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Chuandong Z, Hu J, Li J, Wu Y, Wu C, Lai G, Shen H, Wu F, Tao C, Liu S, Zhang W, Shao H. Distribution and roles of Ligilactobacillus murinus in hosts. Microbiol Res 2024; 282:127648. [PMID: 38367479 DOI: 10.1016/j.micres.2024.127648] [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: 08/30/2023] [Revised: 10/26/2023] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
Ligilactobacillus murinus, a member of the Ligilactobacillus genus, holds significant potential as a probiotic. While research on Ligilactobacillus murinus has been relatively limited compared to well-studied probiotic lactic acid bacteria such as Limosilactobacillus reuteri and Lactobacillus gasseri, a mounting body of evidence highlights its extensive involvement in host intestinal metabolism and immune activities. Moreover, its abundance exhibits a close correlation with intestinal health. Notably, beyond the intestinal context, Ligilactobacillus murinus is gaining recognition for its contributions to metabolism and regulation in the oral cavity, lungs, and vagina. As such, Ligilactobacillus murinus emerges as a potential probiotic candidate with a pivotal role in supporting host well-being. This review delves into studies elucidating the multifaceted roles of Ligilactobacillus murinus. It also examines its medicinal potential and associated challenges, underscoring the imperative to delve deeper into unraveling the mechanisms of its actions and exploring its health applications.
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Affiliation(s)
- Zhou Chuandong
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Jicong Hu
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Jiawen Li
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Yuting Wu
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Chan Wu
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Guanxi Lai
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Han Shen
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Fenglin Wu
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Changli Tao
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Song Liu
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China
| | - Wenfeng Zhang
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China.
| | - Hongwei Shao
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, PR China.
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. Lab Anim (NY) 2024; 53:43-55. [PMID: 38297075 PMCID: PMC10834367 DOI: 10.1038/s41684-023-01322-x] [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: 11/24/2022] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1-P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung-immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.
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Affiliation(s)
- Lan Zhao
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
| | - Christine M Cunningham
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Adam M Andruska
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Katharina Schimmel
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Md Khadem Ali
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Dongeon Kim
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Shenbiao Gu
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Jason L Chang
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Edda Spiekerkoetter
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA
| | - Mark R Nicolls
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, CA, USA.
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
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Sapra L, Saini C, Das S, Mishra PK, Singh A, Mridha AR, Yadav PK, Srivastava RK. Lactobacillus rhamnosus (LR) ameliorates pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS) via targeting neutrophils. Clin Immunol 2024; 258:109872. [PMID: 38113963 DOI: 10.1016/j.clim.2023.109872] [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: 08/11/2023] [Revised: 11/25/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Pulmonary and extrapulmonary acute respiratory distress syndrome (ARDS) is a life-threatening respiratory failure associated with high mortality. Despite progress in our understanding of the pathological mechanism causing the crippling illness, there are currently no targeted pharmaceutical treatments available for it. Recent discoveries have emphasized the existence of a potential nexus between gut and lung health fueling novel approaches including probiotics for the treatment of ARDS. We thus investigated the prophylactic-potential of Lactobacillus rhamnosus-(LR) in lipopolysaccharide (LPS)-induced pulmonary and cecal ligation puncture (CLP) induced extrapulmonary ARDS mice. Our in-vivo findings revealed that pretreatment with LR significantly ameliorated vascular-permeability (edema) of the lungs via modulating the neutrophils along with significantly reducing the expression of inflammatory-cytokines in the BALF, lungs and serum in both pulmonary and extrapulmonary mice-models. Interestingly, our ex-vivo immunofluorescence and flow cytometric data suggested that mechanistically LR via short chain fatty acids (butyrate being the most potent and efficient in ameliorating the pathophysiology of both pulmonary and extra-pulmonary ARDS) targets the phagocytic and neutrophils extracellular traps (NETs) releasing potential of neutrophils. Moreover, our in-vivo data further corroborated our ex-vivo findings and suggested that butyrate exhibits enhanced potential in ameliorating the pathophysiology of ARDS via reducing the infiltration of neutrophils into the lungs. Altogether, our study establishes the prophylactic role of LR and its associated metabolites in the prevention and management of both pulmonary and extrapulmonary ARDS via targeting neutrophils.
