Sudarshan A Shetty
@gutmicrobe.bsky.social
Team Lead Microbiomics @ Danone Research & Innovation | Gut Microbiome | Nutrition | Computational Biology | Academic in previous life | Scientist forever | 🇮🇳 🇳🇱 | Opinions on bsky are mine not of my employer 🕊
Reposted by Sudarshan A Shetty
How I recovered from a collaboration gone wrong www.science.org/content/arti...
How I recovered from a collaboration gone wrong
After learning “how quickly ‘we’ can turn wicked,” this researcher reshaped his approach
www.science.org
November 12, 2025 at 7:00 PM
How I recovered from a collaboration gone wrong www.science.org/content/arti...
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
October 31, 2025 at 6:37 PM
Eukaryotes' closest relatives are internally simple syntrophic archaea https://www.biorxiv.org/content/10.1101/2025.02.26.640444v1
February 27, 2025 at 4:47 AM
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 🕊
January 19, 2025 at 2:58 PM
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 🕊
Reposted by Sudarshan A Shetty
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
January 11, 2025 at 10:11 AM
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! 🐾✨👇
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...
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
January 5, 2025 at 11:03 AM
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...
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...
Reposted by Sudarshan A Shetty
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
#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
January 3, 2025 at 5:03 PM
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
#resistome #amr #microbiome #preterm
If you are a microbial ecologist, add this to your must-read library
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…
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
January 3, 2025 at 1:33 PM
If you are a microbial ecologist, add this to your must-read library
Reposted by Sudarshan A Shetty
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
December 29, 2024 at 7:19 AM
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
Reposted by Sudarshan A Shetty
"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...
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
December 17, 2024 at 2:01 PM
"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...
www.nature.com/artic...
Reposted by Sudarshan A Shetty
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
December 17, 2024 at 9:00 PM
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
Reposted by Sudarshan A Shetty
Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1
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
August 22, 2024 at 4:16 PM
Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1
Reposted by Sudarshan A Shetty
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...
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
June 12, 2024 at 4:16 PM
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...
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...
microsud.github.io/dysbiosisR/a...
Introduction
dysbiosisR
microsud.github.io
May 11, 2024 at 5:01 AM
The dysbiosisR package is a collection of functions to calculate six dysbiosis measures from microbiota profiling data.
microsud.github.io/dysbiosisR/a...
microsud.github.io/dysbiosisR/a...
Reposted by Sudarshan A Shetty
Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1
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
January 7, 2024 at 5:18 AM
Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1
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-...
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
January 7, 2024 at 8:22 AM
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-...
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...
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
January 3, 2024 at 4:13 PM
A tiny fraction of all species forms most of nature: Rarity as a sticky state
doi.org/10.1073/pnas...
doi.org/10.1073/pnas...
Reposted by Sudarshan A Shetty
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
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
December 31, 2023 at 2:18 AM
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
Reposted by Sudarshan A Shetty
Exposure and resistance to lantibiotics impact microbiota composition and function https://www.biorxiv.org/content/10.1101/2023.12.30.573728v1
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
December 31, 2023 at 3:19 AM
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...
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
December 29, 2023 at 11:40 AM
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...
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....
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
December 28, 2023 at 6:40 PM
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....
onlinelibrary.wiley.com/doi/full/10....
Reposted by Sudarshan A Shetty
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
December 28, 2023 at 2:32 PM
Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions www.frontiersin.org/articles/10.... #jcampubs
Reposted by Sudarshan A Shetty
A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1
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
December 28, 2023 at 5:50 PM
A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1
Reposted by Sudarshan A Shetty
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...
@StJudeResearch stjude.wd1.myworkdayjobs.com/stjude/job/M...
December 27, 2023 at 10:01 PM
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...
@StJudeResearch stjude.wd1.myworkdayjobs.com/stjude/job/M...
Reposted by Sudarshan A Shetty
Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1
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
December 28, 2023 at 2:20 AM
Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1