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Bedu-Ferrari C, Biscarrat P, Pepke F, Vati S, Chaudemanche C, Castelli F, Chollet C, Rué O, Hennequet-Antier C, Langella P, Cherbuy C. In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential. mSystems 2024; 9:e0140123. [PMID: 38441031 PMCID: PMC11019791 DOI: 10.1128/msystems.01401-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
The microbial utilization of dietary carbohydrates is closely linked to the pivotal role of the gut microbiome in human health. Inherent to the modulation of complex microbial communities, a prebiotic implies the selective utilization of a specific substrate, relying on the metabolic capacities of targeted microbes. In this study, we investigated the metabolic capacities of 17 commensal bacteria of the human gut microbiome toward dietary carbohydrates with prebiotic potential. First, in vitro experiments allowed the classification of bacterial growth and fermentation profiles in response to various carbon sources, including agave inulin, corn fiber, polydextrose, and citrus pectin. The influence of phylogenetic affiliation appeared to statistically outweigh carbon sources in determining the degree of carbohydrate utilization. Second, we narrowed our focus on six commensal bacteria representative of the Bacteroidetes and Firmicutes phyla to perform an untargeted high-resolution liquid chromatography-mass spectrometry metabolomic analysis: Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Bacteroides intestinalis, Subdoligranulum variabile, Roseburia intestinalis, and Eubacterium rectale exhibited distinct metabolomic profiles in response to different carbon sources. The relative abundance of bacterial metabolites was significantly influenced by dietary carbohydrates, with these effects being strain-specific and/or carbohydrate-specific. Particularly, the findings indicated an elevation in short-chain fatty acids and other metabolites, including succinate, gamma-aminobutyric acid, and nicotinic acid. These metabolites were associated with putative health benefits. Finally, an RNA-Seq transcriptomic approach provided deeper insights into the underlying mechanisms of carbohydrate metabolization. Restricting our focus on four commensal bacteria, including B. xylanisolvens, B. thetaiotaomicron, S. variabile, and R. intestinalis, carbon sources did significantly modulate the level of bacterial genes related to the enzymatic machinery involved in the metabolization of dietary carbohydrates. This study provides a holistic view of the molecular strategies induced during the dynamic interplay between dietary carbohydrates with prebiotic potential and gut commensal bacteria. IMPORTANCE This study explores at a molecular level the interactions between commensal health-relevant bacteria and dietary carbohydrates holding prebiotic potential. We showed that prebiotic breakdown involves the specific activation of gene expression related to carbohydrate metabolism. We also identified metabolites produced by each bacteria that are potentially related to our digestive health. The characterization of the functional activities of health-relevant bacteria toward prebiotic substances can yield a better application of prebiotics in clinical interventions and personalized nutrition. Overall, this study highlights the importance of identifying the impact of prebiotics at a low resolution of the gut microbiota to characterize the activities of targeted bacteria that can play a crucial role in our health.
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Affiliation(s)
- Cassandre Bedu-Ferrari
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- General Mills France, Boulogne Billancourt, France
| | - Paul Biscarrat
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Frederic Pepke
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sarah Vati
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Florence Castelli
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Céline Chollet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments,, CEA, INRAE, Université Paris Saclay, MetaboHUB, Gif-sur-Yvette, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Christelle Hennequet-Antier
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Jang S, Ishigami K, Mergaert P, Kikuchi Y. Ingested soil bacteria breach gut epithelia and prime systemic immunity in an insect. Proc Natl Acad Sci U S A 2024; 121:e2315540121. [PMID: 38437561 PMCID: PMC10945853 DOI: 10.1073/pnas.2315540121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/11/2024] [Indexed: 03/06/2024] Open
Abstract
Insects lack acquired immunity and were thought to have no immune memory, but recent studies reported a phenomenon called immune priming, wherein sublethal dose of pathogens or nonpathogenic microbes stimulates immunity and prevents subsequential pathogen infection. Although the evidence for insect immune priming is accumulating, the underlying mechanisms are still unclear. The bean bug Riptortus pedestris acquires its gut microbiota from ambient soil and spatially structures them into a multispecies and variable community in the anterior midgut and a specific, monospecies Caballeronia symbiont population in the posterior region. We demonstrate that a particular Burkholderia strain colonizing the anterior midgut stimulates systemic immunity by penetrating gut epithelia and migrating into the hemolymph. The activated immunity, consisting of a humoral and a cellular response, had no negative effect on the host fitness, but on the contrary protected the insect from subsequent infection by pathogenic bacteria. Interruption of contact between the Burkholderia strain and epithelia of the gut weakened the host immunity back to preinfection levels and made the insects more vulnerable to microbial infection, demonstrating that persistent acquisition of environmental bacteria is important to maintain an efficient immunity.
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Affiliation(s)
- Seonghan Jang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
| | - Kota Ishigami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, 91198Gif-sur-Yvette, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
- Unit of Applied Biological Chemistry, Graduate School of Agriculture, Hokkaido University, 060-8589Sapporo, Japan
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Lee SW, Park HJ, Van Kaer L, Hong S. Role of CD1d and iNKT cells in regulating intestinal inflammation. Front Immunol 2024; 14:1343718. [PMID: 38274786 PMCID: PMC10808723 DOI: 10.3389/fimmu.2023.1343718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Invariant natural killer T (iNKT) cells, a subset of unconventional T cells that recognize glycolipid antigens in a CD1d-dependent manner, are crucial in regulating diverse immune responses such as autoimmunity. By engaging with CD1d-expressing non-immune cells (such as intestinal epithelial cells and enterochromaffin cells) and immune cells (such as type 3 innate lymphoid cells, B cells, monocytes and macrophages), iNKT cells contribute to the maintenance of immune homeostasis in the intestine. In this review, we discuss the impact of iNKT cells and CD1d in the regulation of intestinal inflammation, examining both cellular and molecular factors with the potential to influence the functions of iNKT cells in inflammatory bowel diseases such as Crohn's disease and ulcerative colitis.
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Affiliation(s)
- Sung Won Lee
- Department of Biomedical Laboratory Science, College of Health and Biomedical Services, Sangji University, Wonju, Republic of Korea
| | - Hyun Jung Park
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Republic of Korea
| | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Seokmann Hong
- Department of Integrative Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, Seoul, Republic of Korea
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Yeh YH, Kelly VW, Pour RR, Sirk SJ. A molecular toolkit for heterologous protein secretion across Bacteroides species. bioRxiv 2023:2023.12.14.571725. [PMID: 38168418 PMCID: PMC10760143 DOI: 10.1101/2023.12.14.571725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
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Affiliation(s)
- Yu-Hsuan Yeh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Vince W. Kelly
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Rahman Rahman Pour
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Perlumi, Berkeley, CA 94704, USA
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead Contact
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Nguyen MR, Ma E, Wyatt D, Knight KL, Osipo C. The effect of an exopolysaccharide probiotic molecule from Bacillus subtilis on breast cancer cells. Front Oncol 2023; 13:1292635. [PMID: 38074643 PMCID: PMC10702531 DOI: 10.3389/fonc.2023.1292635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/27/2023] [Indexed: 02/12/2024] Open
Abstract
Introduction Many well-known risk factors for breast cancer are associated with dysbiosis (an aberrant microbiome). However, how bacterial products modulate cancer are poorly understood. In this study, we investigated the effect of an exopolysaccharide (EPS) produced by the commensal bacterium Bacillus subtilis on breast cancer phenotypes. Although B. subtilis is commonly included in probiotic preparations and its EPS protects against inflammatory diseases, it was virtually unknown whether B. subtilis-derived EPS affects cancer. Methods This work investigated effects of EPS on phenotypes of breast cancer cells as a cancer model. The phenotypes included proliferation, mammosphere formation, cell migration, and tumor growth in two immune compromised mouse models. RNA sequencing was performed on RNA from four breast cancer cells treated with PBS or EPS. IKKβ or STAT1 signaling was assessed using pharmacologic or RNAi-mediated knock down approaches. Results Short-term treatment with EPS inhibited proliferation of certain breast cancer cells (T47D, MDA-MB-468, HCC1428, MDA-MB-453) while having little effect on others (MCF-7, MDA-MB-231, BT549, ZR-75-30). EPS induced G1/G0 cell cycle arrest of T47D cells while increasing apoptosis of MDA-MB-468 cells. EPS also enhanced aggressive phenotypes in T47D cells including cell migration and cancer stem cell survival. Long-term treatment with EPS (months) led to resistance in vitro and promoted tumor growth in immunocompromised mice. RNA-sequence analysis showed that EPS increased expression of pro-inflammatory pathways including STAT1 and NF-κB. IKKβ and/or STAT1 signaling was necessary for EPS to modulate phenotypes of EPS sensitive breast cancer cells. Discussion These results demonstrate a multifaceted role for an EPS molecule secreted by the probiotic bacterium B. subtilis on breast cancer cell phenotypes. These results warrant future studies in immune competent mice and different cancer models to fully understand potential benefits and/or side effects of long-term use of probiotics.
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Affiliation(s)
- Mai R. Nguyen
- M.D./Ph.D. Program, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Emily Ma
- M.D./Ph.D. Program, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Integrated Cell Biology Program, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Debra Wyatt
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Katherine L. Knight
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Clodia Osipo
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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Marco-Fuertes A, Jordá J, Marin C, Lorenzo-Rebenaque L, Montoro-Dasi L, Vega S. Multidrug-Resistant Escherichia coli Strains to Last Resort Human Antibiotics Isolated from Healthy Companion Animals in Valencia Region. Antibiotics (Basel) 2023; 12:1638. [PMID: 37998840 PMCID: PMC10669260 DOI: 10.3390/antibiotics12111638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Failure in antibiotic therapies due to the increase in antimicrobial-resistant (AMR) bacteria is one of the main threats to public and animal health. In recent decades, the perception of companion animals has changed, from being considered as a work tool to a household member, creating a family bond and sharing spaces in their daily routine. Hence, the aim of this study is to assess the current epidemiological situation regarding the presence of AMR and multidrug resistance (MDR) in companion animals in the Valencia Region, using the indicator bacteria Escherichia coli as a sentinel. For this purpose, 244 samples of dogs and cats were collected from veterinary centres to assess antimicrobial susceptibility against a panel of 22 antibiotics with public health relevance. A total of 197 E. coli strains were isolated from asymptomatic dogs and cats. The results showed AMR against all the 22 antibiotics studied, including those critically important to human medicine. Moreover, almost 50% of the strains presented MDR. The present study revealed the importance of monitoring AMR and MDR trends in companion animals, as they could pose a risk due to the spread of AMR and its resistance genes to humans, other animals and the environment they cohabit.