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Affiliation(s)
- Leena Sapra
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Chaman Saini
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Sneha Das
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Pradyumna K Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, MP 462001, India
| | - Anurag Singh
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Asit R Mridha
- Department of Pathology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Pardeep K Yadav
- Central Animal Facility, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Rupesh K Srivastava
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
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Shelton CD, Sing E, Mo J, Shealy NG, Yoo W, Thomas J, Fitz GN, Castro PR, Hickman TT, Torres TP, Foegeding NJ, Zieba JK, Calcutt MW, Codreanu SG, Sherrod SD, McLean JA, Peck SH, Yang F, Markham NO, Liu M, Byndloss MX. An early-life microbiota metabolite protects against obesity by regulating intestinal lipid metabolism. Cell Host Microbe 2023; 31:1604-1619.e10. [PMID: 37794592 PMCID: PMC10593428 DOI: 10.1016/j.chom.2023.09.002] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/07/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023]
Abstract
The mechanisms by which the early-life microbiota protects against environmental factors that promote childhood obesity remain largely unknown. Using a mouse model in which young mice are simultaneously exposed to antibiotics and a high-fat (HF) diet, we show that Lactobacillus species, predominant members of the small intestine (SI) microbiota, regulate intestinal epithelial cells (IECs) to limit diet-induced obesity during early life. A Lactobacillus-derived metabolite, phenyllactic acid (PLA), protects against metabolic dysfunction caused by early-life exposure to antibiotics and a HF diet by increasing the abundance of peroxisome proliferator-activated receptor γ (PPAR-γ) in SI IECs. Therefore, PLA is a microbiota-derived metabolite that activates protective pathways in the small intestinal epithelium to regulate intestinal lipid metabolism and prevent antibiotic-associated obesity during early life.
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Affiliation(s)
- Catherine D Shelton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Elizabeth Sing
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica Mo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicolas G Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Woongjae Yoo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Julia Thomas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gillian N Fitz
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pollyana R Castro
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo 12083-862, Brazil
| | - Tara T Hickman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Teresa P Torres
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nora J Foegeding
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jacob K Zieba
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simona G Codreanu
- Center for Innovative Technology and Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Stacy D Sherrod
- Center for Innovative Technology and Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - John A McLean
- Center for Innovative Technology and Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Sun H Peck
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fan Yang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicholas O Markham
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Min Liu
- Department of Pathology and Molecular Medicine, Metabolic Diseases Institute, University of Cincinnati College of Medicine, Cincinnati, OH 45237, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Digestive Disease Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, TN 37235, USA; Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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Qin T, Yu T, Liu Y, Wu J, Jiang Y, Zhang G. Roseicella aerolata GB24 T from bioaerosol attenuates Streptococcus pneumoniae-introduced inflammation through regulation of gut microbiota and acetic acid. Front Microbiol 2023; 14:1225548. [PMID: 37547684 PMCID: PMC10397393 DOI: 10.3389/fmicb.2023.1225548] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023] Open
Abstract
Streptococcus pneumoniae (Spn) is the most common respiratory pathogen causing community-acquired pneumonia. Probiotics represent a new intervention target for Spn infection. Hence, the discovery and development of new potential probiotic strains are urgently needed. This study was designed to investigate the beneficial effect and mechanism of a new bacterium named Roseicella aerolata GB24T that antagonizes Spn at cellular and animal levels. The results revealed that GB24T strain inhibited the growth of Spn on sheep blood agar plates, forming inhibition circles with a diameter of 20 mm. In cultured bronchial epithelium transformed with Ad 12-SV40 2B (BEAS-2B) cells, Spn infection induced an elevation in the expression levels of interleukin-1β, interleukin-6, and tumor necrosis factor-α to 4.289 ± 0.709, 5.587 ± 2.670, and 5.212 ± 0.772 folds compared to healthy controls, respectively. Moreover, pre-infection with GB24T for 1.5 h almost eliminated the cellular inflammation caused by Spn infection. Additionally, male Sprague-Dawley rats infected with Spn were randomly allocated into two groups: GB24T pre-infection and Spn infection groups, with healthy rats as control. GB24T significantly alleviated inflammatory lung injury caused by Spn infection, which was associated with obvious changes in the abundance of gut microbiota and a trend toward enhanced secretion of short-chain fatty acids, especially acetic acid. Acetic acid was validated to be effective in alleviating inflammation due to Spn infection in cellular assays. Together, these findings highlight that GB24T strain is an important protective feature in the respiratory tract.
