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Tim Straub @timothystraub.com · 1d

I welcome another promising tool to analyze strain-resolved WMS data! #microbiome

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 1d

Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets https://www.biorxiv.org/content/10.1101/2025.10.10.681738v1

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Tim Straub @timothystraub.com · 5d

👀 What an interesting and under-explored idea!

Rachel M. Wheatley @rachelmwheatley.bsky.social · 5d

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The Lancet Microbe @lancetmicrobe.bsky.social · 6d

New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA

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Reposted by Tim Straub

Microbiome Virtual International Forum @microbiomevif.bsky.social · 5d

SAVE THE DATE: 27 October, 2025
and join speakers from both illumina and #MVIF!

Registration for the webinar is free: emea.illumina.com/events/webin...

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Tim Straub @timothystraub.com · 12d

👀 One of the first two articles published for the collection on #Microbiome and Reproductive Health!

link.springer.com/collections/...

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Reposted by Tim Straub

Elaine Hsiao @pipethero.bsky.social · 20d

Happy to share this paper in final form rdcu.be/eH8tj, with more info on neuronal responses and potential mechanism of actions! The results suggest that there is neural interoception of microbial metabolic state 🧠🦠 We hope they can inspire more work in this area!

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Reposted by Tim Straub

Haris Zafeiropoulos @hariszaf.bsky.social · 22d

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology

Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...

doi.org

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Tim Straub @timothystraub.com · 26d

👀 This looks really interesting–being able to understand genomic context and assess species carriage of #ARGs from WMS data. #microbiome

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 26d

CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences https://www.biorxiv.org/content/10.1101/2025.09.15.676352v1

Reposted by Tim Straub

Tami Lieberman @contaminatedsci.bsky.social · Sep 12

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

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Tim Straub @timothystraub.com · Sep 12

🧬 Research from the American Gut Project shows that people who eat 30+ different plants per week tend to have a more diverse gut #microbiome than those eating under 10.
At Tiny Health, we're running a fun 7-day challenge to help you get there—plus one winner gets a gut health test ($199 value)!

Enter Tiny Health's 30 Plants Challenge for your chance to win big

Join Tiny Health’s free 7-day gut health challenge and get expert tips, daily inspiration, and recipes to help you reach 30 different plants and a healthier gut. Why 30? Research shows that eating a w...

www.tinyhealth.com

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Reposted by Tim Straub

Cameron Thrash @jcamthrash.bsky.social · Sep 11

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes genomebiology.biomedcentral.com/articles/10.... #jcampubs

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes - Genome Biology

Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG databa...

genomebiology.biomedcentral.com

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Tim Straub @timothystraub.com · Sep 10

Authors argue that integrating metagenomics, culturing, and experimental validation to study hidden yet ecologically significant microbial species will advance our understanding of the microbiome in health and disease, and inform next-gen therapeutics leveraging the full diversity of the gut.

Alexandre Almeida @alexmsalmeida.bsky.social · Sep 10

🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health

The human gut microbiome plays an important biological role in host health, yet over 60% of gut species remain uncultured and hence inaccessible to experimental manipulation. Here we analysed 11,115 h...

www.biorxiv.org

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Reposted by Tim Straub

Titus Brown @titus.idyll.org · Sep 8

There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed

Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...

pubmed.ncbi.nlm.nih.gov

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Reposted by Tim Straub

Nature Portfolio @natureportfolio.nature.com · Sep 6

A Nature Outlook article reports on the preliminary evidence that microbiota-based treatments can be beneficial for people with mood disorders, such as depression and anxiety. But how these interventions work is not clear, and human trials are needed. #microbiome #medsky 🧪

Why nurturing the gut microbiota could resolve depression and anxiety

Links between gut microbes and mental health could lead to large-scale trials of probiotic interventions.

go.nature.com

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Tim Straub @timothystraub.com · Sep 4

3/3 Why this matters: C-section babies have higher rates of asthma, allergies, and autoimmune conditions later in life. Early microbiome interventions during the critical infancy window could potentially prevent the 'atopic march' - need larger, longer studies to confirm!

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Tim Straub @timothystraub.com · Sep 4

2/3 Key findings from the study:
• ⬆️ Bifidobacterium abundance (p=0.025)
• ⬆️ HMO degradation genes (α-L-fucosidase, p=0.019)
• C-section index normalized to vaginal birth levels
• Atopic dermatitis OR 0.17 (95% CI: 0.023-0.723, p=0.031)

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Tim Straub @timothystraub.com · Sep 4

1/3 🧬 Exciting news from my colleagues at Tiny Health!

New study: A personalized #microbiome program helped C-section babies develop more normal gut microbiomes AND showed 83% lower odds of atopic dermatitis!

