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Ngo VL, Wang Y, Shi Z, Ramani S, Jiang B, T Gewirtz A. Gut-resident C. perfringens impedes rotavirus vaccine efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599343. [PMID: 38948828 PMCID: PMC11212864 DOI: 10.1101/2024.06.17.599343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background & Aims The extent to which live orally-administered rotavirus (RV) vaccines elicit protective immunity is highly heterogeneous. We hypothesized microbiota composition might influence vaccine efficacy. Methods We tested this concept by examining extent to which colonizing mice with segmented filamentous bacteria (SFB) influenced RV vaccine efficacy.Influence of human microbiomes on RV vaccination was studied via administering germ-free mice fecal microbial transplants (FMT) from children with robust or minimal RV vaccine responsiveness. Post-FMT, mice were subjected to vaccination and challenge doses of RV. Results SFB administration resulted in a phenotype reminiscent of RV vaccine failure, i.e. minimal generation of RV antigens and, consequently, lack of anti-RV antibodies resulting in proneness to RV challenge once SFB levels diminished. Transplant of microbiomes from children to mice recapitulated donor vaccination phenotype. Specifically, mice receiving FMT from high-responding children exhibited high levels of fecal RV antigen shedding and RV antibodies in response to RV vaccination and, concomitantly, were impervious to RV challenge. In contrast, mice receiving FMT from children who had not responded to RV vaccination exhibited only modest responses to RV challenge and, accordingly, remained prone to RV challenge. Microbiome analysis ruled out a role for SFB but suggested that RV vaccine failure might involve Clostridium perfringens . Oral administration of cultured C. perfringens to gnotobiotic mice partially recapitulated the RV vaccine non-responder phenotype. Analysis of previously-reported microbiome data found C. perfringens abundance in children associated with RV vaccine failure. Conclusion Microbiota composition influences RV vaccine virus infection and, consequently, protective immunity. C. perfringens may be one, perhaps of many, bacterial species harbored in the intestine of RV-vaccine non-responders that influences RV vaccine outcomes.
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Ngo VL, Lieber CM, Kang HJ, Sakamoto K, Kuczma M, Plemper RK, Gewirtz AT. Intestinal microbiota programming of alveolar macrophages influences severity of respiratory viral infection. Cell Host Microbe 2024; 32:335-348.e8. [PMID: 38295788 PMCID: PMC10942762 DOI: 10.1016/j.chom.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/05/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
Susceptibility to respiratory virus infections (RVIs) varies widely across individuals. Because the gut microbiome impacts immune function, we investigated the influence of intestinal microbiota composition on RVI and determined that segmented filamentous bacteria (SFB), naturally acquired or exogenously administered, protected mice against influenza virus (IAV) infection. Such protection, which also applied to respiratory syncytial virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was independent of interferon and adaptive immunity but required basally resident alveolar macrophages (AMs). In SFB-negative mice, AMs were quickly depleted as RVI progressed. In contrast, AMs from SFB-colonized mice were intrinsically altered to resist IAV-induced depletion and inflammatory signaling. Yet, AMs from SFB-colonized mice were not quiescent. Rather, they directly disabled IAV via enhanced complement production and phagocytosis. Accordingly, transfer of SFB-transformed AMs into SFB-free hosts recapitulated SFB-mediated protection against IAV. These findings uncover complex interactions that mechanistically link the intestinal microbiota with AM functionality and RVI severity.
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Affiliation(s)
- Vu L Ngo
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA
| | - Carolin M Lieber
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA
| | - Hae-Ji Kang
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA
| | - Kaori Sakamoto
- Department of Pathology, University of Georgia College of Veterinary Science, Athens, GA 30602, USA
| | - Michal Kuczma
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA
| | - Richard K Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
| | - Andrew T Gewirtz
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
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Ngo VL, Lieber CM, Kang HJ, Sakamoto K, Kuczma M, Plemper RK, Gewirtz AT. Intestinal microbiota programming of alveolar macrophages influences severity of respiratory viral infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558814. [PMID: 37790571 PMCID: PMC10542499 DOI: 10.1101/2023.09.21.558814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Susceptibility to respiratory virus infections (RVIs) varies widely across individuals. Because the gut microbiome impacts immune function, we investigated the influence of intestinal microbiota composition on RVI and determined that segmented filamentous bacteria (SFB), naturally acquired or exogenously administered, protected mice against influenza virus (IAV) infection. Such protection, which also applied to respiratory syncytial virus and SARS-CoV-2, was independent of interferon and adaptive immunity but required basally resident alveolar macrophages (AM). In SFB-negative mice, AM were quickly depleted as RVI progressed. In contrast, AM from SFB-colonized mice were intrinsically altered to resist IAV-induced depletion and inflammatory signaling. Yet, AM from SFB-colonized mice were not quiescent. Rather, they directly disabled IAV via enhanced complement production and phagocytosis. Accordingly, transfer of SFB-transformed AM into SFB-free hosts recapitulated SFB-mediated protection against IAV. These findings uncover complex interactions that mechanistically link the intestinal microbiota with AM functionality and RVI severity. One sentence summary Intestinal segmented filamentous bacteria reprogram alveolar macrophages promoting nonphlogistic defense against respiratory viruses.