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Affiliation(s)
- Tian Qin
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Ting Yu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yuqi Liu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Jiguo Wu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yunxia Jiang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guoxia Zhang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [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: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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Kim R. Advanced Organotypic In Vitro Model Systems for Host-Microbial Coculture. Biochip J 2023; 17:1-27. [PMID: 37363268 PMCID: PMC10201494 DOI: 10.1007/s13206-023-00103-5] [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] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 06/28/2023]
Abstract
In vitro model systems have been advanced to recapitulate important physiological features of the target organ in vivo more closely than the conventional cell line cultures on a petri dish. The advanced organotypic model systems can be used as a complementary or alternative tool for various testing and screening. Numerous data from germ-free animal studies and genome sequencings of clinical samples indicate that human microbiota is an essential part of the human body, but current in vitro model systems rarely include them, which can be one of the reasons for the discrepancy in the tissue phenotypes and outcome of therapeutic intervention between in vivo and in vitro tissues. A coculture model system with appropriate microbes and host cells may have great potential to bridge the gap between the in vitro model and the in vivo counterpart. However, successfully integrating two species in one system introduces new variables to consider and poses new challenges to overcome. This review aims to provide perspectives on the important factors that should be considered for developing organotypic bacterial coculture models. Recent advances in various organotypic bacterial coculture models are highlighted. Finally, challenges and opportunities in developing organotypic microbial coculture models are also discussed.
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Affiliation(s)
- Raehyun Kim
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
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8
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Zhao L, Cunningham CM, Andruska AM, Schimmel K, Ali MK, Kim D, Gu S, Chang JL, Spiekerkoetter E, Nicolls MR. Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs. bioRxiv 2023:2023.05.19.541527. [PMID: 37293045 PMCID: PMC10245737 DOI: 10.1101/2023.05.19.541527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined a multi-tissue full lifespan microbial biogeography for healthy Fischer 344 rats. Microbial community profiling data was extracted and integrated with host transcriptomic data from the Sequencing Quality Control (SEQC) consortium. Unsupervised machine learning, Spearman's correlation, taxonomic diversity, and abundance analyses were performed to determine and characterize the rat microbial biogeography and the identification of four inter-tissue microbial heterogeneity patterns (P1-P4). The 11 body habitats harbor a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundances progressively declined in lungs from breastfeed newborn to adolescence/adult and was below detectable levels in elderly rats. LAB's presence and levels in lungs were further evaluated by PCR in the two validation datasets. The lung, testes, thymus, kidney, adrenal, and muscle niches were found to have age-dependent alterations in microbial abundance. P1 is dominated by lung samples. P2 contains the largest sample size and is enriched for environmental species. Liver and muscle samples were mostly classified into P3. Archaea species were exclusively enriched in P4. The 357 pattern-specific microbial signatures were positively correlated with host genes in cell migration and proliferation (P1), DNA damage repair and synaptic transmissions (P2), as well as DNA transcription and cell cycle in P3. Our study established a link between metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures would be useful for microbiome therapeutic approaches to human health and good quality of life.
