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Ye Z, Yu L, Zhang C, Gao Y, Zhao J, Narbad A, Chen W, Zhai Q, Tian F. Modulation of gut microbiota and metabolites by Flammulina velutipes polysaccharides during in vitro human fecal fermentation: Unveiling Bacteroides as a potential primary degrader. Food Chem 2024; 450:139309. [PMID: 38631200 DOI: 10.1016/j.foodchem.2024.139309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024]
Abstract
Flammulina velutipes, a widely cultivated species of edible fungus, exhibits diverse functional activities attributed to its polysaccharides. In this study, we employed an in vitro model to investigate the impact of F. velutipes polysaccharides (FVP) fermentation on gut microbiota, with a particular focus on Bacteroides. FVP fermentation resulted in the proliferation of microbiota associated with short-chain fatty acid (SCFA) metabolism and suppression of Escherichia-Shigella. Bacteroides emerged as potential primary degraders of FVP, with species-level analysis identifying the preference of B. thetaiotaomicron and B. intestinalis in FVP degradation. Metabolomics analysis revealed significant increases in hypoxanthine and 7-methyladenine contents, with histidine metabolism emerging as the most enriched pathway. B. nordii and B. xylanisolvens exhibited the most influence on amino acid and SCFA metabolism. Understanding the mechanisms by which gut microbiota metabolize FVP can provide valuable insights into the potential of FVP to promote intestinal health and disease prevention.
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Affiliation(s)
- Zi Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Chuan Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuhang Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Arjan Narbad
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China; Gut Health and Microbiome Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China.
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2
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Yang J, Sun Y, Wang Q, Yu S, Li Y, Yao B, Yang X. Astragalus polysaccharides-induced gut microbiota play a predominant role in enhancing of intestinal barrier function of broiler chickens. J Anim Sci Biotechnol 2024; 15:106. [PMID: 39103958 DOI: 10.1186/s40104-024-01060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND The intestinal barrier is the first line of defense against intestinal invasion by pathogens and foreign antigens and is closely associated with the gut microbiota. Astragalus polysaccharides (APS) have a long history of use in traditional Chinese medicine owing to its protective properties against intestinal barrier function. The mechanism of APS-induced gut microbiota enhancing intestinal barrier function is urgently needed. RESULTS Dietary polysaccharide deprivation induced intestinal barrier dysfunction, decreased growth performance, altered microbial composition (Faecalibacterium, Dorea, and Coprobacillus), and reduced isobutyrate concentration. The results showed that APS facilitates intestinal barrier function in broiler chickens, including a thicker mucus layer, reduced crypt depth, and the growth of tight junction proteins. We studied the landscape of APS-induced gut microbiota and found that APS selectively promoted the growth of Parabacteroides, a commensal bacterium that plays a predominant role in enhancing intestinal barrier function. An in vitro growth assay further verified that APS selectively increased the abundance of Parabacteroides distasonis and Bacteroides uniformis. Dietary APS supplementation increased the concentrations of isobutyrate and bile acid (mainly chenodeoxycholic acid and deoxycholate acid) and activated signaling pathways related to intestinal barrier function (such as protein processing in the endoplasmic reticulum, tight junctions, and adherens junction signaling pathways). CONCLUSIONS APS intervention restored the dietary polysaccharide-induced dysfunction of the intestinal barrier by selectively promoting the abundance of Parabacteroides distasonis, and increasing the concentrations of isobutyrate and bile acids (mainly CDCA and DCA). These findings suggest that APS-induced gut microbiota and metabolic niches are promising strategies for enhancing intestinal barrier function.
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Affiliation(s)
- Jiantao Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanpeng Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agriculture Science, Beijing, China
| | - Qianggang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shanglin Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanhe Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agriculture Science, Beijing, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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De Bruyn F, James K, Cottenet G, Dominick M, Katja J. Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo. Commun Biol 2024; 7:943. [PMID: 39098939 DOI: 10.1038/s42003-024-06628-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
To enhance health benefits, a probiotic can be co-administered with a metabolizable prebiotic forming a synergistic synbiotic. We assessed the synergies resulting from combining Bifidobacterium longum subsp. infantis LMG 11588 and an age-adapted blend of six human milk oligosaccharides (HMOs) in ex vivo colonic incubation bioreactors seeded with fecal background microbiota from infant and toddler donors. When HMOs were combined with B. infantis LMG 11588, they were rapidly and completely consumed. This resulted in increased short chain fatty acid (SCFA) production compared to the summed SCFA production from individual ingredients (synergy). Remarkably, HMOs were partially consumed for specific infant donors in the absence of B. infantis LMG 11588, yet all donors showed increased SCFA production upon B. infantis LMG 11588 supplementation. We found specific bacterial taxa associated with the differential response pattern to HMOs. Our study shows the importance of carefully selecting pre- and probiotic into a synergistic synbiotic that could benefit infants.
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Affiliation(s)
- Florac De Bruyn
- Nestlé Research and Development, Nestléstrasse 3, CH-3510, Konolfingen, Switzerland.
| | - Kieran James
- Nestlé Research and Development, Nestléstrasse 3, CH-3510, Konolfingen, Switzerland
| | - Geoffrey Cottenet
- Nestlé Institute of Food Safety and Analytical Science, Nestlé Research, Route du Jorat 57, CH-1000, Lausanne, Switzerland
| | - Maes Dominick
- Nestlé Research and Development, Nestléstrasse 3, CH-3510, Konolfingen, Switzerland
| | - Johnson Katja
- Nestlé Research and Development, Nestléstrasse 3, CH-3510, Konolfingen, Switzerland
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Zhou Y, Liu D, Li F, Dong Y, Jin Z, Liao Y, Li X, Peng S, Delgado-Baquerizo M, Li X. Superiority of native soil core microbiomes in supporting plant growth. Nat Commun 2024; 15:6599. [PMID: 39097606 PMCID: PMC11297980 DOI: 10.1038/s41467-024-50685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Donghui Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Fengqiao Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili Jin
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Yangwenke Liao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaohui Li
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Shuguang Peng
- Hunan Province Company of China Tobacco Corporation, Changsha, 410004, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
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Mo C, Lou X, Xue J, Shi Z, Zhao Y, Wang F, Chen G. The influence of Akkermansia muciniphila on intestinal barrier function. Gut Pathog 2024; 16:41. [PMID: 39097746 PMCID: PMC11297771 DOI: 10.1186/s13099-024-00635-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 07/20/2024] [Indexed: 08/05/2024] Open
Abstract
Intestinal barriers play a crucial role in human physiology, both in homeostatic and pathological conditions. Disruption of the intestinal barrier is a significant factor in the pathogenesis of gastrointestinal inflammatory diseases, such as inflammatory bowel disease. The profound influence of the gut microbiota on intestinal diseases has sparked considerable interest in manipulating it through dietary interventions, probiotics, and fecal microbiota transplantation as potential approaches to enhance the integrity of the intestinal barrier. Numerous studies have underscored the protective effects of specific microbiota and their associated metabolites. In recent years, an increasing body of research has demonstrated that Akkermansia muciniphila (A. muciniphila, Am) plays a beneficial role in various diseases, including diabetes, obesity, aging, cancer, and metabolic syndrome. It is gaining popularity as a regulator that influences the intestinal flora and intestinal barrier and is recognized as a 'new generation of probiotics'. Consequently, it may represent a potential target and promising therapy option for intestinal diseases. This article systematically summarizes the role of Am in the gut. Specifically, we carefully discuss key scientific issues that need resolution in the future regarding beneficial bacteria represented by Am, which may provide insights for the application of drugs targeting Am in clinical treatment.
