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Ameline C, Seixas E, Barreto HC, Frazão N, Rodrigues MV, Ventura MR, Lourenço M, Gordo I. Evolution of Escherichia coli strains under competent or compromised adaptive immunity. PLoS Pathog 2025; 21:e1012442. [PMID: 40273038 PMCID: PMC12021133 DOI: 10.1371/journal.ppat.1012442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 03/13/2025] [Indexed: 04/26/2025] Open
Abstract
Escherichia coli is a commensal of the intestine of most mammals, but also an important human pathogen. Within a healthy human its population structure is highly dynamic, where typically a dominant E. coli strain is accompanied by several low abundance satellite strains. However, the factors underlying E. coli strain dynamics and evolution within hosts are still poorly understood. Here, we colonised germ-free immune-competent (wild-type) or immune-compromised (Rag2KO) mice, with two phylogenetically distinct strains of E. coli, to determine if strain co-existence and within-strain evolution are shaped by the adaptive immune system. Irrespectively of the immune status of the mice one strain reaches a 100-fold larger abundance than the other. However, the abundance of the dominant strain is significantly higher in Rag2KO mice. Strains co-exist for thousands of generations and accumulate beneficial mutations in genes coding for different resource preferences. A higher rate of mutation accumulation in immune-compromised vs. immune-competent mice is observed and adaptative mutations specific to immune-competent mice are identified. Importantly, the presence of the adaptive immune system selects for mutations that increase stress resistance and the dynamics of such evolutionary events associates with the onset of an antibody response.
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Affiliation(s)
- Camille Ameline
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
| | - Elsa Seixas
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
| | - Hugo C. Barreto
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
- Université Paris Cité, CNRS, Inserm U1016, Institut Cochin, Paris, France
| | - Nelson Frazão
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
- Universidade Católica Portuguesa, Faculdade de Medicina, Centro de Investigação Interdisciplinar em Saúde, Lisboa, Portugal
| | - Miguel V. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - M. Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marta Lourenço
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
| | - Isabel Gordo
- GIMM - Gulbenkian Institute for Molecular Medicine, Evolutionary Biology, Lisboa, Portugal
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2
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Andreani NA, Unterweger D, Schreiber S, Baines JF. Evolutionary Medicine for Chronic Inflammatory Diseases of the Gut: More Than a Clinical Fantasy? Gastroenterology 2025; 168:439-443. [PMID: 39426489 DOI: 10.1053/j.gastro.2024.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/11/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
Affiliation(s)
- Nadia Andrea Andreani
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Daniel Unterweger
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Department of Medicine I, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - John F Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
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3
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Patange O, Breen P, Arsuffi G, Ruvkun G. Hydrogen sulfide mediates the interaction between C. elegans and Actinobacteria from its natural microbial environment. Cell Rep 2025; 44:115170. [PMID: 39786993 DOI: 10.1016/j.celrep.2024.115170] [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: 04/30/2024] [Revised: 10/16/2024] [Accepted: 12/17/2024] [Indexed: 01/12/2025] Open
Abstract
Caenorhabditis elegans proliferates poorly in the presence of abundant Actinobacteria from its natural ecology, but it is unknown why. Here, we show how perturbed levels of hydrogen sulfide modulate the growth rate of both C. elegans and Actinobacteria. From a forward genetic selection, we find C. elegans mutants with faster growth on an Actinobacteria Microbacterium species and mutant alleles of conserved cystathionine gamma-lyase (cth-2/CTH) that improve growth rate. Conversely, null alleles of cth-2 cause developmental arrest of animals grown on Actinobacteria, but not on Proteobacteria, which can be rescued by exogenous H2S. We also find mutations in a leucine-rich-repeat gene that regulates cysteine and H2S production, lrr-2/LRRC58. We place lrr-2 in the animal sulfur metabolism pathway by demonstrating its role in post-translationally regulating levels of cysteine dioxygenase (cdo-1/CDO1). Exogenously supplied H2S inhibits the growth of Actinobacteria but not Proteobacteria. Thus, we conclude that the C. elegans-Actinobacteria interaction is mediated by H2S.
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Affiliation(s)
- Om Patange
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Giulia Arsuffi
- Independent scholar, 00061 Anguillara Sabazia, RM, Italy
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Chen Y, Ye X, Li X, Wang F, Yang J, Sun X, Yan S. Dynamic change of gut microbiota in head and neck concurrent chemoradiotherapy patients and its potential value in the prediction of acute oral mucositis grade as well as quality of life. Clin Transl Oncol 2024; 26:3191-3201. [PMID: 38844739 DOI: 10.1007/s12094-024-03542-0] [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: 01/30/2024] [Accepted: 05/28/2024] [Indexed: 11/15/2024]
Abstract
PURPOSE Radiotherapy is the major therapy for head and neck squamous cell carcinoma (HNSCC). However, whether gut microbiota changes in HNSCC patients who received concurrent chemoradiotherapy remains unclear. This study aimed to investigate the dynamic change of gut microbiota composition, construct the first radiotherapy-related gut microbiota database in these patients and identify the potential value of the gut microbiota changing in the prediction of acute oral mucositis grade as well as patients' life quality. METHODS We enrolled 47 HNSCC patients who scheduled with concurrent chemoradiotherapy. The field was irradiated with a total dose of 66-70 Gy in 33-35 fractions. All the patients received 2-3 cycles of platinum-based chemotherapy. After feces specimens collected, bacterial genomic DNA was isolated using magnetic beads and then analyzed by the Illumina MiSeq Sequencing System based on the V3-V4 hypervariable regions of the 16S rRNA gene. RESULTS 194 genera which belonged to 27 phyla were found in 141 samples. Increased abundance of microbiota in diversity and richness was observed in mid-radiotherapy group. Bacteroides, Blautia, Phascolarctobacterium were three main genera in all three groups and the mid-radiotherapy group had the highest relative abundance of Phascolarctobacterium. What is more, most significantly altered bacteria shared the same variation pattern which was increased in mid-radiotherapy while decreased to the almost same level of as pre-radiotherapy in post-radiotherapy group. Further analysis indicated that Bacteroidetes showing an upward trend while Proteobacteria declining in higher grade of acute mucositis. Moreover, relatively low abundant Proteobacteria was significantly correlated with high-grade acute oral mucositis. As for the quality of life, Lactobacillales and Actinomycetales were specifically found in better life quality group. However, Clostridia_UCG_014, Eubacteriaceae, UCG_010 and Moraxellaceae were unique abundantly present in worse life quality group. CONCLUSION Chemoradiotherapy can affect the composition of the gut microbiota in HNSCC patients during the mid-term of treatment. Yet self-stabilized ability maintained the gut microbiota homeostasis. Dynamic change of specific species could help predict acute oral mucositis grade and characterize different quality of life group in these patients.