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Hamza FN, Daher S, Fakhoury HMA, Grant WB, Kvietys PR, Al-Kattan K. Immunomodulatory Properties of Vitamin D in the Intestinal and Respiratory Systems. Nutrients 2023; 15:nu15071696. [PMID: 37049536 PMCID: PMC10097244 DOI: 10.3390/nu15071696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Vitamin D plays a crucial role in modulating the innate immune response by interacting with its intracellular receptor, VDR. In this review, we address vitamin D/VDR signaling and how it contributes to the regulation of intestinal and respiratory microbiota. We additionally review some components of the innate immune system, such as the barrier function of the pulmonary and intestinal epithelial membranes and secretion of mucus, with their respective modulation by vitamin D. We also explore the mechanisms by which this vitamin D/VDR signaling mounts an antimicrobial response through the transduction of microbial signals and the production of antimicrobial peptides that constitute one of the body’s first lines of defense against pathogens. Additionally, we highlight the role of vitamin D in clinical diseases, namely inflammatory bowel disease and acute respiratory distress syndrome, where excessive inflammatory responses and dysbiosis are hallmarks. Increasing evidence suggests that vitamin D supplementation may have potentially beneficial effects on those diseases.
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Affiliation(s)
- Fatheia N. Hamza
- College of Medicine, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Sarah Daher
- College of Medicine, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Hana M. A. Fakhoury
- College of Medicine, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
- Correspondence:
| | - William B. Grant
- Sunlight, Nutrition, and Health Research Center, P.O. Box 641603, San Francisco, CA 94164-1603, USA
| | - Peter R. Kvietys
- College of Medicine, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, P.O. Box 50927, Riyadh 11533, Saudi Arabia
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10
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Abdullahi IN, Juárez-Fernández G, Höfle Ú, Cardona-Cabrera T, Mínguez D, Pineda-Pampliega J, Lozano C, Zarazaga M, Torres C. Nasotracheal Microbiota of Nestlings of Parent White storks with Different Foraging Habits in Spain. Ecohealth 2023; 20:105-121. [PMID: 37060390 DOI: 10.1007/s10393-023-01626-x] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/11/2023] [Indexed: 06/11/2023]
Abstract
Migratory storks could be vectors of transmission of bacteria of public health concern mediated by the colonization, persistence and excretion of such bacteria. This study aims to determine genera/species diversity, prevalence, and co-colonization indices of bacteria obtained from tracheal (T) and nasal (N) samples from storks in relation to exposure to point sources through foraging. One-hundred and thirty-six samples from 87 nestlings of colonies of parent white storks with different foraging habits (natural habitat and landfills) were obtained (84 T-samples and 52 N-samples) and processed. Morphologically distinct colonies (up to 12/sample) were randomly selected and identified by MALDI-TOF-MS. About 87.2% of the total 806 isolates recovered were identified: 398 from T-samples (56.6%) and 305 from N-samples (43.4%). Among identified isolates, 17 genera and 46 species of Gram-positive and Gram-negative bacteria were detected, Staphylococcus (58.0%) and Enterococcus (20.5%) being the most prevalent genera. S. sciuri was the most prevalent species from T (36.7%) and N (34.4%) cavities of total isolates, followed by E. faecalis (11.1% each from T and N), and S. aureus [T (6.5%), N (13.4%)]. Of N-samples, E. faecium was significantly associated with nestlings of parent storks foraging in landfills (p = 0.018). S. sciuri (p = 0.0034) and M. caseolyticus (p = 0.032) from T-samples were significantly higher among nestlings of parent storks foraging in natural habitats. More than 80% of bacterial species in the T and N cavities showed 1-10% co-colonization indices with one another, but few had ≥ 40% indices. S. sciuri and E. faecalis were the most frequent species identified in the stork nestlings. Moreover, they were highly colonized by other diverse and potentially pathogenic bacteria. Thus, storks could be sentinels of point sources and vehicles of bacterial transmission across the "One Health" ecosystems.
