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Shang J, Li Y, Zhang W, Ma X, Niu L, Wang L, Zheng J. Hysteretic and asynchronous regime shifts of bacterial and micro-eukaryotic communities driven by nutrient loading. WATER RESEARCH 2024; 261:122045. [PMID: 38972236 DOI: 10.1016/j.watres.2024.122045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/14/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
Nutrient pollution is pervasive in many urban rivers, while restoration measures that reduce nutrient loading but fail to improve biological communities often lack effectiveness due to the indispensable role of biota, especially multi-taxa, in enhancing ecosystem stability and function. The investigation of the response patterns of multi-taxa to the nutrient loading in urban rivers is important for the recovery of biota structure and thus ecosystem function. However, little is known about the response patterns of multi-taxa and their impact on ecosystem structure and function in urban rivers. Here, the study, from the perspective of alternative stable states theory, showed the hysteretic response of both bacterial and micro-eukaryotic communities to nutrient loading based on the field investigation and environmental DNA metabarcoding. Bistability was shown to exist in both bacterial and micro-eukaryotic communities, demonstrating that the response of microbiota to nutrient loading was a regime shifts with hysteresis. Potential analysis then indicated that the increased nutrient loading drove regime shifts in the bacterial community and the micro-eukaryotic community towards a state dominated by anaerobic bacteria and benthic Bacillariophyta, respectively. High nutrient loading was found to reduce the relative abundance of metazoan, but increase that of eukaryotic algae, which made the trophic pyramid top-lighter and bottom-heavier, probably exacerbating the degradation of ecosystem function. It should be noted that, in response to the reduced nutrient loading, the recovery threshold of micro-eukaryotic communities (nutrient loading = ∼0.5) was lower than that of bacterial communities (nutrient loading = ∼1.2), demonstrating longer hysteresis of micro-eukaryotic communities. In addition, the markedly positive correlation between the status of microbial communities and N-related enzyme activities suggested the recovery of microbial communities probably will benefit the improvement of N-cycling functionality. The obtained results provide a deep insight into the collapse and recovery trajectories of multi-trophic microbiota to the nutrient loading gradient and their impact on the N transformation potential, therefore benefiting the restoration and management of urban rivers.
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Affiliation(s)
- Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Xin Ma
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Jinhai Zheng
- College of Harbour, Coastal and Offshore Engineering, Hohai University, Nanjing 210098, PR China
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2
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Firrman J, Friedman ES, Hecht A, Strange WC, Narrowe AB, Mahalak K, Wu GD, Liu L. Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota in vitro. mBio 2024; 15:e0094324. [PMID: 38727244 PMCID: PMC11237543 DOI: 10.1128/mbio.00943-24] [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: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 06/13/2024] Open
Abstract
Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota in vitro using human small intestinal ileostomy effluent as the inocula, we show here that the infusion of physiologically relevant levels of oxygen, normally found in the proximal small intestine, reduced deconjugation of primary bile acids, in part, through the expansion of bacterial taxa known to have a low abundance of BSHs. Further recapitulating the small intestinal bile acid composition of the small intestine, limited conversion of primary into secondary bile acids was observed. Remarkably, these effects were preserved among four separate communities, each inoculated with a different small intestinal microbiota, despite a high degree of taxonomic variability under both anoxic and aerobic conditions. In total, these results provide evidence for a previously unrecognized role that the oxygenated environment of the small intestine plays in the maintenance of normal digestive physiology. IMPORTANCE Conjugated primary bile acids are produced by the liver and exist at high concentrations in the proximal small intestine, where they are critical for proper digestion. Deconjugation of these bile acids with subsequent transformation via dehydroxylation into secondary bile acids is regulated by the colonic gut microbiota and reduces their digestive function. Using an in vitro platform modeling the small intestinal microbiota, we analyzed the ability of this community to transform primary bile acids and studied the effect of physiological levels of oxygen normally found in the proximal small intestine (5%) on this metabolic process. We found that oxygenation of the small intestinal microbiota inhibited the deconjugation of primary bile acids in vitro. These findings suggest that luminal oxygen levels normally found in the small intestine may maintain the optimal role of bile acids in the digestive process by regulating bile acid conversion by the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron Hecht
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - William C. Strange
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, USA
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3
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Wang J, Appidi MR, Burdick LH, Abraham PE, Hettich RL, Pelletier DA, Doktycz MJ. Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition. mSystems 2024; 9:e0000624. [PMID: 38470038 PMCID: PMC11019790 DOI: 10.1128/msystems.00006-24] [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: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/13/2024] Open
Abstract
Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.