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Affiliation(s)
- Ana Marco-Fuertes
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (A.M.-F.); (J.J.); (C.M.); (S.V.)
| | - Jaume Jordá
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (A.M.-F.); (J.J.); (C.M.); (S.V.)
| | - Clara Marin
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (A.M.-F.); (J.J.); (C.M.); (S.V.)
| | - Laura Lorenzo-Rebenaque
- Institute of Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Laura Montoro-Dasi
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (A.M.-F.); (J.J.); (C.M.); (S.V.)
| | - Santiago Vega
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (A.M.-F.); (J.J.); (C.M.); (S.V.)
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7
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Lushington GH, Linde A, Melgarejo T. Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog. BioTech (Basel) 2023; 12:61. [PMID: 37987478 PMCID: PMC10660736 DOI: 10.3390/biotech12040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.
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Affiliation(s)
| | - Annika Linde
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
| | - Tonatiuh Melgarejo
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
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8
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Ramírez-Sánchez D, Gibelin-Viala C, Mayjonade B, Duflos R, Belmonte E, Pailler V, Bartoli C, Carrere S, Vailleau F, Roux F. Corrigendum: Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats. Front Microbiol 2023; 14:1304377. [PMID: 37901829 PMCID: PMC10600367 DOI: 10.3389/fmicb.2023.1304377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2022.984832.].
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Affiliation(s)
| | | | | | - Rémi Duflos
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Elodie Belmonte
- Gentyane, UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Vincent Pailler
- Gentyane, UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Claudia Bartoli
- Institute for Genetics, Environment and Plant Protection (IGEPP), INRAE, Institut Agro AgroCampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sébastien Carrere
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
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9
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Kennedy MS, Zhang M, DeLeon O, Bissell J, Trigodet F, Lolans K, Temelkova S, Carroll KT, Fiebig A, Deutschbauer A, Sidebottom AM, Lake J, Henry C, Rice PA, Bergelson J, Chang EB. Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization. Cell Rep 2023; 42:113009. [PMID: 37598339 PMCID: PMC10528517 DOI: 10.1016/j.celrep.2023.113009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/17/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
To understand how a bacterium ultimately succeeds or fails in adapting to a new host, it is essential to assess the temporal dynamics of its fitness over the course of colonization. Here, we introduce a human-derived commensal organism, Bacteroides thetaiotaomicron (Bt), into the guts of germ-free mice to determine whether and how the genetic requirements for colonization shift over time. Combining a high-throughput functional genetics assay and transcriptomics, we find that gene usage changes drastically during the first days of colonization, shifting from high expression of amino acid biosynthesis genes to broad upregulation of diverse polysaccharide utilization loci. Within the first week, metabolism becomes centered around utilization of a predominant dietary oligosaccharide, and these changes are largely sustained through 6 weeks of colonization. Spontaneous mutations in wild-type Bt also evolve around this locus. These findings highlight the importance of considering temporal colonization dynamics in developing more effective microbiome-based therapies.
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Affiliation(s)
- Megan S Kennedy
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA; Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Manjing Zhang
- Committee on Microbiology, The University of Chicago, Chicago, IL, USA
| | - Orlando DeLeon
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jacie Bissell
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Sara Temelkova
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, Department of Biomedical Sciences, The University of Chicago, Chicago, IL, USA
| | - Joash Lake
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
| | - Chris Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Joy Bergelson
- Committee on Microbiology, The University of Chicago, Chicago, IL, USA
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
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10
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Schropp N, Stanislas V, Michels KB, Thriene K. How Do Prebiotics Affect Human Intestinal Bacteria?-Assessment of Bacterial Growth with Inulin and XOS In Vitro. Int J Mol Sci 2023; 24:12796. [PMID: 37628977 PMCID: PMC10454692 DOI: 10.3390/ijms241612796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Prebiotics are believed to exhibit high specificity in stimulating the growth or activity of a limited number of commensal microorganisms, thereby conferring health benefits to the host. However, the mechanism of action of prebiotics depends on multiple factors, including the composition of an individual's gut microbiota, and is therefore difficult to predict. It is known that different bacteria can utilize inulin and xylooligosaccharides (XOS), but an overview of which bacteria in the human gut may be affected is lacking. Detailed knowledge of how bacterial growth is affected by prebiotics is furthermore useful for the development of new synbiotics, which combine a living microorganism with a selective substrate to confer a health benefit to the host. Hence, we developed a statistical model to compare growth in vitro among typical human gut bacteria from different phylogenetic lineages. Based on continuous observation of the optical density (OD600), we compare maximal growth rates (rmax), maximal attained OD600 (ODmax), and area under the growth curve (AUC) of bacteria grown on inulin or XOS. The consideration of these three parameters suggests strain-specific preferences for inulin or XOS and reveals previously unknown preferences such as Streptococcus salivarius growth on XOS.
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Affiliation(s)
| | | | | | - Kerstin Thriene
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79110 Freiburg, Germany; (N.S.); (V.S.); (K.B.M.)
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11
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Luis AS, Hansson GC. Intestinal mucus and their glycans: A habitat for thriving microbiota. Cell Host Microbe 2023; 31:1087-1100. [PMID: 37442097 PMCID: PMC10348403 DOI: 10.1016/j.chom.2023.05.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/07/2023] [Accepted: 05/23/2023] [Indexed: 07/15/2023]
Abstract
The colon mucus layer is organized with an inner colon mucus layer that is impenetrable to bacteria and an outer mucus layer that is expanded to allow microbiota colonization. A major component of mucus is MUC2, a glycoprotein that is extensively decorated, especially with O-glycans. In the intestine, goblet cells are specialized in controlling glycosylation and making mucus. Some microbiota members are known to encode multiple proteins that are predicted to bind and/or cleave mucin glycans. The interactions between commensal microbiota and host mucins drive intestinal colonization, while at the same time, the microbiota can utilize the glycans on mucins and affect the colonic mucus properties. This review will examine this interaction between commensal microbes and intestinal mucins and discuss how this interplay affects health and disease.
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Affiliation(s)
- Ana S Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
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12
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Weckel A, Dhariwala MO, Ly K, Tran VM, Ojewumi OT, Riggs JB, Gonzalez JR, Dwyer LR, Okoro JN, Leech JM, Bacino MS, Cho GD, Merana G, Anandasabapathy N, Kumamoto Y, Scharschmidt TC. Long-term tolerance to skin commensals is established neonatally through a specialized dendritic cell subgroup. Immunity 2023; 56:1239-1254.e7. [PMID: 37028427 PMCID: PMC10330031 DOI: 10.1016/j.immuni.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/29/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023]
Abstract
Early-life establishment of tolerance to commensal bacteria at barrier surfaces carries enduring implications for immune health but remains poorly understood. Here, we showed that tolerance in skin was controlled by microbial interaction with a specialized subset of antigen-presenting cells. More particularly, CD301b+ type 2 conventional dendritic cells (DCs) in neonatal skin were specifically capable of uptake and presentation of commensal antigens for the generation of regulatory T (Treg) cells. CD301b+ DC2 were enriched for phagocytosis and maturation programs, while also expressing tolerogenic markers. In both human and murine skin, these signatures were reinforced by microbial uptake. In contrast to their adult counterparts or other early-life DC subsets, neonatal CD301b+ DC2 highly expressed the retinoic-acid-producing enzyme, RALDH2, the deletion of which limited commensal-specific Treg cell generation. Thus, synergistic interactions between bacteria and a specialized DC subset critically support early-life tolerance at the cutaneous interface.
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Affiliation(s)
- Antonin Weckel
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Miqdad O Dhariwala
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Kevin Ly
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Victoria M Tran
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Oluwasunmisola T Ojewumi
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Julianne B Riggs
- University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Jeanmarie R Gonzalez
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Laura R Dwyer
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Joy N Okoro
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - John M Leech
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Margot S Bacino
- University of California, San Francisco, Oral and Craniofacial Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Grace D Cho
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, Los Angeles, Department of Infectious Diseases, Los Angeles, CA 90095, USA
| | - Geil Merana
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Niroshana Anandasabapathy
- Department of Dermatology, Meyer Cancer Center, Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY, USA
| | - Yosuke Kumamoto
- Department of Pathology, Immunology and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Tiffany C Scharschmidt
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA.
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13
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Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L, Vonaesch P. Corrigendum: A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Front Microbiol 2023; 14:1208177. [PMID: 37283928 PMCID: PMC10241206 DOI: 10.3389/fmicb.2023.1208177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 06/08/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1104707.].