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Affiliation(s)
- Idris Nasir Abdullahi
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Guillermo Juárez-Fernández
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Úrsula Höfle
- SaBio (Health and Biotechnology) Research Group, Game and Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Teresa Cardona-Cabrera
- SaBio (Health and Biotechnology) Research Group, Game and Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - David Mínguez
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Javier Pineda-Pampliega
- Department of Biology, Lund University, Lund, Sweden
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Carmen Lozano
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Myriam Zarazaga
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Carmen Torres
- OneHealth-UR Research Group, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain.
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11
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Chen Q, Liu M, Lin Y, Wang K, Li J, Li P, Yang L, Jia L, Zhang B, Guo H, Li P, Song H. Topography of respiratory tract and gut microbiota in mice with influenza A virus infection. Front Microbiol 2023; 14:1129690. [PMID: 36910185 PMCID: PMC9992211 DOI: 10.3389/fmicb.2023.1129690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Influenza A virus (IAV)-induced dysbiosis may predispose to severe bacterial superinfections. Most studies have focused on the microbiota of single mucosal surfaces; consequently, the relationships between microbiota at different anatomic sites in IAV-infected mice have not been fully studied. Methods We characterized respiratory and gut microbiota using full-length 16S rRNA gene sequencing by Nanopore sequencers and compared the nasopharyngeal, oropharyngeal, lung and gut microbiomes in healthy and IAV-infected mice. Results The oropharyngeal, lung and gut microbiota of healthy mice were dominated by Lactobacillus spp., while nasopharyngeal microbiota were comprised primarily of Streptococcus spp. However, the oropharyngeal, nasopharyngeal, lung, and gut microbiota of IAV-infected mice were dominated by Pseudomonas, Escherichia, Streptococcus, and Muribaculum spp., respectively. Lactobacillus murinus was identified as a biomarker and was reduced at all sites in IAV-infected mice. The microbiota composition of lung was more similar to that of the nasopharynx than the oropharynx in healthy mice. Discussion These findings suggest that the main source of lung microbiota in mice differs from that of adults. Moreover, the similarity between the nasopharyngeal and lung microbiota was increased in IAV-infected mice. We found that IAV infection reduced the similarity between the gut and oropharyngeal microbiota. L. murinus was identified as a biomarker of IAV infection and may be an important target for intervention in post-influenza bacterial superinfections.
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Affiliation(s)
- Qichao Chen
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Yanfeng Lin
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Bei Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu Province, China.,Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, Jiangsu Province, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
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12
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Hu Q, Liu B, Fan Y, Zheng Y, Wen F, Yu U, Wang W. Multi-omics association analysis reveals interactions between the oropharyngeal microbiome and the metabolome in pediatric patients with influenza A virus pneumonia. Front Cell Infect Microbiol 2022; 12:1011254. [PMID: 36389138 PMCID: PMC9651038 DOI: 10.3389/fcimb.2022.1011254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
Children are at high risk for influenza A virus (IAV) infections, which can develop into severe illnesses. However, little is known about interactions between the microbiome and respiratory tract metabolites and their impact on the development of IAV pneumonia in children. Using a combination of liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene sequencing, we analyzed the composition and metabolic profile of the oropharyngeal microbiota in 49 pediatric patients with IAV pneumonia and 42 age-matched healthy children. The results indicate that compared to healthy children, children with IAV pneumonia exhibited significant changes in the oropharyngeal macrobiotic structure (p = 0.001), and significantly lower microbial abundance and diversity (p < 0.05). These changes came with significant disturbances in the levels of oropharyngeal metabolites. Intergroup differences were observed in 204 metabolites mapped to 36 metabolic pathways. Significantly higher levels of sphingolipid (sphinganine and phytosphingosine) and propanoate (propionic acid and succinic acid) metabolism were observed in patients with IAV pneumonia than in healthy controls. Using Spearman’s rank-correlation analysis, correlations between IAV pneumonia-associated discriminatory microbial genera and metabolites were evaluated. The results indicate significant correlations and consistency in variation trends between Streptococcus and three sphingolipid metabolites (phytosphingosine, sphinganine, and sphingosine). Besides these three sphingolipid metabolites, the sphinganine-to-sphingosine ratio and the joint analysis of the three metabolites indicated remarkable diagnostic efficacy in children with IAV pneumonia. This study confirmed significant changes in the characteristics and metabolic profile of the oropharyngeal microbiome in pediatric patients with IAV pneumonia, with high synergy between the two factors. Oropharyngeal sphingolipid metabolites may serve as potential diagnostic biomarkers of IAV pneumonia in children.