Improving immune‐related health outcomes post‐cesarean birth with a gut microbiome‐based program: A randomized controlled trial

Background Infants born via Cesarean section (C-section) often have a distinct gut microbiome and higher risks of atopic and immune-related conditions than vaginally delivered infants. We evaluated ...

onlinelibrary.wiley.com

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Tim Straub @timothystraub.com · Aug 31

Just came across this preprint: groups at @broadinstitute.org and MGH developed a low-cost, #CRISPR based diagnostic for pathogenic bacteria and #AMR genes from blood cultures.

medRxivpreprint @medrxivpreprint.bsky.social · Aug 13

BADLOCK: A Rapid, Portable, Inexpensive Diagnostic for Bacterial Pathogen and Resistance Detection in Resource-Limited Settings https://www.medrxiv.org/content/10.1101/2025.08.11.25332217v1

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Reposted by Tim Straub

Daniel Drucker @danieljdrucker.bsky.social · Aug 28

The potential relevance of FMT as a #microbiome augmenting intervention for #obesity management and metabolic health
www.nature.com/articles/s41...

Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up - Nature Communications

In this 4-year unblinded follow-up study, the authors evaluate 63% of the participants of a double-blind randomised control trial that assessed the effects of faecal microbiota transplantation (FMT) o...

www.nature.com

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Tim Straub @timothystraub.com · Aug 29

This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

Silas Kieser @silask.bsky.social · Aug 29

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

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Reposted by Tim Straub

Hatzios Lab @hatzioslab.bsky.social · Aug 4

Congrats to postdoc Zhe Zhou on her paper out today in @cp-cellhostmicrobe.bsky.social showing that gut bacteria cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Thanks to collaborators Angela Jiang and Xiaofang Jiang at NIH.
www.sciencedirect.com/science/arti...

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Reposted by Tim Straub

Guillaume Méric @gmeric.bsky.social · Aug 5

Is the gut microbiota composition in the 1st week of life linked to viral lower respiratory tract infections (vLRTIs) in early childhood? Here, work using the BBS birth cohort identifies Bifidobacterium longum-dominated cluster linked to lowest vLRTI rates
🔗 www.sciencedirect.com/science/arti...

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics

Early-life gut microbiota affects immune system development, including the lung immune response (gut–lung axis). We aimed to investigate whether gut m…

www.sciencedirect.com

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Tim Straub @timothystraub.com · Jul 31

This study published today finds "a more diverse gut microbiome is generally associated with healthier glucose spike metrics." It's certainly not implying causality, but it is very interesting to see the association!

Eric Topol @erictopol.bsky.social · Jul 31

Our @naturemedicine.bsky.social paper on glucose spikes (CGM sensor) and their relationship with physical activity, gut microbiome, genomics, food intake, and sleep via multimodal A.I. Helps identify people with prediabetes who have high risk of progression (cf HbA1c)
www.nature.com/articles/s41...

Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes - Nature Medicine

Multimodal data from 347 deeply phenotyped individuals including healthy, prediabetic individuals and individuals with T2D report remotely acquired patterns of glucose control via continuous glucose m...

www.nature.com

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Reposted by Tim Straub

Ivan Zanoni @lozanzi.bsky.social · Jul 26

#WeekendRead! #EveryCellIsAnImmuneCell! #TollPower! Kaelberer Bohorquez &co show @nature.com that #TLR5 signaling in response to flagellin drives neuropeptide PYY release by gut colonic neuropod cells, activating vagal neurons that signal to #brain, reducing feeding via a “neurobiotic sense”!

A gut sense for a microbial pattern regulates feeding - Nature

A study reveals a gut–brain sensory pathway through which the microbial component flagellin activates neuropod cells in the colon to signal the brain and reduce feeding in mice.

www.nature.com

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Reposted by Tim Straub

The Benioff Center for Microbiome Medicine @ucsfmicrobiome.bsky.social · Jul 14

The Lynch lab’s latest research delves into the gut microbiome’s influence on peanut oral immunotherapy outcomes. The study identifies specific bile acids and microbial metabolic signatures that predict treatment success. #Microbiome #AllergyResearch #UCSF rdcu.be/ewbEn

Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure

Nature Communications - Peanut oral immunotherapy (POIT) can treat peanut allergy, but only a subset of patients achieve lasting remission. Here, the authors show that POIT efficacy is associated...

rdcu.be

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Reposted by Tim Straub

meisellab.bsky.social @meisellab.bsky.social · Jul 9

Our lab just completed a +6 year #marathon, describing for the first time that the #microbiome is critical for #exercise - induced increases in antitumor CD8 T cell immunity and improved of #cancer #immunotherapy.
www.cell.com/cell/fulltex...

Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy

Exercise enhances antitumor immunity and immunotherapy effectiveness by increasing microbiota-derived formate, which boosts CD8 T cell function and may serve as a biomarker of melanoma suppression.

www.cell.com

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