Sudarshan A Shetty

A Bayesian approach to differential prevalence analysis with applications in microbiome studies Recent evidence suggests that analyzing the presence/absence of taxonomic features can offer a compelling alternative to differential abundance analysis in microbiome studies. However, standard approa...

A Bayesian approach to differential prevalence analysis with applications in microbiome studies ("DiPPER") arxiv.org/abs/2602.05938

BiomeGPT: A foundation model for the human gut microbiome https://www.biorxiv.org/content/10.64898/2026.01.05.697599v1

How I recovered from a collaboration gone wrong After learning “how quickly ‘we’ can turn wicked,” this researcher reshaped his approach

How I recovered from a collaboration gone wrong www.science.org/content/arti...

@antagomir.bsky.social 🙌

With a huge inflow of tweeps to the skies, let us hope the skies will continue to support a spectrum of opinions rather than the division by extremes 🕊

Thanks for sharing the pack! Could you please add me to this list?

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts Animal hosts harbour divergent microbiota, including various Bifidobacterium species and strains, yet their evolutionary relationships, and functional adaptions remain understudied. By integrating tax...

1/ 🚨 New preprint alert! 🚨 We’re thrilled to share our latest work exploring microbiome & genomic #Bifidobacterium co-evolutionary & functional signatures across diverse animal hosts. This has been a long time coming, & huge credit to Magda for her incredible hard work as first author! 🐾✨👇

Hi Jan! Thanks for making the list very useful! Could you please add me to the community 🙏🏽

Ten species comprise half of the bacteriology literature, leaving most species unstudied Microbiology research has historically focused on a few species of model organisms. Our bibliographic analysis finds extreme bias in the distribution of bacteriology research across species, with half...

Fascinating Insights here 👇
50% of all bacteriology papers focus on just 10 species, a disproportionate emphasis on pathogens.
Narrow focus hinders the development of novel health promoting microbes. #microbiome
www.biorxiv.org/content/10.1...

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants Preterm infants (<37 weeks’ gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. Ho...

Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1...
#resistome #amr #microbiome #preterm

If you are a microbial ecologist, add this to your must-read library

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarum https://www.biorxiv.org/content/10.1101/2024.12.28.630609v1

Functional and evolutionary significance of unknown genes from uncultivated taxa Nature - We analysed 149,842 environmental genomes from multiple habitats and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel gene families exclusive to...

"Functional and evolutionary significance of unknown genes from uncultivated taxa", a publication from the lab of @jhcepas.bsky.social (2023), highlights what can be achieved by integrating GMGC and other gene catalogs to hunt for novel gene families in 150k genomes

www.nature.com/artic...

SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap

Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1 Fermented foods are increasingly recognized for their health benefits. Historically, cultures worldw

Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1

Paternal and induced gut microbiota seeding complement mother-to-infant transmission Assembly of the gut microbiome is disrupted in cesarean deliveries. Dubois, Valles-Colomer, et al. assessed the role of both parents and of maternal fecal microbiota transplantation (FMT) in shaping t...

NEW from Willem M. De Vos's lab, HELMi team and our lab:
longitudinal metagenomic analyses on infant gut microbiota seeding dynamics just published!

👏 THANKS to Leonard Dubois, Mireia Valles Colomer and all co-authors, the study participants, and the funding agencies!

www.cell.com/cell-host-mi...

The dysbiosisR package is a collection of functions to calculate six dysbiosis measures from microbiota profiling data.
microsud.github.io/dysbiosisR/a...

Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1 Fermentation products released by the gut microbiota provide energy and important regulatory functio

Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1

'Stickiness' of rarity and the universal dance of dominance In a revelatory exploration of biodiversity, a recent study has exposed the universal principles governing the dominance and rarity of species across ecosystems. The researchers unveil that a mere few...

Prof. Marten Scheffer explains the concept of 'sickness of rarity' in ecosystems. We had an opportunity to collaborate & demonstrate its presence in human gut microbiota(HGM). This has implications for understanding occasional pathobiont blooms in HGM.
www.wur.nl/en/research-...

A tiny fraction of all species forms most of nature: Rarity as a sticky state
doi.org/10.1073/pnas...

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment https://www.biorxiv.org/content/10.1101/2023.12.30.573720v1 Bacterial vaginosis (BV), a common syndrome characterized by Lactobacillus-deficient vaginal microbi

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment https://www.biorxiv.org/content/10.1101/2023.12.30.573720v1

Exposure and resistance to lantibiotics impact microbiota composition and function https://www.biorxiv.org/content/10.1101/2023.12.30.573728v1 The intestinal microbiota is composed of hundreds of distinct microbial species that interact with e

Exposure and resistance to lantibiotics impact microbiota composition and function https://www.biorxiv.org/content/10.1101/2023.12.30.573728v1

Automate Microbiome Analysis Using Quarto
At the beginning of 2023, I created a blog post on how to automate basic and routine microbiome data analysis tasks in R using Quarto.
Here is a tutorial for #Microbiome #blueskiers microsud.github.io/quarto_micro...

Our recent paper is out now in Aging Cell. pre-vaccination immune sytem configuration associate with antibody responses to influenza vaccination and contain signatures that improve our understanding of immune aging and post-vaccination immune subset kinetics.
onlinelibrary.wiley.com/doi/full/10....

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure condi... While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under...

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions www.frontiersin.org/articles/10.... #jcampubs

A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1 Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential role

A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1

Job Alert! We are looking for a Principal Bioinformatics Research Scientist with extensive experience in large-scale microbial genomics to create and direct our new Microbial Computational Genomics and Bioinformatics Lab
@StJudeResearch stjude.wd1.myworkdayjobs.com/stjude/job/M...

Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1 Background. PCR-based diagnostics, predominantly utilized for pathogen detection, have faced chal- l

Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1

I'm happy 😀 to announce I have a PhD position on the mathematical 🧮 modelling 💻 of microbial 🦠 evolution! I'm looking forward to working with an enthousiastic candidate on this project, please contact me with any questions! #JobAlert Please retweet! vacatures.uva.nl/UvA/job/PhD-...