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Affiliation(s)
- Chunyan Mo
- Medical School, Kunming University of Science and Technology, 727 Jingming South Road, Chenggong District, Kunming, 650500, China
| | - Xiran Lou
- Medical School, Kunming University of Science and Technology, 727 Jingming South Road, Chenggong District, Kunming, 650500, China
| | - Jinfang Xue
- Medical School, Kunming University of Science and Technology, 727 Jingming South Road, Chenggong District, Kunming, 650500, China
| | - Zhuange Shi
- Department of Emergency Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650034, China
| | - Yifang Zhao
- Department of Emergency Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650034, China
| | - Fuping Wang
- Department of Emergency Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650034, China
| | - Guobing Chen
- Department of Emergency Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650034, China.
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Sanchez-Gallardo R, Bottacini F, Friess L, Esteban-Torres M, Somers C, Moore RL, McAuliffe FM, Cotter PD, van Sinderen D. Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum. Front Microbiol 2024; 15:1414471. [PMID: 39081887 PMCID: PMC11286577 DOI: 10.3389/fmicb.2024.1414471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024] Open
Abstract
Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.
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Affiliation(s)
- Rocio Sanchez-Gallardo
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Lisa Friess
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Clarissa Somers
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Rebecca L. Moore
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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7
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Cheng T, Zhang T, Zhang P, He X, Sadiq FA, Li J, Sang Y, Gao J. The complex world of kefir: Structural insights and symbiotic relationships. Compr Rev Food Sci Food Saf 2024; 23:e13364. [PMID: 38847746 DOI: 10.1111/1541-4337.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/04/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
Kefir milk, known for its high nutritional value and health benefits, is traditionally produced by fermenting milk with kefir grains. These grains are a complex symbiotic community of lactic acid bacteria, acetic acid bacteria, yeasts, and other microorganisms. However, the intricate coexistence mechanisms within these microbial colonies remain a mystery, posing challenges in predicting their biological and functional traits. This uncertainty often leads to variability in kefir milk's quality and safety. This review delves into the unique structural characteristics of kefir grains, particularly their distinctive hollow structure. We propose hypotheses on their formation, which appears to be influenced by the aggregation behaviors of the community members and their alliances. In kefir milk, a systematic colonization process is driven by metabolite release, orchestrating the spatiotemporal rearrangement of ecological niches. We place special emphasis on the dynamic spatiotemporal changes within the kefir microbial community. Spatially, we observe variations in species morphology and distribution across different locations within the grain structure. Temporally, the review highlights the succession patterns of the microbial community, shedding light on their evolving interactions.Furthermore, we explore the ecological mechanisms underpinning the formation of a stable community composition. The interplay of cooperative and competitive species within these microorganisms ensures a dynamic balance, contributing to the community's richness and stability. In kefir community, competitive species foster diversity and stability, whereas cooperative species bolster mutualistic symbiosis. By deepening our understanding of the behaviors of these complex microbial communities, we can pave the way for future advancements in the development and diversification of starter cultures for food fermentation processes.
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Affiliation(s)
- Tiantian Cheng
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Tuo Zhang
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Pengmin Zhang
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiaowei He
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Faizan Ahmed Sadiq
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff, UK
| | - Jiale Li
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Yaxin Sang
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jie Gao
- Department of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, China
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8
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Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab 2024; 6:1225-1236. [PMID: 38961185 DOI: 10.1038/s42255-024-01074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.
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Affiliation(s)
- Cecilia Noecker
- Department of Biological Sciences, Minnesota State University, Mankato, Mankato, MN, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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9
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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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Yin XF, Ye T, Chen HL, Liu J, Mu XF, Li H, Wang J, Hu YJ, Cao H, Kang WQ. The microbiome compositional and functional differences between rectal mucosa and feces. Microbiol Spectr 2024:e0354923. [PMID: 38916335 DOI: 10.1128/spectrum.03549-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population. IMPORTANCE This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.
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Affiliation(s)
- Xiao-Fei Yin
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Taoyu Ye
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Han-Lin Chen
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Junyan Liu
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Xue-Feng Mu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hao Li
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Jun Wang
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Yuan-Jia Hu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hongzhi Cao
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- Department of Digital Health, South China Hospital of Shenzhen University, Shenzhen, China
| | - Wen-Quan Kang
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
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11
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Ortiz AM, Brenchley JM. Untangling the role of the microbiome across the stages of HIV disease. Curr Opin HIV AIDS 2024:01222929-990000000-00101. [PMID: 38935047 DOI: 10.1097/coh.0000000000000870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design. RECENT FINDINGS Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions. SUMMARY Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland, USA
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12
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Lambert A, Budinich M, Mahé M, Chaffron S, Eveillard D. Community metabolic modeling of host-microbiota interactions through multi-objective optimization. iScience 2024; 27:110092. [PMID: 38952683 PMCID: PMC11215293 DOI: 10.1016/j.isci.2024.110092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/12/2024] [Accepted: 05/21/2024] [Indexed: 07/03/2024] Open
Abstract
The human gut microbiota comprises various microorganisms engaged in intricate interactions among themselves and with the host, affecting its health. While advancements in omics technologies have led to the inference of clear associations between microbiome composition and health conditions, we usually lack a causal and mechanistic understanding of these associations. For modeling mechanisms driving the interactions, we simulated the organism's metabolism using in silico genome-scale metabolic models (GEMs). We used multi-objective optimization to predict and explain metabolic interactions among gut microbes and an intestinal epithelial cell. We developed a score integrating model simulation results to predict the type (competition, neutralism, mutualism) and quantify the interaction between several organisms. This framework uncovered a potential cross-feeding for choline, explaining the predicted mutualism between Lactobacillus rhamnosus GG and the epithelial cell. Finally, we analyzed a five-organism ecosystem, revealing that a minimal microbiota can favor the epithelial cell's maintenance.
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Affiliation(s)
- Anna Lambert
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Marko Budinich
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Maxime Mahé
- Nantes Université, Inserm, TENS UMR1235, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
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13
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Fang Z, Ma M, Wang Y, Dai W, Shang Q, Yu G. Degradation and fermentation of hyaluronic acid by Bacteroides spp. from the human gut microbiota. Carbohydr Polym 2024; 334:122074. [PMID: 38553207 DOI: 10.1016/j.carbpol.2024.122074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/02/2024]
Abstract
Bacteroides spp. are prominent members of the human gut microbiota that play critical roles in the metabolism of complex carbohydrates from the daily diet. Hyaluronic acid (HA) is a multifunctional polysaccharide which has been extensively used in the food and biomedical industry. However, how HA is degraded and fermented by Bacteroides spp. has not been fully characterized. Here, we comprehensively investigated the detailed degradation profiles and fermentation characteristics of four different HAs with discrete molecular weight (Mw) by fourteen distinctive Bacteroides spp. from the human gut microbiota. Our results indicated that high-Mw HAs were more degradable and fermentable than low-Mw HAs. Interestingly, B. salyersiae showed the best degrading capability for both high-Mw and low-Mw HAs, making it a keystone species for HA degradation among Bacteroides spp.. Specifically, HA degradation by B. salyersiae produced significant amounts of unsaturated tetrasaccharide (udp4). Co-culture experiments indicated that the produced udp4 could be further fermented and utilized by non-proficient HA-degraders, suggesting a possible cross-feeding interaction in the utilization of HA within the Bacteroides spp.. Altogether, our study provides novel insights into the metabolism of HA by the human gut microbiota, which has considerable implications for the development of new HA-based nutraceuticals and medicines.
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Affiliation(s)
- Ziyi Fang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Mingfeng Ma
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yamin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Wei Dai
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qingsen Shang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao 266237, China; Qingdao Marine Biomedical Research Institute, Qingdao 266071, China.
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao 266237, China.
