Susan Bullman

We are a group of microbiologists, bacterial and cancer biologists, and computational scientists dedicated to deciphering the role of microbes in cancer.

[Susan Bullman @BullmanLab]

Our work with the @CJohnstonLab1 lab out today @Nature demonstrating the intratumoral microbiota impacts spatial, cellular and transcriptional heterogeneity in human cancer. Monster tweetorial below from Chris.

[CJohnstonLab @CJohnstonLab1]

Finally, two papers out within a day of each other from the @BullmanLab and @CJohnstonLab1 relating to the intratumoral microbiota, today in @Nature (https://t.co/crU4Azm6Ck) and yesterday in @CellReports (https://t.co/ESITlazD6h). 🧵below to those interested!

[Zachary Cooper, PhD @zaccoop]

Thrilled to celebrate my mentor @JenWargoMD on her election to the Fellows of the AACR Academy. This honor recognizes visionary leaders whose work has transformed cancer research—no one more deserving. Inspiring to learn from the best.

[UT MD Anderson @UTMDAnderson]

The relationship between the tumor microenvironment and tumor-infiltrating microbes is bidirectional in colorectal cancer; each affects the other, our Dr. Susan Bullman said at #AACR26. How they do so may help us create new clinical interventions. Learn more: https://t.co/NklvzW82BY @BullmanLab #EndCancer

[CJohnstonLab @CJohnstonLab1]

Great to be back in Boston for #Immunology2026. Looking forward to presenting our lab @UTMDAnderson the @BullmanLab's work on tumor-infiltrating microbes - in this giant ballroom! Join us bright and early for awesome session and speaker line up! (April 16th 8am)

[Gang Fang @gangfang_1]

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing

Have you heard about #cancer microbiome or #intratumor microbiome? Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much of the microbial signal is real ❓ and how much is background noise from the lab or the environment ❓

We tackle this with a simple idea: look at DNA fragment sizes using #longread sequencing. If microbes are truly present as intact cells, their DNA should show up as long, genome-like fragment distributions, not mostly short broken (degraded) pieces. Long-read data lets us distinguish those two cases! To make this more robust across datasets, we developed a #metric that normalizes microbial DNA fragment lengths to human DNA fragment lengths within the same sample.

Negative #controls: germ-free mice and human cell culture datasets, where true resident microbes are not expected and any microbial signal is most likely introduced during workflows (i.e. contaminations).

Positive #controls: bacteria spike-in, and importantly, GI tumors with well established bacteria: e.g. #Helicobacter #pylori in #gastric cancer, #Fusobacterium in #colorectal cancer.

Across multiple tumor types and tissues (public + new data), we find that long microbial reads are mainly seen in tissues with natural microbial exposure (such as #gut, #stomach, #skin, #vagina and #cervix, etc). Outside those settings, most microbial signals look more like fragmented, and the occasional long fragments often match well-known #contaminant organisms.

One finding that stood out to us was the #lung, which is constantly exposed to microbes we breathe in, yet in our analysis, the microbial signal appeared mostly as short, fragmented DNA, which is more consistent with transient exposure and rapid clearance than with stable resident microbes in deep lung tissue.

The new metric also helps #unify earlier debates about microbiomes reported in #placenta and #blood. When we reanalyzed long-read data from those settings using the same read length-based approach, we found no evidence for a stable resident microbiome under normal conditions, consistent with the current consensus that most signals reflect background contamination, with true positives mainly expected during active infection.

Long story short, but this was a 4+ years effort led by Yanchun Zhang and Andy Mead. Grateful to all collaborators who contributed valuable samples and feedback: Mi Ni, @MagdalenaKsi, @clannabel7, @LauraZuluagaJim, Gintaras Deikus, Robert Sebra, Rachel Brody, Raymund Yong, @NYCRoboticTeam, @Xue_Song__Zhang. @SinaiGenetics @IcahnInstitute

Link: https://t.co/MHGNCFY447

We’d love your thoughts!