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Affiliation(s)
- Ying Chen
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xianghua Ye
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xinke Li
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Fang Wang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Jinsong Yang
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiaoli Sun
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Senxiang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
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Sauers LA, Bassingthwaite T, Sierra-Rivera B, Hampton KJ, Duffield KR, Gore H, Ramirez JL, Sadd BM. Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction. Microbiol Spectr 2024; 12:e0086124. [PMID: 39373496 PMCID: PMC11536996 DOI: 10.1128/spectrum.00861-24] [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: 04/04/2024] [Accepted: 08/26/2024] [Indexed: 10/08/2024] Open
Abstract
Understanding factors influencing the composition and maintenance of beneficial host-associated microbial communities is central to understanding their ecological, evolutionary, and health consequences for hosts. Host immunity is often implicated as a regulator of these microbiota, but immunity may also play a disruptive role, with responses to infection perturbing beneficial communities. Such effects may be more prominent from innate immune responses, with more rapid-acting and often non-specific components, compared to adaptive responses. We investigated how upregulation of antibacterial immunity in the bumble bee Bombus impatiens affects its core gut microbiota, testing the hypothesis that immunity-induced perturbation impacts the microbiota structure. Freshly emerged adult bees were fed a microbiota inoculum before receiving a non-pathogenic immune stimulation injection. We quantified microbial communities using 16S rRNA amplicon sequencing and targeted quantitative PCR. Coarse community membership shows apparent robustness, but we find that immune stimulation alters the abundance of two core community members, Gilliamella and Snodgrassella. Moreover, a positive association in communities between these bacteria is perturbed following a Gram-negative challenge. The observed changes in the gut microbial community are suggestive of immune response-induced dysbiosis, linking ecological interactions across levels between hosts, their pathogens, and their beneficial gut microbiota. The potential for collateral perturbation of the natural gut microbiota following an innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment depending on the ecological context. IMPORTANCE Our work demonstrates how innate immunity may influence the host-associated microbiota. While previous work has demonstrated the role of adaptive immunity in regulating the microbiota, we show that stimulation of an innate immune response in bumble bees may disrupt the native gut microbial community by shifting individual abundances of some members and pairwise associations. This work builds upon previous work in bumble bees demonstrating factors determining microbe colonization of hosts and microbiota membership, implicating immune response-induced changes as a factor shaping these important gut communities. While some microbiota members appear unaffected, changes in others and the community overall suggests that collateral perturbation of the native gut microbiota upon an innate immune response may serve as an additional selective pressure that shapes the evolution of host innate immunity.
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Affiliation(s)
- Logan A. Sauers
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Toby Bassingthwaite
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Bryan Sierra-Rivera
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Kylie J. Hampton
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Kristin R. Duffield
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Haley Gore
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - José L. Ramirez
- Crop BioProtection Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Ben M. Sadd
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
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6
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Torrillo PA, Lieberman TD. Reversions mask the contribution of adaptive evolution in microbiomes. eLife 2024; 13:e93146. [PMID: 39240756 PMCID: PMC11379459 DOI: 10.7554/elife.93146] [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: 09/29/2023] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.
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Affiliation(s)
- Paul A Torrillo
- Institute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Tami D Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
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7
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El Jarkass HT, Reinke AW. Pathogen evolution: Protective microbes act as a double-edged sword. Curr Biol 2024; 34:R247-R249. [PMID: 38531318 DOI: 10.1016/j.cub.2024.02.013] [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: 03/28/2024]
Abstract
Vaccines and infection can sometimes cause incomplete immunity, which allows for pathogen re-infection with decreased disease severity but also contributes to the evolution of pathogen virulence. A new study demonstrates that incomplete immunity from resident protective microbes results in similar evolutionary trajectories.
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Affiliation(s)
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto ON M5G 1M1, Canada.
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8
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Hoang KL, Read TD, King KC. Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence. Curr Biol 2024; 34:1357-1363.e3. [PMID: 38430909 PMCID: PMC10962313 DOI: 10.1016/j.cub.2024.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/18/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Kayla C King
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [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: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Decaestecker E, Van de Moortel B, Mukherjee S, Gurung A, Stoks R, De Meester L. Hierarchical eco-evo dynamics mediated by the gut microbiome. Trends Ecol Evol 2024; 39:165-174. [PMID: 37863775 DOI: 10.1016/j.tree.2023.09.013] [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: 04/17/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.
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Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium.
| | - Broos Van de Moortel
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Laboratory of Reproductive Genomics, KU Leuven, B-3000 Leuven, Belgium
| | - Aditi Gurung
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium
| | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, B-3000 Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), D-12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
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11
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Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
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Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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12
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Roland MM, Peacock TE, Hall N, Mohammed AD, Ball R, Jolly A, Alexeev S, Dopkins N, Nagarkatti M, Nagarkatti P, Kubinak JL. B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner. Front Immunol 2023; 14:1253674. [PMID: 38187389 PMCID: PMC10766766 DOI: 10.3389/fimmu.2023.1253674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Background The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown. Methods Here, we developed a novel Rag1 -/- adoptive co-transfer model to answer this question. In this model, Rag1 -/- mice were reconstituted with naïve CD4+ T cells and either MhcII-sufficient or MhcII-deficient naïve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities. Results Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 -/- mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities. Conclusion Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jason L. Kubinak
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
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13
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Viney M, Cheynel L. Gut immune responses and evolution of the gut microbiome-a hypothesis. DISCOVERY IMMUNOLOGY 2023; 2:kyad025. [PMID: 38567055 PMCID: PMC10917216 DOI: 10.1093/discim/kyad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/22/2023] [Indexed: 04/04/2024]
Abstract
The gut microbiome is an assemblage of microbes that have profound effects on their hosts. The composition of the microbiome is affected by bottom-up, among-taxa interactions and by top-down, host effects, which includes the host immune response. While the high-level composition of the microbiome is generally stable over time, component strains and genotypes will constantly be evolving, with both bottom-up and top-down effects acting as selection pressures, driving microbial evolution. Secretory IgA is a major feature of the gut's adaptive immune response, and a substantial proportion of gut bacteria are coated with IgA, though the effect of this on bacteria is unclear. Here we hypothesize that IgA binding to gut bacteria is a selection pressure that will drive the evolution of IgA-bound bacteria, so that they will have a different evolutionary trajectory than those bacteria not bound by IgA. We know very little about the microbiome of wild animals and even less about their gut immune responses, but it must be a priority to investigate this hypothesis to understand if and how host immune responses contribute to microbiome evolution.