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Affiliation(s)
- Qian Hu
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Baiming Liu
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yanqun Fan
- Department of Trans-omics Research, Biotree Metabolomics Technology Research Center, Shanghai, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Uet Yu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Wenjian Wang, ; Uet Yu,
| | - Wenjian Wang
- Department of Respiratory Diseases, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Wenjian Wang, ; Uet Yu,
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13
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Jha A, Ward T, Walker S, Goodwin AT, Chalmers JD. Review of the British Thoracic Society Winter Meeting 2021, 24-26 November 2021. Thorax 2022; 77:1030-1035. [PMID: 35907640 DOI: 10.1136/thorax-2022-219150] [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: 04/29/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022]
Abstract
The Winter Meeting of the British Thoracic Society (BTS) is a platform for the latest clinical and scientific research in respiratory medicine. This review summarises the key symposia and presentations from the BTS Winter Meeting 2021 held online due to the COVID-19 pandemic.
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Affiliation(s)
- Akhilesh Jha
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Tom Ward
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Steven Walker
- School of Clinical Sciences, University of Bristol Academic Respiratory Unit, Westbury on Trym, UK
| | - Amanda T Goodwin
- Nottingham NIHR Respiratory Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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14
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Yildiz S, Mazel-Sanchez B, Bonifacio JPP, Schmolke M. A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model. NPJ Biofilms Microbiomes 2022; 8:51. [PMID: 35780244 DOI: 10.1038/s41522-022-00315-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
In adult animals, acute viral infections only temporarily alter the composition of both respiratory and intestinal commensal microbiota, potentially due to the intrinsic stability of this microbial ecosystem. In stark contrast, commensal bacterial communities are rather vulnerable to perturbation in infancy. Animal models proved that disruption of a balanced microbiota development e.g., by antibiotics treatment early in life, increases the probability for metabolic disorders in adults. Importantly, infancy is also a phase in life with high incidence of acute infections. We postulated that acute viral infections in early life might pose a similarly severe perturbation and permanently shape microbiota composition with long-term physiological consequences for the adult host. As a proof of concept, we infected infant mice with a sub-lethal dose of influenza A virus. We determined microbiota composition up to early adulthood (63 days) from small intestine by 16S rRNA gene-specific next-generation sequencing. Infected mice underwent long-lasting changes in microbiota composition, associated with increase in fat mass. High-fat-high-glucose diet promoted this effect while co-housing with mock-treated animals overwrote the weight gain. Our data suggest that in the critical phase of infancy even a single silent viral infection could cast a long shadow and cause long-term microbiota perturbations, affecting adult host physiology.
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15
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Abstract
Respiratory diseases cause a high incidence and mortality worldwide. As a natural immunobiotic, Lactobacillus has excellent immunomodulatory ability. Administration of some Lactobacillus species can alleviate the symptoms of respiratory diseases such as respiratory tract infections, asthma, lung cancer and cystic fibrosis in animal studies and clinical trials. The beneficial effect of Lactobacillus on the respiratory tract is strain dependent. Moreover, the efficacy of Lactobacillus may be affected by many factors, such as bacteria dose, timing and host background. Here, we summarized the beneficial effect of administered Lactobacillus on common respiratory diseases with a focus on the mechanism and safety of Lactobacillus in regulating respiratory immunity.
