Professor Lesley Hoyles

@bugsinyourguts

And all this science I don't understand, it's just my job five days a week. Professor of Microbiome and Systems Biology @ Nottingham Trent University. 🏳️‍🌈 Working predominantly on the human gut microbiota. All views my own.

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Professor Lesley Hoyles@bugsinyourguts· 25d

Dear predatory journal, you've clearly never met me and my RBF.

Start of email from a predatory journal...
"Dear Dr. Lesley Hoyles, I hope everything is good as bright as smile your face."
I am known for my resting bitch face.

Professor Lesley Hoyles@bugsinyourguts· Jul 7

It was good fun working on this with Margaret Lubwama and @jodywinter.bsky.social. I'm looking forward to presenting the Klebsiella story (among other things) at IUMS 2026 in November.

Comparison of 137 Klebsiella pneumoniae species complex (KpSC) isolates recovered in Uganda. (a) Dendrogram showing the genomic relatedness of the isolates, including 31 we sequenced for our study. Also includes Kleborate virulence and resistance scores. (b) Bar graph summarizing Kleborate capsule (K) type data for the 137 isolates. (c) Bar graph summarizing MLST data for 329 KpSC isolates recovered in Uganda.

Professor Lesley Hoyles@bugsinyourguts· May 8

The 1st Klebsiella Epidemiology and Biology Symposium in 2024 was much needed and a great event, so I'm really looking forward to the 2nd in 2027.

2nd KLEBS meeting will be convened in Cape Town, South Africa in 2027!
When? November 17-19, 2027
Where? Century City Conference Centre, Cape Town, South Africa

Professor Lesley Hoyles@bugsinyourguts· Jan 26

Dr @mohamedeladawy.bsky.social knocked it out of the park presenting his PhD work to his Egyptian home crowd. *proud former supervisor* 🥹

Professor Lesley Hoyles@bugsinyourguts· Jan 6

🧬 Free @microbesng.bsky.social PopUp ECR symposium 🧬 UK-based MRes or PhD student, research assistant or postdoc working on microbial genomics or metagenomics? Present your work and/or chair a session, plus excellent keynote speakers: @halllab.bsky.social and @alexmsalmeida.bsky.social. #MNGPopUp

Professor Lesley Hoyles@bugsinyourguts· Sep 11

Over 17,000 submissions for this year's MSCA Postdoctoral Fellowships, and it's really no surprise where most applicants are applying from.

Almost half of all applications are from the US.

Professor Lesley Hoyles@bugsinyourguts· Aug 4

Microbiome Innovation One Health Conference 2025. 15-16 September 2025, University of Oxford. #microbiomesky

Professor Lesley Hoyles@bugsinyourguts· Jun 18

Great to have the opportunity to present our work on CAUTI-associated bacteria at #HISCON. Good to get feedback from clinicians on the work.

Poster on our work showing that growing uropathogens in urine under hypoxia produces clinically relevant metabolomic profiles.

Professor Lesley Hoyles@bugsinyourguts· Jun 12

The pinnacle of my scientific career.

Professor Lesley Hoyles@bugsinyourguts· Jun 8

Interested in seeing whether your favourite bacterium is well represented in the AllTheBacteria database of 2,440,377 assembled (and annotated) genomes? 96 % of all genomes are high quality. Species-level assemblies represented at >=0.1 % of the total dataset. #microsky

2346079 genomes (96 %) represent high-quality, short-read assemblies.

Top 10 bacteria: Salmonella enterica genomes make up over a quarter of the dataset, followed by Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pneumoniae, Campylobacter jejuni, Klebsiella pneumoniae, Neisseria gonnorhoeae, Streptococcus pyogenes and Pseudomonas aeruginosa.

Professor Lesley Hoyles@bugsinyourguts· Apr 24

The leupeptin BGC looks to be pretty much restricted to K. michiganensis. >90 % of all genomes encode the complete BGC. Our annotations mean that this BGC will be included in the next release of antiSMASH (unexpected bonus 😀). (AllTheBacteria a huge help here - thanks @zaminiqbal.bsky.social!)