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14
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Swaney MH, Henriquez N, Campbell T, Handelsman J, Kalan LR. Skin-associated Corynebacterium amycolatum shares cobamides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591522. [PMID: 38712214 PMCID: PMC11071462 DOI: 10.1101/2024.04.28.591522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B12 family of cofactors, are essential for metabolism in many bacteria, but are only synthesized by a small fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and show that C. amycolatum produces sufficient cobamides to support E. coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK and cobO and confirm that disruption of cobamide biosynthesis abolishes support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.
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Affiliation(s)
- M H Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - N Henriquez
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - T Campbell
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - J Handelsman
- Wisconsin Institute for Discovery, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - L R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, CAN
- David Braley Centre for Antibiotic Discovery, Hamilton, ON, CAN
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15
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Facchin S, Bertin L, Bonazzi E, Lorenzon G, De Barba C, Barberio B, Zingone F, Maniero D, Scarpa M, Ruffolo C, Angriman I, Savarino EV. Short-Chain Fatty Acids and Human Health: From Metabolic Pathways to Current Therapeutic Implications. Life (Basel) 2024; 14:559. [PMID: 38792581 PMCID: PMC11122327 DOI: 10.3390/life14050559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The gastrointestinal tract is home to trillions of diverse microorganisms collectively known as the gut microbiota, which play a pivotal role in breaking down undigested foods, such as dietary fibers. Through the fermentation of these food components, short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate are produced, offering numerous health benefits to the host. The production and absorption of these SCFAs occur through various mechanisms within the human intestine, contingent upon the types of dietary fibers reaching the gut and the specific microorganisms engaged in fermentation. Medical literature extensively documents the supplementation of SCFAs, particularly butyrate, in the treatment of gastrointestinal, metabolic, cardiovascular, and gut-brain-related disorders. This review seeks to provide an overview of the dynamics involved in the production and absorption of acetate, propionate, and butyrate within the human gut. Additionally, it will focus on the pivotal roles these SCFAs play in promoting gastrointestinal and metabolic health, as well as their current therapeutic implications.
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Affiliation(s)
- Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Luisa Bertin
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Erica Bonazzi
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Greta Lorenzon
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Caterina De Barba
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Brigida Barberio
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Fabiana Zingone
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Daria Maniero
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Marco Scarpa
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Cesare Ruffolo
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Imerio Angriman
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
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16
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Knobloch S, Skirnisdóttir S, Dubois M, Mayolle L, Kolypczuk L, Leroi F, Leeper A, Passerini D, Marteinsson VÞ. The gut microbiome of farmed Arctic char ( Salvelinus alpinus) is shaped by feeding stage and nutrient presence. FEMS MICROBES 2024; 5:xtae011. [PMID: 38745980 PMCID: PMC11092275 DOI: 10.1093/femsmc/xtae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Food Technology, University of Applied Sciences Fulda, Leipziger Strasse 123, 36037 Fulda, Germany
| | | | - Marianne Dubois
- ESBS/University of Strasbourg, 300 Bd Sébastien Brant, 67085 Strasbourg, France
| | - Lucie Mayolle
- University of Technology of Compiègne, Rue Roger Couttolenc, 60203 Compiègne, France
| | - Laetitia Kolypczuk
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Françoise Leroi
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Alexandra Leeper
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, 1430 Ås, Norway
- Iceland Ocean Cluster, Department of Research and Innovation, Grandagarður 16, 101 Reykjavík, Iceland
| | - Delphine Passerini
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Viggó Þ Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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17
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Elford JD, Becht N, Garssen J, Kraneveld AD, Perez-Pardo P. Buty and the beast: the complex role of butyrate in Parkinson's disease. Front Pharmacol 2024; 15:1388401. [PMID: 38694925 PMCID: PMC11061429 DOI: 10.3389/fphar.2024.1388401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/02/2024] [Indexed: 05/04/2024] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease which is often associated with gastrointestinal (GI) dysfunction. The GI tract is home to a wide range of microorganisms, among which bacteria, that can influence the host through various mechanisms. Products produced by these bacteria can act in the gut but can also exert effects in the brain via what is now well established to be the microbiota-gut-brain axis. In those with PD the gut-bacteria composition is often found to be different to that of non-PD individuals. In addition to compositional changes, the metabolic activity of the gut-microbiota is also changed in PD. Specifically, it is often reported that key producers of short chain fatty acids (SCFAs) as well as the concentration of SCFAs themselves are altered in the stool and blood of those with PD. These SCFAs, among which butyrate, are essential nutrients for the host and are a major energy source for epithelial cells of the GI tract. Additionally, butyrate plays a key role in regulating various host responses particularly in relation to inflammation. Studies have demonstrated that a reduction in butyrate levels can have a critical role in the onset and progression of PD. Furthermore, it has been shown that restoring butyrate levels in those with PD through methods such as probiotics, prebiotics, sodium butyrate supplementation, and fecal transplantation can have a beneficial effect on both motor and non-motor outcomes of the disease. This review presents an overview of evidence for the altered gut-bacteria composition and corresponding metabolite production in those with PD, with a particular focus on the SCFA butyrate. In addition to presenting current studies regarding SCFA in clinical and preclinical reports, evidence for the possibility to target butyrate production using microbiome based approaches in a therapeutic context is discussed.
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Affiliation(s)
- Joshua D. Elford
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nanette Becht
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
- Danone Nutricia Research, Utrecht, Netherlands
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
- Department of Neuroscience, Faculty of Science, Vrije Universiteit, Amsterdam, Netherlands
| | - Paula Perez-Pardo
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
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18
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Li N, Han J, Zhou Y, Zhang H, Xu X, He B, Liu M, Wang J, Wang Q. A rumen-derived bifunctional glucanase/mannanase uncanonically releases oligosaccharides with a high degree of polymerization preferentially from branched substrates. Carbohydr Polym 2024; 330:121828. [PMID: 38368107 DOI: 10.1016/j.carbpol.2024.121828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Abstract
Glycoside hydrolases (GHs) are known to depolymerize polysaccharides into oligo-/mono-saccharides, they are extensively used as additives for both animals feed and our food. Here we reported the characterization of IDSGH5-14(CD), a weakly-acidic mesophilic bifunctional mannanase/glucanase of GH5, originally isolated from sheep rumen microbes. Biochemical characterization studies revealed that IDSGH5-14(CD) exhibited preferential hydrolysis of mannan-like and glucan-like substrates. Interestingly, the enzyme exhibited significantly robust catalytic activity towards branched-substrates compared to linear polysaccharides (P < 0.05). Substrate hydrolysis pattern indicated that IDSGH5-14(CD) predominantly liberated oligosaccharides with a degree of polymerization (DP) of 3-7 as the end products, dramatically distinct from canonical endo-acting enzymes. Comparative modeling revealed that IDSGH5-14(CD) was mainly comprised of a (β/α)8-barrel-like structure with a spacious catalytic cleft on surface, facilitating the enzyme to target high-DP or branched oligosaccharides. Molecular dynamics (MD) simulations further suggested that the branched-ligand, 64-α-D-galactosyl-mannohexose, was steadily accommodated within the catalytic pocket via a two-sided clamp formed by the aromatic residues. This study first reports a bifunctional GH5 enzyme that predominantly generates high-DP oligosaccharides, preferentially from branched-substrates. This provides novel insights into the catalytic mechanism and molecular underpinnings of polysaccharide depolymerization, with potential implications for feed additive development and high-DP oligosaccharides preparation.
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Affiliation(s)
- Nuo Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Junyan Han
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yebo Zhou
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Huien Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Xiaofeng Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Bo He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqi Liu
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Qian Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China.