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Gerasco JE, Hathaway‐Schrader JD, Poulides NA, Carson MD, Okhura N, Westwater C, Hatch NE, Novince CM. Commensal Microbiota Effects on Craniofacial Skeletal Growth and Morphology. JBMR Plus 2023; 7:e10775. [PMID: 37614301 PMCID: PMC10443078 DOI: 10.1002/jbm4.10775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 08/25/2023] Open
Abstract
Microbes colonize anatomical sites in health to form commensal microbial communities (e.g., commensal gut microbiota, commensal skin microbiota, commensal oral microbiota). Commensal microbiota has indirect effects on host growth and maturation through interactions with the host immune system. The commensal microbiota was recently introduced as a novel regulator of skeletal growth and morphology at noncraniofacial sites. Further, we and others have shown that commensal gut microbes, such as segmented filamentous bacteria (SFB), contribute to noncraniofacial skeletal growth and maturation. However, commensal microbiota effects on craniofacial skeletal growth and morphology are unclear. To determine the commensal microbiota's role in craniofacial skeletal growth and morphology, we performed craniometric and bone mineral density analyses on skulls from 9-week-old female C57BL/6T germ-free (GF) mice (no microbes), excluded-flora (EF) specific-pathogen-free mice (commensal microbiota), and murine-pathogen-free (MPF) specific-pathogen-free mice (commensal microbiota with SFB). Investigations comparing EF and GF mice revealed that commensal microbiota impacted the size and shape of the craniofacial skeleton. EF versus GF mice exhibited an elongated gross skull length. Cranial bone length analyses normalized to skull length showed that EF versus GF mice had enhanced frontal bone length and reduced cranial base length. The shortened cranial base in EF mice was attributed to decreased presphenoid, basisphenoid, and basioccipital bone lengths. Investigations comparing MPF mice and EF mice demonstrated that commensal gut microbes played a role in craniofacial skeletal morphology. Cranial bone length analyses normalized to skull length showed that MPF versus EF mice had reduced frontal bone length and increased cranial base length. The elongated cranial base in MPF mice was due to enhanced presphenoid bone length. This work, which introduces the commensal microbiota as a contributor to craniofacial skeletal growth, underscores that noninvasive interventions in the gut microbiome could potentially be employed to modify craniofacial skeletal morphology. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Joy E. Gerasco
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Stomatology‐Division of Periodontics, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Pediatrics‐Division of Endocrinology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Orthodontics, Adam's School of DentistryUniversity of North CarolinaChapel HillNCUSA
| | - Jessica D. Hathaway‐Schrader
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Stomatology‐Division of Periodontics, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Pediatrics‐Division of Endocrinology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
| | - Nicole A. Poulides
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Stomatology‐Division of Periodontics, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Pediatrics‐Division of Endocrinology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
| | - Matthew D. Carson
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Stomatology‐Division of Periodontics, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Pediatrics‐Division of Endocrinology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
| | - Naoto Okhura
- Department of Orthodontics and Pediatric Dentistry, School of DentistryUniversity of MichiganAnn ArborMIUSA
| | - Caroline Westwater
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Microbiology and Immunology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
| | - Nan E. Hatch
- Department of Orthodontics and Pediatric Dentistry, School of DentistryUniversity of MichiganAnn ArborMIUSA
| | - Chad M. Novince
- Department of Oral Health Sciences, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Stomatology‐Division of Periodontics, College of Dental MedicineMedical University of South CarolinaCharlestonSCUSA
- Department of Pediatrics‐Division of Endocrinology, College of MedicineMedical University of South CarolinaCharlestonSCUSA
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Ritter AC, Ricart Arbona RJ, Mourino AJ, Palillo MB, Aydin M, Fahey JR, Lipman NS. Mechanical Washing Prevents Transmission of Bacterial, Viral, and Protozoal Murine Pathogens from Cages. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2023; 62:131-138. [PMID: 36746440 PMCID: PMC10078927 DOI: 10.30802/aalas-jaalas-22-000105] [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: 11/09/2022] [Revised: 12/01/2022] [Accepted: 12/20/2022] [Indexed: 02/08/2023]
Abstract
