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Rothenberger CM, Yu M, Kim HM, Cheung YW, Chang YW, Davey ME. An outer membrane vesicle specific lipoprotein promotes Porphyromonas gingivalis aggregation on red blood cells. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100249. [PMID: 38974668 PMCID: PMC11225709 DOI: 10.1016/j.crmicr.2024.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Porphyromonas gingivalis uses a variety of mechanisms to actively interact with and promote the hydrolysis of red blood cells (RBCs) to obtain iron in the form of heme. In this study, we investigated the function of lipoprotein PG1881 which was previously shown to be up-regulated during subsurface growth and selectively enriched on outer membrane vesicles (OMVs). Our results show that wildtype strain W83 formed large aggregates encompassing RBCs whereas the PG1881 deletion mutant remained predominately as individual cells. Using a PG1881 antibody, immunofluorescence revealed that the wildtype strain's aggregation to RBCs involves an extracellular matrix enriched with PG1881. Our findings discover that RBCs elicit cell aggregation and matrix formation by P. gingivalis and that this process is promoted by an OMV-specific lipoprotein. We propose this strategy is advantageous for nutrient acquisition as well as dissemination from the oral cavity and survival of this periodontal pathogen.
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Affiliation(s)
- Christina M. Rothenberger
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
- Department of Oral Microbiology, University of Florida College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Manda Yu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Hey-Min Kim
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mary Ellen Davey
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
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Salavati Schmitz S, Salgado JPA, Glendinning L. Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial. Access Microbiol 2024; 6:000774.v4. [PMID: 38868374 PMCID: PMC11165627 DOI: 10.1099/acmi.0.000774.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/20/2024] [Indexed: 06/14/2024] Open
Abstract
Even though dietary fibres are often used as prebiotic supplements in dogs, the effect of individual types of fibres on canine microbiota composition is unknown. The objective of this study was to assess changes in faecal microbiota richness, diversity and taxonomic abundance with three different fibre supplements in dogs. These were psyllium husk, resistant starch from banana flour and methylcellulose. They were administered to 17 healthy dogs in a cross-over trial after transition to the same complete feed. Faecal scores and clinical activity indices were recorded, and faecal samples were collected before and at the end of supplementation, as well as 2 weeks after each supplement (washout). Illumina NovaSeq paired-end 16S rRNA gene sequencing was performed on all samples. After quality control and chimera removal, alpha diversity indices were calculated with QIIME. Differences in specific taxa between groups were identified using Metastats. Methylcellulose significantly increased faecal scores but had no effect on microbiota. Psyllium resulted in minor changes in the abundance of specific taxa, but with questionable biological significance. Resistant starch reduced microbiota richness and resulted in the most abundant changes in taxa, mostly a reduction in short-chain fatty acid-producing genera of the phylum Bacillota, with an increase in genera within the Bacteroidota, Pseudomonadota, Actinomycetota and Saccharibacteria. In conclusion, while psyllium and methylcellulose led to few changes in the microbiota composition, the taxonomic changes seen with resistant starch may indicate a less favourable composition. Based on this, the type of resistant starch used here cannot be recommended as a prebiotic in dogs.