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Affiliation(s)
- Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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4
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Ng E, Tay JRH, Mattheos N, Bostanci N, Belibasakis GN, Seneviratne CJ. A Mapping Review of the Pathogenesis of Peri-Implantitis: The Biofilm-Mediated Inflammation and Bone Dysregulation (BIND) Hypothesis. Cells 2024; 13:315. [PMID: 38391928 PMCID: PMC10886485 DOI: 10.3390/cells13040315] [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: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
This mapping review highlights the need for a new paradigm in the understanding of peri-implantitis pathogenesis. The biofilm-mediated inflammation and bone dysregulation (BIND) hypothesis is proposed, focusing on the relationship between biofilm, inflammation, and bone biology. The close interactions between immune and bone cells are discussed, with multiple stable states likely existing between clinically observable definitions of peri-implant health and peri-implantitis. The framework presented aims to explain the transition from health to disease as a staged and incremental process, where multiple factors contribute to distinct steps towards a tipping point where disease is manifested clinically. These steps might be reached in different ways in different patients and may constitute highly individualised paths. Notably, factors affecting the underlying biology are identified in the pathogenesis of peri-implantitis, highlighting that disruptions to the host-microbe homeostasis at the implant-mucosa interface may not be the sole factor. An improved understanding of disease pathogenesis will allow for intervention on multiple levels and a personalised treatment approach. Further research areas are identified, such as the use of novel biomarkers to detect changes in macrophage polarisation and activation status, and bone turnover.
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Affiliation(s)
- Ethan Ng
- Department of Restorative Dentistry, National Dental Centre Singapore, Singapore 168938, Singapore;
| | - John Rong Hao Tay
- Department of Restorative Dentistry, National Dental Centre Singapore, Singapore 168938, Singapore;
| | - Nikos Mattheos
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand;
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, 14152 Stockholm, Sweden; (N.B.); (G.N.B.)
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, 14152 Stockholm, Sweden; (N.B.); (G.N.B.)
| | - Georgios N. Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institute, 14152 Stockholm, Sweden; (N.B.); (G.N.B.)
| | - Chaminda Jayampath Seneviratne
- School of Dentistry, The University of Queensland, Brisbane, QLD 4006, Australia
- School of Dentistry, Center for Oral-Facial Regeneration, Rehabilitation and Reconstruction (COR3), The University of Queensland, Brisbane, QLD 4072, Australia
- National Dental Research Institute Singapore, National Dental Centre Singapore, Singapore 168938, Singapore
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5
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Choi W, Mangal U, Park JY, Kim JY, Jun T, Jung JW, Choi M, Jung S, Lee M, Na JY, Ryu DY, Kim JM, Kwon JS, Koh WG, Lee S, Hwang PTJ, Lee KJ, Jung UW, Cha JK, Choi SH, Hong J. Occlusive membranes for guided regeneration of inflamed tissue defects. Nat Commun 2023; 14:7687. [PMID: 38001080 PMCID: PMC10673922 DOI: 10.1038/s41467-023-43428-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Guided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration therapy period. We apply the symbiotically integrating occlusive membrane to treat inflammatory-challenged cases in vivo, namely, the open and closed healing of canine premolars with severe periodontitis. We find that the membrane promotes symbiosis, prevents negative inflammatory responses, and improves cellular integration. Finally, we show that guided bone regeneration therapy with the symbiotically integrating occlusive membrane achieves fast healing of gingival soft tissue and alveolar bone.
