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Armbruster KM, Jiang J, Sartorio MG, Scott NE, Peterson JM, Sexton JZ, Feldman MF, Koropatkin NM. Identification and Characterization of the Lipoprotein N-acyltransferase in Bacteroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596883. [PMID: 38853980 PMCID: PMC11160734 DOI: 10.1101/2024.05.31.596883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Members of the Bacteroidota compose a large portion of the human gut microbiota, contributing to overall gut health via the degradation of various polysaccharides. This process is facilitated by lipoproteins, globular proteins anchored to the cell surface by a lipidated N-terminal cysteine. Despite their importance, lipoprotein synthesis by these bacteria is understudied. In E. coli, the α-amino linked lipid of lipoproteins is added by the lipoprotein N-acyltransferase Lnt. Herein, we have identified a protein distinct from Lnt responsible for the same process in Bacteroides, named lipoprotein N-acyltransferase in Bacteroides (Lnb). Deletion of Lnb yields cells that synthesize diacylated lipoproteins, with impacts on cell viability and morphology, growth on polysaccharides, and protein composition of membranes and outer membrane vesicles (OMVs). Our results not only challenge the accepted paradigms of lipoprotein biosynthesis in Gram-negative bacteria, but also support the establishment of a new family of lipoprotein N-acyltransferases.
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Affiliation(s)
- Krista M Armbruster
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jiawen Jiang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Mariana G Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, 3000, Australia
| | - Jenna M Peterson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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2
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Wang Y, Hunt A, Danziger L, Drwiega EN. A Comparison of Currently Available and Investigational Fecal Microbiota Transplant Products for Recurrent Clostridioides difficile Infection. Antibiotics (Basel) 2024; 13:436. [PMID: 38786164 PMCID: PMC11117328 DOI: 10.3390/antibiotics13050436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Clostridioides difficile infection (CDI) is an intestinal infection that causes morbidity and mortality and places significant burden and cost on the healthcare system, especially in recurrent cases. Antibiotic overuse is well recognized as the leading cause of CDI in high-risk patients, and studies have demonstrated that even short-term antibiotic exposure can cause a large and persistent disturbance to human colonic microbiota. The recovery and sustainability of the gut microbiome after dysbiosis have been associated with fewer CDI recurrences. Fecal microbiota transplantation (FMT) refers to the procedure in which human donor stool is processed and transplanted to a patient with CDI. It has been historically used in patients with pseudomembranous colitis even before the discovery of Clostridioides difficile. More recent research supports the use of FMT as part of the standard therapy of recurrent CDI. This article will be an in-depth review of five microbiome therapeutic products that are either under investigation or currently commercially available: Rebyota (fecal microbiota, live-jslm, formerly RBX2660), Vowst (fecal microbiota spores, live-brpk, formerly SER109), VE303, CP101, and RBX7455. Included in this review is a comparison of the products' composition and dosage forms, available safety and efficacy data, and investigational status.
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Affiliation(s)
- Yifan Wang
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
| | - Aaron Hunt
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
| | - Larry Danziger
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
- Division of Infectious Diseases, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Emily N. Drwiega
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
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3
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Duckett M, Taylor MN, Bowman C, Vega NM. Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans. FEMS Microbiol Ecol 2024; 100:fiae039. [PMID: 38549432 PMCID: PMC11004935 DOI: 10.1093/femsec/fiae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.
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Affiliation(s)
- Marissa Duckett
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Megan N Taylor
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Claire Bowman
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
| | - Nic M Vega
- Department of Biology, Emory University, 1510 Clifton Road NE #2006, Atlanta, GA 30322, United States
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30322, United States
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4
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Kijner S, Ennis D, Shmorak S, Florentin A, Yassour M. CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat Commun 2024; 15:105. [PMID: 38167825 PMCID: PMC10761964 DOI: 10.1038/s41467-023-44437-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
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Affiliation(s)
- Sivan Kijner
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dena Ennis
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimrit Shmorak
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Florentin
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Kuvin Center for the Study of Infectious and Tropical Diseases, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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5
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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6
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Hullahalli K, Dailey KG, Waldor MK. Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose. Proc Natl Acad Sci U S A 2023; 120:e2309151120. [PMID: 37669395 PMCID: PMC10500177 DOI: 10.1073/pnas.2309151120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
To cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These bottlenecks restrict the inoculum and largely determine whether pathogen exposure results in disease. Infection bottlenecks therefore quantify the effectiveness of immune barriers. Here, using a model of Escherichia coli systemic infection, we identify bottlenecks that tighten or widen with higher inoculum sizes, revealing that the efficacy of innate immune responses can increase or decrease with pathogen dose. We term this concept "dose scaling". During E. coli systemic infection, dose scaling is tissue specific, dependent on the lipopolysaccharide (LPS) receptor TLR4, and can be recapitulated by mimicking high doses with killed bacteria. Scaling therefore depends on sensing of pathogen molecules rather than interactions between the host and live bacteria. We propose that dose scaling quantitatively links innate immunity with infection bottlenecks and is a valuable framework for understanding how the inoculum size governs the outcome of pathogen exposure.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
| | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham & Women’s Hospital, Boston, MA02115
- HHMI, Boston, MA02115
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