How do people combine their 16S human microbiome studies and what do they call them? Check out our scoping review in AJE advances. @ajeadvances.bsky.social academic.oup.com/ajeadvances/... TL;DR: Lots of heterogeneity in methods, analysis, reporting: we need field standards (1/7)

In harmony? A scoping review of methods to combine multiple 16S amplicon datasets

Abstract. Robust evidence on relationships between the human microbiome and health is critical for understanding and improving the human condition. However

academic.oup.com

Excited for my first #ISME20 conference next week! I’ll present "community conservatism"- closely related microbes tend to occur in similar communities - on Monday the 17th, 3:15 pm (AS03,ToL). Paper: www.nature.com/articles/s41559-025-02957-4 Feel free to reach out -happy to meet new colleagues!

Community conservatism is widespread across microbial phyla and environments - Nature Ecology & Evolution

This study reveals that closely related microorganisms tend to inhabit similar communities across all major environments and phyla. The authors term this phenomenon ‘community conservatism’, extending...

nature.com

Adding my 2 cents about using agents for scientific work, with a focus on what's dear for German academia: "Datenschutz" and independence from foreign influence. Plus some concrete examples on how to use and sandbox the excellent pi harness! www.microbial-pangenomes-lab.org/2026/07/08/A...

📢 Season 6 is currently in the works. In the meantime, #MVIF recordings from Season 5 are available for you to enjoy. If you missed any of the talks, now's a great time to catch up 👉 cassyni.com/c/mvif/series

Microbiome Virtual International Forum@microbiomevif.bsky.social · 10mo ago

💫 #MVIF Season 5 💫 Feel free to join the keynotes by presenting your work–abstract submission is open: www.microbiome-vif.org/en-US/how-to... #MVIF is proudly supported by #illumina @corundumsb.bsky.social and our non-commercial co-organizing partners Seerave Foundation @cunysph.bsky.social

🔵Candidatus Cibionibacter quicibialis 🟡Catenibacterium tridentinum have a new friend 💜Bacillus subtilis

We're cooking up a new season for September, but that doesn't mean you have to wait for great content! Check out #MVIF 42 w/ Brooke Wilson & her prize-winning presentation on how FMT is changing outcomes for adolescents with obesity: www.youtube.com/watch?v=_ErR...

Brooke Wilson – Long-term health in obese adolescents after fecal transplant: 4-year | MVIF42 S05

YouTube video by Microbiome Virtual International Forum

youtube.com

🎉 Exciting news from our lab! cFMDv1.3.2 is now live. This release marks a significant expansion of cFMD: 📊 681 newly integrated food metagenomes from 22 public datasets 18,180 total MAGs across 4,125 metagenomes 54 countries (now including 🇲🇦) 100+ food-related studies 1/3

Not many entries this time in the reading list, as times are busy with other things. A few new interesting papers that came to my attention on the human microbiome and some other population health studies. Hopefully helpful to some. mericlab.com/blog/2026-06b/

I’ve been maintaining a list of shotgun #metagenomics tools and resources which I got Claude to turn into a GitHub repo. It has 300+ entries. Please share and tell me if I’ve missed anything! github.com/feargalr/Met... #microbiota #bioinformatics #microbiome #genomics

GitHub - feargalr/Metagenomics-tools-atlas: An inventory of tools and resources for short-read shotgun metagenomics.

An inventory of tools and resources for short-read shotgun metagenomics. - feargalr/Metagenomics-tools-atlas

github.com

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Excited to share my summer plans! 🌞 This summer, 3 incredible microbiome study curation teams we'll be selecting, curating, reviewing, analyzing, & expanding two key microbiome databases: cMD & BugSigDB. A huge thank you to @cibiocm.bsky.social & @bioconductor.bsky.social for making this possible.

Excited to share my summer plans! 🌞 This summer, 3 incredible microbiome study curation teams we'll be selecting, curating, reviewing, analyzing, & expanding two key microbiome databases: cMD & BugSigDB. A huge thank you to @cibiocm.bsky.social & @bioconductor.bsky.social for making this possible.