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19
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Mukherjee A, Breselge S, Dimidi E, Marco ML, Cotter PD. Fermented foods and gastrointestinal health: underlying mechanisms. Nat Rev Gastroenterol Hepatol 2024; 21:248-266. [PMID: 38081933 DOI: 10.1038/s41575-023-00869-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 12/20/2023]
Abstract
Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in particular. It is important that any such perceived benefits are underpinned by rigorous scientific research to understand the associated mechanisms of action. Here, we review in vitro, ex vivo and in vivo studies that have provided insights into the ways in which the specific food components, including FF microorganisms and a variety of bioactives, can contribute to health-promoting activities. More specifically, we draw on representative examples of FFs to discuss the mechanisms through which functional components are produced or enriched during fermentation (such as bioactive peptides and exopolysaccharides), potentially toxic or harmful compounds (such as phytic acid, mycotoxins and lactose) are removed from the food substrate, and how the introduction of fermentation-associated live or dead microorganisms, or components thereof, to the gut can convey health benefits. These studies, combined with a deeper understanding of the microbial composition of a wider variety of modern and traditional FFs, can facilitate the future optimization of FFs, and associated microorganisms, to retain and maximize beneficial effects in the gut.
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Affiliation(s)
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Eirini Dimidi
- Department of Nutritional Sciences, King's College London, London, UK
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, CA, USA
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
- VistaMilk, Cork, Ireland.
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20
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Chiang BH, Vega G, Dunwoody SC, Patnode ML. Bacterial interactions on nutrient-rich surfaces in the gut lumen. Infect Immun 2024:e0048023. [PMID: 38506518 DOI: 10.1128/iai.00480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.
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Affiliation(s)
- Bo Huey Chiang
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Giovanni Vega
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
- Graduate Program in Biological Sciences and Engineering, University of California, Santa Cruz, California, USA
| | - Sarah C Dunwoody
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Michael L Patnode
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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21
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Li J, Chen Z, Wang Q, Du L, Yang Y, Guo F, Li X, Chao Y, Ma Y. Microbial and metabolic profiles unveil mutualistic microbe-microbe interaction in obesity-related colorectal cancer. Cell Rep Med 2024; 5:101429. [PMID: 38378003 PMCID: PMC10982962 DOI: 10.1016/j.xcrm.2024.101429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/30/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Obesity is a risk factor for colorectal cancer (CRC), and the involvement of gut microbiota in the pathogenesis of obesity and CRC is widely recognized. However, the landscape of fecal microbiome and metabolome distinguishing patients with obesity-related CRC from obesity remains unknown. Here, we utilize metagenomic sequencing and metabolomics from 522 patients with CRC and healthy controls to identify the characteristics of obese CRC. Our integrated analysis reveals that obesity-related CRC is characterized by elevated Peptostreptococcus stomatis, dysregulated fatty acids and phospholipids, and altered Kyoto Encyclopedia of Genes and Genomes pathways involving glycerophospholipid metabolism and lipopolysaccharide synthesis. Correlation analysis unveils microbial interactions in obesity, where the probiotic Faecalibacterium prausnitzii and the tumor-promoting species P. stomatis may engage in cross-feeding, thereby promoting tumorigenesis. In vitro experiments affirm enhanced growth under cross-feeding conditions. The mutualistic microbe-microbe interaction may contribute to the association between obesity and elevated CRC risk. Additionally, diagnostic models incorporating BMI-specific microbial biomarkers display promise for precise CRC screening.
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Affiliation(s)
- Jinming Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziying Chen
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qinying Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong Province, China
| | - Yongzhi Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fanying Guo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanjie Chao
- CAS Key Laboratory of Molecular Virology and Immunology, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Young SM, Woode RA, Williams EC, Ericsson AC, Clarke LL. Fecal dysbiosis and inflammation in intestinal-specific Cftr knockout mice on regimens preventing intestinal obstruction. Physiol Genomics 2024; 56:247-264. [PMID: 38073491 PMCID: PMC11283905 DOI: 10.1152/physiolgenomics.00077.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/26/2023] Open
Abstract
Chronic intestinal inflammation is a poorly understood manifestation of cystic fibrosis (CF), which may be refractory to ion channel CF transmembrane conductance regulator (CFTR) modulator therapy. People with CF exhibit intestinal dysbiosis, which has the potential for stimulating intestinal and systemic inflammation. CFTR is expressed in organ epithelia, leukocytes, and other tissues. Here, we investigate the contribution of intestinal epithelium-specific loss of Cftr [iCftr knockout (KO)] to dysbiosis and inflammation in mice treated with either of two antiobstructive dietary regimens necessary to maintain CF mouse models [polyethylene glycol (PEG) laxative or a liquid diet (LiqD)]. Feces collected from iCftr KO mice and their wild-type (WT) sex-matched littermates were used to measure fecal calprotectin to evaluate inflammation and to perform 16S rRNA sequencing to characterize the gut microbiome. Fecal calprotectin was elevated in iCftr KO relative to WT mice that consumed either PEG or LiqD. PEG iCftr KO mice did not show a change in α diversity versus WT mice but demonstrated a significant difference in microbial composition (β diversity) with included increases in the phylum Proteobacteria, the family Peptostreptococcaceae, four genera of Clostridia including C. innocuum, and the mucolytic genus Akkermansia. Fecal microbiome analysis of LiqD-fed iCftr KO mice showed both decreased α diversity and differences in microbial composition with increases in the Proteobacteria family Enterobacteriaceae, Firmicutes families Clostridiaceae and Peptostreptococcaceae, and enrichment of Clostridium perfringens, C. innocuum, C. difficile, mucolytic Ruminococcus gnavus, and reduction of Akkermansia. It was concluded that epithelium-specific loss of Cftr is a major driver of CF intestinal dysbiosis and inflammation with significant similarities to previous studies of pan Cftr KO mice.NEW & NOTEWORTHY Chronic intestinal inflammation is a manifestation of cystic fibrosis (CF), a disease caused by loss of the anion channel CF transmembrane conductance regulator (CFTR) that is expressed in many tissues. This study shows that intestinal epithelial cell-specific loss of CFTR [inducible Cftr knockout (KO)] in mice is sufficient to induce intestinal dysbiosis and inflammation. Experiments were performed on mice consuming two dietary regimens routinely used to prevent obstruction in CF mice.
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Affiliation(s)
- Sarah M Young
- College of Veterinary Medicine, University of Missouri Comparative Medicine Program, Columbia, Missouri, United States
| | - Rowena A Woode
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Estela C Williams
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Aaron C Ericsson
- College of Veterinary Medicine, University of Missouri Comparative Medicine Program, Columbia, Missouri, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
- College of Veterinary Medicine, University of Missouri Metagenomics Center, Columbia, Missouri, United States
| | - Lane L Clarke
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, United States
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23
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Chen S, Mei H, Xu L, Zhan L, Yang Y, Zhao D, Bao G, Li X, Cao Z. Impact of fermented feed of soybean hulls and rapeseed cake on immunity, antioxidant capacity, and gut microbiota in Chahua chicken. Poult Sci 2024; 103:103451. [PMID: 38301497 PMCID: PMC10847688 DOI: 10.1016/j.psj.2024.103451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/25/2023] [Accepted: 01/06/2024] [Indexed: 02/03/2024] Open
Abstract
The present study investigated the effects of replacing part of the basal diet with 2-stage fermented feed (FF) (soybean hulls:rapeseed cake (2:1, m/m)) on the growth performance, immunity, antioxidant capacity, and intestinal health of Chahua chicken. A total of 160 Chahua chickens were randomly divided into 4 groups to receive a control diet or diet with 5%, 10%, or 15% of the basal diet replaced by FF, respectively for 56 d. The results showed that FF significantly improved the average daily gain (ADG) and average daily feed intake (ADFI) of Chahua chickens (P < 0.05). Furthermore, the serum immunoglobulin (Ig) A, glutathione peroxidase (GSH-Px), and superoxide dismutase (SOD) in Chahua chicken receiving the diet added with 15% FF significantly increased (P < 0.05). Chahua chicken in both the 10% and 15% groups showed increased serum IgG and IgM and decreased malondialdehyde. Serum interleukin-2 and interferon-gamma significantly increased in all FF groups. Compared with the CON group, higher ileal villus height (VH) was found in the 10% FF group. Treatment with FF significantly increased the ileal villus height/crypt depth (VH/CD) ratio, jejunal VH, and jejunal VH/CD ratio while reducing ileal and jejunal CD. The modified gut microbiota composition was observed in the Chahua chicken fed a diet containing FF, in particular, with the increased abundance of Faecalibacterium and Lactobacillus. The abundance of Lactobacillus significantly increased in the 10% and 15% FF groups (all P < 0.05). Correlation analysis revealed a positive correlation between Lactobacillus and VH (R = 0.38, P = 0.10, Figure 3B), AH/CD ratio (R = 0.63, P = 0.003), and a negative correlation with CD (R = -0.72, P = 0.001). These results indicate that FF improves immunity, antioxidant capacity, and intestinal health and consequently enhances growth performance in Chahua chicken.