#longread @PacBio @nanopore
#metagenomics #pacbio #nanopore

[NYU Langone Health @nyulangone]

We’re excited to announce that Anirban Maitra, MD (@Aiims1742)—a pre-eminent physician-scientist whose work has widely influenced the field of pancreatic cancer research—has been appointed the new director of @Perlmutter_CC here at NYU Langone.

For more: https://t.co/a710zOE04c

[The Mark Foundation for Cancer Research @TheMarkFdn]

Christopher Johnston (@CJohnstonLab1) is engineering human-derived bacteria to act as "cellular therapies," infiltrating solid tumors to deliver medicine directly into the most treatment-resistant environments. 🧫 @MDAndersonNews

[Susan Bullman @BullmanLab]

New from the Bullman Lab in Cancer Cell!
Tumor-infiltrating bacteria, including Fusobacterium, disrupt cell-cell contacts & trigger quiescence, uncovering a pathway of bacteria-induced therapy resistance
🔗 https://t.co/Bd3L6izEAl
Thanks to @MDAndersonNews, @FredHutch, @UTEPnews

[UT MD Anderson @UTMDAnderson]

Bacteria can impact cancer progression and treatment.

A new study shows how a particular bacteria can induce a reversible state in cancer epithelial cells, which allows tumors to evade the immune system and resist chemotherapy: https://t.co/wSE0NecCYF @BullmanLab #EndCancer

[Prof. Nikolai Slavov @slavov_n]

These findings add to the increasing evidence that cancer is not driven solely by DNA mutations.

🧵

[Jose M. Adrover @niseto]

I’m happy to share our latest work on tumour necrosis! During my time in the @megeblad lab, we found that tumour necrosis is not a passive phenomenon secondary to tumour growth, but an active phenomenon driven by neutrophils and NETs! Thread below: (1/13)
https://t.co/Tr0nHLXRzz

[Anirban Maitra @Aiims1742]

Absolutely insane amount of data in this resource from @mason_lab
The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs
https://t.co/rwKWVtidfZ
Spatial data on 15million cells from 100 donors across multiple ages, mainly GI

[Cancer Cell @Cancer_Cell]

Stromal lipid species dictate melanoma metastasis and tropism https://t.co/2UlLo144Ze

[Lukas Valihrach @LukasValihrach]

Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq https://t.co/qMUGI4at5w

[CJohnstonLab @CJohnstonLab1]

Our team is hiring! 🦠 🧫 🥼🧑‍🔧 https://t.co/GW9BK3lXaW

[CJohnstonLab @CJohnstonLab1]

What exactly does "Fusobacterium nucleatum" refer to? It depends who you ask (and when you asked them). Our new perspective on taxonomy and naming challenges @GutMicrobes, proposing a genomics-based framework for Fusobacterium species designations. 🦠
https://t.co/8jS3e9agYJ

[Denis Wirtz @deniswirtz]

If your stack of images is full of defects, don't panic!

InterpolaAI, a deep learning-based optical flow method, will fix issue tears, photobleaching and sticking artifacts for improved 3D imaging.

Read our paper in Nature Methods: https://t.co/LIpzl3heoB

[Anirban Maitra @Aiims1742]

Second paper on HMGA2 mediated basal identity in #PancreaticCancer from Sita Kugel @fredhutch. This one is an elegant mechanistic dissection of the multi step cascade through which HMGA2 overexpression orchestrates basal lineage state:
https://t.co/vUgXCW6vNL

[Susan Bullman @BullmanLab]

@JessicaRQueen1 @Nature_NPJ Congratulations, Jessica and team!

[Cyrus Ghajar @GhajarLab]

Powerful new story from the Srivastava Lab @sriv4000

[Susan Bullman @BullmanLab]

@AACR @PeterMKWestcott Congratulations, Peter!

[CJohnstonLab @CJohnstonLab1]

Looking forward to presenting and hearing from the other speakers this evening @AACR25, at the microbiota and cancer prevention, diagnosis, and treatment session! Room S105 @MDAndersonNews