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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

It is demonstrated that periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts, and integrative analysis identified microbial, biochemical, and host factors central to this dysregulation.
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Gut microbiome structure and metabolic activity in inflammatory bowel disease

Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort, providing an improved understanding of perturbations of the microbiome–metabolome interface in IBD.
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Control of cell fate by the formation of an architecturally complex bacterial community.

It is proposed that sporulation is a culminating feature of biofilm formation, and that spore formation is coupled to the formation of an architecturally complex community of cells.
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Sticking together: building a biofilm the Bacillus subtilis way

This Review focuses on the molecular mechanisms that control B. subtilis biofilm assembly, and then briefly summarize the current state of knowledge regarding biofilm disassembly.
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Generation of multiple cell types in Bacillus subtilis.

This review discusses how individual cells within a population control their gene expression to ensure that proper regulation of differentiation occurs, and how this regulation relies primarily on the activity of three major transcriptional regulators: Spo0A, DegU, and ComK.
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Bacillus subtilis biofilm induction by plant polysaccharides

It is demonstrated that B. subtilis root attachment depends on production of an extracellular matrix that holds the cells together in multicellular communities termed biofilms, and it is found that plant polysaccharides act as an environmental cue that triggers biofilm formation by the bacterium.
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Paracrine signaling in a bacterium.

The results demonstrate that extracellular signaling was unidirectional, with one subpopulation producing a signal and a different subpopulation responding to it, and some cells produce a signal to which only certain target cells respond.
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Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

A longitudinal strain-level analysis of the infant gut microbiome after repeated antibiotic treatments reveals decreased diversity and stability, as well as transient increases in antibiotic resistance genes, which highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the newborn gut microbiome.
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The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes.
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A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

A consortium of 11 bacterial strains from the healthy human gut microbiota can strongly induce interferon-γ-producing CD8 T cells in the intestine, and enhance both resistance to bacterial infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models.
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