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Affiliation(s)
- Shiyu Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Huiyou Mei
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Le Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China; Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Heilongtan, Kunming 650201, People's Republic of China
| | - Limei Zhan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Yuhao Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Dexuan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Guoying Bao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Xiaoye Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China
| | - Zhenhui Cao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Heilongtan, Kunming 650201, People's Republic of China; Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Heilongtan, Kunming 650201, People's Republic of China.
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24
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Wang Y, Ma M, Dai W, Shang Q, Yu G. Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota. MICROBIOME 2024; 12:41. [PMID: 38419055 PMCID: PMC10902947 DOI: 10.1186/s40168-024-01768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
Chondroitin sulfate (CS) has widely been used as a symptomatic slow-acting drug or a dietary supplement for the treatment and prevention of osteoarthritis. However, CS could not be absorbed after oral intake due to its polyanionic nature and large molecular weight. Gut microbiota has recently been proposed to play a pivotal role in the metabolism of drugs and nutrients. Nonetheless, how CS is degraded by the human gut microbiota has not been fully characterized. In the present study, we demonstrated that each human gut microbiota was characterized with a unique capability for CS degradation. Degradation and fermentation of CS by the human gut microbiota produced significant amounts of unsaturated CS oligosaccharides (CSOSs) and short-chain fatty acids. To uncover which microbes were responsible for CS degradation, we isolated a total of 586 bacterial strains with a potential CS-degrading capability from 23 human fecal samples. Bacteroides salyersiae was a potent species for CS degradation in the human gut microbiota and produced the highest amount of CSOSs as compared to other well-recognized CS-degraders, including Bacteroides finegoldii, Bacteroides thetaiotaomicron, Bacteroides xylanisolvens, and Bacteroides ovatus. Genomic analysis suggested that B. salyersiae was armed with multiple carbohydrate-active enzymes that could potentially degrade CS into CSOSs. By using a spent medium assay, we further demonstrated that the unsaturated tetrasaccharide (udp4) produced by the primary degrader B. salyersiae could serve as a "public goods" molecule for the growth of Bacteroides stercoris, a secondary CS-degrader that was proficient at fermenting CSOSs but not CS. Taken together, our study provides insights into the metabolism of CS by the human gut microbiota, which has promising implications for the development of medical and nutritional therapies for osteoarthritis. Video Abstract.
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Affiliation(s)
- Yamin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Mingfeng Ma
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wei Dai
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qingsen Shang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China.
- Qingdao Marine Biomedical Research Institute, Qingdao, 266071, China.
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China.
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25
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Yu L, Xiao M, Tian F, Chen W, Zhai Q. Glycan utilization properties govern the cross-feeding network in gut microbiota: A focus on Bifidobacteria. Sci Bull (Beijing) 2024; 69:299-302. [PMID: 38129235 DOI: 10.1016/j.scib.2023.11.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Meifang Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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26
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Bedani R, Cucick ACC, Albuquerque MACD, LeBlanc JG, Saad SMI. B-Group Vitamins as Potential Prebiotic Candidates: Their Effects on the Human Gut Microbiome. J Nutr 2024; 154:341-353. [PMID: 38176457 DOI: 10.1016/j.tjnut.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024] Open
Abstract
In recent years, thousands of studies have demonstrated the importance of the gut microbiome for human health and its relationship with certain diseases. The search for new gut microbiome modulators has thus become an objective to beneficially alter the gut microbiome composition and/or metabolic activity, which may modify intestinal physiology. Growing evidence has shown that B-group vitamins might be considered as potential candidates as gut microbiome modulators. However, the relationship between the B-group vitamins and the gut microbiome remains largely unexplored. Studies have suggested that non-absorbed B-group vitamins administered orally can reach the distal intestine or even the colon where these vitamins may have potential health benefits for the host. Clinical trials supporting this effect are still limited. In this review, we discuss evidence regarding the modulatory effects of B-group vitamins on the gut microbiome with a focus on their potential role as prebiotic candidates.
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Affiliation(s)
- Raquel Bedani
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.
| | - Ana Clara Candelaria Cucick
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marcela Albuquerque Cavalcanti de Albuquerque
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Susana Marta Isay Saad
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil; Food Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
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27
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Miyakoshi M. Multilayered regulation of amino acid metabolism in Escherichia coli. Curr Opin Microbiol 2024; 77:102406. [PMID: 38061078 DOI: 10.1016/j.mib.2023.102406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024]
Abstract
Amino acid metabolism in Escherichia coli has long been studied and has established the basis for regulatory mechanisms at the transcriptional, posttranscriptional, and posttranslational levels. In addition to the classical signal transduction cascade involving posttranslational modifications (PTMs), novel PTMs in the two primary nitrogen assimilation pathways have recently been uncovered. The regulon of the master transcriptional regulator NtrC is further expanded by a small RNA derived from the 3´UTR of glutamine synthetase mRNA, which coordinates central carbon and nitrogen metabolism. Furthermore, recent advances in sequencing technologies have revealed the global regulatory networks of transcriptional and posttranscriptional regulators, Lrp and GcvB. This review provides an update of the multilayered and interconnected regulatory networks governing amino acid metabolism in E. coli.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 305-8575 Ibaraki, Japan.
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28
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Roth-Walter F, Berni Canani R, O'Mahony L, Peroni D, Sokolowska M, Vassilopoulou E, Venter C. Nutrition in chronic inflammatory conditions: Bypassing the mucosal block for micronutrients. Allergy 2024; 79:353-383. [PMID: 38084827 DOI: 10.1111/all.15972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024]
Abstract
Nutritional Immunity is one of the most ancient innate immune responses, during which the body can restrict nutrients availability to pathogens and restricts their uptake by the gut mucosa (mucosal block). Though this can be a beneficial strategy during infection, it also is associated with non-communicable diseases-where the pathogen is missing; leading to increased morbidity and mortality as micronutritional uptake and distribution in the body is hindered. Here, we discuss the acute immune response in respect to nutrients, the opposing nutritional demands of regulatory and inflammatory cells and particularly focus on some nutrients linked with inflammation such as iron, vitamins A, Bs, C, and other antioxidants. We propose that while the absorption of certain micronutrients is hindered during inflammation, the dietary lymph path remains available. As such, several clinical trials investigated the role of the lymphatic system during protein absorption, following a ketogenic diet and an increased intake of antioxidants, vitamins, and minerals, in reducing inflammation and ameliorating disease.