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Affiliation(s)
- Mark Viney
- Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool, UK
| | - Louise Cheynel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
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14
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Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
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Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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15
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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16
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Dapa T, Wong DP, Vasquez KS, Xavier KB, Huang KC, Good BH. Within-host evolution of the gut microbiome. Curr Opin Microbiol 2023; 71:102258. [PMID: 36608574 PMCID: PMC9993085 DOI: 10.1016/j.mib.2022.102258] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Gut bacteria inhabit a complex environment that is shaped by interactions with their host and the other members of the community. While these ecological interactions have evolved over millions of years, mounting evidence suggests that gut commensals can evolve on much shorter timescales as well, by acquiring new mutations within individual hosts. In this review, we highlight recent progress in understanding the causes and consequences of short-term evolution in the mammalian gut, from experimental evolution in murine hosts to longitudinal tracking of human cohorts. We also discuss new opportunities for future progress by expanding the repertoire of focal species, hosts, and surrounding communities, and by combining deep-sequencing technologies with quantitative frameworks from population genetics.
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Affiliation(s)
- Tanja Dapa
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Daniel Pgh Wong
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
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17
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Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [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: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
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Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
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18
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Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
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Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
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19
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Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations. Nat Commun 2022; 13:5604. [PMID: 36153389 PMCID: PMC9509342 DOI: 10.1038/s41467-022-33412-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show how rapid ecotype formation and phage domestication can be in the mammalian gut. Here, the authors show that a colonizing bacterial strain evolves in the gut by either generating ecotypes or continuously fixing beneficial mutations. They associate the first mode to metabolic mutations and the second to domestication of bacteriophages that are incorporated into the bacterial genome.
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20
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Barreto HC, Abreu B, Gordo I. Fluctuating selection on bacterial iron regulation in the mammalian gut. Curr Biol 2022; 32:3261-3275.e4. [PMID: 35793678 DOI: 10.1016/j.cub.2022.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Iron is critical in host-microbe interactions, and its availability is tightly regulated in the mammalian gut. Antibiotics and inflammation can perturb iron availability in the gut, which could alter host-microbe interactions. Here, we show that an adaptive allele of iscR, a major regulator of iron homeostasis of Escherichia coli, is under fluctuating selection in the mouse gut. In vivo competitions in immune-competent, immune-compromised, and germ-free mice reveal that the selective pressure on an iscR mutant E. coli is modulated by the presence of antibiotics, the microbiota, and the immune system. In vitro assays show that iron availability is an important mediator of the iscR allele fitness benefits or costs. We identify Lipocalin-2, a host's immune protein that prevents bacterial iron acquisition, as a major host mechanism underlying fluctuating selection of iscR. Our results provide a remarkable example of strong fluctuating selection acting on bacterial iron regulation in the mammalian gut.
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Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| | - Beatriz Abreu
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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21
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Abstract
Akkermansia muciniphila is a commensal bacterium using mucin as its sole carbon and nitrogen source. A. muciniphila is a promising candidate for next-generation probiotics to prevent inflammatory and metabolic disorders, including diabetes and obesity, and to increase the response to cancer immunotherapy. In this study, a comparative pan-genome analysis was conducted to investigate the genomic diversity and evolutionary relationships between complete genomes of 27 A. muciniphila strains, including KGMB strains isolated from healthy Koreans. The analysis showed that A. muciniphila strains formed two clades of group A and B in a phylogenetic tree constructed using 1,219 orthologous single-copy core genes. Interestingly, group A comprised of strains from human feces in Korea, whereas most of group B comprised strains from human feces in Europe and China, and from mouse feces. As group A and B branched, mucin hydrolysis played an important role in the stability of the core genome and drove evolution in the direction of defense against invading pathogens, survival in, and colonization in the mucus layer. In addition, WapA and anSME, which function in competition and post-translational modification of sulfatase, respectively, have been a particularly important selective pressure in the evolution of group A. KGMB strains in group A with anSME gene showed sulfatase activity, but KCTC 15667T in group B without anSME did not. Our findings revealed that KGMB strains evolved to gain an edge in the competition with other gut bacteria by increasing the utilization of sulfated mucin, which will allow it to become highly colonized in the gut environment.
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea,Department of Environmental Biotechnology, University of Science and Technology, Yuseong-gu, Republic of Korea,CONTACT Jung-Sook Lee Korean Collection for Type Cultures,Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si56212Republic of Korea
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22
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Feng S, Wu Z, Liang W, Zhang X, Cai X, Li J, Liang L, Lin D, Stoesser N, Doi Y, Zhong LL, Liu Y, Xia Y, Dai M, Zhang L, Chen X, Yang JR, Tian GB. Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase. Mol Biol Evol 2022; 39:msac086. [PMID: 35485492 PMCID: PMC9087888 DOI: 10.1093/molbev/msac086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The antibiotic resistance crisis continues to threaten human health. Better predictions of the evolution of antibiotic resistance genes could contribute to the design of more sustainable treatment strategies. However, comprehensive prediction of antibiotic resistance gene evolution via laboratory approaches remains challenging. By combining site-specific integration and high-throughput sequencing, we quantified relative growth under the respective selection of cefotaxime or ceftazidime selection in ∼23,000 Escherichia coli MG1655 strains that each carried a unique, single-copy variant of the extended-spectrum β-lactamase gene blaCTX-M-14 at the chromosomal att HK022 site. Significant synergistic pleiotropy was observed within four subgenic regions, suggesting key regions for the evolution of resistance to both antibiotics. Moreover, we propose PEARP and PEARR, two deep-learning models with strong clinical correlations, for the prospective and retrospective prediction of blaCTX-M-14 evolution, respectively. Single to quintuple mutations of blaCTX-M-14 predicted to confer resistance by PEARP were significantly enriched among the clinical isolates harboring blaCTX-M-14 variants, and the PEARR scores matched the minimal inhibitory concentrations obtained for the 31 intermediates in all hypothetical trajectories. Altogether, we conclude that the measurement of local fitness landscape enables prediction of the evolutionary trajectories of antibiotic resistance genes, which could be useful for a broad range of clinical applications, from resistance prediction to designing novel treatment strategies.