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Affiliation(s)
- Paul Tetteh Asare
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Chi-Hsien Lee
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Vera Hürlimann
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Youzheng Teo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Nermin Akduman
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Cordula Gekeler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Myriam Corthesy
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Claire Kohout
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | | | | | - Gilbert Greub
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Eric G Pamer
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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14
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Wilson A, Manuzak JA, Liang H, Leda AR, Klatt N, Lynch RM. Probiotic Therapy During Vaccination Alters Antibody Response to Simian-Human Immunodeficiency Virus Infection But Not to Commensals. AIDS Res Hum Retroviruses 2023; 39:222-231. [PMID: 36517984 PMCID: PMC10171943 DOI: 10.1089/aid.2022.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The induction of robust circulating antibody titers is a key goal of HIV-1 vaccination. Probiotic supplementation is an established strategy to enhance microbiota and boost antibody responses to vaccines. A recent study tested whether oral probiotics could enhance vaccine-specific mucosal immunity by testing vaccination with and without supplementation in a Rhesus macaque Simian-Human Immunodeficiency Virus challenge model. Although supplementation was not associated with protection, the effects of probiotics on immunity after infection were not examined. To address this question, we measured antibody titers to HIV Env and commensal bacteria in plasma from the vaccination/supplementation time points as well as after Simian-Human Immunodeficiency Virus (SHIV) acquisition. We found that a trend toward lower HIV Env-specific titers in the animals given probiotics plus vaccine became greater after SHIV infection. Significantly lower Immunoglobulin (Ig) A titers were observed in animals vaccinated and supplemented compared with vaccine alone due to a delay in antibody kinetics at week 2 postinfection. We observed no difference, however, in titers to commensal bacteria during probiotic supplementation or after SHIV infection. These results suggest that probiotic supplementation may be a strategy for reducing IgA-specific HIV antibodies in the plasma, a correlate associated with increased HIV infection in the RV144 clinical trial.
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Affiliation(s)
- Andrew Wilson
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
| | - Jennifer A. Manuzak
- Division of Immunology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Hua Liang
- Department of Statistics, George Washington University, Washington, District of Columbia, USA
| | - Ana R. Leda
- Department of Microbiology and Immunology, Scripps Biomedical Research, University of Florida, Jupiter, Florida, USA
| | - Nichole Klatt
- Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rebecca M. Lynch
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
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15
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Di Nardo A, Chang YL, Alimohammadi S, Masuda-Kuroki K, Wang Z, Sriram K, Insel PA. Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts. Cell Rep 2023; 42:112453. [PMID: 37120813 DOI: 10.1016/j.celrep.2023.112453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/16/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023] Open
Abstract
Activation and degranulation of mast cells (MCs) is an essential aspect of innate and adaptive immunity. Skin MCs, the most exposed to the external environment, are at risk of quickly degranulating with potentially severe consequences. Here, we define how MCs assume a tolerant phenotype via crosstalk with dermal fibroblasts (dFBs) and how this phenotype reduces unnecessary inflammation when in contact with beneficial commensal bacteria. We explore the interaction of human MCs (HMCs) and dFBs in the human skin microenvironment and test how this interaction controls MC inflammatory response by inhibiting the nuclear factor κB (NF-κB) pathway. We show that the extracellular matrix hyaluronic acid, as the activator of the regulatory zinc finger (de)ubiquitinating enzyme A20/tumor necrosis factor α-induced protein 3 (TNFAIP3), is responsible for the reduced HMC response to commensal bacteria. The role of hyaluronic acid as an anti-inflammatory ligand on MCs opens new avenues for the potential treatment of inflammatory and allergic disorders.
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Affiliation(s)
- Anna Di Nardo
- Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
| | - Yu-Ling Chang
- Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Shahrzad Alimohammadi
- Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Kana Masuda-Kuroki
- Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Zhenping Wang
- Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Krishna Sriram
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA; Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Paul A Insel
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA; Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
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16
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Conrado FO, Stacy NI, Wellehan JFX. Out with the old, in with the new: What's up with Simonsiella spp.? Vet Clin Pathol 2023. [PMID: 37029600 DOI: 10.1111/vcp.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 04/09/2023]
Affiliation(s)
- Francisco O Conrado
- Departments of Comparative Pathobiology, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Nicole I Stacy
- Comparative, Diagnostic, & Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - James F X Wellehan
- Comparative, Diagnostic, & Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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17
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Ma Z, Wang H, Shi Z, Yan F, Li Q, Chen J, Cui ZK, Zhang Y, Jin X, Jia YG, Wang L. Inhalable GSH-Triggered Nanoparticles to Treat Commensal Bacterial Infection in In Situ Lung Tumors. ACS Nano 2023; 17:5740-5756. [PMID: 36884352 DOI: 10.1021/acsnano.2c12165] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bacterial infection has been considered one of the primary reasons for low survival rate of lung cancer patients. Herein, we demonstrated that a kind of mesoporous silica nanoparticles loaded with anticancer drug doxorubicin (DOX) and antimicrobial peptide HHC36 (AMP) (MSN@DOX-AMP) can kill both commensal bacteria and tumor cells under GSH-triggering, modulating the immunosuppressive tumor microenvironment, significantly treating commensal bacterial infection, and eliminating in situ lung tumors in a commensal model. Meanwhile, MSN@DOX-AMP encapsulated DOX and AMP highly efficiently via a combined strategy of physical adsorption and click chemistry and exhibited excellent hemocompatibility and biocompatibility. Importantly, MSN@DOX-AMP could be inhaled and accumulate in lung by a needle-free nebulization, achieving a better therapeutic effect. This system is expected to serve as a straightforward platform to treat commensal bacterial infections in tumors and promote the translation of such inhaled GSH-triggered MSN@DOX-AMP to clinical treatments of lung cancer.
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Affiliation(s)
- Zunwei Ma
- School of Materials Science & Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huaiming Wang
- Department of Colorectal Surgery, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510655, China
| | - Zhifeng Shi
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Fengying Yan
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Qingtao Li
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Junjian Chen
- Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China
| | - Zhong-Kai Cui
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yunjiao Zhang
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Xin Jin
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Yong-Guang Jia
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
| | - Lin Wang
- School of Materials Science & Engineering, South China University of Technology, Guangzhou 510006, China
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18
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Mosby CA, Edelmann MJ, Jones MK. Murine Norovirus Interaction with Enterobacter cloacae Leads to Changes in Membrane Stability and Packaging of Lipid and Metabolite Vesicle Content. Microbiol Spectr 2023; 11:e0469122. [PMID: 36943087 PMCID: PMC10100888 DOI: 10.1128/spectrum.04691-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Outer membrane vesicles (OMVs) are a primary means of communication for Gram-negative bacteria. The specific role of vesicle components in cellular communication and how components are packaged are still under investigation, but a correlation exists between OMV biogenesis and content. The two primary mechanisms of OMV biogenesis are membrane blebbing and explosive cell lysis, and vesicle content is based on the biogenesis mechanism. Hypervesiculation, which can be induced by stress conditions, also influences OMV content. Norovirus interaction with Enterobacter cloacae induces stress responses leading to increased OMV production and changes in DNA content, protein content, and vesicle size. The presence of genomic DNA and cytoplasmic proteins in these OMVs suggests some of the vesicles are formed by explosive cell lysis, so reduction or loss of these components indicates a shift away from this mechanism of biogenesis. Based on this, further investigation into bacterial stability and OMV content was conducted. Results showed that norovirus induced a dramatic shift in OMV lipid content. Specifically, the increased accumulation of phospholipids is associated with increased blebbing, thereby supporting previous observations that noroviruses shift the mechanism of OMV biogenesis. Slight differences in OMV metabolite content were also observed. While norovirus induced changes in OMV content, it did not change the lipid content of the bacterial outer membrane or the metabolite content of the bacterial cell. Overall, these results indicate that norovirus induces significant changes to OMV lipid architecture and cargo, which may be linked to a change in the mechanism of vesicle biogenesis. IMPORTANCE Extracellular vesicles from commensal bacteria are recognized for their importance in modulating host immune responses, and vesicle content is related to their impact on the host. Therefore, understanding how vesicles are formed and how their content shifts in response to stress conditions is necessary for elucidating their downstream functions. Our recent work has demonstrated that interactions between noroviruses and Enterobacter cloacae induce bacterial stress responses leading to hypervesiculation. In this article, we characterize and compare the lipid and metabolomic cargo of E. cloacae vesicles generated in the presence and absence of norovirus and show that viral interactions induce significant changes in vesicle content. Furthermore, we probe how these changes and changes to the bacterial cell may be indicative of a shift in the mechanism of vesicle biogenesis. Importantly, we find that noroviruses induce significant changes in vesicle lipid architecture and cargo that may be responsible for the immunogenic activity of these vesicles.
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Affiliation(s)
- Chanel A. Mosby
- Microbiology and Cell Science Department, IFAS, University of Florida, Gainesville, Florida, USA
| | - Mariola J. Edelmann
- Microbiology and Cell Science Department, IFAS, University of Florida, Gainesville, Florida, USA
| | - Melissa K. Jones
- Microbiology and Cell Science Department, IFAS, University of Florida, Gainesville, Florida, USA
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19
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Luu M, Schütz B, Lauth M, Visekruna A. The Impact of Gut Microbiota-Derived Metabolites on the Tumor Immune Microenvironment. Cancers (Basel) 2023; 15:cancers15051588. [PMID: 36900377 PMCID: PMC10001145 DOI: 10.3390/cancers15051588] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Prevention of the effectiveness of anti-tumor immune responses is one of the canonical cancer hallmarks. The competition for crucial nutrients within the tumor microenvironment (TME) between cancer cells and immune cells creates a complex interplay characterized by metabolic deprivation. Extensive efforts have recently been made to understand better the dynamic interactions between cancer cells and surrounding immune cells. Paradoxically, both cancer cells and activated T cells are metabolically dependent on glycolysis, even in the presence of oxygen, a metabolic process known as the Warburg effect. The intestinal microbial community delivers various types of small molecules that can potentially augment the functional capabilities of the host immune system. Currently, several studies are trying to explore the complex functional relationship between the metabolites secreted by the human microbiome and anti-tumor immunity. Recently, it has been shown that a diverse array of commensal bacteria synthetizes bioactive molecules that enhance the efficacy of cancer immunotherapy, including immune checkpoint inhibitor (ICI) treatment and adoptive cell therapy with chimeric antigen receptor (CAR) T cells. In this review, we highlight the importance of commensal bacteria, particularly of the gut microbiota-derived metabolites that are capable of shaping metabolic, transcriptional and epigenetic processes within the TME in a therapeutically meaningful way.