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Affiliation(s)
- Franziska Roth-Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Roberto Berni Canani
- Department of Translational Medical Science and ImmunoNutritionLab at CEINGE-Advanced Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Liam O'Mahony
- Department of Medicine, School of Microbiology, APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Diego Peroni
- Section of Paediatrics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Emilia Vassilopoulou
- Pediatric Area, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
- Department of Nutritional Sciences and Dietetics, International Hellenic University, Thessaloniki, Greece
| | - Carina Venter
- Children's Hospital Colorado, University of Colorado, Aurora, Colorado, USA
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29
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Michellod D, Liebeke M. Host-microbe metabolic dialogue. Nat Microbiol 2024; 9:318-319. [PMID: 38316925 DOI: 10.1038/s41564-023-01592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Affiliation(s)
- Dolma Michellod
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Liebeke
- Max-Planck Institute for Marine Microbiology, Bremen, Germany.
- Department for Metabolomics, Institute for Human Nutrition and Food Science, University of Kiel, Kiel, Germany.
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30
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Lee NR, Kwon TJ, Chung EC, Bae J, Soung SH, Tak HJ, Choi JY, Lee YE, Won Hwang N, Lee JS, Shin KJ, Lee CH, Kim K, Kim S. Combination of Lacticaseibacillus paracasei BEPC22 and Lactiplantibacillus plantarum BELP53 attenuates fat accumulation and alters the metabolome and gut microbiota in mice with high-fat diet-induced obesity. Food Funct 2024; 15:647-662. [PMID: 38099933 DOI: 10.1039/d3fo03557c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This study evaluated the effects of formulations with Lacticaseibacillus paracasei BEPC22 and Lactiplantibacillus plantarum BELP53 on adiposity, the alteration of microbiota, and the metabolome in high-fat diet-fed mice. The strains were selected based on their fat and glucose absorption inhibitory activities and potential metabolic interactions. The optimal ratio of the two strains in the probiotic formulation was determined based on their adipocyte differentiation inhibitory activities. Treatment of formulations with BEPC22 and BELP53 for 10 weeks decreased body weight gain at 6 weeks; it also decreased the food efficiency ratio, white adipose tissue volume, and adipocyte size. Moreover, it decreased the expression of the lipogenic gene Ppar-γ in the liver, while significantly increasing the expression of the fat oxidation gene Ppar-α in the white adipose tissue. Notably, treatment with a combination of the two strains significantly reduced the plasma levels of the obesity hormone leptin and altered the microbiota and metabolome. The omics data also indicated the alteration of anti-obesity microbes and metabolites such as Akkermansia and indolelactic acid, respectively. These findings suggest that treatment with a combination of BEPC22 and BELP53 exerts synergistic beneficial effects against obesity.
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Affiliation(s)
- Na-Rae Lee
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae-Jun Kwon
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea.
| | - Eui-Chun Chung
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
| | - Jaewoong Bae
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
| | - Song-Hui Soung
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05209, Republic of Korea
| | - Hyun-Ji Tak
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05209, Republic of Korea
| | - Jun-Young Choi
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea.
| | - Young-Eun Lee
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Nak Won Hwang
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
| | - Jong Seo Lee
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
| | - Kum-Joo Shin
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
| | - Choong Hwan Lee
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul 05029, Republic of Korea
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05209, Republic of Korea
| | - KilSoo Kim
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea.
- College of Veterinary Medicine, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu 41566, Korea
| | - Seokjin Kim
- R&D Center, Hecto Healthcare Co., Ltd, Seoul 06142, Republic of Korea.
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31
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Yang Y, Ke Y, Liu X, Zhang Z, Zhang R, Tian F, Zhi L, Zhao G, Lv B, Hua S, Wu H. Navigating the B vitamins: Dietary diversity, microbial synthesis, and human health. Cell Host Microbe 2024; 32:12-18. [PMID: 38211561 DOI: 10.1016/j.chom.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
B vitamins are intricately involved in various physiological processes vital for health. Their significance is complicated by the heterogeneous landscape of B vitamin distribution in diets and the contributions of the gut microbiota. Here, we delve into the impact of these factors on B vitamins and introduce strategies, with a focus on microbiota-based therapeutic options, to enhance their availability for improved well-being. Additionally, we provide an ecological and evolutionary perspective on the importance of B vitamins to human-microbiota interactions. In the dynamic realms of nutrition and microbiome science, these essential micronutrients continue to play a fundamental role in our understanding of disease development.
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Affiliation(s)
- Yudie Yang
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Yize Ke
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Xinyan Liu
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Zhidong Zhang
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Rongji Zhang
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Fang Tian
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Luqian Zhi
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Bomin Lv
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China.
| | - Sha Hua
- Department of Cardiovascular Medicine, Heart Failure Center, Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Hao Wu
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
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32
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Plata G, Krishnamurthy M, Herron L, Dixit P. Designing host-associated microbiomes using the consumer/resource model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.28.538625. [PMID: 37162888 PMCID: PMC10168316 DOI: 10.1101/2023.04.28.538625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A key step towards rational microbiome engineering is the in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously model compositions of host-associated microbiomes and host phenotypes. To that end, we present a machine learning model based on the consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (latent variables) while species' resource preferences remain conserved. Variation in the same latent variables is used to model phenotypic variation across hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address two salient questions in microbiome design: (1) which host phenotypes maximally constrain the composition of the host-associated microbiome? and (2) what are plausible microbiome compositions corresponding to user-specified host phenotypes? Thus, our model aids the design and analysis of microbial communities associated with host phenotypes of interest.
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Pei TT, Luo H, Wang Y, Li H, Wang XY, Zhang YQ, An Y, Wu LL, Ma J, Liang X, Yan A, Yang L, Chen C, Dong T. Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa. THE ISME JOURNAL 2024; 18:wrad025. [PMID: 38365255 PMCID: PMC10837833 DOI: 10.1093/ismejo/wrad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Filamentous prophages are widespread among bacteria and play crucial functions in virulence, antibiotic resistance, and biofilm structures. The filamentous Pf4 particles, extruded by an important pathogen Pseudomonas aeruginosa, can protect producing cells from adverse conditions. Contrary to the conventional belief that the Pf4-encoding cells resist reinfection, we herein report that the Pf4 prophage is reciprocally and commonly exchanged within P. aeruginosa colonies, which can repair defective Pf4 within the community. By labeling the Pf4 locus with antibiotic resistance and fluorescence markers, we demonstrate that the Pf4 locus is frequently exchanged within colony biofilms, in artificial sputum media, and in infected mouse lungs. We further show that Pf4 trafficking is a rapid process and capable of rescuing Pf4-defective mutants. The Pf4 phage is highly adaptable and can package additional DNA doubling its genome size. We also report that two clinical P. aeruginosa isolates are susceptible to the Pf4-mediated exchange, and the Pf5 prophage can be exchanged between cells as well. These findings suggest that the genetic exchanging interactions by filamentous prophages may facilitate defect rescue and the sharing of prophage-dependent benefits and costs within the P. aeruginosa community.