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Affiliation(s)
- Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Zhuoxing Wu
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wanfei Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Xin Zhang
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiujuan Cai
- Department of Genetics and Cellular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiachen Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Lujie Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Daixi Lin
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh 15261, PA, USA
- Department of Microbiology, Fujita Health University School of Medicine, Aichi 470-1192, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi 470-1192, Japan
| | - Lan-lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Yan Liu
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, China
| | - Liyan Zhang
- Department of Clinical Laboratory, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Xiaoshu Chen
- Department of Genetics and Cellular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jian-Rong Yang
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Guo-bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
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23
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Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe 2022; 30:183-199.e10. [PMID: 35085504 DOI: 10.1016/j.chom.2022.01.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet causes microbiota imbalances that underlay many pathological conditions (i.e., dysbiosis). Although the effects of dietary changes on microbiota composition and functions are well documented, their impact in gut bacterial evolution remains unexplored. We followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly in the gut and Western-style diet selected for mutations that promote degradation of mucin-derived glycans. Periodic dietary changes caused fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intraspecies genetic diversity compared to constant dietary regimens. These results show that dietary changes leave a genetic signature in microbiome members and suggest that B. thetaiotaomicron genetic diversity could be a biomarker for dietary differences among individuals.
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24
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Jian YP, Yang G, Zhang LH, Liang JY, Zhou HL, Wang YS, Xu ZX. Lactobacillus plantarum alleviates irradiation-induced intestinal injury by activation of FXR-FGF15 signaling in intestinal epithelia. J Cell Physiol 2021; 237:1845-1856. [PMID: 34881818 DOI: 10.1002/jcp.30651] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/23/2022]
Abstract
Abdominal irradiation (IR) may destroy the intestinal mucosal barrier, leading to severe intestinal infection and multiple organ dysfunction syndromes. The role of intestinal microbiota in the development of IR-induced intestinal injury remains largely unknown. Herein, we reported that abdominal IR altered the composition of the microbiota and reduced the abundance and diversity of the gut microbiome. Alterations of bacteria, in particular reduction of Lactobacillus, played a critical role in IR-induced intestinal injury. Fecal microbiota transplant (FMT) from normal mice or administration of Lactobacillus plantarum to intestinal microbiota-eliminated mice substantially reduced IR-induced intestinal damage and prevented mice from IR-induced death. We further characterized that L. plantarum activated the farnesoid X receptor (FXR) - fibroblast growth factor 15 (FGF15) signaling in intestinal epithelial cells and hence promoted DNA-damage repair. Application of GW4064, an activator of FXR, to microbiota eliminated mice markedly mitigated IR-induced intestinal damage, reduced intestinal epithelial cell death and promoted the survival of IR mice. In contrast, suppression of FXR with Gly-β-MCA, a bile acid and an intestine-selective and high-affinity FXR inhibitor, abrogated L. Plantarum-mediated protection on the ileum of IR mice. Taken together, our findings not only provide new insights into the role of intestinal flora in radiation-induced intestinal injury but also shed new light on the application of probiotics for the protection of radiation-damaged individuals.
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Affiliation(s)
- Yong-Ping Jian
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China
| | - Ge Yang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China
| | - Li-Hong Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China
| | - Ji-Yong Liang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, Texas, USA
| | - Hong-Lan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yi-Shu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China
| | - Zhi-Xiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China.,School of Life Sciences, Henan University, Kaifeng, Henan, China
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25
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Vasquez KS, Willis L, Cira NJ, Ng KM, Pedro MF, Aranda-Díaz A, Rajendram M, Yu FB, Higginbottom SK, Neff N, Sherlock G, Xavier KB, Quake SR, Sonnenburg JL, Good BH, Huang KC. Quantifying rapid bacterial evolution and transmission within the mouse intestine. Cell Host Microbe 2021; 29:1454-1468.e4. [PMID: 34473943 PMCID: PMC8445907 DOI: 10.1016/j.chom.2021.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/25/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022]
Abstract
Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.
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Affiliation(s)
- Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nate J Cira
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Katharine M Ng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Miguel F Pedro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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26
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Teulière J, Bernard C, Bapteste E. Interspecific interactions that affect ageing: Age-distorters manipulate host ageing to their own evolutionary benefits. Ageing Res Rev 2021; 70:101375. [PMID: 34082078 DOI: 10.1016/j.arr.2021.101375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
Genetic causes for ageing are traditionally investigated within a species. Yet, the lifecycles of many organisms intersect. Additional evolutionary and genetic causes of ageing, external to a focal species/organism, may thus be overlooked. Here, we introduce the phrase and concept of age-distorters and its evidence. Age-distorters carry ageing interfering genes, used to manipulate the biological age of other entities upon which the reproduction of age-distorters relies, e.g. age-distorters bias the reproduction/maintenance trade-offs of cells/organisms for their own evolutionary interests. Candidate age-distorters include viruses, parasites and symbionts, operating through specific, genetically encoded interferences resulting from co-evolution and arms race between manipulative non-kins and manipulable species. This interference results in organismal ageing when age-distorters prompt manipulated organisms to favor their reproduction at the expense of their maintenance, turning these hosts into expanded disposable soma. By relying on reproduction/maintenance trade-offs affecting disposable entities, which are left ageing to the reproductive benefit of other physically connected lineages with conflicting evolutionary interests, the concept of age-distorters expands the logic of the Disposable Soma theory beyond species with fixed germen/soma distinctions. Moreover, acknowledging age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of the mutation accumulation and of the antagonistic pleiotropy theories.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
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27
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Jian Y, Zhang D, Liu M, Wang Y, Xu ZX. The Impact of Gut Microbiota on Radiation-Induced Enteritis. Front Cell Infect Microbiol 2021; 11:586392. [PMID: 34395308 PMCID: PMC8358303 DOI: 10.3389/fcimb.2021.586392] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Radiotherapy is an important treatment for abdominal tumors. A critical side effect for this therapy is enteritis. In this review, we aim to summarize recent findings in radiation enteritis, in particular the role of gut microbiota dysbiosis in the development and therapy of the disease. Gut microbiota dysbiosis plays an important role in the occurrence of various diseases, such as radiation enteritis. Abdominal radiation results in changes in the composition of microbiota and reduces its diversity, which is mainly reflected in the decrease of Lactobacillus spp. and Bifidobacterium spp. and increase of Escherichia coli and Staphylococcus spp. Gut microbiota dysbiosis aggravates radiation enteritis, weakens intestinal epithelial barrier function, and promotes inflammatory factor expression. Pathogenic Escherichia coli induce the rearrangement and redistribution of claudin-1, occludin, and ZO-1 in tight junctions, a critical component in intestinal epithelial barrier. In view of the role that microbiome plays in radiation enteritis, we believe that intestinal flora could be a potential biomarker for the disease. Correction of microbiome by application of probiotics, fecal microbiota transplantation (FMT), and antibiotics could be an effective method for the prevention and treatment of radiation-induced enteritis.