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Affiliation(s)
- Maik Luu
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Burkhard Schütz
- Institute of Anatomy and Cell Biology, Philipps-University Marburg, 35037 Marburg, Germany
| | - Matthias Lauth
- Department of Gastroenterology, Center for Tumor and Immune Biology (ZTI), Philipps-University Marburg, 35043 Marburg, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, 35043 Marburg, Germany
- Correspondence:
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20
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Meslé MM, Gray CR, Dlakić M, DuBois JL. Bacteroides thetaiotaomicron, a Model Gastrointestinal Tract Species, Prefers Heme as an Iron Source, Yields Protoporphyrin IX as a Product, and Acts as a Heme Reservoir. Microbiol Spectr 2023; 11:e0481522. [PMID: 36862015 PMCID: PMC10100974 DOI: 10.1128/spectrum.04815-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
Members of the phylum Bacteroidetes are abundant in healthy gastrointestinal (GI) tract flora. Bacteroides thetaiotaomicron is a commensal heme auxotroph and representative of this group. Bacteroidetes are sensitive to host dietary iron restriction but proliferate in heme-rich environments that are also associated with colon cancer. We hypothesized that B. thetaiotaomicron may act as a host reservoir for iron and/or heme. In this study, we defined growth-promoting quantities of iron for B. thetaiotaomicron. B. thetaiotaomicron preferentially consumed and hyperaccumulated iron in the form of heme when presented both heme and nonheme iron sources in excess of its growth needs, leading to an estimated 3.6 to 8.4 mg iron in a model GI tract microbiome consisting solely of B. thetaiotaomicron. Protoporphyrin IX was identified as an organic coproduct of heme metabolism, consistent with anaerobic removal of iron from the heme leaving the intact tetrapyrrole as the observed product. Notably, no predicted or discernible pathway for protoporphyrin IX generation exists in B. thetaiotaomicron. Heme metabolism in congeners of B. thetaiotaomicron has previously been associated with the 6-gene hmu operon, based on genetic studies. A bioinformatics survey demonstrated that the intact operon is widespread in but confined to members of the Bacteroidetes phylum and ubiquitous in healthy human GI tract flora. Anaerobic heme metabolism by commensal Bacteroidetes via hmu is likely a major contributor to human host metabolism of the heme from dietary red meat and a driver for the selective growth of these species in the GI tract consortium. IMPORTANCE Research on bacterial iron metabolism has historically focused on the host-pathogen relationship, where the host suppresses pathogen growth by cutting off access to iron. Less is known about how host iron is shared with bacterial species that live commensally in the anaerobic human GI tract, typified by members of phylum Bacteroidetes. While many facultative pathogens avidly produce and consume heme iron, most GI tract anaerobes are heme auxotrophs whose metabolic preferences we aimed to describe. Understanding iron metabolism by model microbiome species like Bacteroides thetaiotaomicron is essential for modeling the ecology of the GI tract, which serves the long-term biomedical goals of manipulating the microbiome to facilitate host metabolism of iron and remediate dysbiosis and associated pathologies (e.g., inflammation and cancer).
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Affiliation(s)
- Margaux M. Meslé
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Chase R. Gray
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Mensur Dlakić
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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21
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Lee KW, Shin JS, Lee CM, Han HY, O Y, Kim HW, Cho TJ. Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship? Nutrients 2023; 15:nu15051131. [PMID: 36904133 PMCID: PMC10005057 DOI: 10.3390/nu15051131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Bacterial co-culture studies using synthetic gut microbiomes have reported novel research designs to understand the underlying role of bacterial interaction in the metabolism of dietary resources and community assembly of complex microflora. Since lab-on-a-chip mimicking the gut (hereafter "gut-on-a-chip") is one of the most advanced platforms for the simulative research regarding the correlation between host health and microbiota, the co-culture of the synthetic bacterial community in gut-on-a-chip is expected to reveal the diet-microbiota relationship. This critical review analyzed recent research on bacterial co-culture with perspectives on the ecological niche of commensals, probiotics, and pathogens to categorize the experimental approaches for diet-mediated management of gut health as the compositional and/or metabolic modulation of the microbiota and the control of pathogens. Meanwhile, the aim of previous research on bacterial culture in gut-on-a-chip has been mainly limited to the maintenance of the viability of host cells. Thus, the integration of study designs established for the co-culture of synthetic gut consortia with various nutritional resources into gut-on-a-chip is expected to reveal bacterial interspecies interactions related to specific dietary patterns. This critical review suggests novel research topics for co-culturing bacterial communities in gut-on-a-chip to realize an ideal experimental platform mimicking a complex intestinal environment.
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Affiliation(s)
- Ki Won Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Jin Song Shin
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Chan Min Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hea Yeon Han
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Yun O
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tae Jin Cho
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Correspondence: ; Tel.: +82-44-860-1433
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22
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Yang R, Shan S, Shi J, Li H, An N, Li S, Cui K, Guo H, Li Z. Coprococcus eutactus, a Potent Probiotic, Alleviates Colitis via Acetate-Mediated IgA Response and Microbiota Restoration. J Agric Food Chem 2023; 71:3273-3284. [PMID: 36786768 DOI: 10.1021/acs.jafc.2c06697] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Inflammatory bowel disease (IBD) is a complex disease characterized by relapsing episodes of inflammation of the colonic mucosa. Research into IBD suggests that this disease condition is caused by alterations in resident mucosal bacterial populations. Our previous study showed that Coprococcus was significantly elevated during the improvement of IBD. Human metagenome database GMrepo also indicates Coprococcus, in particular, Coprococcus eutactus (C. eutactus), which was negatively associated with IBD. The current study implied the alleviated effects and mechanisms of C. eutactus on dextran sodium sulfate-induced experimental colitis mice. Gavage with C. eutactus-ameliorated acute colitis, as evidenced, relieved weight loss, decreased concentrations of proinflammatory cytokines TNF-α, IL-1β, and IL-6, and increased anti-inflammatory factors, IL-4, IL-5, and IL-10. In addition, C. eutactus enhanced the maturation of goblet cells and the expressions of mucins and restored the expressions of tight junction proteins such as claudin-1, occludin, and ZO-1. As a short-chain fatty acid-producing bacterium, C. eutactus mainly generates acetic acid. Interestingly, not only high levels of secretory immunoglobulin A (SIgA) but also increased IgA-producing plasma cells were observed in colitis mice during the administration of C. eutactus. Importantly, our data demonstrated that colonic SIgA is specifically coated on pathogens of Enterobacteriaceae. Owing to the selective binding effect of SIgA on microorganisms, the microbial diversity in the intestinal lumen and mucosa of C. eutactus-treated colitis mice was significantly restored, and the microbiota structure was remodeled. These findings provide substantial insight that C. eutactus as a promising probiotic can ameliorate colitis. In conclusion, our findings may deliver a novel approach to the prevention and biotherapy of IBD.
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Affiliation(s)
- Ruipeng Yang
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Shuhua Shan
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiangying Shi
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Hanqing Li
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Ning An
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Songtao Li
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Kaili Cui
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Huiqin Guo
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhuoyu Li
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of National Ministry of Education, Shanxi University, Taiyuan 030006, China
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23
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Spring J, Beilinson V, DeFelice BC, Sanchez JM, Fischbach M, Chervonsky A, Golovkina T. Retroviral Infection and Commensal Bacteria Dependently Alter the Metabolomic Profile in a Sterile Organ. Viruses 2023; 15:386. [PMID: 36851600 PMCID: PMC9967258 DOI: 10.3390/v15020386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Both viruses and bacteria produce "pathogen associated molecular patterns" that may affect microbial pathogenesis and anti-microbial responses. Additionally, bacteria produce metabolites, while viruses could change the metabolic profiles of the infected cells. Here, we used an unbiased metabolomics approach to profile metabolites in spleens and blood of murine leukemia virus-infected mice monocolonized with Lactobacillus murinus to show that viral infection significantly changes the metabolite profile of monocolonized mice. We hypothesize that these changes could contribute to viral pathogenesis or to the host response against the virus and thus open a new avenue for future investigations.
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Affiliation(s)
- Jessica Spring
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Vera Beilinson
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Michael Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Alexander Chervonsky
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Tatyana Golovkina
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Genetics, Genomics and System Biology, University of Chicago, Chicago, IL 60637, USA
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Sher AA, VanAllen ME, Ahmed H, Whitehead-Tillery C, Rafique S, Bell JA, Zhang L, Mansfield LS. Conjugative RP4 Plasmid-Mediated Transfer of Antibiotic Resistance Genes to Commensal and Multidrug-Resistant Enteric Bacteria In Vitro. Microorganisms 2023; 11. [PMID: 36677486 DOI: 10.3390/microorganisms11010193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Many antibiotic-resistant bacteria carry resistance genes on conjugative plasmids that are transferable to commensals and pathogens. We determined the ability of multiple enteric bacteria to acquire and retransfer a broad-host-range plasmid RP4. We used human-derived commensal Escherichia coli LM715-1 carrying a chromosomal red fluorescent protein gene and green fluorescent protein (GFP)-labeled broad-host-range RP4 plasmid with ampR, tetR, and kanR in in vitro matings to rifampicin-resistant recipients, including Escherichia coli MG1655, Dec5α, Vibrio cholerae, Pseudomonas putida, Pseudomonas aeruginosa, Klebsiella pneumoniae, Citrobacter rodentium, and Salmonella Typhimurium. Transconjugants were quantified on selective media and confirmed using fluorescence microscopy and PCR for the GFP gene. The plasmid was transferred from E. coli LM715-1 to all tested recipients except P. aeruginosa. Transfer frequencies differed between specific donor-recipient pairings (10-2 to 10-8). Secondary retransfer of plasmid from transconjugants to E. coli LM715-1 occurred at frequencies from 10-2 to 10-7. A serial passage plasmid persistence assay showed plasmid loss over time in the absence of antibiotics, indicating that the plasmid imposed a fitness cost to its host, although some plasmid-bearing cells persisted for at least ten transfers. Thus, the RP4 plasmid can transfer to multiple clinically relevant bacterial species without antibiotic selection pressure.
