Dan Sprockett
@danielsprockett.bsky.social
New Assistant Professor. My lab works on the ecology and evolution of the microbiome.
Former CIHMID Postdoc Fellow at Cornell. Stanford M&I Alum. NMDC Microbiome Data Champion @microbiomedata.org
Former CIHMID Postdoc Fellow at Cornell. Stanford M&I Alum. NMDC Microbiome Data Champion @microbiomedata.org
Reposted by Dan Sprockett
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:13 PM
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
If anyone happens to be around UNC Chapel Hill this week, I'll be speaking on Tuesday: www.med.unc.edu/cgibd/event/... @microbiomeunc.bsky.social #microbiome
"The Assembly, Evolution, and Clinical Implications of the Gut Microbiota in Early Life" With Daniel Sprockett, PhD, MSc | Center for Gastrointestinal Biology and Disease
www.med.unc.edu
September 6, 2025 at 1:55 PM
If anyone happens to be around UNC Chapel Hill this week, I'll be speaking on Tuesday: www.med.unc.edu/cgibd/event/... @microbiomeunc.bsky.social #microbiome
Reposted by Dan Sprockett
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...
www.biorxiv.org
August 16, 2025 at 6:25 PM
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
Check out this incredible analysis!
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...
www.biorxiv.org
August 16, 2025 at 4:19 AM
Check out this incredible analysis!
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
www.biorxiv.org/content/10.1...
Reposted by Dan Sprockett
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
July 17, 2025 at 8:32 PM
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Reposted by Dan Sprockett
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Garud Lab
garud.eeb.ucla.edu
July 22, 2025 at 5:51 PM
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Looks like it'll be a good one!
Cell Symposia: Host-microbiome dynamics
May 10–12, 2026 | Bruges, Belgium
by @cp-immunity.bsky.social @cp-cellhostmicrobe.bsky.social and @cp-trendsmicrobiol.bsky.social
www.cell-symposia.com/microbiome-2...
May 10–12, 2026 | Bruges, Belgium
by @cp-immunity.bsky.social @cp-cellhostmicrobe.bsky.social and @cp-trendsmicrobiol.bsky.social
www.cell-symposia.com/microbiome-2...
August 14, 2025 at 6:59 PM
Looks like it'll be a good one!
Reposted by Dan Sprockett
Excited to share the Compendium Manager -- our new tool for scaling bioinformatics pipelines! Launch thousands of analyses, track progress, and maintain reproducibility. Developed by @richabdill.com. Check it out: arxiv.org/abs/2505.11385
May 20, 2025 at 12:59 AM
Excited to share the Compendium Manager -- our new tool for scaling bioinformatics pipelines! Launch thousands of analyses, track progress, and maintain reproducibility. Developed by @richabdill.com. Check it out: arxiv.org/abs/2505.11385
Reposted by Dan Sprockett
#NatureMicroPicks
Microbial integrons in focus 🦠🧬
Two studies showing microbial integrons encoding phage defense systems
#MicroSky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Microbial integrons in focus 🦠🧬
Two studies showing microbial integrons encoding phage defense systems
#MicroSky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
www.science.org
May 14, 2025 at 3:55 PM
#NatureMicroPicks
Microbial integrons in focus 🦠🧬
Two studies showing microbial integrons encoding phage defense systems
#MicroSky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Microbial integrons in focus 🦠🧬
Two studies showing microbial integrons encoding phage defense systems
#MicroSky
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A very open-ended question:
Has anyone developed a lab policy for for AI use in their biomedical research that they'd be willing to share?
Have people even thought about defining what should be allowed/encouraged, and what should be outright banned?
Please share with anyone who might have ideas.
Has anyone developed a lab policy for for AI use in their biomedical research that they'd be willing to share?
Have people even thought about defining what should be allowed/encouraged, and what should be outright banned?
Please share with anyone who might have ideas.
May 14, 2025 at 2:14 PM
A very open-ended question:
Has anyone developed a lab policy for for AI use in their biomedical research that they'd be willing to share?
Have people even thought about defining what should be allowed/encouraged, and what should be outright banned?
Please share with anyone who might have ideas.
Has anyone developed a lab policy for for AI use in their biomedical research that they'd be willing to share?
Have people even thought about defining what should be allowed/encouraged, and what should be outright banned?
Please share with anyone who might have ideas.
Reposted by Dan Sprockett
🔬 New Perspective in mBio (@asm.org)!
We call for a shift from disease surveillance to microbial stewardship, and highlight testable, cross-system hypotheses to unravel central rules of microbial life–spanning multiple scales, taxa, and environments. 🦠🌎
journals.asm.org/doi/10.1128/...