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Affiliation(s)
- Yongping Jian
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Dan Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Mingdi Liu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Zhi-Xiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China.,School of Life Sciences, Henan University, Kaifeng, China
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28
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Comparative genomics of in vitro and in vivo evolution of probiotics reveals energy restriction not the main evolution driving force in short term. Genomics 2021; 113:3373-3380. [PMID: 34311046 DOI: 10.1016/j.ygeno.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/15/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022]
Abstract
Probiotics have attracted much attention because of their health-promoting effects, but little is known about the in vivo evolution of probiotics. This study analyzed the genome adaptation of the probiotic Lactiplantibacillus plantarum P-8 strain cultivated in ordinary and glucose restrictive growth media. Then, this study re-analyzed genomes of P-8 isolates recovered from the gut contents of subjects in two feeding trials (in rat and human). The sampling time points were similar to that of the in vitro evolution experiment, which might give parallel comparison of the in vitro and in vivo evolution processes. Our results showed that intra-individual specific microbial genomic variants of the original strain were detected in all human and some rat subjects. The divergent patterns of evolution within the host gastrointestinal tract suggested intra-individual-specific environmental adaptation. Based on comprehensive analysis of adapted-isolates recovered from these experiments, our results showed that the energy restriction was not the main driving force for evolution of probiotics. The individual-specific adaptation of probiotics might partially explain the varying extent of health effects seen between different individuals after probiotic consumption. In addition, the results suggest that probiotics should not only adapt to the environment of the birth canal, but also adapt to other species in the gut, revealing the Red Queen hypothesis in the process of intestinal flora.
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29
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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30
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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31
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van Best N, Hornef MW. Early life host regulation of the mammalian enteric microbiota composition. Int J Med Microbiol 2021; 311:151498. [PMID: 33774478 DOI: 10.1016/j.ijmm.2021.151498] [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: 09/11/2020] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
The enteric microbiota exerts a major influence on the host. It promotes food degradation, nutrient absorption, immune maturation and protects from infection with pathogenic microorganisms. However, certain compositional alterations also enhance the risk to develop metabolic, inflammatory and immune-mediated diseases. This suggests that the enteric microbiota is subject to strong evolutionary pressure. Here, we hypothesize that endogenous, genetically determined mechanisms exist that shape and optimize the enteric microbiota. We discuss that the postnatal period as the starting point of the host-microbial interaction bears the greatest chance to identify such regulatory mechanisms and report on two recently identified ways how the neonate host favours or disfavours colonization by certain bacteria and thereby manipulates the postnatally emerging bacterial ecosystem. A better understanding of these mechanisms might ultimately help to define the features of a beneficial enteric microbiota and to develop interventional strategies to overcome adverse microbiota alterations.
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Affiliation(s)
- Niels van Best
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University Aachen, Aachen, Germany; Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University Aachen, Aachen, Germany.
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32
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Singh S, Thompson JA, Yilmaz B, Li H, Weis S, Sobral D, Truglio M, Aires da Silva F, Aguiar S, Carlos AR, Rebelo S, Cardoso S, Gjini E, Nuñez G, Soares MP. Loss of α-gal during primate evolution enhanced antibody-effector function and resistance to bacterial sepsis. Cell Host Microbe 2021; 29:347-361.e12. [DOI: 10.1016/j.chom.2020.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/17/2020] [Accepted: 12/22/2020] [Indexed: 12/29/2022]
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33
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Abstract
Ecological interactions can generate strong selection. Two new studies reveal that the tempo and patterns of evolutionary change in a mammalian gut commensal can be altered dramatically during interactions with both the host and its microbiome.
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Affiliation(s)
- Kayla C King
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.
| | - Emily Stevens
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Georgia C Drew
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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34
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Racine PJ, Janvier X, Clabaut M, Catovic C, Souak D, Boukerb AM, Groboillot A, Konto-Ghiorghi Y, Duclairoir-Poc C, Lesouhaitier O, Orange N, Chevalier S, Feuilloley MGJ. Dialog between skin and its microbiota: Emergence of "Cutaneous Bacterial Endocrinology". Exp Dermatol 2020; 29:790-800. [PMID: 32682345 DOI: 10.1111/exd.14158] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022]
Abstract
Microbial endocrinology is studying the response of microorganisms to hormones and neurohormones and the microbiota production of hormones-like molecules. Until now, it was mainly applied to the gut and revealed that the intestinal microbiota should be considered as a real organ in constant and bilateral interactions with the whole human body. The skin harbours the second most abundant microbiome and contains an abundance of nerve terminals and capillaries, which in addition to keratinocytes, fibroblasts, melanocytes, dendritic cells and endothelial cells, release a huge diversity of hormones and neurohormones. In the present review, we will examine recent experimental data showing that, in skin, molecules such as substance P, calcitonin gene-related peptide, natriuretic peptides and catecholamines can directly affect the physiology and virulence of common skin-associated bacteria. Conversely, bacteria are able to synthesize and release compounds including histamine, glutamate and γ-aminobutyric acid or peptides showing partial homology with neurohormones such as α-melanocyte-stimulating hormone (αMSH). The more surprising is that some viruses can also encode neurohormones mimicking proteins. Taken together, these elements demonstrate that there is also a cutaneous microbial endocrinology and this emerging concept will certainly have important consequences in dermatology.
