🌟 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

Our article includes a checklist that we hope will be useful for the community to summarize the lines of evidence that have been provided in a study! @natmicrobiol.nature.com @nature.com @cp-cell.bsky.social

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 the presence of mic...

A key message is the need for extensive controls (particularly sampling controls) which can be missing in some studies. We also highlight the need for orthogonal validation beyond just sequencing based detection: www.nature.com/articles/s43...

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...

🎆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

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...

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...

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

Say hello to Heliusvirales, Astravirales and Suryavirales! 👋These are the first TEM images of members of these highly prevalent gut phage clades. Genomic characterization identified many interesting features (particularly DGRs) that could explain their ability to infect diverse hosts. [5/5]

Interestingly, many of the highly prevalent phage families have diverse Firmicutes hosts. They seem to frequently have temperate lifestyles, but are also spontaneously induced from their hosts! [4/5]

Using these genomes to identify viral families, we noted that 11 out of the 12 most prevalent families in our cohort have never been described before. Even more strikingly, 6 of them are globally among the most prevalent based on analysis of >3000 gut metagenomes! [3/5]

It turns out that short-read assemblies might be consistently fragmenting viral genomes and thus affecting viral family-level clustering workflows. Long read assemblies allowed us to discover nearly 20,000 novel viruses from just a 100 odd samples! [2/5]

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...

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! :)

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.

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

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

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...

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.

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...

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 - Nature Biotechnology Skin metagenomic and metatranscriptomic analysis shows divergence between microbial abundance and activity.

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

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...

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...

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👇:

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.

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...

Thank you - bluesky feels like a mirror world :)

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

5. Exciting days ahead as we try to decipher the contributions of diverse factors that shape skin microbiome dermotypes, and in turn their influence on skin health! @cherrychengchenli.bsky.social

4. Dermotypes exhibit distinct associations w/ host, where ethnicity and gender play a role in some cases, while others are linked to skincare behaviors. Skin sensitivity, itch and eczema may be affected by dermotype function, highlighting utility for patient stratification & therapeutics

3. Microbes behave very differently across dermotypes in terms of who they co-occur with! We can confirm this with culture-based experiments that show that oxygen gradients and nutrient availability likely shape why we see distinct dermotypes in various individuals.
@atVidu

2. Dermotypes are highly coordinated across sites. For some sites, we can predict the dermotype just by knowing dermotype of another site. Left and right sides of the body are also highly correlated, suggesting that individual intrinsic factors strongly shape the skin microbiome.

Many exciting results to follow-up on!
1. The skin microbiome has unique “types” in every site - we call them dermotypes. The underarm has as many as 5 distinct ones defined by diverse microbes. We built ML classifiers to predict them w/ near-perfect accuracy with 5 species!

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...

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

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).