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Wang W, Li D, Qiu X, Yang J, Liu L, Wang E, Yuan H. Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. ENVIRONMENTAL MICROBIOME 2024; 19:2. [PMID: 38178261 PMCID: PMC10768371 DOI: 10.1186/s40793-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.
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Affiliation(s)
- Wenqian Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Dongmei Li
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Xiaoqian Qiu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11340, Ciudad de México, México
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian District, 100193, Beijing, China.
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Reens AL, Cosetta CM, Saur R, Trofimuk O, Brooker SL, Lee ML, Sun AK, McKenzie GJ, Button JE. Tunable control of B. infantis abundance and gut metabolites by co-administration of human milk oligosaccharides. Gut Microbes 2024; 16:2304160. [PMID: 38235736 PMCID: PMC10798361 DOI: 10.1080/19490976.2024.2304160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
Precision engineering of the gut microbiome holds promise as an effective therapeutic approach for diseases associated with a disruption in this microbial community. Engrafting a live biotherapeutic product (LBP) in a predictable, controllable manner is key to the consistent success of this approach and has remained a challenge for most LBPs under development. We recently demonstrated high-level engraftment of Bifidobacterium longum subsp. infantis (B. infantis) in adults when co-dosed with a specific prebiotic, human milk oligosaccharides (HMO). Here, we present a cellular kinetic-pharmacodynamic approach, analogous to pharmacokinetic-pharmacodynamic-based analyses of small molecule- and biologic-based drugs, to establish how HMO controls expansion, abundance, and metabolic output of B. infantis in a human microbiota-based model in gnotobiotic mice. Our data demonstrate that the HMO dose controls steady-state abundance of B. infantis in the microbiome, and that B. infantis together with HMO impacts gut metabolite levels in a targeted, HMO-dependent manner. We also found that HMO creates a privileged niche for B. infantis expansion across a 5-log range of bacterial inocula. These results demonstrate remarkable control of both B. infantis levels and the microbiome community metabolic outputs using this synbiotic approach, and pave the way for precision engineering of desirable microbes and metabolites to treat a range of diseases.
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Affiliation(s)
| | | | | | | | | | - Martin L. Lee
- Prolacta Bioscience, Duarte, CA, USA
- Department of Biostatistics, University of California Los Angeles Fielding School of Public Health, Los AngelesCA, USA
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Shi Z, Li H, Song W, Zhou Z, Li Z, Zhang M. Emerging roles of the gut microbiota in cancer immunotherapy. Front Immunol 2023; 14:1139821. [PMID: 36911704 PMCID: PMC9992551 DOI: 10.3389/fimmu.2023.1139821] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Gut microbiota represents a hidden treasure vault encompassing trillions of microorganisms that inhabit the intestinal epithelial barrier of the host. In the past decade, numerous in-vitro, animal and clinical studies have revealed the profound roles of gut microbiota in maintaining the homeostasis of various physiological functions, especially immune modulation, and remarkable differences in the configuration of microbial communities between cancers and healthy individuals. In addition, although considerable efforts have been devoted to cancer treatments, there remain many patients succumb to their disease with the incremental cancer burden worldwide. Nevertheless, compared with the stability of human genome, the plasticity of gut microbiota renders it a promising opportunity for individualized treatment. Meanwhile, burgeoning findings indicate that gut microbiota is involved in close interactions with the outcomes of diverse cancer immunotherapy protocols, including immune checkpoint blockade therapy, allogeneic hematopoietic stem cell transplantation, and chimeric antigen receptor T cell therapy. Here, we reviewed the evidence for the capacity of gut microflora to modulate cancer immunotherapies, and highlighted the opportunities of microbiota-based prognostic prediction, as well as microbiotherapy by targeting the microflora to potentiate anticancer efficacy while attenuating toxicity, which will be pivotal to the development of personalized cancer treatment strategies.
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Affiliation(s)
- Zhuangzhuang Shi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China.,Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongwen Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Wenting Song
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China.,Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhiyuan Zhou
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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