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Affiliation(s)
- Pierre-Jean Racine
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Xavier Janvier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Maximilien Clabaut
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Chloe Catovic
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Djouhar Souak
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Amine M Boukerb
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Anne Groboillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Cécile Duclairoir-Poc
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA4312, University of Rouen Normandy, Normandie Université, Evreux, France
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35
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Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut. Nat Ecol Evol 2020; 4:1268-1278. [PMID: 32632259 DOI: 10.1038/s41559-020-1235-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 06/02/2020] [Indexed: 12/18/2022]
Abstract
In the absence of antibiotics, it is essential that antibiotic resistance has a fitness cost for microorganisms if suspending antibiotics treatment is to be a useful strategy for reducing antibiotic resistance. However, the cost of antibiotic resistance within the complex ecosystem of the mammalian gut is not well understood. Here, using mice, we show that the same antibiotic resistance mutation can reduce fitness in one host, while being neutral or even increasing fitness in other hosts. Such antagonistic pleiotropy is shaped by the microbiota because resistance in germ-free mice is consistently costly across all hosts, and the host-specific effect on antibiotic resistance is reduced in hosts with similar microbiotas. Using an eco-evolutionary model of competition for resources, we identify a general mechanism that underlies between-host variation and predicts that the dynamics of compensatory evolution of resistant bacteria should be host specific, a prediction that was supported by experimental evolution in vivo. The microbiome of each human is close to unique, and our results suggest that the short-term cost of resistances and their long-term within-host evolution are also highly personalized, a finding that may contribute to the observed variable outcome of withdrawing antibiotics to reduce resistance levels.
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36
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Barreto HC, Frazão N, Sousa A, Konrad A, Gordo I. Mutation accumulation and horizontal gene transfer in Escherichia coli colonizing the gut of old mice. Commun Integr Biol 2020; 13:89-96. [PMID: 33014261 PMCID: PMC7518454 DOI: 10.1080/19420889.2020.1783059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/03/2022] Open
Abstract
The ecology and environment of the microbes that inhabit the mammalian intestine undergoes several changes as the host ages. Here, we ask if the selection pressure experienced by a new strain colonizing the aging gut differs from that in the gut of young adults. Using experimental evolution in mice after a short antibiotic treatment, as a model for a common clinical situation, we show that a new colonizing E. coli strain rapidly adapts to the aging gut via both mutation accumulation and bacteriophage-mediated horizontal gene transfer (HGT). The pattern of evolution of E. coli in aging mice is characterized by a larger number of transposable element insertions and intergenic mutations compared to that in young mice, which is consistent with the gut of aging hosts harboring a stressful and iron limiting environment.
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Affiliation(s)
| | | | - Ana Sousa
- IBiMed, Institute for Biomedicine, Universidade de Aveiro, Aveiro, Portugal
| | - Anke Konrad
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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37
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Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol 2020; 18:e3000465. [PMID: 32310938 PMCID: PMC7192512 DOI: 10.1371/journal.pbio.3000465] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/30/2020] [Accepted: 04/02/2020] [Indexed: 01/05/2023] Open
Abstract
Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.
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Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Katia R. Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Alex R. Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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38
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Barreto HC, Sousa A, Gordo I. The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice. Curr Biol 2020; 30:1102-1109.e5. [PMID: 32142696 DOI: 10.1016/j.cub.2020.01.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022]
Abstract
Aging is a complex process, with many associated time-dependent phenotypes. The gut microbiota have long been postulated as an important factor in shaping healthy aging [1, 2]. During aging, changes in the microbiota composition occur, with taxa that are rare in adults becoming dominant in the elderly [3, 4]. Increased inflammation associated with aging is also known to modulate and be modulated by the microbiota [5]. Ecological interactions are known to affect the evolution of bacteria both in vitro [6] and in vivo [7], but the extent to which these and the host age-dependent inflammatory environment can alter the pattern of evolutionary change of a gut commensal lineage is still unknown [8]. Here, we provide the first genomic analysis of such evolution in cohorts of old mice, under controlled host genetics and lifestyle conditions. We find that Escherichia coli evolution when colonizing the gut of old mice significantly differs from its evolution in young mice. Evolution toward metabolic adaptation is slower in old than young mice, and mutational targets concerning stress-related functions were found specifically in the inflamed gut of old mice. Taking the genetic basis of E. coli short-term evolution as a reflection of the environment it experiences, the sequencing data indicate that aging imposes a more stressful environment to this important colonizer of the mammalian gut.
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Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciências, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Ana Sousa
- iBiMed, Institute for Biomedicine, Universidade de Aveiro, Agra do Crasto, Edifício 30, 3810-193 Aveiro, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciências, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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39
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Kumar P, Monteiro M, Dabdoub S, Miranda G, Casati M, Ribeiro F, Cirano F, Pimentel S, Casarin R. Subgingival Host-Microbial Interactions in Hyperglycemic Individuals. J Dent Res 2020; 99:650-657. [DOI: 10.1177/0022034520906842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is an established risk factor for periodontitis, yet its contribution to creating host-bacterial disequilibrium in the subgingival crevice is poorly understood. The present investigation aimed to quantify the impact of hyperglycemia on host-bacterial interactions in established periodontitis and to map shifts in these dynamics following mechanical nonsurgical therapy. Seventeen T2DM and 17 non-T2DM subjects with generalized severe chronic periodontitis were recruited along with 20 periodontally healthy individuals. Subjects with periodontitis were treated with scaling and root planing (SRP). Samples of subgingival biofilm and gingival crevicular fluid were collected at baseline and at 1-, 3-, and 6 mo postoperatively. Correlations were generated between 13.7 million 16S ribosomal DNA sequences and 8 immune mediators. Intermicrobial and host-microbial interactions were modeled using differential network analysis. Periodontal health was characterized by a sparse interbacterial and highly connected cytokine-bacterial network, while both normoglycemics and T2DM subjects with periodontitis demonstrated robust congeneric and intergeneric hubs but significantly fewer cytokine-bacterial connections. Following SRP, the cytokine-bacterial edges demonstrated a 2-fold increase 1 mo postoperatively and a 10-fold increase at 6 mo in normoglycemics. In hyperglycemics, there was a doubling at 1 mo but no further changes thereafter. These shifts accompanied an increasingly sparse interbacterial network. In normoglycemics, the nodes anchored by interleukin (IL)–4, IL-6, and IL-10 demonstrated greatest rewiring, while in hyperglycemics, IL-1β, IL-6, INF-γ, and IL-17 exhibited progressive rewiring. Thus, the present investigation points to a breakdown in host-bacterial mutualism in periodontitis, with interbacterial interactions rather than host-bacterial interactions primarily determining community assembly. Hyperglycemia further exacerbates this uncoupled mutualism. Our data also demonstrate that while nonsurgical therapy might not consistently alter microbial abundances or lower proinflammatory molecules, it “reboots” the interaction between the immunoinflammatory system and the newly colonizing microbiome, restoring a role for the immune system in determining bacterial colonization. However, this outcome is lower and delayed in hyperglycemics.
