Host preferences of commensal bacteria in the root microbiota are revealed using systematic analyses of synthetic bacterial communities in a gnotobiotic system.

Published in bioRxiv : the preprint server for biology

The root microbiota remains an untapped resource for sustainable agriculture — resolving its recruitment cues is a research priority for moving towards translational applications. Family-conserved functional repertoires emerge as building blocks of the root microbiota in distinct plants, opening new avenues for the rational manipulation of biological interactions at the root–soil continuum.

Dung beetles (Coleoptera, Scarabaeoidea) support several ecological processes and services making them important ecosystem engineers. The dung beetle gut mic...

Gut bacteria affect host physiology, but the underlying mechanisms are not completely understood. We identify a pathway whereby gut microbes convert inorganic nitrate and non-heme iron into mobile bio...

A host’s immune responses may shape its microbiota, but the microbiota are just as likely to shape the host’s responses.

Gut bacteria convert inorganic nitrate and non-heme iron into bioactive dinitrosyl iron complexes (DNICs) that distribute systemically and signal independently of free nitric oxide. These microbe-deri...

Seed-derived bacterial communities tracked host phylogeny across wild Medicago, revealing a phylosymbiotic pattern, whereas fungal communities did not. In cultivated alfalfa, bacterial composition di...

What drives recurrent C. difficile infections? Research suggests host immune responses play a crucial role in recovery. Improved understanding could lead to new therapies. #InfectionResearch #Microbio...

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This review proposes a multidimensional chitinase–microbiota axis integrating enzymatic chitin processing, nonenzymatic chitinase-like protein signaling, h

Nature Microbiology, Published online: 19 October 2026; doi:10.1038/s41564-026-02453-wUsing a computational tool called CompoRes, the authors show that antibiotics can alter feeding behaviour, immunity and circadian regulation, revealing a non-microbial pathway by which antibiotic treatment reshapes host physiology.

Using a computational tool called CompoRes, the authors show that antibiotics can alter feeding behaviour, immunity and circadian regulation, revealing a non-microbial pathway by which antibiotic trea...

Antibiotics can be administered via multiple routes in the clinic and in experiments. Yet, whether the administration route affects treatment outcomes is unclear. To test this, we treated mice reared in a specific pathogen-free (SPF) barrier facility with four commonly used antibiotics (that is, vancomycin, ampicillin, metronidazole and neomycin), either separately or combined (a four-antibiotic mix). Antibiotics were administered orally via gavage or systemically via intraperitoneal (i.p.) or intravenous (i.v.) injection. Mimicking real-world conditions, mice were treated twice a day for 3.5 days (to reflect real-world observations and the shift towards shorter regimen periods22,23,24,25,26), after which stool and colonic tissue samples were collected (Fig. 1a). Faecal samples were also collected before treatment, to establish a baseline. We first analysed the bacterial composition of faecal samples using 16S ribosomal RNA (rRNA) amplicon sequencing. We calculated the effective number of genera (using the Shannon diversity index27) and performed a pairwise community-level comparison of the effect of the antibiotic treatment using Adonis2 (ref. 28) (Fig. 1b,c). We detail our observations on the effects of ampicillin, metronidazole, neomycin and a mix of these three antibiotics on microbial composition in Extended Data Fig. 1. Herein, we focus on the results relating to vancomycin. Contrary to...

A new study sheds light on how gut microbiota-derived metabolites can influence host immune and metabolic pathways. Focusing on trimethylamine (TMA) and IRAK4 signaling, the findings help clarify the mechanisms linking microbial metabolism with metabolic inflammation and glycemic regulation.