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Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L, Vonaesch P. A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Front Microbiol 2023; 14:1104707. [PMID: 36896425 PMCID: PMC9990839 DOI: 10.3389/fmicb.2023.1104707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Chi-Hsien Lee
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vera Hürlimann
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Youzheng Teo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Nermin Akduman
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Cordula Gekeler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Myriam Corthesy
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Claire Kohout
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | | | | | - Gilbert Greub
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Eric G Pamer
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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26
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Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
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Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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Abstract
In light of the demonstrated antagonism of Wnt5A signaling toward the growth of several bacterial pathogens, it was important to study the influence of Wnt5A on gut-resident bacteria and its outcome. Here, we demonstrate that in contrast to inhibiting the survival of the established gut pathogen Salmonella enterica, Wnt5A clearly promotes the survival of the common gut commensals Enterococcus faecalis and Lactobacillus rhamnosus within macrophages through a self-perpetuating Wnt5A-actin axis. A Wnt5A-actin axis furthermore regulates the subsistence of the natural bacterial population of the Peyer's patches, as is evident from the diminution in the countable bacterial CFU therein through the application of Wnt5A signaling and actin assembly inhibitors. Wnt5A dependency of the gut-resident bacterial population is also manifested in the notable difference between the bacterial diversities associated with the feces and Peyer's patches of Wnt5A heterozygous mice, which lack a functional copy of the Wnt5A gene, and their wild-type counterparts. Alterations in the gut commensal bacterial population resulting from either the lack of a copy of the Wnt5A gene or inhibitor-mediated attenuation of Wnt5A signaling are linked with significant differences in cell surface major histocompatibility complex (MHC) II levels and regulatory versus activated CD4 T cells associated with the Peyer's patches. Taken together, our findings reveal the significance of steady state Wnt5A signaling in shaping the gut commensal bacterial population and the T cell repertoire linked to it, thus unveiling a crucial control device for the maintenance of gut bacterial diversity and T cell homeostasis. IMPORTANCE Gut commensal bacterial diversity and T cell homeostasis are crucial entities of the host innate immune network, yet the molecular details of host-directed signaling pathways that sustain the steady state of gut bacterial colonization and T cell activation remain unclear. Here, we describe the protective role of a Wnt5A-actin axis in the survival of several gut bacterial commensals and its necessity in shaping gut bacterial colonization and the associated T cell repertoire. This study opens up new avenues of investigation into the role of the Wnt5A-actin axis in protection of the gut from dysbiosis-related inflammatory disorders.
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28
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Bharathi SV, Rajamohan G. Biocide-Resistant Escherichia coli ST540 Co-Harboring ESBL, dfrA14 Confers QnrS-Dependent Plasmid-Mediated Quinolone Resistance. Antibiotics (Basel) 2022; 11. [PMID: 36551381 DOI: 10.3390/antibiotics11121724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 12/04/2022] Open
Abstract
Emerging sequence types of pathogenic bacteria have a dual ability to acquire resistance islands/determinants, and remain renitent towards disinfection practices; therefore, they are considered "critical risk factors" that contribute significantly to the global problem of antimicrobial resistance. Multidrug-resistant Escherichia coli was isolated, its genome sequenced, and its susceptibilities characterized, in order to understand the genetic basis of its antimicrobial resistance.The draft genome sequencing of E. coli ECU32, was performed with Illumina NextSeq 500, and annotated using a RAST server. The antibiotic resistome, genomic island, insertion sequences, and prophages were analyzed using bioinformatics tools. Subsequently, analyses including antibiotic susceptibility testing, E-test, bacterial growth, survival, and efflux inhibition assays were performed.The draft genome of E. coli ECU32 was 4.7 Mb in size, the contigs were 107, and the G+C content was 50.8%. The genome comprised 4658 genes, 4543 CDS, 4384 coding genes, 115 RNA genes, 88 tRNAs, and 3 CRISPR arrays. The resistome characterization of ST540 E. coli ECU32 revealed the presence of ESBL, APH(6)-Id, APH(3')-IIa, dfrA14, and QnrS1, with broad-spectrum multidrug and biocide resistance. Comparative genome sequence analysis revealed the presence of transporter and several virulence genes. Efflux activity and growth inhibition assays, which were performed with efflux substrates in the presence of inhibitor PAβN, exhibited significant reduced growth relative to its control.This study discusses the genotypic and phenotypic characterization of the biocide-tolerant multidrug-resistant E. coli O9:H30 strain, highlighting the contributory role of qnrS-dependent plasmid-mediated quinolone resistance, in addition to innate enzymatic modes of multidrug resistance mechanisms.
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Huang W, Zhang Y, Li Z, Li M, Li F, Mortimer M, Guo LH. Silver and Hyaluronic Acid-Coated Gold Nanoparticles Modulate the Metabolism of a Model Human Gut Bacterium Lactobacillus casei. Nanomaterials (Basel) 2022; 12:nano12193377. [PMID: 36234503 PMCID: PMC9565723 DOI: 10.3390/nano12193377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/11/2022] [Accepted: 09/23/2022] [Indexed: 05/19/2023]
Abstract
Medical applications of nanotechnology are promising in creating efficient and targeted therapies. However, so far, nanodrug design has not taken into consideration possible effects on human microbiota. The beneficial functions of bacteria could be stimulated by nanodrugs while negative effects on beneficial bacteria could cause risks to human health. Here, simulated intestinal fluid (IF) was optimized for culturing a human commensal and probiotic bacterial strain, Lactobacillus casei, to study the effects of medically relevant NPs—Ag and hyaluronic acid-coated Au NPs (HA-Au NPs)—in conditions pertinent to the gastrointestinal tract. When cultivated either aerobically or anaerobically, the specific growth rates of L. casei were ~0.2 h−1 in IF and ~0.4 h−1 in the standard medium of lactobacilli (MRS). Ag NPs inhibited the growth of L. casei in IF at lower concentrations (EC50 ~ 65 and 15 mg/L in aerobic and anaerobic conditions, respectively) than in MRS (EC50 > 100 mg/L), likely caused by differences in the composition of the two media and different intrinsic growth rates of bacteria in IF and MRS. Ag NP dissolution in IF and MRS did not explain the differences in growth inhibition, implying NP-specific effects. HA-Au NPs were not growth-inhibitory to L. casei up to 250 mg/L. Still, both NPs at sub-growth-inhibitory concentrations suppressed the expression of bacteriocin genes in L. casei, suggesting an inhibitory effect of NPs on the probiotic properties of L. casei, i.e., its competitiveness in microbial communities. However, HA-Au NPs did not appear to affect or even stimulated the immunomodulatory properties of L. casei in human intestinal epithelial cells. Thus, medically relevant NPs at low, sub-bacteriostatic levels can affect the metabolism of beneficial human bacteria and potentially induce changes in the microbiota and immune signaling.
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Affiliation(s)
- Wenqian Huang
- College of Life Science, China Jiliang University, Hangzhou 310018, China
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yirong Zhang
- College of Life Science, China Jiliang University, Hangzhou 310018, China
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhi Li
- College of Life Science, China Jiliang University, Hangzhou 310018, China
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
| | - Minjie Li
- College of Quality and Safety Engineering, China Jiliang University, Hangzhou 310018, China
| | - Fangfang Li
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
- College of Quality and Safety Engineering, China Jiliang University, Hangzhou 310018, China
| | - Monika Mortimer
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
- College of Quality and Safety Engineering, China Jiliang University, Hangzhou 310018, China
- Correspondence: (M.M.); (L.-H.G.)
| | - Liang-Hong Guo
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou 310018, China
- College of Quality and Safety Engineering, China Jiliang University, Hangzhou 310018, China
- Correspondence: (M.M.); (L.-H.G.)
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30
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Goytia M, Wadsworth CB. Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria. mBio 2022;:e0199122. [PMID: 36154280 DOI: 10.1128/mbio.01991-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is widespread within Neisseria gonorrhoeae populations. Recent work has highlighted the importance of commensal Neisseria (cN) as a source of AMR for their pathogenic relatives through horizontal gene transfer (HGT) of AMR alleles, such as mosaic penicillin binding protein 2 (penA), multiple transferable efflux pump (mtr), and DNA gyrase subunit A (gyrA) which impact beta-lactam, azithromycin, and ciprofloxacin susceptibility, respectively. However, nonpathogenic commensal species are rarely characterized. Here, we propose that surveillance of the universally carried commensal Neisseria may play the role of the "canary in the coal mine," and reveal circulating known and novel antimicrobial resistance determinants transferable to pathogenic Neisseria. We summarize the current understanding of commensal Neisseria as an AMR reservoir, and call to increase research on commensal Neisseria species, through expanding established gonococcal surveillance programs to include the collection, isolation, antimicrobial resistance phenotyping, and whole-genome sequencing (WGS) of commensal isolates. This will help combat AMR in the pathogenic Neisseria by: (i) determining the contemporary AMR profile of commensal Neisseria, (ii) correlating AMR phenotypes with known and novel genetic determinants, (iii) qualifying and quantifying horizontal gene transfer (HGT) for AMR determinants, and (iv) expanding commensal Neisseria genomic databases, perhaps leading to the identification of new drug and vaccine targets. The proposed modification to established Neisseria collection protocols could transform our ability to address AMR N. gonorrhoeae, while requiring minor modifications to current surveillance practices. IMPORTANCE Contemporary increases in the prevalence of antimicrobial resistance (AMR) in Neisseria gonorrhoeae populations is a direct threat to global public health and the effective treatment of gonorrhea. Substantial effort and financial support are being spent on identifying resistance mechanisms circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci-the commensal Neisseria. Commensal Neisseria and pathogenic Neisseria frequently share DNA through horizontal gene transfer, which has played a large role in rendering antibiotic therapies ineffective in pathogenic Neisseria populations. Here, we propose the expansion of established gonococcal surveillance programs to integrate a collection, AMR profiling, and genomic sequencing pipeline for commensal species. This proposed expansion will enhance the field's ability to identify resistance in and from nonpathogenic reservoirs and anticipate AMR trends in pathogenic Neisseria.