Prevalence of the complete leupeptin (leup) BGC across the Klebsiella oxytoca species complex. PhyloPhlAn v3.1.68 was used to generate a phylogenetic tree (low diversity; rooted at the midpoint) from the Bakta-annotated proteomes of 2716 genome sequences available from AllTheBacteria v1: K. michiganensis, n=1298 (1176 BGC-positive, 90.6 %); K. oxytoca, n=865; K. grimontii, n=443 (4 BGC-positive, 0.9 %); K. pasteurii, n=82 (2 BGC-positive, 2.4 %); K. spallanzanii, n=12; Klebsiella taxon 3, n=7 (4 BGC-positive, 71.4 %); Klebsiella taxon 1, n=5; K. huaxiensis, n=4. Only genomes encoding contiguous transporter–LeupA–LeupB–LeupC–LeupD sequences were annotated as having a complete leup BGC. The inner coloured circle represents Klebsiella species, while the outer circle shows those genomes that encode the complete leup BGC (refer to colour legends).

Professor Lesley Hoyles@bugsinyourguts· Apr 24

We've covered histamine, ethanol, colibactin, tilivalline, tilimycin, pyrazinones, pyrazines and N-acyl amides. This is one area of research where much more is known about non-pneumoniae Klebsiella spp. than K. pneumoniae.

Proposed mechanisms through which metabolites produced by Klebsiella spp. interact with the mammalian histamine GPCRs HRH4 and HRH1, and the responses elicited. Some strains of K. planticola, K. ornithinolytica, K. terrigena and K. aerogenes encode a histidine decarboxylase (HDC) that converts histidine to histamine in the skeletal muscles of fish; a histidine (His)/histamine antiporter facilitates uptake of L-histidine (light-blue dots) and export of histamine (red dots) out of the bacterial cell. When histamine-rich fish is ingested, the histamine interacts with HRH4 on mast cells in the gut to produce a proinflammatory response, which can lead to respiratory and cardiac distress in some individuals. High-histamine-producing, K. aerogenes-rich microbiotas in mice have been shown to activate HRH4, leading to mast-cell infiltration and abdominal pain (i.e. visceral hypersensitivity) in these animals. Activation of the leupeptin operon by N-acetylneuraminic acid (Neu5Ac; red diamonds) in K. michiganensis, via the nan operon (nanRATEK), leads to the production of leupeptin (a protease inhibitor; dark-blue dots), pyrazinones and pyrazines. Leupeptin produced by K. michiganensis may increase survival of the bacterium during infections because the leupeptin inhibits subunit beta2i of the immunoproteasome, thereby decreasing immune activity. Pyrazinone 3 (yellow dots) is a selective agonist of HRH4, potentially eliciting histamine release from mast cells and activating proinflammatory and allergic responses similar to those seen via activation of HRH4 by histamine. Presence of HRH4 and HRH1
(plus HRH2 and HRH3) on a range of proinflammatory cells suggests that there is still much work to be done with respect to host–microbiota interactions in the context of histamine production.

Professor Lesley Hoyles@bugsinyourguts· Mar 29

This has made @drsimonmcarthur.bsky.social and I laugh this morning (but in a good - and very middle class - way). #gutbrainaxis #IShopAtWaitroseBecause

Waitrose magazine discussing the effects of SCFAs on the gut-brain axis, specifically their protective effects on the blood-brain barrier.

Professor Lesley Hoyles@bugsinyourguts· Nov 20

Ziyaad Dangor talking on Klebsiella pneumoniae as an important infectious cause of death in infants in LMIC settings. K. pneumoniae contributes to "pathway to death" in almost a quarter of infants between months 1 and 59 months of life. #KLEBS2024

Professor Lesley Hoyles@bugsinyourguts· Nov 15

With a bit of curation* sandpiper (sandpiper.qut.edu.au/About) data is useful for summarizing species prevalence across different metagenomic datasets. (*Figure my own after wrangling with the myriad source descriptors provided under the heading 'organism'.)