Our paper on Trimmomatic v0.40 is officially published in Bioinformatics! A decade after the original, the ~50,000-times-cited NGS trimmer gets a major overhaul. Here's what's new 🧵 doi.org/10.1093/bioi... #Bioinformatics #NGS

Trimmomatic: A decade of feature-rich, high-performance NGS read preprocessing

AbstractMotivation. Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its

doi.org

New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/29/m... • root microbiome/ @algazuccaro.bsky.social   • gut microbiome-epigenetics/ @gangfang.bsky.social   • resistome annotation/ @bigdatabiology.bsky.social   • invitation for #MVIF 50🎂 / @microbiomevif.bsky.social & more. Happy Friday!

May 29, 2026

See you next week at MVIF! Global microbiome Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISM…

microbiomedigest.com

New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/29/m... • root microbiome/ @algazuccaro.bsky.social   • gut microbiome-epigenetics/ @gangfang.bsky.social   • resistome annotation/ @bigdatabiology.bsky.social   • invitation for #MVIF 50🎂 / @microbiomevif.bsky.social & more. Happy Friday!

May 29, 2026

See you next week at MVIF! Global microbiome Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISM…

microbiomedigest.com

Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com : academic.oup.com/bioinformati... Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social ! See the thread below for more details.

microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and

academic.oup.com

Sebastian Schmidt@tsbschm.bsky.social · 7mo ago

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...

#MVIFconversations podcast episode 5 with Alexandre Soares Rosado is OUT! ▶️ Spotify: open.spotify.com/episode/01tU... ▶️ Amazon music: music.amazon.com/podcasts/81c... ▶️ Apple Music: podcasts.apple.com/us/podcast/e... ▶️ YouTube podcast: youtu.be/wMZ63S2BVVE?... 1/2

Microbe Decoder uncovers functional traits of microbes in microbiome datasets academic.oup.com/nar/article/...

Microbe Decoder uncovers functional traits of microbes in microbiome datasets

Abstract. Microbe Decoder is a web server that predicts functional traits of microbes in microbiome sequencing datasets. Sequencing has revealed thousands

academic.oup.com

June is right around the corner and the #MVIF 50 program is officially out! 🤩 Highlights: 🇧🇩 Dipto Kundu 🇸🇪 @joseecologist.bsky.social Keynote: 🇺🇸 @julesdeep.bsky.social Talks: 🇺🇸 Samuel Degregori 🇺🇸 Anna Samarra 🇨🇳 Dehan Cai

You missed the last #MVIF... No problem, now you can enjoy reading #MVIF 49 reflections! Muhammad Shah Zaib (ATL) and @kate-lagerstrom.bsky.social (PAC) opened the event w/highlights: Netta Barak presented LAMPP: Live Assessment of Metagenomics-based tools for host Phenotype Prediction, 1/n

Join #MVIF 50 cassyni.com/s/mvif-50 and #MeetTheSpeakers Samuel Degregori will present the Gut Microbiome Tree of Life (GMToL), a curated 16S amplicon dataset of 17,366 samples from 1,553 host species across 26 host classes from 284 studies, enabling analysis of large-scale evolutionary trends.

Happy Tuesday, Svetlana!

Happy to follow #HCMPH2026 virtually! hsph.harvard.edu/research/mic...

HCMPH Symposium | Harvard Chan Microbiome in Public Health Center | Harvard T.H. Chan School of Public Health

We are delighted to welcome everyone to the eighth annual Harvard Chan Microbiome in Public Health Center (HCMPH) symposium. As microbial community science

hsph.harvard.edu

Hutlab@hutlab.bsky.social · 3mo ago

Dr. Robert Britton from Baylor College of Medicine gave an excellent talk on "The impact of the infant microbiome on brain development and cognition"!

🎉 @bioconductor.bsky.social welcomes Firdaws Lamidi and Peace Daniel as our May 2026 #Outreachy interns! To all applicants: you were amazing and this community is still yours. We'd love for you to keep contributing to #BugSigDB and #OpenScience 💙🚀

We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project? That question sent us down a rabbit hole. Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles. 1/3

Today is the final day to nominate your favorite biocurator for the early and advanced career awards. The award includes a small cash prize and speaking slot at the ISB meeting in October. See www.biocuration.org/community/bi... #biocuration

We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project? That question sent us down a rabbit hole. Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles. 1/3

This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.

@bigdatabiology.bsky.social · 3mo ago

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...

Explore the results interactively: arg-pipelines.big-data-biology.org Project led by Juan Inda-Diaz with a great team across the whole SEARCHER Consortium!