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Sudarshan A Shetty @gutmicrobe.bsky.social · Feb 27

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Feb 27

Eukaryotes' closest relatives are internally simple syntrophic archaea https://www.biorxiv.org/content/10.1101/2025.02.26.640444v1

Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 19

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 🕊

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 15

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

Reposted by Sudarshan A Shetty

Hall Lab @halllab.bsky.social · Jan 11

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! 🐾✨👇

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...

doi.org

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 7

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

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 5

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...

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...

www.biorxiv.org

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Reposted by Sudarshan A Shetty

Raymond Kiu @raymondkiu.bsky.social · Jan 3

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

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...

www.biorxiv.org

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 3

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

Brett Baker @archaeal.bsky.social · Jan 3

After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social

rdcu.be/d5put

A thread…

Two decades of bacterial ecology and evolution in a freshwater lake

Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...

rdcu.be

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Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 29

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

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Reposted by Sudarshan A Shetty

Bork Group at EMBL Heidelberg @borklab.bsky.social · Dec 17

"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...

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...

www.nature.com

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Reposted by Sudarshan A Shetty

Stephen Turner @stephenturner.us · Dec 17

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

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Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Aug 22

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

www.biorxiv.org

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Reposted by Sudarshan A Shetty

Segata Lab @cibiocm.bsky.social · Jun 12

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...

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...

www.cell.com

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Sudarshan A Shetty @gutmicrobe.bsky.social · May 11

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

Introduction

dysbiosisR

microsud.github.io

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Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jan 7

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

www.biorxiv.org

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 7

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-...

'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...

www.wur.nl

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Sudarshan A Shetty @gutmicrobe.bsky.social · Jan 3

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

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

doi.org

Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 31

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

www.biorxiv.org

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Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 31

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

www.biorxiv.org

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Sudarshan A Shetty @gutmicrobe.bsky.social · Dec 29

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...

Automate microbiome analysis - Automate Microbiome Analysis Using Quarto

microsud.github.io

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Sudarshan A Shetty @gutmicrobe.bsky.social · Dec 28

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....

Pre‐vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination

Aging Cell is an open access geroscience journal addressing the biology of aging, from molecular mechanisms of aging to age-related disease.

onlinelibrary.wiley.com

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Reposted by Sudarshan A Shetty

Cameron Thrash @jcamthrash.bsky.social · Dec 28

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

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...

www.frontiersin.org

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Reposted by Sudarshan A Shetty

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Dec 28

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

www.biorxiv.org

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Reposted by Sudarshan A Shetty

Victor J. Torres @torreslab.bsky.social · Dec 27

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...

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Reposted by Sudarshan A Shetty

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 28

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

www.biorxiv.org

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