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Affiliation(s)
- P.S. Kumar
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - M.F. Monteiro
- Division of Periodontology, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - S.M. Dabdoub
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - G.L. Miranda
- Division of Periodontology, School of Dentistry, Paulista University, São Paulo, Brazil
| | - M.Z. Casati
- Division of Periodontology, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
- Division of Periodontology, School of Dentistry, Paulista University, São Paulo, Brazil
| | - F.V. Ribeiro
- Division of Periodontology, School of Dentistry, Paulista University, São Paulo, Brazil
| | - F.R. Cirano
- Division of Periodontology, School of Dentistry, Paulista University, São Paulo, Brazil
| | - S.P. Pimentel
- Division of Periodontology, School of Dentistry, Paulista University, São Paulo, Brazil
| | - R.C.V. Casarin
- Division of Periodontology, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
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40
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Ramiro RS, Durão P, Bank C, Gordo I. Low mutational load and high mutation rate variation in gut commensal bacteria. PLoS Biol 2020; 18:e3000617. [PMID: 32155146 PMCID: PMC7064181 DOI: 10.1371/journal.pbio.3000617] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteria generally live in species-rich communities, such as the gut microbiota. Yet little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensal Escherichia coli in the mouse gut. We observe the emergence of mutation rate polymorphism, ranging from wild-type levels to 1,000-fold higher. By combining experiments, whole-genome sequencing, and in silico simulations, we identify the molecular causes and explore the evolutionary conditions allowing these hypermutators to emerge and coexist within the microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III proofreading and catalytic subunits, which increase mutation rate by approximately 1,000-fold and stabilise hypermutator fitness, respectively. Strong mutation rate variation persists for >1,000 generations, with coexistence between lineages carrying 4 to >600 mutations. The in vivo molecular evolution pattern is consistent with fitness effects of deleterious mutations sd ≤ 10−4/generation, assuming a constant effect or exponentially distributed effects with a constant mean. Such effects are lower than typical in vitro estimates, leading to a low mutational load, an inference that is observed in in vivo and in vitro competitions. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but could be explained by other evolutionary mechanisms that maintain genetic diversity. Thus, microbial evolution in the gut is likely characterised by partial sweeps of beneficial mutations combined with hitchhiking of slightly deleterious mutations, which take a long time to be purged because they impose a low mutational load. The combination of these two processes could allow for the long-term maintenance of intraspecies genetic diversity, including mutation rate polymorphism. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we have identified key evolutionary processes shaping the genetic composition of this community. Weak-effect deleterious mutations and negative frequency–dependent selection, acting on beneficial mutations, shape the dynamics of molecular evolution within the mouse gut microbiota.
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Affiliation(s)
- Ricardo S. Ramiro
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (RSR); (IG)
| | - Paulo Durão
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (RSR); (IG)
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41
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Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Curr Biol 2020; 30:1049-1062.e7. [PMID: 32142697 DOI: 10.1016/j.cub.2020.01.050] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/21/2019] [Accepted: 01/15/2020] [Indexed: 02/08/2023]
Abstract
Members of the gut microbiota are thought to experience strong competition for nutrients. However, how such competition shapes their evolutionary dynamics and depends on intra- and interspecies interactions is poorly understood. Here, we test the hypothesis that Escherichia coli evolution in the mouse gut is more predictable across hosts in the absence of interspecies competition than in the presence of other microbial species. In support, we observed that lrp, a gene encoding a global regulator of amino acid metabolism, was repeatedly selected in germ-free mice 2 weeks after mono-colonization by this bacterium. We established that this specific genetic adaptation increased E. coli's ability to compete for amino acids, and analysis of gut metabolites identified serine and threonine as the metabolites preferentially consumed by E. coli in the mono-colonized mouse gut. Preference for serine consumption was further supported by testing a set of mutants that showed loss of advantage of an lrp mutant impaired in serine metabolism in vitro and in vivo. Remarkably, the presence of a single additional member of the microbiota, Blautia coccoides, was sufficient to alter the gut metabolome and, consequently, the evolutionary path of E. coli. In this environment, the fitness advantage of the lrp mutant bacteria is lost, and mutations in genes involved in anaerobic respiration were selected instead, recapitulating the eco-evolutionary context from mice with a complex microbiota. Together, these results highlight the metabolic plasticity and evolutionary versatility of E. coli, tailored to the specific ecology it experiences in the gut.
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42
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Campbell C, Rudensky A. Roles of Regulatory T Cells in Tissue Pathophysiology and Metabolism. Cell Metab 2020; 31:18-25. [PMID: 31607562 PMCID: PMC7657366 DOI: 10.1016/j.cmet.2019.09.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Regulatory T (Treg) cells expressing the X-chromosome-encoded transcription factor Foxp3 represent a specialized immunosuppressive lineage with a well-recognized, essential function in preventing fatal autoimmunity and inflammation. Recent studies revealed that Treg cells can also exert systemic effects on metabolism and partake in tissue repair, suggesting a dual role for these cells in serving and protecting tissues. Here, we review multiple means by which Treg cells support tissue function and organismal homeostasis.
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Affiliation(s)
- Clarissa Campbell
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA; Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Alexander Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA; Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA.
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43
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Soderholm AT, Pedicord VA. Intestinal epithelial cells: at the interface of the microbiota and mucosal immunity. Immunology 2019; 158:267-280. [PMID: 31509239 PMCID: PMC6856932 DOI: 10.1111/imm.13117] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
The intestinal epithelium forms a barrier between the microbiota and the rest of the body. In addition, beyond acting as a physical barrier, the function of intestinal epithelial cells (IECs) in sensing and responding to microbial signals is increasingly appreciated and likely has numerous implications for the vast network of immune cells within and below the intestinal epithelium. IECs also respond to factors produced by immune cells, and these can regulate IEC barrier function, proliferation and differentiation, as well as influence the composition of the microbiota. The mechanisms involved in IEC-microbe-immune interactions, however, are not fully characterized. In this review, we explore the ability of IECs to direct intestinal homeostasis by orchestrating communication between intestinal microbes and mucosal innate and adaptive immune cells during physiological and inflammatory conditions. We focus primarily on the most recent findings and call attention to the numerous remaining unknowns regarding the complex crosstalk between IECs, the microbiota and intestinal immune cells.
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Affiliation(s)
- Amelia T. Soderholm
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUK
| | - Virginia A. Pedicord
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUK
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44
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Frazão N, Sousa A, Lässig M, Gordo I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc Natl Acad Sci U S A 2019; 116:17906-17915. [PMID: 31431529 PMCID: PMC6731689 DOI: 10.1073/pnas.1906958116] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.