Infectious agents have varying susceptibilities to thermal inactivation and/or mechanical removal from cages by the use of heated, pressurized water. In this study, we tested whether 5 specific infectious organisms (Candidatus savagella [segmented filamentous bacterium (SFB)], Helicobacter sp., mouse norovirus (MNV), Tritrichomonas sp., and Entamoeba muris) could survive the cage wash process and still infect naïve mice. These 5 organisms were chosen due to their prevalence in rodent colonies, environmental stability, and/or potential to influence experimental outcomes. Cages that had housed mice shedding all 5 organisms were assigned to 1 of 3 treatment groups: 1) sanitization in a tunnel washer followed by autoclaving (121 °C [250 °F] for 20 min; n = 40 cages); 2) sanitization in a tunnel washer (82 °C [180 °F] for an average of 30 s; n = 40 cages); or 3) control (bedding change only; n = 40 cages). The presence of these agents in the cage was assessed by performing PCR on swabs of the empty soiled cage interior before and after the treatment. In addition, to determine if any residual nucleic acid was infectious, 2 Swiss outbred (J:ARC(S)) female mice were housed for 7 d in cages from each treatment group. The above procedures were then repeated so that every week each pair of J:ARC(S) mice ( n = 10 pairs of mice/treatment group) were housed in another cage that underwent the same treatment; this was done for a total of 4 consecutive, 1-wk-long periods. Swabs collected from soiled cages were PCR-positive for SFB, Helicobacter, MNV, Tritrichomonas, and Entamoeba in 99%, 97%, 39%, 63%, and 73% of the cages tested, respectively. Cages in the tunnel wash group that were PCR-positive for SFB, Helicobacter, Tritrichomonas, and Entamoeba before treatment remained PCR-positive in 8%, 15%, 43%, and 10% of positive cages, respectively. None of the cages from the autoclave group were PCR-positive for any of the agents after treatment. None of the mice housed in cages in either the autoclave or tunnel wash groups became infected with any of the agents. However, 80%, 60%, and 100% of the pairs of mice housed in untreated cages were PCR-positive for SFB, MNV, and Entamoeba, respectively. None of the mice housed in untreated cages were positive for Helicobacter or Tritrichomonas. Our results suggest that nucleic acids from these bacterial and protozoal organisms may remain in cages after mechanical cage washing, but these nucleic acids are not infectious, and autoclaving is not necessary to prevent transmission.
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Affiliation(s)
- Amanda C Ritter
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, New York;,
| | - Rodolfo J Ricart Arbona
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, New York
| | | | - Michael B Palillo
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, New York
| | - Mert Aydin
- The Jackson Laboratory, Bar Harbor, Maine
| | | | - Neil S Lipman
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, The Rockefeller University, New York, New York; Center for Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, New York;,
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Commensal gut bacterium critically regulates alveolar bone homeostasis. J Transl Med 2022; 102:363-375. [PMID: 34934182 PMCID: PMC8967765 DOI: 10.1038/s41374-021-00697-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022] Open
Abstract
The alveolar bone is a unique osseous tissue due to the presence of the teeth and the proximity of commensal oral microbes. Commensal microbe effects on alveolar bone homeostasis have been attributed to the oral microbiota, yet the impact of commensal gut microbes is unknown. Study purpose was to elucidate whether commensal gut microbes regulate osteoimmune mechanisms and skeletal homeostasis in alveolar bone. Male C57BL/6T germfree (GF) littermate mice were maintained as GF or monoassociated with segmented filamentous bacteria (SFB), a commensal gut bacterium. SFB has been shown to elicit broad immune response effects, including the induction of TH17/IL17A immunity, which impacts the development and homeostasis of host tissues. SFB colonized the gut, but not oral cavity, and increased IL17A levels in the ileum and serum. SFB had catabolic effects on alveolar bone and non-oral skeletal sites, which was attributed to enhanced osteoclastogenesis. The alveolar bone marrow of SFB vs. GF mice had increased dendritic cells, activated helper T-cells, TH1 cells, TH17 cells, and upregulated Tnf. Primary osteoblast cultures from SFB and GF mice were stimulated with vehicle-control, IL17A, or TNF to elucidate osteoblast-derived signaling factors contributing to the pro-osteoclastic phenotype in SFB mice. Treatment of RAW264.7 osteoclastic cells with supernatants from vehicle-stimulated SFB vs. GF osteoblasts recapitulated the osteoclast phenotype found in vivo. Supernatants from TNF-stimulated osteoblasts normalized RAW264.7 osteoclast endpoints across SFB and GF cultures, which was dependent on the induction of CXCL1 and CCL2. This report reveals that commensal gut microbes have the capacity to regulate osteoimmune processes in alveolar bone. Outcomes from this investigation challenge the current paradigm that alveolar bone health and homeostasis is strictly regulated by oral microbes.
