๐ 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 ๐
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
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...
๐Very 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...
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! ๐These 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 ๐คฉ
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
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 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 ๐
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
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 researchersโAssociate Director @niranjantw.bsky.social, GIS Innovation Fellow Chayaporn Suphavilai and Dr Karrie Koโdiscovered a new variation of ๐๐ข๐ฏ๐ฅ๐ช๐ฅ๐ข ๐ข๐ถ๐ณ๐ช๐ด (๐.๐ข๐ถ๐ณ๐ช๐ด)โ๐ฐ๐น๐ฎ๐ฑ๐ฒ ๐ฉ๐โa drug-resistant yeast that kept infectious disease experts on high alert worldwide.
Full story below๐:
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 ๐ค Check out our exciting work from the Asian Skin Microbiome Program offering new insights of skin microbiome population heterogeneity๐ #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 โtypesโ 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!
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).