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Ramírez-Sánchez D, Gibelin-Viala C, Mayjonade B, Duflos R, Belmonte E, Pailler V, Bartoli C, Carrere S, Vailleau F, Roux F. Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats. Front Microbiol 2022; 13:984832. [PMID: 36212843 PMCID: PMC9537739 DOI: 10.3389/fmicb.2022.984832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Microbiota modulates plant health and appears as a promising lever to develop innovative, sustainable and eco-friendly agro-ecosystems. Key patterns of microbiota assemblages in plants have been revealed by an extensive number of studies based on taxonomic profiling by metabarcoding. However, understanding the functionality of microbiota is still in its infancy and relies on reductionist approaches primarily based on the establishment of representative microbial collections. In Arabidopsis thaliana, most of these microbial collections include one strain per OTU isolated from a limited number of habitats, thereby neglecting the ecological potential of genetic diversity within microbial species. With this study, we aimed at estimating the extent of genetic variation between strains within the most abundant and prevalent leaf-associated non-pathogenic bacterial species in A. thaliana located south-west of France. By combining a culture-based collection approach consisting of the isolation of more than 7,000 bacterial colonies with an informative-driven approach, we isolated 35 pure strains from eight non-pathogenic bacterial species. We detected significant intra-specific genetic variation at the genomic level and for growth rate in synthetic media. In addition, significant host genetic variation was detected in response to most bacterial strains in in vitro conditions, albeit dependent on the developmental stage at which plants were inoculated, with the presence of both negative and positive responses on plant growth. Our study provides new genetic and genomic resources for a better understanding of the plant-microbe ecological interactions at the microbiota level. We also highlight the need of considering genetic variation in both non-pathogenic bacterial species and A. thaliana to decipher the genetic and molecular mechanisms involved in the ecologically relevant dialog between hosts and leaf microbiota.
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Affiliation(s)
| | | | | | - Rémi Duflos
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Elodie Belmonte
- Gentyane, UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Vincent Pailler
- Gentyane, UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Claudia Bartoli
- Institute for Genetics, Environment and Plant Protection (IGEPP), INRAE, Institut Agro AgroCampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sébastien Carrere
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
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32
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Vinayamohan PG, Locke SR, Portillo-Gonzalez R, Renaud DL, Habing GG. Antimicrobial Use and Resistance in Surplus Dairy Calf Production Systems. Microorganisms 2022; 10:1652. [PMID: 36014070 PMCID: PMC9413162 DOI: 10.3390/microorganisms10081652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Surplus calves, which consist predominately of male calves born on dairy farms, are an underrecognized source of antimicrobial-resistant (AMR) pathogens. Current production systems for surplus calves have important risk factors for the dissemination of pathogens, including the high degree of commingling during auction and transportation and sometimes inadequate care early in life. These circumstances contribute to an increased risk of respiratory and other infectious diseases, resulting in higher antimicrobial use (AMU) and the development of AMR. Several studies have shown that surplus calves harbor AMR genes and pathogens that are resistant to critically important antimicrobials. This is a potential concern as the resistant pathogens and genes can be shared between animal, human and environmental microbiomes. Although knowledge of AMU and AMR has grown substantially in dairy and beef cattle systems, comparable studies in surplus calves have been mostly neglected in North America. Therefore, the overall goal of this narrative review is to summarize the existing literature regarding AMU and AMR in surplus dairy calf production, highlight the management practices contributing to the increased AMU and the resulting AMR, and discuss potential strategies and barriers for improved antimicrobial stewardship in surplus calf production systems.
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Affiliation(s)
- Poonam G. Vinayamohan
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Samantha R. Locke
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Rafael Portillo-Gonzalez
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - David L. Renaud
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Gregory G. Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
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33
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Song CH, Kim YH, Naskar M, Hayes BW, Abraham MA, Noh JH, Suk G, Kim MJ, Cho KS, Shin M, Lee EJ, Abraham SN, Choi HW. Lactobacillus crispatus Limits Bladder Uropathogenic E. coli Infection by Triggering a Host Type I Interferon Response. Proc Natl Acad Sci U S A 2022; 119:e2117904119. [PMID: 35939684 PMCID: PMC9388105 DOI: 10.1073/pnas.2117904119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many urinary tract infections (UTIs) are recurrent because uropathogens persist within the bladder epithelial cells (BECs) for extended periods between bouts of infection. Because persistent uropathogens are intracellular, they are often refractive to antibiotic treatment. The recent discovery of endogenous Lactobacillus spp. in the bladders of healthy humans raised the question of whether these endogenous bacteria directly or indirectly impact intracellular bacterial burden in the bladder. Here, we report that in contrast to healthy women, female patients experiencing recurrent UTIs have a bladder population of Lactobacilli that is markedly reduced. Exposing infected human BECs to L. crispatus in vitro markedly reduced the intracellular uropathogenic Escherichia coli (UPEC) load. The adherence of Lactobacilli to BECs was found to result in increased type I interferon (IFN) production, which in turn enhanced the expression of cathepsin D within lysosomes harboring UPECs. This lysosomal cathepsin D-mediated UPEC killing was diminished in germ-free mice and type I IFN receptor-deficient mice. Secreted metabolites of L. crispatus seemed to be responsible for the increased expression of type I IFN in human BECs. Intravesicular administration of Lactobacilli into UPEC-infected murine bladders markedly reduced their intracellular bacterial load suggesting that components of the endogenous microflora can have therapeutic effects against UTIs.
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Affiliation(s)
- Chang Hyun Song
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Young Ho Kim
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon-si, 14584, South Korea
| | - Manisha Naskar
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Byron W Hayes
- Department of Pathology, Duke University Medical Center, Durham, NC 27710
| | - Mathew A Abraham
- Department of Pathology, Duke University Medical Center, Durham, NC 27710
| | - Joo Hwan Noh
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Gyeongseo Suk
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Min Jung Kim
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Kyu Sang Cho
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Minhye Shin
- Department of Microbiology, Inha University School of Medicine, Incheon, 22212, South Korea
| | - Eun-Jin Lee
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Soman N Abraham
- Department of Pathology, Duke University Medical Center, Durham, NC 27710
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Hae Woong Choi
- Division of Life Sciences, Korea University, Seoul, 02841, South Korea
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Bellanti JA. Seasonal-specific Variations of the Upper Airway Microbiome and Childhood Asthma: Friend or Foe? J Allergy Clin Immunol 2022; 150:62-63. [PMID: 35623413 DOI: 10.1016/j.jaci.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Joseph A Bellanti
- Professor of Pediatrics and Microbiology-Immunology (Emeritus), Director, International Center for Interdisciplinary Studies of Immunology (ICISI), Georgetown University Medical Center, 3900 Reservoir Road, NW, Room 308 NW, Washington, DC 20057
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35
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Wu X, Gu B, Yang H. The role of γδ T cells in the interaction between commensal and pathogenic bacteria in the intestinal mucosa. Int Rev Immunol 2022; 42:379-392. [PMID: 35583374 DOI: 10.1080/08830185.2022.2076846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/22/2022]
Abstract
The intestinal mucosa is an important structure involved in resistance to pathogen infection. It is mainly composed of four barriers, which have different but interrelated functions. Pathogenic bacteria can damage these intestinal mucosal barriers. Here, we mainly review the mechanisms of pathogen damage to biological barriers. Most γδ T cells are located on the surface of the intestinal mucosa, with the ability to migrate and engage in crosstalk with microorganisms. Commensal bacteria are involved in the activation and migration of γδ T cells to monitor the invasion of pathogens. Pathogen invasion alters the migration pattern of γδ T cells. γδ T cells accelerate pathogen clearance and limit opportunistic invasion of commensal bacteria. By discussing these interactions among γδ T cells, commensal bacteria and pathogenic bacteria, we suggest that γδ T cells may link the interactions between commensal bacteria and pathogenic bacteria.
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Affiliation(s)
- Xiaoxiao Wu
- Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Bing Gu
- Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Yang
- Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, China
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36
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Dey P, Ray Chaudhuri S. Cancer-Associated Microbiota: From Mechanisms of Disease Causation to Microbiota-Centric Anti-Cancer Approaches. Biology (Basel) 2022; 11:757. [PMID: 35625485 PMCID: PMC9138768 DOI: 10.3390/biology11050757] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori infection is the only well-established bacterial cause of cancer. However, due to the integral role of tissue-resident commensals in maintaining tissue-specific immunometabolic homeostasis, accumulated evidence suggests that an imbalance of tissue-resident microbiota that are otherwise considered as commensals, can also promote various types of cancers. Therefore, the present review discusses compelling evidence linking tissue-resident microbiota (especially gut bacteria) with cancer initiation and progression. Experimental evidence supporting the cancer-causing role of gut commensal through the modulation of host-specific processes (e.g., bile acid metabolism, hormonal effects) or by direct DNA damage and toxicity has been discussed. The opportunistic role of commensal through pathoadaptive mutation and overcoming colonization resistance is discussed, and how chronic inflammation triggered by microbiota could be an intermediate in cancer-causing infections has been discussed. Finally, we discuss microbiota-centric strategies, including fecal microbiota transplantation, proven to be beneficial in preventing and treating cancers. Collectively, this review provides a comprehensive understanding of the role of tissue-resident microbiota, their cancer-promoting potentials, and how beneficial bacteria can be used against cancers.