We call for a shift from disease surveillance to microbial stewardship, and highlight testable, cross-system hypotheses to unravel central rules of microbial life–spanning multiple scales, taxa, and environments. 🦠🌎
journals.asm.org/doi/10.1128/...
Ecologically expanding the One Health framework to unify the microbiome sciences | mBio
Microbiome research rapidly expanded in the last two decades, with nearly 200,000
peer-reviewed articles that use the word “microbiome” and significant microbial lineage
discoveries reshaping the evol...
journals.asm.org
May 13, 2025 at 12:59 PM
🔬 New Perspective in mBio (@asm.org)!
We call for a shift from disease surveillance to microbial stewardship, and highlight testable, cross-system hypotheses to unravel central rules of microbial life–spanning multiple scales, taxa, and environments. 🦠🌎
journals.asm.org/doi/10.1128/...
We call for a shift from disease surveillance to microbial stewardship, and highlight testable, cross-system hypotheses to unravel central rules of microbial life–spanning multiple scales, taxa, and environments. 🦠🌎
journals.asm.org/doi/10.1128/...
From 2 of my favorite scientists:
“We are deeply concerned about the current funding climate. When we think about new professors or postdocs starting their own labs, we worry that funding challenges could easily result in losing a generation of talented scientists.”
news.stanford.edu/stories/2025...
“We are deeply concerned about the current funding climate. When we think about new professors or postdocs starting their own labs, we worry that funding challenges could easily result in losing a generation of talented scientists.”
news.stanford.edu/stories/2025...
‘We can change diet to generate a healthier microbiome and a healthy individual’
Microbiologists Justin and Erica Sonnenburg are working to understand the complex microbial community that resides within the human gut and its potential for helping people live healthier, longer live...
news.stanford.edu
May 10, 2025 at 1:33 PM
From 2 of my favorite scientists:
“We are deeply concerned about the current funding climate. When we think about new professors or postdocs starting their own labs, we worry that funding challenges could easily result in losing a generation of talented scientists.”
news.stanford.edu/stories/2025...
“We are deeply concerned about the current funding climate. When we think about new professors or postdocs starting their own labs, we worry that funding challenges could easily result in losing a generation of talented scientists.”
news.stanford.edu/stories/2025...
Reposted by Dan Sprockett
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
This is exciting! Top reporting on Science, Biotech, Health Policy, and Public Health news.
Wake Forest University School of Medicine affiliates can access @statnews.com for the next 2 weeks!
Visit www.statnews.com/register/ & enter a valid @wakehealth.edu email address
@wakeforest.bsky.social
Wake Forest University School of Medicine affiliates can access @statnews.com for the next 2 weeks!
Visit www.statnews.com/register/ & enter a valid @wakehealth.edu email address
@wakeforest.bsky.social
Register
Register for your free STAT account.
www.statnews.com
April 29, 2025 at 6:41 PM
This is exciting! Top reporting on Science, Biotech, Health Policy, and Public Health news.
Wake Forest University School of Medicine affiliates can access @statnews.com for the next 2 weeks!
Visit www.statnews.com/register/ & enter a valid @wakehealth.edu email address
@wakeforest.bsky.social
Wake Forest University School of Medicine affiliates can access @statnews.com for the next 2 weeks!
Visit www.statnews.com/register/ & enter a valid @wakehealth.edu email address
@wakeforest.bsky.social
WOW -- this is awesome:
Stealth plasmids: rapid evolution of deleted plasmids can displace antibiotic resistance plasmids under selection for horizontal transmission. https://www.biorxiv.org/content/10.1101/2025.03.30.646151v1
March 31, 2025 at 1:54 PM
WOW -- this is awesome:
"...creativity in science, as in the arts, cannot be organized."
March 19, 2025 at 2:17 AM
"...creativity in science, as in the arts, cannot be organized."
Are Microbiomes Contagious?
Check out this awesome video on the social #microbiome.
asm.org/Videos/Are-M...
@asm.org
Check out this awesome video on the social #microbiome.
asm.org/Videos/Are-M...
@asm.org
Are Microbiomes Contagious? Microbial Minutes
ASM is a nonprofit professional society that publishes scientific journals and advances microbiology through advocacy, global health and diversity in STEM programs.
asm.org
March 14, 2025 at 6:43 PM
Are Microbiomes Contagious?
Check out this awesome video on the social #microbiome.
asm.org/Videos/Are-M...
@asm.org
Check out this awesome video on the social #microbiome.
asm.org/Videos/Are-M...
@asm.org
This is such a cool finding...