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Grześkowiak Ł, Martínez-Vallespín B, Zentek J, Vahjen W. A Preliminary Survey of the Distribution of Segmented Filamentous Bacteria in the Porcine Gastrointestinal Tract. Curr Microbiol 2021; 78:3757-3761. [PMID: 34476557 PMCID: PMC8435515 DOI: 10.1007/s00284-021-02636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
Segmented filamentous bacteria (SFB) are present in various animal species including pigs. The aim of this work was to analyze the occurrence of SFB in different parts of the gastrointestinal tract of piglets of different ages. A total of 377 DNA extracts from stomach, jejunum, ileum, cecum and colon digesta, and from feces collected on different time points, originating from 155 animals, were screened by qPCR method with primers specific for the SFB. SFB sequences were detected in 74 of 377 samples (19.6%) from 155 animals in total. SFB were most abundant in ileum (50.0%), cecum (45.0%), and colon (37.0%), followed by feces (14.6%). SFB prevalence in sows was 12.9% (13/101) and 75.9% (41/54) in individual piglets. Of the 41 SFB-positive piglets, only two samples were from pre-weaning animals, while the rest of samples originated from post-weaning piglets. SFB sequences are abundant in post-weaning piglets, but not in suckling or adult animals. They are most abundant in the ileum and cecum of pigs. Further studies are warranted to reveal the role of SFB in pigs.
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Affiliation(s)
- Łukasz Grześkowiak
- Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany.
| | | | - Jürgen Zentek
- Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany
| | - Wilfried Vahjen
- Institute of Animal Nutrition, Freie Universität Berlin, Berlin, Germany
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Wagner C, Torow N, Hornef MW, Lelouard H. Spatial and temporal key steps in early-life intestinal immune system development and education. FEBS J 2021; 289:4731-4757. [PMID: 34076962 DOI: 10.1111/febs.16047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/15/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
Education of our intestinal immune system early in life strongly influences adult health. This education strongly relies on series of events that must occur in well-defined time windows. From initial colonization by maternal-derived microbiota during delivery to dietary changes from mother's milk to solid foods at weaning, these early-life events have indeed long-standing consequences on our immunity, facilitating tolerance to environmental exposures or, on the contrary, increasing the risk of developing noncommunicable diseases such as allergies, asthma, obesity, and inflammatory bowel diseases. In this review, we provide an outline of the recent advances in our understanding of these events and how they are mechanistically related to intestinal immunity development and education. First, we review the susceptibility of neonates to infections and inflammatory diseases, related to their immune system and microbiota changes. Then, we highlight the maternal factors involved in protection and education of the mucosal immune system of the offspring, the role of the microbiota, and the nature of neonatal immune system until weaning. We also present how the development of some immune responses is intertwined in temporal and spatial windows of opportunity. Finally, we discuss pending questions regarding the neonate particular immune status and the activation of the intestinal immune system at weaning.
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Affiliation(s)
- Camille Wagner
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Natalia Torow
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
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Genome sequence of segmented filamentous bacteria present in the human intestine. Commun Biol 2020; 3:485. [PMID: 32887924 PMCID: PMC7474095 DOI: 10.1038/s42003-020-01214-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host’s intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65–71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment. Hans Jonsson et al. report the metagenomic reconstruction of the genome of a potentially immune modulatory segmented filamentous bacteria (SFB) from a human ileostomy sample. They demonstrate that the genome clusters closely with SFB genomes from other species. They also detect the unique SFB variant in human faecal metagenomics datasets.
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