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Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Saumya Ray Chaudhuri
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh 160036, India;
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37
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Oladeinde A, Abdo Z, Zwirzitz B, Woyda R, Lakin SM, Press MO, Cox NA, Thomas JC, Looft T, Rothrock MJ, Zock G, Plumblee Lawrence J, Cudnik D, Ritz C, Aggrey SE, Liachko I, Grove JR, Wiersma C. Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens. Appl Environ Microbiol 2022; 88:e0251721. [PMID: 35416680 PMCID: PMC9107613 DOI: 10.1128/aem.02517-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/06/2022] [Indexed: 12/15/2022] Open
Abstract
Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.
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Affiliation(s)
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Benjamin Zwirzitz
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Steven M Lakin
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | | | - Nelson A Cox
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Jesse C Thomas
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Torey Looft
- National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | | | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | - Denice Cudnik
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Casey Ritz
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | | | - Crystal Wiersma
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
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38
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Udayan S, Stamou P, Crispie F, Hickey A, Floyd AN, Hsieh CS, Cotter PD, O'Sullivan O, Melgar S, O'Toole PW, Newberry RD, Rossini V, Nally K. Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice. Gut Microbes 2022; 14:2007743. [PMID: 35023810 PMCID: PMC8765072 DOI: 10.1080/19490976.2021.2007743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD88-/- mice. Shotgun metagenomic-sequencing revealed a marked increase in the relative abundance of L. johnsonii in intestinal tissues of MyD88-/- mice compared to WT mice. Lactobacillus johnsonii was detected most frequently from multiple systemic tissues and at higher levels in MyD88-/- mice compared to WT mice. Viable L. johnsonii strains were recovered from different cell types sorted from intestinal and systemic tissues of WT and MyD88-/- mice. L. johnsonii could persist in dendritic cells and may represent murine immunomodulatory endosymbionts.
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Affiliation(s)
- Sreeram Udayan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Center, Moorepark, Cork, Ireland
| | - Ana Hickey
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Alexandria N Floyd
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Center, Moorepark, Cork, Ireland
| | - Orla O'Sullivan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Center, Moorepark, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Rodney D Newberry
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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39
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Mosby CA, Bhar S, Phillips MB, Edelmann MJ, Jones MK. Interaction with mammalian enteric viruses alters outer membrane vesicle production and content by commensal bacteria. J Extracell Vesicles 2022; 11:e12172. [PMID: 34981901 PMCID: PMC8725172 DOI: 10.1002/jev2.12172] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 01/22/2023] Open
Abstract
Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The importance of these organisms is further demonstrated by the widespread ability of enteric viruses to exploit commensal bacteria to enhance viral infection. These viruses interact directly with commensal bacteria, and while the impact of this interaction on viral infection is well described for several viruses, the impact on the commensal bacteria has yet to be explored. In this article, we demonstrate, for the first time, that enteric viruses alter the gene expression and phenotype of individual commensal bacteria. Human and murine norovirus interaction with bacteria resulted in genome-wide differential gene expression and marked changes in the surface architecture of the bacterial cells. Furthermore, the interaction of the virus with bacteria led to increased production of smaller outer membrane vesicles (OMVs). Enhanced production of smaller vesicles was also observed when noroviruses were incubated with other commensal bacteria, indicating a potentially broad impact of norovirus interaction. The vesicle production observed in the in vivo model followed a similar trend where an increased quantity of smaller bacterial vesicles was observed in stool collected from virus-infected mice compared to mock-infected mice. Furthermore, changes in vesicle size were linked to changes in protein content and abundance, indicating that viral binding induced a shift in the mechanism of the OMV biogenesis. Collectively, these data demonstrate that enteric viruses induce specific changes in bacterial gene expression, leading to changes in bacterial extracellular vesicle production that can potentially impact host responses to infection.
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Affiliation(s)
- Chanel A. Mosby
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Sutonuka Bhar
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Matthew B. Phillips
- Department of Molecular Genetics and MicrobiologyCollege of MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Mariola J. Edelmann
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
| | - Melissa K. Jones
- Microbiology and Cell Science DepartmentIFASUniversity of FloridaGainesvilleFloridaUSA
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40
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Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, Cross JR, Almeida A, Lawley TD, Pedicord VA. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe 2021; 30:124-138.e8. [PMID: 34971560 PMCID: PMC8763404 DOI: 10.1016/j.chom.2021.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Abstract
Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.
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Affiliation(s)
- Benjamin S Beresford-Jones
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Mark D Stares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - George Notley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elisa Viciani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Hilary P Browne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel J Boehmler
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amelia T Soderholm
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Nitin Kumar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Vervier
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandre Almeida
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Trevor D Lawley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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41
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Chen Y, Cui W, Li X, Yang H. Interaction Between Commensal Bacteria, Immune Response and the Intestinal Barrier in Inflammatory Bowel Disease. Front Immunol 2021; 12:761981. [PMID: 34858414 PMCID: PMC8632219 DOI: 10.3389/fimmu.2021.761981] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
In inflammatory bowel disease (IBD), intestinal mucosa cell and intestinal epithelial cell are severely damaged, and then their susceptibility to bacteria increases, so many commensal bacteria become pathogenic. The pathogenic commensal bacteria can stimulate a series of compensatory immune responses in the intestine. However, the immune response prevents the intestinal tract from restoring homeostasis, which in turn produces an indispensable inflammatory response. On the contrary, in IBD, the fierce inflammatory response contributes to the development of IBD. However, the effect of commensal bacteria on inflammation in IBD has not been clearly studied. Therefore, we further summarize the changes brought about by the changes of commensal bacteria to the inflammation of the intestines and their mutual influence. This article reviews the protective mechanism of commensal bacteria in healthy people and the mechanism of commensal bacteria and immune response to the destruction of the intestinal barrier when IBD occurs. The treatment and prevention of IBD are also briefly summarized.
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Affiliation(s)
| | | | - Xiao Li
- Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Huan Yang
- Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
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Jollet M, Nay K, Chopard A, Bareille MP, Beck A, Ollendorff V, Vernus B, Bonnieu A, Mariadassou M, Rué O, Derbré F, Goustard B, Koechlin-Ramonatxo C. Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model. Nutrients 2021; 13:3865. [PMID: 34836120 DOI: 10.3390/nu13113865] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota, a major contributor to human health, is influenced by physical activity and diet, and displays a functional cross-talk with skeletal muscle. Conversely, few data are available on the impact of hypoactivity, although sedentary lifestyles are widespread and associated with negative health and socio-economic impacts. The study aim was to determine the effect of Dry Immersion (DI), a severe hypoactivity model, on the human gut microbiota composition. Stool samples were collected from 14 healthy men before and after 5 days of DI to determine the gut microbiota taxonomic profiles by 16S metagenomic sequencing in strictly controlled dietary conditions. The α and β diversities indices were unchanged. However, the operational taxonomic units associated with the Clostridiales order and the Lachnospiraceae family, belonging to the Firmicutes phylum, were significantly increased after DI. Propionate, a short-chain fatty acid metabolized by skeletal muscle, was significantly reduced in post-DI stool samples. The finding that intestine bacteria are sensitive to hypoactivity raises questions about their impact and role in chronic sedentary lifestyles.
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43
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Luu M, Binder K, Hartmann S, Kespohl M, Bazant J, Romero R, Schütz B, Steinhoff U, Visekruna A. Transcription factor c-Rel mediates communication between commensal bacteria and mucosal lymphocytes. J Leukoc Biol 2021; 111:1001-1007. [PMID: 34622991 DOI: 10.1002/jlb.3ab0621-350r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The NF-κB transcription factor c-Rel plays a crucial role in promoting and regulating immune responses and inflammation. However, the function of c-Rel in modulating the mucosal immune system is poorly understood. T follicular helper (Tfh) cells and IgA production in gut-associated lymphoid tissues (GALT) such as Peyer's patches (PPs) are important for maintaining the intestinal homeostasis. Here, c-Rel was identified as an essential factor regulating intestinal IgA generation and function of Tfh cells. Genetic deletion of c-Rel resulted in the aberrant formation of germinal centers (GCs) in PPs, significantly reduced IgA generation and defective Tfh cell differentiation. Supporting these findings, the Ag-specific IgA response to Citrobacter rodentium was strongly impaired in c-Rel-deficient mice. Interestingly, an excessive expansion of segmented filamentous bacteria (SFB) was observed in the small intestine of animals lacking c-Rel. Yet, the production of IL-17A, IgA, and IL-21, which are induced by SFB, was impaired due to the lack of transcriptional control by c-Rel. Collectively, the transcriptional activity of c-Rel regulates Tfh cell function and IgA production in the gut, thus preserving the intestinal homeostasis.
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Affiliation(s)
- Maik Luu
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany.,Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Kai Binder
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany
| | - Sabrina Hartmann
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany.,Institute for Pathology, Universitätsklinikum Giessen, Giessen, Germany
| | - Meike Kespohl
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany.,Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jasmin Bazant
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany.,Institute for Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Rossana Romero
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany
| | - Burkhard Schütz
- Institute for Anatomy and Cell Biology, Philipps-University, Marburg, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University, Marburg, Germany
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44
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Hotinger JA, Morris ST, May AE. The Case against Antibiotics and for Anti-Virulence Therapeutics. Microorganisms 2021; 9:2049. [PMID: 34683370 PMCID: PMC8537500 DOI: 10.3390/microorganisms9102049] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
Although antibiotics have been indispensable in the advancement of modern medicine, there are downsides to their use. Growing resistance to broad-spectrum antibiotics is leading to an epidemic of infections untreatable by first-line therapies. Resistance is exacerbated by antibiotics used as growth factors in livestock, over-prescribing by doctors, and poor treatment adherence by patients. This generates populations of resistant bacteria that can then spread resistance genes horizontally to other bacterial species, including commensals. Furthermore, even when antibiotics are used appropriately, they harm commensal bacteria leading to increased secondary infection risk. Effective antibiotic treatment can induce bacterial survival tactics, such as toxin release and increasing resistance gene transfer. These problems highlight the need for new approaches to treating bacterial infection. Current solutions include combination therapies, narrow-spectrum therapeutics, and antibiotic stewardship programs. These mediate the issues but do not address their root cause. One emerging solution to these problems is anti-virulence treatment: preventing bacterial pathogenesis instead of using bactericidal agents. In this review, we discuss select examples of potential anti-virulence targets and strategies that could be developed into bacterial infection treatments: the bacterial type III secretion system, quorum sensing, and liposomes.
