Vitor Heidrich

Excited and proud to share our new work with @cibiocm.bsky.social, @vheidrich.bsky.social and @michal puncochar!

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

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

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

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)

Shotgun Metagenomics Identifies in a Cross‐Sectional Setting Improved Plaque Microbiome Biomarkers for Peri‐Implant Diseases Aim This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases. Materials and Methods Patients were in.....

In this study just published at the Journal of Clinical Periodontology - a collaboration between @cibiocm.bsky.social and PreBiomics - we evaluated the microbiome of dental implants using metagenomic sequencing

onlinelibrary.wiley.com/doi/10.1111/...

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

www.nature.com/articles/s41...

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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…

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...

Full-text: t.co/G8zk3j9Vtm

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:

Human microbiome acquisition and transmission - Nature Reviews Microbiology 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...

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

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

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

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

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

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

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We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)

🔗 Get it here: github.com/SegataLab/cFMD

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Wrong figure here, right one below

Newly identified species from the dog dental plaque microbiome highlight little overlap with humans npj Biofilms and Microbiomes - Newly identified species from the dog dental plaque microbiome highlight little overlap with humans

Link to the publication: rdcu.be/eajx6

@fackelmeister.bsky.social @raj09.bsky.social @cengoni.bsky.social @cibiocm.bsky.social

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)

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)

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)

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)

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

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)

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)

In this study just published at npj Biofilms and Microbiomes, we collected dental swab samples from dogs to shed light on the hardly studied dog dental plaque microbiome (1/7)