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Affiliation(s)
- Nelson Frazão
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Ana Sousa
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, 50923 Cologne, Germany
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal;
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45
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Remigi P, Masson-Boivin C, Rocha EP. Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions. Trends Microbiol 2019; 27:623-634. [DOI: 10.1016/j.tim.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
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46
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The Unique Lifestyle of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. J Mol Biol 2019; 431:2970-2981. [PMID: 31029703 DOI: 10.1016/j.jmb.2019.04.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Escherichia coli is one of the most genetically and phenotypically diverse species of bacteria. This remarkable diversity produces a plethora of clinical outcomes following infection and has informed much of what we currently know about host-pathogen interactions for a wide range of bacteria-host relationships. In studying the role of microbes in disease, adherent-invasive E. coli (AIEC) has emerged as having a strong association with Crohn's disease (CD). Thus, there has been an equally strong effort to uncover the root origins of AIEC, to appreciate how AIEC differs from other well-known pathogenic E. coli variants, and to understand its connection to disease. Emerging from a growing body of research on AIEC is the understanding that AIEC itself is remarkably diverse, both in phylogenetic origins, genetic makeup, and behavior in the host setting. Here, we describe the unique lifestyle of CD-associated AIEC and review recent research that is uncovering the inextricable link between AIEC and its host in the context of CD.
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47
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Friberg IM, Taylor JD, Jackson JA. Diet in the Driving Seat: Natural Diet-Immunity-Microbiome Interactions in Wild Fish. Front Immunol 2019; 10:243. [PMID: 30837993 PMCID: PMC6389695 DOI: 10.3389/fimmu.2019.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
Natural interactions between the diet, microbiome, and immunity are largely unstudied. Here we employ wild three-spined sticklebacks as a model, combining field observations with complementary experimental manipulations of diet designed to mimic seasonal variation in the wild. We clearly demonstrate that season-specific diets are a powerful causal driver of major systemic immunophenotypic variation. This effect occurred largely independently of the bulk composition of the bacterial microbiome (which was also driven by season and diet) and of host condition, demonstrating neither of these, per se, constrain immune allocation in healthy individuals. Nonetheless, through observations in multiple anatomical compartments, differentially exposed to the direct effects of food and immunity, we found evidence of immune-driven control of bacterial community composition in mucus layers. This points to the interactive nature of the host-microbiome relationship, and is the first time, to our knowledge, that this causal chain (diet → immunity → microbiome) has been demonstrated in wild vertebrates. Microbiome effects on immunity were not excluded and, importantly, we identified outgrowth of potentially pathogenic bacteria (especially mycolic-acid producing corynebacteria) as a consequence of the more animal-protein-rich summertime diet. This may provide part of the ultimate explanation (and possibly a proximal cue) for the dramatic immune re-adjustments that we saw in response to diet change.
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Affiliation(s)
- Ida M Friberg
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
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48
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Elhenawy W, Tsai CN, Coombes BK. Host-Specific Adaptive Diversification of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. Cell Host Microbe 2019; 25:301-312.e5. [PMID: 30683582 DOI: 10.1016/j.chom.2018.12.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/05/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Abstract
Crohn's disease (CD) is an inflammatory bowel disease influenced by bacteria. Adherent-invasive E. coli (AIEC) is associated with CD, yet the adaptations facilitating AIEC gut colonization are unknown. AIEC isolates exhibit high genetic diversity, suggesting strains evolve independently across different gut environments. We tracked the adaptive evolution of AIEC in a murine model of chronic colonization across multiple hosts and transmission events. We detected evolved lineages that outcompeted the ancestral strain in the host through independent mechanisms. One lineage was hypermotile because of a mobile insertion sequence upstream of the master flagellar regulator, flhDC, which enhanced AIEC invasion and establishment of a mucosal niche. Another lineage outcompeted the ancestral strain through improved use of acetate, a short-chain fatty acid in the gut. The presence of hypermotile and acetate-consuming lineages discriminated E. coli isolated from CD patients from healthy controls, suggesting an evolutionary trajectory that distinguishes AIEC from commensal E. coli.
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Affiliation(s)
- Wael Elhenawy
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Caressa N Tsai
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Brian K Coombes
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Hamilton, ON, Canada.
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49
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Li M, Li L, Huang T, Liu Y, Lei A, Ma C, Chen F, Chen M. Effects of Attenuated S. agalactiae Strain YM001 on Intestinal Microbiota of Tilapia Are Recoverable. Front Microbiol 2019; 9:3251. [PMID: 30687255 PMCID: PMC6333689 DOI: 10.3389/fmicb.2018.03251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/14/2018] [Indexed: 11/25/2022] Open
Abstract
Previously, we constructed and characterized the vaccine efficacy of attenuated S. agalactiae strain YM001 in tilapia. In this study, the potential impacts of YM001 on the tilapia intestinal microbiota were assessed by qPCR and 16S rRNA sequencing methods. The results showed that YM001 distributed unevenly in different parts of intestine, peaked in the intestine at 12 h after oral administration, and then declined gradually. YM001 caused 0% mortality of fish during the entire experimental period, while the referent strain HN016 caused 100% mortality at 3 d after oral administration. However, the intestinal microbiota could be changed by YM001, the diversity of intestinal microbiota decreased first and gradually recovered after oral administration. The diversity of intestinal microbiota of tilapia was negatively correlated with the content of HN016 in the intestinal tract. The oral YM001 mainly changed the abundance of Streptococcus, Cetobacterium, Akkermansia, Romboutsia, Bacteroides, Brevinema, Lachnospiraceae_NK4A136-group, coprothermobactter, presiomonas, and Roseburia in intestine. The present study indicate that oral administration of YM001 altered the diversity and composition of intestinal microbiota in tilapia, but these change were only temporary, non-lethal, and recoverable. The results provide a more comprehensive experimental basis for the safety of oral YM001 vaccines.
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Affiliation(s)
- Ming Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Liping Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Ting Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Yu Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Aiying Lei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Chunxia Ma
- Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Department of Bacteriology, Guangxi Veterinary Research Institute, Nanning, China
| | - Fuyan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
| | - Ming Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China
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50
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Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol 2019; 17:e3000102. [PMID: 30673701 PMCID: PMC6361464 DOI: 10.1371/journal.pbio.3000102] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.
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Affiliation(s)
- Nandita R. Garud
- Gladstone Institutes, San Francisco, California, United States of America
| | - Benjamin H. Good
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
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