Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE
Niranjan Nagarajan
@niranjantw.bsky.social
Computational Biologist and Microbiome Scientist at the National University of Singapore
We are organizing an intense 10-day summer school for new PhD/master's students in computational genomics & metagenomics at IISER Pune (July 18th-27th, 2026) - please do spread the word! cospi.iiserpune.ac.in/workshop2026...
Genomics Workshop 2026 – IISER Pune
cospi.iiserpune.ac.in
Finally out in @natmethods.nature.com 🎉 Our work with Wan Yue's lab shows that signal alignments from direct RNA @nanopore sequencing can reveal structural heterogeneity in RNA. Huge implications for RNA therapeutics! Read all about it here: www.nature.com/articles/s41...
Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell - Nature Methods
sm-PORE-cupine combines SHAPE-based chemical probing with nanopore-based direct RNA sequencing to identify RNA structural ensembles in the SARS-CoV-2 genome and the Candida albicans transcriptome.
nature.com
🌟 We finally have a brand new lab webpage, with blog-style articles describing our work, and exciting *open positions* in culturomics and metagenomics! Please spread the word 🙏 mtms-lab.github.io csb5.github.io/open-positions
Redirecting to https://csb5.github.io/ ...
mtms-lab.github.io
🎆Very excited to share our perspective piece calling for higher standards in reports on microbial detection in cancers! It was great to put this together with some of the leaders in the field including @stevensalzberg.bsky.social @rafalab.bsky.social Barry Marshall and Eske Willerslev: rdcu.be/e4IaU
Setting higher standards for reports of microbial species in human cancers
Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...
rdcu.be
Are you still relying on quality values to do QC for genome sequencing data? What if there was an ultra-fast method that does not need quality values or alignments to genomes? If this sounds interesting, check out our latest preprint w/ @guzhenhao.bsky.social: www.biorxiv.org/content/10.6...
biorxiv.org
Happy to share this free link to our new paper on the perils of trying to find microbes in human cancers, which appeared today in NatureCancer. Co-authors include Nobel laureate Barry Marshall, ancient DNA Eske Willerslev, @niranjantw.bsky.social, Jacques Neefjes, @rafalab.bsky.social: rdcu.be/e4IaU
Setting higher standards for reports of microbial species in human cancers
Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...
rdcu.be
Thrilled to share our labor of love over the last 5 years 🤩 Leveraging long-read metagenomics (@nanoporetech.com) we identified some of the most prevalent gut phage families that have previously been overlooked in short-read based studies. [1/5] Read more here: www.biorxiv.org/content/10.6...
GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome
Despite being important ecological modulators of the gut microbiome, bacteriophage diversity and function remain under-characterized. We show that short-read metagenomic surveys can miss even globally highly prevalent viral family-level clusters (VFCs), that can be readily assembled and characterized with long-read metagenomic data from a relatively small cohort (n=109). While gut Bacteroidota phages have been the prevailing focus in the literature, we show that highly prevalent gut phage families frequently have Firmicutes hosts (termed GuFi phages), with broad host ranges verified using proximity-ligation (Hi-C) sequencing data. High-throughput sequencing of virus-like particles from fecal samples detected frequent enrichment of GuFi phages across samples, revealing their under-appreciated impact on the gut microbiome. We report the first in vitro induction and imaging of members of prevalent GuFi clades including the candidate orders Heliusvirales , Astravirales (VFC 2) and Suryavirales (VFC 4). Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease. ### Competing Interest Statement IL is an employee of Phase Genomics. National Medical Research Council, 23-0614 National Research Foundation, NRFI09-0015 A*STAR, C210812044
biorxiv.org
Our new paper on high-throughput isolation of Bifidobacterium just got published! A very nice adventure starting with the supervision of @lamhaiha.bsky.social, a talented intern, and a nice collab with our BSight expert @isaacyueyuan.bsky.social! Stay tuned for more isolation and Bifido work! :)
@isaacyueyuan.bsky.social · 7mo agoThrilled to share our high-throughput Bifidobacterium isolation work in Microbiology Spectrum! journals.asm.org/doi/10.1128/... By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
Excited to share my first-ever publication on high-throughput Bifidobacterium isolation! Special thanks to my co-author, @isaacyueyuan.bsky.social, for this wonderful write-up. I would also want to thank @niranjantw.bsky.social and @jsgounot.bsky.social for their uwavering support and guidance.