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Affiliation(s)
- Woojin Choi
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Utkarsh Mangal
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Jin-Young Park
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Ji-Yeong Kim
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Taesuk Jun
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Ju Won Jung
- Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Moonhyun Choi
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sungwon Jung
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Milae Lee
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Ji-Yeong Na
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Du Yeol Ryu
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jin Man Kim
- Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Sung Kwon
- Department and Research Institute of Dental Biomaterials and Bioengineering, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Won-Gun Koh
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sangmin Lee
- School of Mechanical Engineering, Chung-ang University, 84, Heukserok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Patrick T J Hwang
- Cardiovascular Institute, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, 201 Mullica Hill Rd., Glassboro, NJ, 08028, USA
| | - Kee-Joon Lee
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Ui-Won Jung
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Jae-Kook Cha
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea.
| | - Sung-Hwan Choi
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea.
| | - Jinkee Hong
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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6
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Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [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: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
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Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
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7
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Poceviciute R, Bogatyrev SR, Romano AE, Dilmore AH, Mondragón-Palomino O, Takko H, Pradhan O, Ismagilov RF. Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa. NPJ Biofilms Microbiomes 2023; 9:64. [PMID: 37679412 PMCID: PMC10485000 DOI: 10.1038/s41522-023-00423-2] [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: 08/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Because the small intestine (SI) epithelium lacks a thick protective mucus layer, microbes that colonize the thin SI mucosa may exert a substantial effect on the host. For example, bacterial colonization of the human SI may contribute to environmental enteropathy dysfunction (EED) in malnourished children. Thus far, potential bacterial colonization of the mucosal surface of the SI has only been documented in disease states, suggesting mucosal colonization is rare, likely requiring multiple perturbations. Furthermore, conclusive proof of bacterial colonization of the SI mucosal surface is challenging, and the three-dimensional (3D) spatial structure of mucosal colonies remains unknown. Here, we tested whether we could induce dense bacterial association with jejunum mucosa by subjecting mice to a combination of malnutrition and oral co-gavage with a bacterial cocktail (E. coli and Bacteroides spp.) known to induce EED. To visualize these events, we optimized our previously developed whole-tissue 3D imaging tools with third-generation hybridization chain reaction (HCR v3.0) probes. Only in mice that were malnourished and gavaged with the bacterial cocktail did we detect dense bacterial clusters surrounding intestinal villi suggestive of colonization. Furthermore, in these mice we detected villus loss, which may represent one possible consequence that bacterial colonization of the SI mucosa has on the host. Our results suggest that dense bacterial colonization of jejunum mucosa is possible in the presence of multiple perturbations and that whole-tissue 3D imaging tools can enable the study of these rare events.
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Affiliation(s)
- Roberta Poceviciute
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Said R Bogatyrev
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Medically Associated Science and Technology Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anna E Romano
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Amanda H Dilmore
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Biomedical Sciences Program, University of California San Diego, San Diego, CA, USA
| | - Octavio Mondragón-Palomino
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Heli Takko
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ojas Pradhan
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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8
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Datseris G, Luiz Rossi K, Wagemakers A. Framework for global stability analysis of dynamical systems. CHAOS (WOODBURY, N.Y.) 2023; 33:073151. [PMID: 37499248 DOI: 10.1063/5.0159675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Dynamical systems that are used to model power grids, the brain, and other physical systems can exhibit coexisting stable states known as attractors. A powerful tool to understand such systems, as well as to better predict when they may "tip" from one stable state to the other, is global stability analysis. It involves identifying the initial conditions that converge to each attractor, known as the basins of attraction, measuring the relative volume of these basins in state space, and quantifying how these fractions change as a system parameter evolves. By improving existing approaches, we present a comprehensive framework that allows for global stability analysis of dynamical systems. Notably, our framework enables the analysis to be made efficiently and conveniently over a parameter range. As such, it becomes an essential tool for stability analysis of dynamical systems that goes beyond local stability analysis offered by alternative frameworks. We demonstrate the effectiveness of our approach on a variety of models, including climate, power grids, ecosystems, and more. Our framework is available as simple-to-use open-source code as part of the DynamicalSystems.jl library.
