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Items tagged with: microbiome
Novel research reveals thriving microbial life in trees phys.org/news/2025-08-reveals-…
A diverse and distinct #microbiome inside living trees nature.com/articles/s41586-025…
"A single tree hosts about one trillion #bacteria in its woody tissue... #microbes are partitioned between heartwood and sapwood with each having its own unique microbiomes with minimal similarity to other tissues... They are actively producing gases and cycling nutrients... these communities may have coevolved with #trees over time"
Novel research reveals thriving microbial life in trees
There's a thriving community of diverse microbes living in tree wood, a new study led by a Yale School of the Environment team of scientists has found. A single tree hosts about one trillion bacteria in its woody tissue.Yale University (Phys.org)
Exciting work from the Hsu lab at Virginia Tech! They developed a cool way too knock down phage abundances to examine their role in the gut.
"A bacteriophage-conditional mouse model reveals the impact of phages within a conventionally colonized gut microbiota"
Interesting perspectives on the microbiome here.
I always had the somewhat quaint idea that our guts are full of friendly microbes, but what if the microbiome is largely parasitic, at least in the long run?
newscientist.com/article/mg265…
The shocking discovery that our gut microbiome drives ageing
A new understanding of our relationship with our "friendly" gut microbes shows they actually have a dark side and help cause ageing. Here's how to fight backGraham Lawton (New Scientist)
We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! embl.org/jobs/position/HD02727
In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the expedition. (1/4)
EMBL Jobs
We offer a wide range of challenging scientific and non-scientific positions at all of our European locations and encourage applications from international candidates at all career levels.www.embl.org
#Plankton mark #seasons in the #sea, just like leaves and flowers on land.
theconversation.com/plankton-m…
Plankton mark seasons in the sea, just like leaves and flowers on land
Plankton bloom and wither with the seasons much as plants do on land.The Conversation
What's that you say? You want an undergraduate practical course that teaches #MinION sequencing of the skin microbiome? Here you go:
biorxiv.org/content/10.1101/20…
#Biology #Hull #microbiome #UKHE
Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding
We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow.bioRxiv
A tiny fraction of all species forms most of nature: Rarity as a sticky state
Identifying keystone species in microbial communities using deep learning
"Study proposes new framework to identify keystone microbial species"
Lay summary
phys.org/news/2023-11-framewor…
Source
nature.com/articles/s41559-023…
#KeystoneSpecies #DeepLearningModel #ecology #microbiome
Study proposes new framework to identify keystone microbial species
Microbial communities are thought to contain keystone species, which can disproportionately affect the stability of the communities, even if only present in low abundances.Science X (Phys.org)
Very interesting preprint by Ran Blekhman's lab (@blekhman): biorxiv.org/content/10.1101/20… on microbiomap.org/ , a resource integrating 168k human gut 16S samples for a global overview. Seems similar to microbeatlas.org/ , which combines >2 million samples (both 16S and WGS across all habitats)
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Understanding the factors that shape variation in the human microbiome is a major goal of research in biology.bioRxiv
Preprint from Salzberg team questioning a 2020 Nature paper from Rob Knight 😮
"the raw read counts were vastly over-estimated for nearly every bacterial species, often by a factor of 1000 or more."
"Our conclusion after re-analysis is that the near-perfect association between microbes and cancer types reported in the study is, simply put, a fiction."
Major data analysis errors invalidate cancer microbiome findings
biorxiv.org/content/10.1101/20…
#microbiome #genomics #research #science
Major data analysis errors invalidate cancer microbiome findings
We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cance…bioRxiv
Our new Perspective is out in Nature Microbiology today. It covers some common/emerging myths and misconceptions in the human #microbiome field, and explains why they are likely incorrect: nature.com/articles/s41564-023…
A hopefully helpful primer against uncritical repetition.
Thanks to @fragilismatters for providing me and Alan with the original inspiration for this piece.
Human microbiome myths and misconceptions - Nature Microbiology
Walker and Hoyles highlight selected myths and misconceptions in the human microbiota literature.Nature
Interesting: *Vaginal Microbiota Transplantation (VMT)*
We're probably going to start seeing a lot more of this as we appreciate how microbiomes of different organs impact health and disease.
Personally the key is to have clinical measures of success, as here, not just measuring % of different species changing.
#IDMastodon #MedMastodon #AMR #antibiotics #microbiology #microbiome #transplant
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses
nature.com/articles/s43705-023…
#microbiology #bioinformatics #microbiome
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses - ISME Communications
ISME Communications - Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analysesNature
The best practice for microbiome analysis using R
Abstract. With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis toolWen, Tao (Oxford University Press)
Plant domestication shapes rhizosphere microbiome assembly and metabolic functions
microbiomejournal.biomedcentra…
Plant domestication shapes rhizosphere microbiome assembly and metabolic functions - Microbiome
Background The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth.BioMed Central
In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem
microbiomejournal.biomedcentra…
In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem - Microbiome
Background In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known.BioMed Central
Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics
"the abrupt community changes observed through the time-series could be described as shifts between “alternative stable states“ or dynamics around complex attractors."
microbiomejournal.biomedcentra…
Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics - Microbiome
Background Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications.BioMed Central
Bacterial aerobic methane cycling by the marine sponge-associated microbiome
microbiomejournal.biomedcentra…
Bacterial aerobic methane cycling by the marine sponge-associated microbiome - Microbiome
Background Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfa…BioMed Central
We are all too familiar with the all-too-often catastrophic impacts of #COVID19 #infection on human #health.
This fascinating new #metagenomics research in mBio explores a potentially important and intriguing link between the presence and relative abundance of different functional guilds present in the human gut #microbiome (including short chain fatty acid biosynthesis and virulence functions) and disease severity and outcomes resulting from the virus. Clearly a subject for future extended studies to explore potential increases in severity due to infection and exacerbated or mitigated by differences in gut microbiomes.
Explore the research on:
journals.asm.org/doi/10.1128/m…
Happy to announce this #preprint , the culmination of last 10 years. 🥳
We find that #antimicrobialpeptides are evolved to control specific #microbiome #bacteria. This example is a textbook case of host #immune #evolution being shaped by the microbiome 🦠 which depends on host #ecology.
Thanks for comments! Bit of an experiment: we are posting pre-submit to get feedback 🙂.
biorxiv.org/content/10.1101/20…
#immunity #Drosophila #EvolutionaryBiology #inflammation #NFkB
Single innate immune effectors control ecological microbiome bacteria across evolutionary timescales
Antimicrobial peptides are host-encoded antibiotics that combat invading microbes and help shape the microbiome in plants and animals.bioRxiv