Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the rhizosphere were combined and passaged in two different media environments to form stable microbial communities. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium. To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. A fast growth rate is identified as one factor that can provide an advantage for maintaining presence in the community. Final community selection can also depend on selective antagonistic relationships and metabolic exchanges. Revealing the mechanisms of interaction among plant-associated microorganisms provides insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic communities with desired biological functions.
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http://dx.doi.org/10.1016/j.csbj.2021.03.034 | DOI Listing |
Mol Cancer
January 2025
Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, No. 20, Section 3, Renmin South Road, Chengdu, Sichuan Province, 610041, China.
The polymorphic microbiome is considered a new hallmark of cancer. Advances in High-Throughput Sequencing have fostered rapid developments in microbiome research. The interaction between cancer cells, immune cells, and microbiota is defined as the immuno-oncology microbiome (IOM) axis.
View Article and Find Full Text PDFWorld J Microbiol Biotechnol
January 2025
Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, HP, 176061, India.
Understanding the change in plant-associated microbial diversity and secondary metabolite biosynthesis in medicinal plants due to their cultivation in non-natural habitat (NNH) is important to maintain their therapeutic importance. Here, the bacterial endomicrobiome of Podophyllum hexandrum plants of natural habitat (NH; Kardang and Triloknath locations) and NNH (Palampur location) was identified and its association with the biosynthesis of podophyllotoxin (PTOX) was revealed. Rhizomes (source of PTOX) of plants of NH had highest endophytic bacterial diversity compared to NNH-plants.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Health and Nutrition, Yamagata Prefectural Yonezawa University of Nutrition Sciences, 6-15-1, Torimachi, Yonezawa, Yamagata, 992-0025, Japan.
Colorectal cancer has the second highest mortality among cancer sites worldwide, with increasing morbidity, high recurrence rates, and even poorer postoperative quality of life. Therefore, preventive strategies for colorectal cancer should be established. This study aimed to cross-sectionally explore dietary patterns affecting the intestinal metabolism of bile acids (BAs), a risk factor for colorectal cancer, in young Japanese women.
View Article and Find Full Text PDFNature
January 2025
Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Tertiary lymphoid structures (TLSs) are de novo ectopic lymphoid aggregates that regulate immunity in chronically inflamed tissues, including tumours. Although TLSs form due to inflammation-triggered activation of the lymphotoxin (LT)-LTβ receptor (LTβR) pathway, the inflammatory signals and cells that induce TLSs remain incompletely identified. Here we show that interleukin-33 (IL-33), the alarmin released by inflamed tissues, induces TLSs.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, 0372, Oslo, Norway.
The respiratory tract is colonized with low-density microbial communities, which have been shown to impact human respiratory health through microbiota-host interactions. However, a lack of fast and cost-effective nucleic acid extraction method for low-microbial biomass samples hinders investigation of respiratory microbiota. Here, we performed a pilot study to assess the suitability of the NAxtra nucleic acid extraction protocol for profiling bacterial microbiota in respiratory samples.
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