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Affiliation(s)
- George Datseris
- Department of Mathematics and Statistics, University of Exeter, North Park Road, Exeter EX4 4QF, United Kingdom
| | - Kalel Luiz Rossi
- Theoretical Physics/Complex Systems, ICBM, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Alexandre Wagemakers
- Nonlinear Dynamics, Chaos and Complex Systems Group, Departamento de Física, Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain
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9
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Mangal U, Noh K, Lee S, Cha JK, Song JS, Cha JY, Lee KJ, Kim KM, Kwon JS, Choi SH. Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies? J Periodontal Res 2023; 58:381-391. [PMID: 36641544 DOI: 10.1111/jre.13098] [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: 09/12/2022] [Revised: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Microbiome from a "healthy cohort" is used as a reference for comparison to cases and intervention. However, the studies with cohort-based clinical research have not sufficiently accounted for the multistability in oral microbial community. The screening is limited to phenotypic features with marked variations in microbial genomic markers. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention-free "healthy" cohort. METHODS We obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at 1-month (T1) and 3-month (T2) intervals for 16S ribosomal RNA gene sequencing analysis. RESULTS We observed that taxonomic profiling had a similar pattern of dominant genera, namely, Rothia, Prevotella, and Hemophilus, at all time points. Shannon diversity revealed a significant increase from T0 (p < .05). Bray Curtis dissimilarity was significant (R = -.02, p < .01) within the cohort at each time point. Community stability had negative correlation to synchrony (r = -.739; p = .009) and variance (r = -.605; p = .048) of the species. Clustering revealed marked differences in the grouping patterns between the three time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers. CONCLUSION Our observations indicate towards the presence of multistable states within the oral microbiome in an intervention-free healthy cohort. For a conclusive and meaningful long-term reference, dental clinical research should account for multistability in the personalized therapy approach to improve the identification and classification of reliable markers.
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Affiliation(s)
- Utkarsh Mangal
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kowoon Noh
- Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea.,Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Seeyoon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Kook Cha
- Department of Periodontology, Research Institute of Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea
| | - Je Seon Song
- Department of Pediatric Dentistry, Yonsei University College of Dentistry, Seoul, Korea.,Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea
| | - Jung-Yul Cha
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kee-Joon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kwang-Mahn Kim
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Sung Kwon
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Sung-Hwan Choi
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
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10
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Rios Garza D, Gonze D, Zafeiropoulos H, Liu B, Faust K. Metabolic models of human gut microbiota: Advances and challenges. Cell Syst 2023; 14:109-121. [PMID: 36796330 DOI: 10.1016/j.cels.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 02/17/2023]
Abstract
The human gut is a complex ecosystem consisting of hundreds of microbial species interacting with each other and with the human host. Mathematical models of the gut microbiome integrate our knowledge of this system and help to formulate hypotheses to explain observations. The generalized Lotka-Volterra model has been widely used for this purpose, but it does not describe interaction mechanisms and thus does not account for metabolic flexibility. Recently, models that explicitly describe gut microbial metabolite production and consumption have become popular. These models have been used to investigate the factors that shape gut microbial composition and to link specific gut microorganisms to changes in metabolite concentrations found in diseases. Here, we review how such models are built and what we have learned so far from their application to human gut microbiome data. In addition, we discuss current challenges of these models and how these can be addressed in the future.
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Affiliation(s)
- Daniel Rios Garza
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP 231, Université Libre de Bruxelles, Bvd du Triomphe, 1050 Bruxelles, Belgium
| | - Haris Zafeiropoulos
- Biology Department, University of Crete, Heraklion 700 13, Greece; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Bin Liu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Karoline Faust
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
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11
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Chen PC, Lin MS, Lin TC, Kang TW, Ruan JW. The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling. Bioinform Biol Insights 2023; 17:11779322231166229. [PMID: 37077899 PMCID: PMC10108413 DOI: 10.1177/11779322231166229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/11/2023] [Indexed: 04/21/2023] Open
Abstract
Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the Akkermansia genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of Akkermansia induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower Akkermansiaceae/Lachnospiraceae (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.
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Affiliation(s)
- Pei-Chen Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
| | - Ming-Shian Lin
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi
| | - Tien-Ching Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan
| | - Ting-Wei Kang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
| | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan
- Jhen-Wei Ruan, Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, No. 1, University Road, Tainan 701.
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12
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Cao X, Zhao D, Li C, Röttjers L, Faust K, Zhang H. Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake. MICROBIAL ECOLOGY 2022; 84:336-350. [PMID: 34585289 DOI: 10.1007/s00248-021-01878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.
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Affiliation(s)
- Xinyi Cao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Chaoran Li
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
| | - Lisa Röttjers
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
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13
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Li C, Xie H, Sun Y, Zeng Y, Tian Z, Chen X, Sanganyado E, Lin J, Yang L, Li P, Liang B, Liu W. Insights on Gut and Skin Wound Microbiome in Stranded Indo-Pacific Finless Porpoise (Neophocaena phocaenoides). Microorganisms 2022; 10:microorganisms10071295. [PMID: 35889014 PMCID: PMC9318903 DOI: 10.3390/microorganisms10071295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome is a unique marker for cetaceans’ health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (Neophocaena phocaenoides). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. Fusobacteria (67.51% ± 5.10%), Firmicutes (22.00% ± 2.60%), and Proteobacteria (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), Firmicutes (22.00% ± 2.60%), and Bacteroidetes (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera Photobacterium, Actinobacillus, Vibrio, Erysipelothrix, Tenacibaculum, and Psychrobacter, considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.