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Affiliation(s)
- Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Han Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Wang
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing-Yu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi-Qiu Zhang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying An
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junhua Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoye Liang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Changbin Chen
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Zeng M, Oh JH, van Pijkeren JP, Pan X. Selective utilization of gluco-oligosaccharides by lactobacilli: A mechanism study revealing the impact of glycosidic linkages and degree of polymerization on their utilization. J Food Sci 2024; 89:523-539. [PMID: 38010727 DOI: 10.1111/1750-3841.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023]
Abstract
Gluco-oligosaccharides (GlcOS) are potential prebiotics that positively modulate beneficial gut commensals like lactobacilli. For the rational design of GlcOS as prebiotics or combined with lactobacilli as synbiotics, it is important to establish the structure requirements of GlcOS and specificity toward lactobacilli. Herein, the utilization of 10 GlcOS with varied degrees of polymerization (DP) and glycosidic linkages by 7 lactobacilli strains (Levilactobacillus brevis ATCC 8287, Limosilactobacillus reuteri ATCC PTA 6475, Lacticaseibacillus rhamnosus ATCC 53103, Lentilactobacillus buchneri ATCC 4005, Limosilactobacillus fermentum FUA 3589, Lactiplantibacillus plantarum WCFS1, and Lactobacillus gasseri ATCC 33323) was studied. L. brevis ATCC 8287 was the only strain that grew on α/β-(1→4/6) linked disaccharides, whereas other strains showed diverse patterns, dependent on the availability of genes encoding sugar transporters and catabolic enzymes. The effect of DP on GlcOS utilization was strain dependent. β-(1→4) Linked cello-oligosaccharides (COS) supported the growth of L. brevis ATCC 8287 and L. plantarum WCFS1, and shorter COS (DP 2-3) were preferentially utilized over longer COS (DP 4-7) (consumption ≥90% vs. 40%-60%). α-(1→4) Linked maltotriose and maltodextrin (DP 2-11) were effectively utilized by L. brevis ATCC 8287, L. reuteri ATCC 6475, and L. plantarum WCFS1, but not L. fermentum FUA 3589. Growth of L. brevis ATCC 8287 on branched isomalto-oligosaccharides (DP 2-6) suggested preferential consumption of DP 2-3, but no preference between α-(1→6) and α-(1→4) linkages. The knowledge of the structure-specific GlcOS utilization by different lactobacilli from this study helps the structural rationale of GlcOS for prebiotic development.
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Affiliation(s)
- Meijun Zeng
- Department of Biological Systems Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Xuejun Pan
- Department of Biological Systems Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Paudel D, Nair DVT, Tian S, Hao F, Goand UK, Joseph G, Prodes E, Chai Z, Robert CE, Chassaing B, Patterson AD, Singh V. Dietary fiber guar gum-induced shift in gut microbiota metabolism and intestinal immune activity enhances susceptibility to colonic inflammation. Gut Microbes 2024; 16:2341457. [PMID: 38630030 PMCID: PMC11028019 DOI: 10.1080/19490976.2024.2341457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
With an increasing interest in dietary fibers (DFs) to promote intestinal health and the growth of beneficial gut bacteria, there is a continued rise in the incorporation of refined DFs in processed foods. It is still unclear how refined fibers, such as guar gum, affect the gut microbiota activity and pathogenesis of inflammatory bowel disease (IBD). Our study elucidated the effect and underlying mechanisms of guar gum, a fermentable DF (FDF) commonly present in a wide range of processed foods, on colitis development. We report that guar gum containing diet (GuD) increased the susceptibility to colonic inflammation. Specifically, GuD-fed group exhibited severe colitis upon dextran sulfate sodium (DSS) administration, as evidenced by reduced body weight, diarrhea, rectal bleeding, and shortening of colon length compared to cellulose-fed control mice. Elevated levels of pro-inflammatory markers in both serum [serum amyloid A (SAA), lipocalin 2 (Lcn2)] and colon (Lcn2) and extensive disruption of colonic architecture further affirmed that GuD-fed group exhibited more severe colitis than control group upon DSS intervention. Amelioration of colitis in GuD-fed group pre-treated with antibiotics suggest a vital role of intestinal microbiota in GuD-mediated exacerbation of intestinal inflammation. Gut microbiota composition and metabolite analysis in fecal and cecal contents, respectively, revealed that guar gum primarily enriches Actinobacteriota, specifically Bifidobacterium. Guar gum also altered multiple genera belonging to phyla Bacteroidota and Firmicutes. Such shift in gut microbiota composition favored luminal accumulation of intermediary metabolites succinate and lactate in the GuD-fed mice. Colonic IL-18 and tight junction markers were also decreased in the GuD-fed group. Importantly, GuD-fed mice pre-treated with recombinant IL-18 displayed attenuated colitis. Collectively, unfavorable changes in gut microbiota activity leading to luminal accumulation of lactate and succinate, reduced colonic IL-18, and compromised gut barrier function following guar gum feeding contributed to increased colitis susceptibility.
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Affiliation(s)
- Devendra Paudel
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Divek V. T. Nair
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Sangshan Tian
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Umesh K. Goand
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Grace Joseph
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eleni Prodes
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhi Chai
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chloé E.M. Robert
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université Paris Cité, Paris, France
- INSERM U1306, Microbiome-Host Interaction group, Institut Pasteur, Université Paris Cité, Paris, France
| | - Benoit Chassaing
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université Paris Cité, Paris, France
- INSERM U1306, Microbiome-Host Interaction group, Institut Pasteur, Université Paris Cité, Paris, France
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Vishal Singh
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
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Liu K, Yang P, Zhang X, Zhang D, Wu L, Zhang L, Zhang H, Li G, Li R, Rong L. Metabolic cross-feeding enhances branched-chain aldehydes production in a synthetic community of fermented sausages. Int J Food Microbiol 2023; 407:110373. [PMID: 37696140 DOI: 10.1016/j.ijfoodmicro.2023.110373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/30/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Microbial interactions play an important role in regulating the metabolic function of fermented food communities, especially the production of key flavor compounds. However, little is known about specific molecular mechanisms that regulate the production of key flavor compounds through microbial interactions. Here, we designed a synthetic consortium containing Debaryomyces hansenii D1, Staphylococcus xylosus S1, and Pediococcus pentosaceus PP1 to explore the mechanism of the microbial interactions underlying the branched-chain aldehydes production. In this consortium, firstly, D. hansenii secreted amino acids that promoted the growth of P. pentosaceus and S. xylosus. Specifically, D. hansenii D1 secreted alanine, aspartate, glutamate, glutamine, glycine, phenylalanine, serine, and threonine, which were the primary nutrients for bacterial growth. P. pentosaceus PP1 utilized all these eight amino acids through cross-feeding, whereas S. xylosus S1 did not utilize aspartate and serine. Furthermore, D. hansenii D1 promoted the production of branched-chain aldehydes from S. xylosus and P. pentosaceus through cross-feeding of α-keto acids (intermediate metabolites). Thus, the accumulation of 2-methyl-butanal was promoted in all co-culture. Overall, this work revealed the mechanism by which D. hansenii and bacteria cross-feed to produce branched-chain aldehydes in fermented sausages.
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Affiliation(s)
- Kaihao Liu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Peng Yang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Xudong Zhang
- Comprehensive Technology Service Center of Jinzhou Customs, Jinzhou, Liaoning 121013, China
| | - Di Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Liu Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Lan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Huan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Ruren Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
| | - Liangyan Rong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
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37
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Malwe AS, Sharma VK. Application of artificial intelligence approaches to predict the metabolism of xenobiotic molecules by human gut microbiome. Front Microbiol 2023; 14:1254073. [PMID: 38116528 PMCID: PMC10728657 DOI: 10.3389/fmicb.2023.1254073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 12/21/2023] Open
Abstract
A highly complex, diverse, and dense community of more than 1,000 different gut bacterial species constitutes the human gut microbiome that harbours vast metabolic capabilities encoded by more than 300,000 bacterial enzymes to metabolise complex polysaccharides, orally administered drugs/xenobiotics, nutraceuticals, or prebiotics. One of the implications of gut microbiome mediated biotransformation is the metabolism of xenobiotics such as medicinal drugs, which lead to alteration in their pharmacological properties, loss of drug efficacy, bioavailability, may generate toxic byproducts and sometimes also help in conversion of a prodrug into its active metabolite. Given the diversity of gut microbiome and the complex interplay of the metabolic enzymes and their diverse substrates, the traditional experimental methods have limited ability to identify the gut bacterial species involved in such biotransformation, and to study the bacterial species-metabolite interactions in gut. In this scenario, computational approaches such as machine learning-based tools presents unprecedented opportunities and ability to predict the gut bacteria and enzymes that can potentially metabolise a candidate drug. Here, we have reviewed the need to identify the gut microbiome-based metabolism of xenobiotics and have provided comprehensive information on the available methods, tools, and databases to address it along with their scope and limitations.