Summary of 17 different Klebsiella spp. found in different sample types - 'Animal, bird, insect, plant' or environment. Data were retrieved from the sandpiper database.

Professor Lesley Hoyles@bugsinyourguts· Nov 8

Any excuse for a video of my favourite bird.

Professor Lesley Hoyles@bugsinyourguts· Nov 2

Presented, this morning at the Scottish Microbiology Association autumn meeting, on our work on non-pneumoniae Klebsiella spp. in clinical and veterinary settings. Very happy with the Klebsiella bowl I was given by my hosts!

Black bowl with green bacteria in the middle.

Professor Lesley Hoyles@bugsinyourguts· Jun 12

Long may the downward trend regarding gut-brain axis reviews continue.

Graphs showing ridiculous number of reviews published on the gut-brain axis in recent years, though for last few years the percentage has dropped below 40 %.

Professor Lesley Hoyles@bugsinyourguts· Apr 19

EXTREME!

Professor Lesley Hoyles@bugsinyourguts· Apr 9

Not able to attend #MicroSoc24, but my team is being represented by Sam Dawson and Mohamed Eladawy. Today, check out Mohamed's poster (no. 181) on the first detailed genomic analyses of uropathogens in an Egyptian clinical setting, and the importance of comparing genotypic and phenotypic AMR data.

Professor Lesley Hoyles@bugsinyourguts· Feb 15

I know what that pathway is missing...

Professor Lesley Hoyles@bugsinyourguts· Dec 19

Post a meme made by you

Professor Lesley Hoyles@bugsinyourguts· Oct 30

Importance of Mohamed's study in an Egyptian clinical context.

In-depth genotypic and phenotypic characterization of clinical pathogens contributing to the antimicrobial resistance burden in low- and middle-income countries is often not possible due to limited resources. Characterized 31 P. aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital over a 3 month period. Even with small number of isolates, genetically diverse isolates and high-risk clones (i.e. ST357 and ST773) of P. aeruginosa are present in this clinical setting, and novel resistance determinants can be readily detected in genomic data. We provide the first report of a pBT2436-like megaplasmid in a clinical P. aeruginosa isolate recovered in the Middle East and North Africa region.

Professor Lesley Hoyles@bugsinyourguts· Oct 1

Reading a clinical FMT paper where the only screening criterion for donors was pretty much "yep, jobby's a good 'un".

Professor Lesley Hoyles@bugsinyourguts· Sep 19

Share your #thesis quotes! #academia My dogs were also thanked for keeping me sane.

Lyrics quoted from the Beach Boys "You still believe in me" and Martha Wainwright's "Bloody Mother Fucking Asshole" (abbreviated to BMFA in my thesis acknowledgements, to avoid my mother shouting at me for swearing in print).

Professor Lesley Hoyles@bugsinyourguts· Sep 1

TFW you've done a comprehensive genome-based analysis and a reviewer wants a 16S rRNA gene-based tree for the same strains.

Professor Lesley Hoyles@bugsinyourguts· Aug 12

Latest purchase, which will never be seen in public.

Professor Lesley Hoyles@bugsinyourguts· Aug 5

TFW you're trying to find guidance on getting ethics and questions together for interviewing patients and all the people who could help you are on holiday until September.

Alan Rickman as the Sheriff of Nottingham asking "...am I thwarted?"

Professor Lesley Hoyles@bugsinyourguts· Jul 30

Excellent opportunity for anyone wanting to undertake a postdoc in phage research, with Professor Andrey Shkoporov @AShkoporov at UCC. Contact Andrey directly about this position.

Job advert for postdoctoral position at University College Cork, working on phages in the research team of Professor Andrey Shkoporov.

Professor Lesley Hoyles@bugsinyourguts· Jul 27

TFW you haven't looked at a dataset for a while, and now have to spend 2 days getting your head round exactly where things were when you had to turn your attention elsewhere.