Thrilled to share my postdoctoral work with @microbiome.bsky.social on BioRxiv. Ever wonder why you got a fever after your booster shot, but your friend didn’t? We find that both diet and the gut microbiome are associated with risk of fever after vaccination (1/4).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Flagellin in the human gut microbiome is a diet-adjustable adjuvant for vaccination
The intestinal microbiota is thought to modulate immune responsiveness to vaccines. Human studies on this topic, however, have yielded inconsistent results[1][1],[2][2]. We hypothesized that the micro...
www.biorxiv.org
February 27, 2025 at 4:21 PM
This is such a cool finding...
I’m excited to share that I’ll be starting a new position as an Assistant Professor at @wakeforest.bsky.social School of Medicine!
The Sprockett Lab will focus on understanding the assembly, transmission, and evolution of the microbiome, and how these forces impact host health and physiology.
The Sprockett Lab will focus on understanding the assembly, transmission, and evolution of the microbiome, and how these forces impact host health and physiology.
January 17, 2025 at 3:56 PM
I’m excited to share that I’ll be starting a new position as an Assistant Professor at @wakeforest.bsky.social School of Medicine!
The Sprockett Lab will focus on understanding the assembly, transmission, and evolution of the microbiome, and how these forces impact host health and physiology.
The Sprockett Lab will focus on understanding the assembly, transmission, and evolution of the microbiome, and how these forces impact host health and physiology.
Reposted by Dan Sprockett
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
rdcu.be
January 8, 2025 at 1:19 PM
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
More cool strain-level findings from @mattolm.bsky.social -- kind of unbelievable that this hadn't been done yet!
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
www.nature.com
January 3, 2025 at 1:51 PM
More cool strain-level findings from @mattolm.bsky.social -- kind of unbelievable that this hadn't been done yet!
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut"
www.nature.com/articles/s41...
I have a New Years Day tradition of closing all of the open tabs/windows on my phone and computer, and then clearing out all of the old emails and papers that I've been meaning to read. It's a small but meaningful way to wipe the slate clean, and start the new year feeling mentally refreshed.
January 3, 2025 at 1:35 PM
I have a New Years Day tradition of closing all of the open tabs/windows on my phone and computer, and then clearing out all of the old emails and papers that I've been meaning to read. It's a small but meaningful way to wipe the slate clean, and start the new year feeling mentally refreshed.
MICROBIOME DATA ANALYSIS WORKSHOP AT CORNELL UNIVERSITY
Nov 6th, 2023
10AM – noon, Corson-Mudd Hall, Room A409
Topics Include:
- Standardized Workflows for Metagenomic Analysis
- Metadata Management
- F.A.I.R. Data Use
Pre-Register Here: tinyurl.com/cornellmicrobiome
#microsky 🦠 🧫
Nov 6th, 2023
10AM – noon, Corson-Mudd Hall, Room A409
Topics Include:
- Standardized Workflows for Metagenomic Analysis
- Metadata Management
- F.A.I.R. Data Use
Pre-Register Here: tinyurl.com/cornellmicrobiome
#microsky 🦠 🧫
October 16, 2023 at 2:57 PM
MICROBIOME DATA ANALYSIS WORKSHOP AT CORNELL UNIVERSITY
Nov 6th, 2023
10AM – noon, Corson-Mudd Hall, Room A409
Topics Include:
- Standardized Workflows for Metagenomic Analysis
- Metadata Management
- F.A.I.R. Data Use
Pre-Register Here: tinyurl.com/cornellmicrobiome
#microsky 🦠 🧫
Nov 6th, 2023
10AM – noon, Corson-Mudd Hall, Room A409
Topics Include:
- Standardized Workflows for Metagenomic Analysis
- Metadata Management
- F.A.I.R. Data Use
Pre-Register Here: tinyurl.com/cornellmicrobiome
#microsky 🦠 🧫
As stressful and uncertain as it is to be on the faculty job market, I have REALLY been enjoying having the opportunity to read dozens upon dozens of departmental and lab websites (not to mention papers I've overlooked ) from all over the world. Everywhere people are doing such fascinating work!!
October 15, 2023 at 1:07 AM
As stressful and uncertain as it is to be on the faculty job market, I have REALLY been enjoying having the opportunity to read dozens upon dozens of departmental and lab websites (not to mention papers I've overlooked ) from all over the world. Everywhere people are doing such fascinating work!!
Just mindlessly went to the "applications" folder on my computer and wondered why my faculty applications weren't there. I could probably use some more sleep.
October 3, 2023 at 6:12 PM
Just mindlessly went to the "applications" folder on my computer and wondered why my faculty applications weren't there. I could probably use some more sleep.