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Affiliation(s)
- Chengzhang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Huiying Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yajing Sun
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ying Zeng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ziyao Tian
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiaohan Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Edmond Sanganyado
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK;
| | - Jianqing Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liangliang Yang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ping Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Bo Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (B.L.); (W.L.)
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou 515063, China; (C.L.); (H.X.); (Y.S.); (Y.Z.); (Z.T.); (X.C.); (J.L.); (L.Y.); (P.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (B.L.); (W.L.)
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14
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Khalighi M, Sommeria-Klein G, Gonze D, Faust K, Lahti L. Quantifying the impact of ecological memory on the dynamics of interacting communities. PLoS Comput Biol 2022; 18:e1009396. [PMID: 35658019 PMCID: PMC9200327 DOI: 10.1371/journal.pcbi.1009396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 06/15/2022] [Accepted: 05/12/2022] [Indexed: 12/21/2022] Open
Abstract
Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent modeling studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can be introduced in such models using the framework of fractional calculus. We study how the dynamics of a well-characterized interaction model is affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory introduces inertia into the dynamics. This favors species coexistence under perturbation, enhances system resistance to state shifts, mitigates hysteresis, and can affect system resilience both ways depending on the time scale considered. Memory also promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Our study highlights the fundamental role of memory in communities, and provides quantitative tools to introduce it in ecological models and analyse its impact under varying conditions. An ecosystem is said to exhibit ecological memory when its future states do not only depend on its current state but also on its initial state and trajectory. Memory may arise through various mechanisms as organisms adapt to their environment, modify it, and accumulate biotic and abiotic material. It may also emerge from phenotypic heterogeneity at the population level. Despite its commonness in nature, ecological memory and its potential influence on ecosystem dynamics have been so far overlooked in many applied contexts. Here, we use modeling to investigate how memory can influence the dynamics, composition, and stability landscape of communities. We incorporate long-term memory effects into a multi-species model recently introduced to investigate alternative stable states in microbial communities. We assess the impact of memory on key aspects of model behavior and further examine our findings using a model parameterized by empirical data from the human gut microbiota. Our approach for modeling long-term memory and studying its implications has the potential to improve our understanding of microbial community dynamics and ultimately our ability to predict, manipulate, and experimentally design microbial ecosystems. It could also be applied more broadly in the study of systems composed of interacting components.
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Affiliation(s)
- Moein Khalighi
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
- * E-mail: (MK); (LL)
| | | | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences CP 231, Université Libre de Bruxelles, Brussels, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
- * E-mail: (MK); (LL)
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15
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Barlow JT, Leite G, Romano AE, Sedighi R, Chang C, Celly S, Rezaie A, Mathur R, Pimentel M, Ismagilov RF. Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome. MICROBIOME 2021; 9:214. [PMID: 34724979 PMCID: PMC8561862 DOI: 10.1186/s40168-021-01162-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/14/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine microbiota have been linked to several GI diseases, the microbiota of the human small intestine and its relation to human disease has been understudied. The small intestine is the major site for immune surveillance in the gut, and compared with the large intestine, it has greater than 100 times the surface area and a thinner and more permeable mucus layer. RESULTS Using quantitative sequencing, we evaluated total and taxon-specific absolute microbial loads from 250 duodenal-aspirate samples and 21 paired duodenum-saliva samples from participants in the REIMAGINE study. Log-transformed total microbial loads spanned 5 logs and were normally distributed. Paired saliva-duodenum samples suggested potential transmission of oral microbes to the duodenum, including organisms from the HACEK group. Several taxa, including Klebsiella, Escherichia, Enterococcus, and Clostridium, seemed to displace strict anaerobes common in the duodenum, so we refer to these taxa as disruptors. Disruptor taxa were enriched in samples with high total microbial loads and in individuals with small intestinal bacterial overgrowth (SIBO). Absolute loads of disruptors were associated with more severe GI symptoms, highlighting the value of absolute taxon quantification when studying small-intestine health and function. CONCLUSION This study provides the largest dataset of the absolute abundance of microbiota from the human duodenum to date. The results reveal a clear relationship between the oral microbiota and the duodenal microbiota and suggest an association between the absolute abundance of disruptor taxa, SIBO, and the prevalence of severe GI symptoms. Video Abstract.