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Affiliation(s)
| | - Vineet K. Sharma
- MetaBioSys Lab, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Huang Q, Zhang H, Zhang L, Xu B. Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence. Crit Rev Food Sci Nutr 2023:1-16. [PMID: 37905560 DOI: 10.1080/10408398.2023.2272770] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.
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Affiliation(s)
- Qianli Huang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Huijuan Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Zhang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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Kim HW, Kim NK, Phillips APR, Parker DA, Liu P, Whitaker RJ, Rao CV, Mackie RI. Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Front Microbiol 2023; 14:1232587. [PMID: 37822751 PMCID: PMC10562698 DOI: 10.3389/fmicb.2023.1232587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Alicyclobacillus has been isolated from extreme environments such as hot springs, volcanoes, as well as pasteurized acidic beverages, because it can tolerate extreme temperatures and acidity. In our previous study, Alicyclobacillus was isolated during the enrichment of methane oxidizing bacteria from Yellowstone Hot Spring samples. Methods Physiological characterization and genomic exploration of two new Alicyclobacillus isolates, AL01A and AL05G, are the main focus of this study to identify their potential relationships with a thermoacidophilic methanotroph (Methylacidiphilum) isolated from the same hot spring sediments. Results and discussion In the present study, both Alicyclobacillus isolates showed optimal growth at pH 3.5 and 55°C, and contain ω-alicyclic fatty acids as a major lipid (ca. 60%) in the bacterial membrane. Genomic analysis of these strains revealed specific genes and pathways that the methanotroph genome does not have in the intermediary carbon metabolism pathway such as serC (phosphoserine aminotransferase), comA (phosphosulfolactate synthase), and DAK (glycerone kinase). Both Alicyclobacillus strains were also found to contain transporter systems for extracellular sulfate (ABC transporter), suggesting that they could play an important role in sulfur metabolism in this extreme environment. Genomic analysis of vitamin metabolism revealed Alicyclobacillus and Methylacidiphilum are able to complement each other's nutritional deficiencies, resulting in a mutually beneficial relationship, especially in vitamin B1(thiamin), B3 (niacin), and B7 (biotin) metabolism. These findings provide insights into the role of Alicyclobacillus isolates in geothermal environments and their unique metabolic adaptations to these environments.
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Affiliation(s)
- Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Na Kyung Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Alex P. R. Phillips
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Ping Liu
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Rachel J. Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Roderick I. Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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Jensen BAH, Heyndrickx M, Jonkers D, Mackie A, Millet S, Naghibi M, Pærregaard SI, Pot B, Saulnier D, Sina C, Sterkman LGW, Van den Abbeele P, Venlet NV, Zoetendal EG, Ouwehand AC. Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration. Cell Rep Med 2023; 4:101190. [PMID: 37683651 PMCID: PMC10518632 DOI: 10.1016/j.xcrm.2023.101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Research on gut microbiota has generally focused on fecal samples, representing luminal content of the large intestine. However, nutrient uptake is restricted to the small intestine. Abundant immune cell populations at this anatomical site combined with diminished mucus secretion and looser junctions (partly to allow for more efficient fluid and nutrient absorption) also results in intimate host-microbe interactions despite more rapid transit. It is thus crucial to dissect key differences in both ecology and physiology between small and large intestine to better leverage the immense potential of human gut microbiota imprinting, including probiotic engraftment at biological sensible niches. Here, we provide a detailed review unfolding how the physiological and anatomical differences between the small and large intestine affect gut microbiota composition, function, and plasticity. This information is key to understanding how gut microbiota manipulation, including probiotic administration, may strain-dependently transform host-microbe interactions at defined locations.
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Affiliation(s)
| | - Marc Heyndrickx
- Flanders Research Institute of Agriculture, Fisheries and Food, Belgium & Ghent University, Department Pathobiology, Pharmacology and Zoological Medicine, B-9090 Melle, 9820 Merelbeke, Belgium
| | - Daisy Jonkers
- Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht 6229 ER, the Netherlands
| | - Alan Mackie
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Sam Millet
- Flanders Research Institute of Agriculture, Fisheries and Food, 9090 Melle, Belgium
| | | | - Simone Isling Pærregaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bruno Pot
- Yakult Europe BV, 1332 Almere, the Netherlands
| | | | - Christian Sina
- Institute of Nutritional Medicine, University Medical Center of Schleswig-Holstein & University of Lübeck, 23538 Lübeck, Germany
| | | | | | - Naomi Vita Venlet
- International Life Science Institute, European Branch, Brussels, Belgium.
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
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Yan XY, Yao JP, Li YQ, Xiao XJ, Yang WQ, Chen SJ, Tang TC, Yang YQ, Qu L, Hou YJ, Chen M, Li Y. Effects of acupuncture on gut microbiota and short-chain fatty acids in patients with functional constipation: a randomized placebo-controlled trial. Front Pharmacol 2023; 14:1223742. [PMID: 37719865 PMCID: PMC10502303 DOI: 10.3389/fphar.2023.1223742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023] Open
Abstract
Objective: To comprehensively evaluate the effect of acupuncture on gut microbiota, identify specific microbes closely related to the clinical efficacy of acupuncture, and explored the role of short-chain fatty acids (SCFAs). Methods: A randomized placebo-controlled trial was conducted with 80 FC patients and 28 healthy controls (HCs). FC patients randomly received 16 acupuncture (n = 40) or sham acupuncture (n = 40) sessions over 4 weeks; HCs received no treatment. The change in the proportion of patients with mean weekly complete spontaneous bowel movements (CSBMs) was considered as the primary outcome measure. Moreover, the composition and the predictive metabolic function of the gut microbiota from feceal samples were analyzed by 16S rRNA gene sequencing, while feceal SCFAs were identified via gas chromatography-mass spectrometry (GC-MS). Results: Compared to sham acupuncture, acupuncture significantly increased the proportion of CSBM responders, and improved spontaneous bowel movements (SBMs), straining, stool consistency, and quality of life. Moreover, Sequencing of 16S rRNA genes revealed that acupuncture improved β-diversity and restored the composition of gut microbiota. Specifically, the abundance of beneficial bacteria such as g_Lactobacillus increased while that of pathogenic bacteria such as g_Pseudomonas decreased after acupuncture, which were significantly correlated with alleviated symptoms. Moreover, ten microbes including g_Coprobacter, g_Lactobacillus, and g_Eubacterium_coprostanoligenes_group might be considered acupuncture-specific microbes, and formed a stable interaction network. Additionally, GC-MS analysis indicated that acupuncture increased the content of butyrate acid in the gut, which was positively correlated with an increase in defecation frequency and a decrease in acupuncture-related pathogens. Finally, acupuncture specific-microbes including g_Coprobacter, g_Lactobacillus, g_Pseudomonas, g_Eubacterium_coprostanoligenes_group, g_Erysipelotrichaceae_UCG.003, g_Prevotellaceae_UCG.001, and g_Rolstonia could accurately predict the clinical efficacy of acupuncture (AUC = 0.918). Conclusion: Acupuncture could effectively improve clinical symptoms in FC patients, and was associated with gut microbiota reshaping and increased butyrate acid levels. Moreover, key microbial genera such as g_Coprobacter and g_Lactobacillus was predictive of acupuncture efficacy in treating FC. Future studies are required to validate the causal relationship between key microbial genera and acupuncture clinical efficacy, and should explore further metabolic pathways for designing personalized treatment strategies. Clinical Trial Registration: http://www.chictr.org.cn, Identifier: ChiCTR2100048831.
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Affiliation(s)
- Xiang-Yun Yan
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jun-Peng Yao
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan-Qiu Li
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xian-Jun Xiao
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wan-Qing Yang
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Si-Jue Chen
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tai-Chun Tang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu-Qing Yang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liu Qu
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu-Jun Hou
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying Li
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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