@isaacyueyuan.bsky.social · 7mo agoThrilled to share our high-throughput Bifidobacterium isolation work in Microbiology Spectrum! journals.asm.org/doi/10.1128/... By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
High-throughput isolation of probiotic species from the gut microbiome! Great to have this work out early in the year: journals.asm.org/eprint/KHNHX... We report our experience with the B.SIGHT system from @cytena.bsky.social
High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome | Microbiology Spectrum
The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for adva...
journals.asm.org
@isaacyueyuan.bsky.social · 7mo agoThrilled to share our high-throughput Bifidobacterium isolation work in Microbiology Spectrum! journals.asm.org/doi/10.1128/... By integrating a single-cell dispenser into a culturomics workflow, we accelerated the isolation of individual bacterial cells, allowing robust strain-level resolution.
Published finally! Our study describing the use of metagenomics for AMR/pathogen surveillance in food-centres island-wide in Singapore is out in npj Antimicrobial & Resistance: nature.com/articles/s44...
Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment
nature.com
Skin #metatranscriptomics could be transformational in a way not seen in gut/oral studies as 1) Defined spatial sampling can provide in vivo relevant insights 2) Microbial mRNA is dominant, but human mRNA is also readily detected and quantified www.nature.com/articles/s41...
Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body - Nature Biotechnology
Skin metagenomic and metatranscriptomic analysis shows divergence between microbial abundance and activity.
nature.com
Our study developing a skin metatranscriptomics protocol is now out in @natbiotech.nature.com! We finally have the ability to study microbial activity on skin and identify key functional genes playing a role in diseases. Amazing team of Chia Minghao and Amanda Ng 👏 nature.com/articles/s41...
Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body - @niranjantw.bsky.social @astar-gis.bsky.social go.nature.com/4fVg95j
Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body - Nature Biotechnology
Skin metagenomic and metatranscriptomic analysis shows divergence between microbial abundance and activity.
go.nature.com
Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com! Read all about it here: nature.com/articles/s41... Great collab with Chew and Hirao lab x.com/NiranjanTW/s...
Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning - Nature Communications
Perez, Kimoto, Rajakumar and colleagues present a fast and accurate DNA sequencing method that reads canonical and non-canonical bases using AI and nanopore technology. The approach enables an expande...
nature.com
Find out how our researchers—Associate Director @niranjantw.bsky.social, GIS Innovation Fellow Chayaporn Suphavilai and Dr Karrie Ko—discovered a new variation of 𝘊𝘢𝘯𝘥𝘪𝘥𝘢 𝘢𝘶𝘳𝘪𝘴 (𝘊.𝘢𝘶𝘳𝘪𝘴)—𝗰𝗹𝗮𝗱𝗲 𝗩𝗜—a drug-resistant yeast that kept infectious disease experts on high alert worldwide. Full story below👇:
research.a-star.edu.sg
Studying low-biomass environments in microbiome research? The struggle is real when it comes to contamination! Even the tiniest sprinkle of external microbes can throw off your results, making traditional methods a no-go. Details in link below: @niranjantw.bsky.social www.nature.com/articles/s41...
Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology
In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.
nature.com
Which skin microbiome type do you have 🤔 Check out our exciting work from the Asian Skin Microbiome Program offering new insights of skin microbiome population heterogeneity👇 #skinmicrobiome #microbiomescience
Niranjan Nagarajan@niranjantw.bsky.social · last yr.Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites
The human skin microbiome is increasingly recognized to influence skin health, immune function and disease susceptibility. However, large-scale, multi-site metagenomic studies in the general populatio...
biorxiv.org
A bit late to joining the Bluesky party, but it's great to see all the amazing scientists who are on this platform! Looking forward to connecting with all of you here (on twitter as @niranjantw ... so keeping the handle consistent).