9yo) or a good connection with schools, here is the English version of Fila&Bubbee! We deliver it for free to schools and we also respond to children's questions by visioconference with schools.

Very happy to see this work finally published! Many thanks to all authors, my lab mates and special thanks to @AlvSanMillan ! The full paper can be read here --> nature.com/articles/s4155… If you want to know about it keep scrolling down! (1/5)

@UliKluemper @DSWAP1 @biorxivpreprint Aaaaaaah! Enlightened I am now 😅

@jnesme @DSWAP1 @biorxivpreprint two separate tweets, two separate stories ;). sorry… here is the epic stuff: EpicPCR improved method paper: mdpi.com/2076-2607/9/8/… Environmental hosts paper: sciencedirect.com/science/articl… Both Roman et al. from the Merlin lab…

Christophe Merlin presenting neat epicPCR based evidence that plasmid transfer from wasrewater effluents to environmental bacteria is happening. #treWAG2022

@UliKluemper @DSWAP1 @biorxivpreprint I must miss the obvious, but there is no mention of epicPCR in the preprint? 🤔

Natural reservoirs harbouring diverse microbial communities might act as a barrier to the spread of AMR from wastewater - Christophe Merlin #treWAG2022 @DSWAP1 Read more in Leao et al. @biorxivpreprint biorxiv.org/content/10.110…

📣We have open PhD positions on the early life human gut microbiome & microbial interactions therein @microUCPH 🔥Exciting project on #metagenomics & #metabolomics 🤝 Great collaborators @COPSAC_com ✍️Application deadline: Nov 4, 2022 jobportal.ku.dk/phd/?show=1577… 🙏Please retweet

our follow-up study on disposal of sewage biosolids: Influence of sewage sludge stabilization method on microbial community... sciencedirect.com/science/articl…

@Metlab_DTU @chalmersuniv What are latent ARGs? Non functional and/or in unimportant saprophytes hosts ARGs?

#EDAR6 latent #ARG are abundant in all environments ➡️ current repositories are incomplete ! prof Erik Kristianssson From @chalmersuniv

Life comes at you fast: pundits on Russian TV realize that their military is failing and their country is in trouble. They are starting to play the blame game. Some of them finally understand that their genocidal denial of the Ukrainian identity isn't working in Russia's favor.

Lettuce grown in soil with organic fertilization history had higher fitness in presence of pathogen Rh. solani compared to mineral fertilization yet showed growth/defense tradeoff. DiControl: @igz_leibniz @UniHohenheim @HSAnhalt @HelmholtzMunich @JKI_Bund @BonaRes4u @jnesme

Why did one AMR plasmid disseminate globally and one die out? Find out inside this awesome work bit.ly/3oMRrup led by @MalakaDeS with @Jaws_Stenhouse @GraceBlackwell @RJBengtsson @ClaireJenkins2 @JPJHall 1/8

@BioMickWatson 'cause all your regants bear the mention "For research use only, not diagnostic"- I am not an expert in that matter but the legal ramification must be crazy...

But even though we're a few years away from sequencing diagnostics on the high street, service providers could produce rapid data for the NHS within hours if necessary. Why aren't we doing this?

As a sequencing expert, the lack of rapid diagnostics available on the NHS is extremely frustrating Thread

New preprint out! We know that plasmid spread depends on the specific bacterial host. But are initial phenotypes of strain-plasmid pairs or evolutionary changes in their plasmid-stability traits the more relevant predictor of plasmid spread? 1/3

Latest #preprint at @PlantEvolution lab: we fully exploit pool-based amplicon sequencing with @PacBio long-reads to preserve the haplotype information of the targeted locus. Lead by @Kersten_Sonja in collaboration with @agris42 @zevkronenberg @kjschmid biorxiv.org/content/10.110…

A fully funded PhD position is available in my lab: - 3 years - project: metabolic and regulatory drivers of metabolic cross-feeding interactions in microbial communities - deadline: 28.07.22 - experience in LC-MS analyses and/or transcriptomics is a plus uni-osnabrueck.de/universitaet/s…

@tomodelmont What's microdiversity? Pun intended.

A reminder that deadline for the fantastic *EBAME7* #bioinformatics #workshop (international teachers and students) is around the corner (July 10). A substantial part is dedicated to environmental genomics (domains of life and viruses), pangenomics and microdiversity using #anvio

@epcrocha @IbeidLabex @FRM_officiel Excellent as usual! Though fwiw it is a bit RefSeq plasmid is not a random sampling of plasmid sequence diversity. We are trying to change this @microUCPH with massive sequencing of envt. plasmids and novel methods to assemble & bin these from short reads @simonrasmu @CeBiTec