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Affiliation(s)
| | | | - Aaron E. May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA; (J.A.H.); (S.T.M.)
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Abstract
The gastrointestinal tract harbors numerous commensal bacteria, referred to as the microbiota, that benefit host health by digesting dietary components and eliminating pathogens. The intestinal microbiota maintains epithelial barrier integrity and shapes the mucosal immune system, balancing host defense and oral tolerance with microbial metabolites, components, and attachment to host cells. To avoid aberrant immune responses, epithelial cells segregate the intestinal microbiota from immune cells by constructing chemical and physical barriers, leading to the establishment of host-commensal mutualism. Furthermore, intestinal immune cells participate in the maintenance of a healthy microbiota community and reinforce epithelial barrier functions. Perturbations of the microbiota composition are commonly observed in patients with autoimmune diseases and chronic inflammatory disorders. An understanding of the intimate interactions between the intestinal microbiota, epithelial cells, and immune cells that are crucial for the maintenance of intestinal homeostasis might promote advances in diagnostic and therapeutic approaches for various diseases.
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Affiliation(s)
- Hisako Kayama
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryu Okumura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kiyoshi Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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Kovale L, Nimonkar Y, Green SJ, Shouche YS, Prakash O. Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions. Microbes Infect 2021;:104847. [PMID: 34116163 DOI: 10.1016/j.micinf.2021.104847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 11/23/2022]
Abstract
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.
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Bonifacio JPP, Schmolke M. Visualization of Respiratory Commensal Bacteria in Context of Their Natural Host Environment. Front Microbiol 2021; 12:678389. [PMID: 34149669 PMCID: PMC8212125 DOI: 10.3389/fmicb.2021.678389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Commensal microbes are an integral component of mammalian physiology. 16S rRNA gene-specific next generation sequencing from DNA of total organs, swabs or lavages has revolutionized the characterization of bacterial communities in virtually every ecological niche of the body. Culturomics, next allowed the isolation and characterization of commensal bacteria in the lab and the establishment of artificial communities of bacteria, which were eventually reintroduced in model organisms. Spatial organization of microbiota within a given host environment is critical to the physiological or pathological phenotypes provoked by commensal microbiota. In situ hybridization (ISH) is a complementary technique to sequencing and culturing to visualize the presence of individual bacterial operational taxonomic unit (OTUs) in context of the colonized organ. We recently applied highly sensitive in situ RNA hybridization to detection of commensal bacteria in low abundance respiratory tract samples of mice housed under specific pathogen free conditions. This technique allows species-specific detection of living bacteria using RNAScopeTM technology, while preserving the natural environment of the organ. We here provide a detailed step-by-step protocol describing the detection of commensal lung bacteria in respiratory tissue.
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Affiliation(s)
- Joao P P Bonifacio
- Microbiology and Molecular Medicine Department, University of Geneva, Geneva, Switzerland
| | - Mirco Schmolke
- Microbiology and Molecular Medicine Department, University of Geneva, Geneva, Switzerland
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Vandehoef C, Molaei M, Karpac J. Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP. Cell Rep 2021; 31:107736. [PMID: 32521261 DOI: 10.1016/j.celrep.2020.107736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/22/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Dietary nutrients shape complex interactions between hosts and their commensal gut bacteria, further promoting flexibility in host-microbiota associations that can drive nutritional symbiosis. However, it remains less clear if diet-dependent host signaling mechanisms also influence these associations. Using Drosophila, we show here that nuclear factor κB (NF-κB)/Relish, an innate immune transcription factor emerging as a signaling node linking nutrient-immune-metabolic interactions, is vital to adapt gut microbiota species composition to host diet macronutrient composition. We find that Relish is required within midgut enterocytes to amplify host-Lactobacillus associations, an important bacterial mediator of nutritional symbiosis, and thus modulate microbiota composition in response to dietary adaptation. Relish limits diet-dependent transcriptional inducibility of the cap-dependent translation inhibitor 4E-BP/Thor to control microbiota composition. Furthermore, maintaining cap-dependent translation in response to dietary adaptation is critical to amplify host-Lactobacillus associations. These results highlight that NF-κB-dependent host signaling mechanisms, in coordination with host translation control, shape diet-microbiota interactions.
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Affiliation(s)
- Crissie Vandehoef
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Maral Molaei
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Jason Karpac
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA.
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Sallustio F, Curci C, Chaoul N, Fontò G, Lauriero G, Picerno A, Divella C, Di Leo V, De Angelis M, Ben Mkaddem S, Macchia L, Gallone A, Monteiro RC, Pesce F, Gesualdo L. High levels of gut-homing immunoglobulin A+ B lymphocytes support the pathogenic role of intestinal mucosal hyperresponsiveness in immunoglobulin A nephropathy patients. Nephrol Dial Transplant 2021; 36:452-464. [PMID: 33200215 PMCID: PMC7898021 DOI: 10.1093/ndt/gfaa264] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Background Immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulonephritis.
The role of the microbiota and mucosal immunity in the pathogenesis of IgAN remains a
key element. To date, the hypothetical relationship between commensal bacteria, elevated
tumour necrosis factor (TNF) superfamily member 13 [also known as B-cell activating
factor (BAFF)] levels, perturbed homoeostasis of intestinal-activated B cells and
intestinal IgA class switch has not been clearly shown in IgAN patients. Methods We studied the intestinal–renal axis connections, analysing levels of BAFF, TNF ligand
superfamily member 13 (APRIL) and intestinal-activated B cells in IgAN patients, healthy
subjects (HSs) and patients with non-IgA glomerulonephritides. Results IgAN patients had increased serum levels of BAFF cytokine, correlating with higher
amounts of five specific microbiota metabolites, and high APRIL cytokine serum levels.
We also found that subjects with IgAN have a higher level of circulating gut-homing
(CCR9+ β7 integrin+) regultory B cells, memory B cells and
IgA+ memory B cells compared with HSs. Finally, we found that IgAN patients
had high levels of both total plasmablasts (PBs) and intestinal-homing PBs.
Interestingly, PBs significantly increased in IgAN but not in patients with other
glomerulonephritides. Conclusions Our results demonstrate a significant difference in the amount of intestinal-activated
B lymphocytes between IgAN patients and HSs, confirming the hypothesis of the pathogenic
role of intestinal mucosal hyperresponsiveness in IgAN. The intestinal–renal axis plays
a crucial role in IgAN and several factors may contribute to its complex pathogenesis
and provide an important area of research for novel targeted therapies to modulate
progression of the disease.
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Affiliation(s)
- Fabio Sallustio
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Claudia Curci
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Bari, Italy.,Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Nada Chaoul
- Allergology Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Giulia Fontò
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Gabriella Lauriero
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Angela Picerno
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Chiara Divella
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Vincenzo Di Leo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Sanae Ben Mkaddem
- Faculty of Medicine, Center for Research on Inflammation, Paris Diderot University, INSERM U1149, ELR8252 CNRS, Paris, France
| | - Luigi Macchia
- Allergology Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Anna Gallone
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - Renato C Monteiro
- Faculty of Medicine, Center for Research on Inflammation, Paris Diderot University, INSERM U1149, ELR8252 CNRS, Paris, France
| | - Francesco Pesce
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University "Aldo Moro", Bari, Italy
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Abstract
OBJECTIVES Commensal bacteria in the nasal cavity may act as opportunistic pathogens that cause infections under certain conditions. Screening for commensal bacteria in the nasal cavity may aid in understanding their roles in microbiota balance and preventing potential infections. METHODS Nasal samples were collected from healthy preclinical medical students and used to inoculate various bacterial culture media, by means of the WaspLab microbiology automated system. Bacterial colonies were then identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Antibiotic resistance phenotypes of Staphylococcus aureus were determined by antibiotic susceptibility tests. RESULTS In total, 549 bacterial strains were isolated from 161 participants. These strains included the following genera: Staphylococcus, Streptococcus, Corynebacterium, Dolosigranulum, Bacillus, Micrococcus, Haemophilus, Neisseria, Moraxella, Pseudomonas, and members of Enterobacteriaceae (e.g., Escherichia, Klebsiella, Citrobacter, Enterobacter, and Serratia). Approximately 25.5% of students were carriers of S. aureus; most S. aureus isolates were resistant to penicillin, erythromycin, and clindamycin. The prevalence of methicillin-resistant S. aureus in nasal samples was 4.3%. CONCLUSIONS A diverse group of nasal commensal bacteria inhabited our population of healthy volunteers. These data can improve comprehension of the potential roles of these nasal commensal bacteria in regulating microbiota balance and promoting or mitigating potential future infections.
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Affiliation(s)
- Ke Zhou
- Center of Clinical Laboratory Medicine of PLA, Department of Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fei Sun
- Department of Otolaryngology Head and Neck Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiu-Li Xu
- Center of Clinical Laboratory Medicine of PLA, Department of Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiao-Ke Hao
- Center of Clinical Laboratory Medicine of PLA, Department of Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jia-Yun Liu
- Center of Clinical Laboratory Medicine of PLA, Department of Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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