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Affiliation(s)
- Silke Salavati Schmitz
- Hospital for Small Animals, Royal (Dick) School of Veterinary Studies, College of Medicine and Veterinary Medicine,, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jorge Perez-Accino Salgado
- Hospital for Small Animals, Royal (Dick) School of Veterinary Studies, College of Medicine and Veterinary Medicine,, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Laura Glendinning
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X. Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. THE ISME JOURNAL 2024; 18:wrad034. [PMID: 38366018 PMCID: PMC10939385 DOI: 10.1093/ismejo/wrad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/07/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
Saccharibacteria (formerly TM7) are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to Candidate Phyla Radiation, a large monophyletic lineage with poorly understood biology. Nanosynbacter lyticus type strain TM7x is the first Saccharibacteria member isolated from the human oral microbiome. With restrained metabolic capacities, TM7x lives on the surface of, and forms an obligate episymbiotic relationship with its bacterial host, Schaalia odontolytica strain XH001. The symbiosis allows TM7x to propagate but presents a burden to host bacteria by inducing stress response. Here, we employed super-resolution fluorescence imaging to investigate the physical association between TM7x and XH001. We showed that the binding with TM7x led to a substantial alteration in the membrane fluidity of XH001. We also revealed the formation of intracellular lipid droplets in XH001 when forming episymbiosis with TM7x, a feature that has not been reported in oral bacteria. The TM7x-induced lipid droplets accumulation in XH001 was confirmed by label-free Raman spectroscopy, which also unveiled additional phenotypical features when XH001 cells are physically associated with TM7x. Further exploration through culturing XH001 under various stress conditions showed that lipid droplets accumulation was a general response to stress. A survival assay demonstrated that the presence of lipid droplets plays a protective role in XH001, enhancing its survival under adverse conditions. In conclusion, our study sheds new light on the intricate interaction between Saccharibacteria and their host bacteria, highlighting the potential benefit conferred by TM7x to its host and further emphasizing the context-dependent nature of symbiotic relationships.
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Affiliation(s)
- Pu-Ting Dong
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
| | - Jing Tian
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Koseki J Kobayashi-Kirschvink
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Lujia Cen
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, United States
| | - Batbileg Bor
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
| | - Wenyuan Shi
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
| | - Xuesong He
- Department of Microbiology, The ADA Forsyth Institute, Boston, MA 02142, United States
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
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Hendrickson EL, Bor B, Kerns KA, Cen L, Shi W, He X, McLean JS. Ultrasmall epibiont Nanosynbacter lyticus strain TM7x and host bacteria transcriptional activity after initial host parasitism. J Oral Microbiol 2023; 16:2287349. [PMID: 38188073 PMCID: PMC10768705 DOI: 10.1080/20002297.2023.2287349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024] Open
Abstract
Background Oral Saccharibacteria Nanosynbacter lyticus strain TM7× lives as an ultrasmall epibiont on the surface of its host, Schaalia odontolytica strain XH001. Establishing this interaction is a poorly understood multi-step process. The recovery phase marks a shift in the TM7×/host interaction, switching from the early killing phase, with extensive host cell death, to a stable symbiosis phase where the host and epibiont can grow together. Results Transcriptomes of TM7× and host, XH001, were captured during the recovery phase and compared to uninfected host and the early host/epibiont interaction (initial encounter). XH001 showed increased expression for rhamnose cell wall components and for the precursor to peptidoglycan while TM7× showed increases in the peptidoglycan pathway. Transporter expression was generally increased for both organisms during recovery compared to the initial encounter, though, XH001 showed lower amino acid transporter expression. Consistent with host parasitism, XH001 showed increased expression of various stress-related genes during recovery while TM7× showed reduced stress. TM7× displayed higher expression of type IV pili, consistent with increased attachment to new hosts. Conclusion As TM7× is a member of the broadly distributed Candidate Phyla Radiation with small genomes lacking numerous biosynthetic pathways, this study provides further insights into how these epibionts interact and modulate their host bacteria.
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Affiliation(s)
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | | | - Lujia Cen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, USA
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
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Baker JL. Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiol Rev 2023; 47:fuad051. [PMID: 37667515 PMCID: PMC10503653 DOI: 10.1093/femsre/fuad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/02/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.
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Affiliation(s)
- Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, School of Dentistry, Oregon Health & Science University, 3181 Sam Jackson Park Road, Portland, OR 97202, United States
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA 92093, United States
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Culture-based approaches to studying "microbial dark matter". Proc Natl Acad Sci U S A 2023; 120:e2219691120. [PMID: 36595687 PMCID: PMC9926201 DOI: 10.1073/pnas.2219691120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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