iiinova — where your digital self keeps evolving

Paolo Ghensi, V Heidrich, D Bazzani, F Asnicar (@fasnicar.bsky.social), F Armanini, A Bertelle, F Dell'Acqua, E Dellasega, R Waldner, D Vicentini, M Bolzan, L Trevisiol, C Tomasi, E Pasolli (@epasolli.bsky.social), Nicola Segata

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We also used machine learning to show that diseased implants could be identified from microbiome profiles alone, reinforcing the potential of assessing the peri-implant microbiome in the clinical setting as a supportive diagnostic tool

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These included many functional and taxonomic unknowns, but also the well-studied for its role in periodontitis Fusobacterium nucleatum, with specific F. nuc clades associated differentially with mucositis and peri-implantitis

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Sergio Andreu-Sanchez @seandreu.bsky.social · 30/04/2025

Here we expanded our previous cohort (Ghensi et al. 2020) and used improved metagenomic profiling tools to identify strong microbiome markers of implant health and disease (mucositis or peri-implantitis)

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Reposted by Vitor Heidrich

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...

sciencedirect.com

Global genetic structure of human gut microbiome species is related to geographic location and host health

The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

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Reposted by Vitor Heidrich

Mireia Valles-Colomer @mireiavallesc.bsky.social · 21/03/2025

Our review on the acquisition and transmission of the human microbiome, now out @naturerevmicro.bsky.social 🦠 🔄 This was a fun writing process with @vheidrich.bsky.social and Nicola Segata! See Vitor's summary thread below:

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Human microbiome acquisition and transmission - Nature Reviews Microbiology

Finally, we discuss the impact that microbiome transmission can have on human health and disease, and how it is possible to leverage this knowledge for the design of effective microbiome-targeting strategies www.nature.com/articles/s41... Have a nice read! @cibiocm.bsky.social

nature.com

Each human hosts a unique microbiome, but only recently have we started to uncover how such uniqueness can arise. In this Review, Heidrich, Valles-Colomer and Segata highlight studies that surveyed ho...

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We also list the social, host-related, and microbial factors potentially associated with human microbiome transmission, and talk about the methodological challenges associated with microbiome transmission inference

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Since this includes microbial exchange not only with the main fount of our microbes - other humans, we dissect all the potential sources of human microbiome strains, including animals and foods

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We discuss how the building blocks of our microbiome - single microbial strains - are dynamically exchanged with the surroundings, leading to the continued acquisition and transmission of microbiome members

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Segata Lab @cibiocm.bsky.social · 12/03/2025

Thrilled to share our review (with @mireiavallesc.bsky.social and Nicola Segata) on "Human microbiome acquisition and transmission" just published @naturerevmicro.bsky.social

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Reposted by Vitor Heidrich

🥁 We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD) 🔗 Get it here: github.com/SegataLab/cFMD 🧵👇 1/5

github.com

GitHub - SegataLab/cFMD: Public repository for cFMD - curatedFoodMetagenomicData

Public repository for cFMD - curatedFoodMetagenomicData - SegataLab/cFMD

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Wrong figure here, right one below

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In conclusion, we hope our results and the better ability to metagenomically profile oral samples from dogs enabled by our study will encourage further efforts to characterize the microbiomes of pets (7/7)

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This finding provides some support for the continued use of dogs as models of periodontal conditions in humans and, more interestingly, hints at the possibility of the acquisition of oral pathogens from companion animals (6/7)

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This is probably linked to the very different anatomy, environmental conditions, and hygiene levels found in each host species' oral cavity. Despite this limited overlap, we noticed that species found in both hosts were often periodontal pathobionts, such as Campylobacter rectus (5/7)

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We found the dog plaque microbiome is more diverse than the human plaque microbiome and that there is very little microbial overlap between the dental plaque of dogs and humans (only ~6% of species found in both host species) (4/7)

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GitHub - biobakery/MetaPhlAn: MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

We then added these new dog plaque species to the database of MetaPhlAn 4 (github.com/biobakery/Me...) to be able to quantify their abundance in metagenomes. This allowed us to evaluate the overlap between the plaque microbiome of dogs and humans (3/7)

github.com

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data - biobakery/MetaPhlAn

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Through metagenomic sequencing and assembly, we reconstructed genomes for 347 dog plaque microbial species (spanning one archaeal and 17 bacterial phyla), 265 of which had never been identified before (2/7)

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