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Affiliation(s)
- Jacob T. Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
| | - Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Anna E. Romano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Christine Chang
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Rustem F. Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
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16
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Qian Y, Lan F, Venturelli OS. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr Opin Microbiol 2021; 62:84-92. [PMID: 34098512 PMCID: PMC8286325 DOI: 10.1016/j.mib.2021.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
Microbial communities and their functions are shaped by complex networks of interactions among microbes and with their environment. While the critical roles microbial communities play in numerous environments have become increasingly appreciated, we have a very limited understanding of their interactions and how these interactions combine to generate community-level behaviors. This knowledge gap hinders our ability to predict community responses to perturbations and to design interventions that manipulate these communities to our benefit. Dynamic models are promising tools to address these questions. We review existing modeling techniques to construct dynamic models of microbial communities at different scales and suggest ways to leverage multiple types of models and data to facilitate our understanding and engineering of microbial communities.
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Affiliation(s)
- Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States.
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17
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Lee JA, Baugh AC, Shevalier NJ, Strand B, Stolyar S, Marx CJ. Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community. Microorganisms 2021; 9:321. [PMID: 33557371 PMCID: PMC7914493 DOI: 10.3390/microorganisms9020321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal "Model Lignocellulose" growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.
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Affiliation(s)
- Jessica A. Lee
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
| | - Alyssa C. Baugh
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Nicholas J. Shevalier
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Brandi Strand
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Sergey Stolyar
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
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18
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Thiel AL, Ragab M, Wagner AE, Divanovic S, Derer S, Sina C. Purification and Functional Characterization of the Chloroform/Methanol-Soluble Protein 3 (CM3) From Triticum aestivum in Drosophila melanogaster. Front Nutr 2021; 7:607937. [PMID: 33425975 PMCID: PMC7785803 DOI: 10.3389/fnut.2020.607937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Non-celiac wheat sensitivity (NCWS) has been proposed to be an independent disease entity that is characterized by intestinal (e.g., abdominal pain, flatulence) and extra-intestinal symptoms (e.g., headache, fatigue), which are propagated following the ingestion of wheat products. Increased activity of amylase trypsin inhibitors (ATIs) in modern wheat is suggested to be major trigger of NCWS, while underlying mechanisms still remain elusive. Here, we aimed to generate and functionally characterize the most abundant ATI in modern wheat, chloroform/methanol-soluble protein 3 (CM3), in vitro and in Drosophila melanogaster. We demonstrate that CM3 displays α-glucosidase but not α-amylase or trypsin inhibitory activity in vitro. Moreover, fruit flies fed a sucrose-containing diet together with CM3 displayed significant overgrowth of intestinal bacteria in a sucrose-dependent manner while the consumption of α-amylase and α-glucosidase inhibitors was sufficient to limit bacterial quantities in the intestine. Notably, both CM3 and acarbose-treated flies showed a reduced lifespan. However, this effect was absent in amylase inhibitor (AI) treated flies. Together, given α-glucosidase is a crucial requirement for disaccharide digestion, we suggest that inhibition of α-glucosidase by CM3 enhances disaccharide load in the distal gastrointestinal tract, thereby promoting intestinal bacteria overgrowth. However, it remains speculative if this here described former unknown function of CM3 might contribute to the development of gastrointestinal symptoms observed in NCWS patients which are very similar to symptoms of patients with small intestinal bacterial overgrowth.
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Affiliation(s)
- Anna-Lena Thiel
- Institute of Nutritional Medicine, Molecular Gastroenterology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Mohab Ragab
- Institute of Nutritional Medicine, Molecular Gastroenterology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Anika E Wagner
- Institute of Nutritional Sciences, Nutrition and Immune System, Justus-Liebig University Giessen, Giessen, Germany
| | - Senad Divanovic
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Stefanie Derer
- Institute of Nutritional Medicine, Molecular Gastroenterology, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christian Sina
- Institute of Nutritional Medicine and 1st Department of Medicine, Section of Nutritional Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
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