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16
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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17
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Nunzi E, Renga G, Palmieri M, Pieraccini G, Pariano M, Stincardini C, D’Onofrio F, Santarelli I, Bellet MM, Bartoli A, Costantini C, Romani L. A Shifted Composition of the Lung Microbiota Conditions the Antifungal Response of Immunodeficient Mice. Int J Mol Sci 2021; 22:ijms22168474. [PMID: 34445184 PMCID: PMC8395209 DOI: 10.3390/ijms22168474] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 01/04/2023] Open
Abstract
The microbiome, i.e., the communities of microbes that inhabit the surfaces exposed to the external environment, participates in the regulation of host physiology, including the immune response against pathogens. At the same time, the immune response shapes the microbiome to regulate its composition and function. How the crosstalk between the immune system and the microbiome regulates the response to fungal infection has remained relatively unexplored. We have previously shown that strict anaerobes protect from infection with the opportunistic fungus Aspergillus fumigatus by counteracting the expansion of pathogenic Proteobacteria. By resorting to immunodeficient mouse strains, we found that the lung microbiota could compensate for the lack of B and T lymphocytes in Rag1–/– mice by skewing the composition towards an increased abundance of protective anaerobes such as Clostridia and Bacteroidota. Conversely, NSG mice, with major defects in both the innate and adaptive immune response, showed an increased susceptibility to infection associated with a low abundance of strict anaerobes and the expansion of Proteobacteria. Further exploration in a murine model of chronic granulomatous disease, a primary form of immunodeficiency characterized by defective phagocyte NADPH oxidase, confirms the association of lung unbalance between anaerobes and Proteobacteria and the susceptibility to aspergillosis. Consistent changes in the lung levels of short-chain fatty acids between the different strains support the conclusion that the immune system and the microbiota are functionally intertwined during Aspergillus infection and determine the outcome of the infection.
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Affiliation(s)
- Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
- University Research Center on Functional Genomics (C.U.R.Ge.F), University of Perugia, 06132 Perugia, Italy
| | - Giorgia Renga
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Melissa Palmieri
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Giuseppe Pieraccini
- Mass Spectrometry Centre (CISM), University of Florence, 50019 Florence, Italy;
| | - Marilena Pariano
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Claudia Stincardini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Fiorella D’Onofrio
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Ilaria Santarelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Marina Maria Bellet
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Andrea Bartoli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
- Correspondence: (C.C.); (L.R.)
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (E.N.); (G.R.); (M.P.); (M.P.); (C.S.); (F.D.); (I.S.); (M.M.B.); (A.B.)
- University Research Center on Functional Genomics (C.U.R.Ge.F), University of Perugia, 06132 Perugia, Italy
- Correspondence: (C.C.); (L.R.)
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18
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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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19
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Rowe HM, Rosch JW. Polymicrobial Interactions Operative during Pathogen Transmission. mBio 2021; 12:e01027-21. [PMID: 34006664 DOI: 10.1128/mBio.01027-21] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pathogen transmission is a key point not only for infection control and public health interventions but also for understanding the selective pressures in pathogen evolution. The “success” of a pathogen lies not in its ability to cause signs and symptoms of illness but in its ability to be shed from the initial hosts, survive between hosts, and then establish infection in a new host. Recent insights have shown the importance of the interaction between the pathogen and both the commensal microbiome and coinfecting pathogens on shedding, environmental survival, and acquisition of infection. Pathogens have evolved in the context of cooperation and competition with other microbes, and the roles of these cooperations and competitions in transmission can inform novel preventative and therapeutic strategies.
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