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Bajagai YS, Petranyi F, J Yu S, Lobo E, Batacan R, Kayal A, Horyanto D, Ren X, M Whitton M, Stanley D. Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers. Sci Rep 2022; 12:11033. [PMID: 35773309 PMCID: PMC9246849 DOI: 10.1038/s41598-022-14925-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.
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Affiliation(s)
- Yadav S Bajagai
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Friedrich Petranyi
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Sung J Yu
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Edina Lobo
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Romeo Batacan
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Advait Kayal
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Darwin Horyanto
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Xipeng Ren
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Maria M Whitton
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia
| | - Dragana Stanley
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD, 4702, Australia.
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Questionnaires or Serum Immunoglobulin G Testing in the Diagnosis of Hypersensitivity Pneumonitis among Patients with Interstitial Lung Disease. Ann Am Thorac Soc 2021; 18:130-147. [PMID: 32780584 DOI: 10.1513/annalsats.202005-419oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rationale: Hypersensitivity pneumonitis (HP) results from exposure to a variety of stimuli, which are challenging to identify. Questionnaires and serum immunoglobulin G (IgG) testing are methods to identify potentially causative exposures.Objectives: To perform a systematic review to determine the usefulness of questionnaires and serum IgG testing in identifying exposures that may have caused HP.Methods: This systematic review informed an international, multidisciplinary panel that developed a clinical practice guideline on the diagnosis of HP for the American Thoracic Society, Japanese Respiratory Society, and Asociación Latinoamericana del Tórax. MEDLINE, the Cochrane Library, and EMBASE were searched from January 1946 to October 2019 for studies that used a questionnaire or serum IgG testing to identify exposures that may have caused HP. The Grading of Recommendations, Assessment, Development, and Evaluation approach was used to appraise the quality of the evidence.Results: Searches identified 1,141 and 926 potentially relevant articles for questionnaires and serum IgG testing, respectively. The full texts of 32 and 49 articles, respectively, were reviewed. Two observational studies for questionnaires and 15 accuracy studies for serum IgG testing were selected. Questionnaires were better at detecting potentially relevant exposures than clinical history (100% vs. 26%; risk ratio [RR], 3.80; 95% confidence interval [95% CI], 1.79-8.06) and serum IgG testing (100% vs. 63%; RR, 1.58; 95% CI, 1.12-2.23) but did not differ from serum IgG testing plus bronchial challenge testing (59% vs. 65%; RR, 0.90; 95% CI, 0.65-1.24). Longer, detailed questionnaires were more likely to lead to identification of potential exposures. Only 70% of potential exposures identified by questionnaires were subsequently confirmed by environmental testing. Serum IgG testing distinguished HP from healthy exposed and unexposed control subjects with high sensitivity (90% and 92%, respectively) and high specificity (91% and 100%, respectively) but did not distinguish HP as effectively from interstitial lung diseases (ILDs; sensitivity of 83% and specificity of 68%).Conclusions: Using a questionnaire may help clinicians identify potentially relevant exposures when evaluating a patient with newly identified ILD for HP. Serum IgG testing may also lead to identification of potentially relevant exposures, but its usefulness for distinguishing HP from other types of ILD is poor.
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Johannson KA, Barnes H, Bellanger AP, Dalphin JC, Fernández Pérez ER, Flaherty KR, Huang YCT, Jones KD, Kawano-Dourado L, Kennedy K, Millerick-May M, Miyazaki Y, Morisset J, Morell F, Raghu GR, Robbins C, Sack CS, Salisbury ML, Selman M, Vasakova M, Walsh SLF, Rose CS. Exposure Assessment Tools for Hypersensitivity Pneumonitis. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2020; 17:1501-1509. [PMID: 33258669 PMCID: PMC7706597 DOI: 10.1513/annalsats.202008-942st] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
This report is based on proceedings from the Exposure Assessment Tools for Hypersensitivity Pneumonitis (HP) Workshop, sponsored by the American Thoracic Society, that took place on May 18, 2019, in Dallas, Texas. The workshop was initiated by members from the Environmental, Occupational, and Population Health and Clinical Problems Assemblies of the American Thoracic Society. Participants included international experts from pulmonary medicine, occupational medicine, radiology, pathology, and exposure science. The meeting objectives were to 1) define currently available tools for exposure assessment in evaluation of HP, 2) describe the evidence base supporting the role for these exposure assessment tools in HP evaluation, 3) identify limitations and barriers to each tool's implementation in clinical practice, 4) determine which exposure assessment tools demonstrate the best performance characteristics and applicability, and 5) identify research needs for improving exposure assessment tools for HP. Specific discussion topics included history-taking and exposure questionnaires, antigen avoidance, environmental assessment, specific inhalational challenge, serum-specific IgG testing, skin testing, lymphocyte proliferation testing, and a multidisciplinary team approach. Priorities for research in this area were identified.
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Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes 2020; 8:proteomes8030017. [PMID: 32781532 PMCID: PMC7563651 DOI: 10.3390/proteomes8030017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty & Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum Gesundheitscampus, 4 44801 Bochum, Germany;
| | - Cécile Lelong
- CBM UMR CNRS5249, Université Grenoble Alpes, CEA, CNRS, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France;
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, 38054 Grenoble, France
- Correspondence: ; Tel.: +33-438-783-212
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Raghu G, Remy-Jardin M, Ryerson CJ, Myers JL, Kreuter M, Vasakova M, Bargagli E, Chung JH, Collins BF, Bendstrup E, Chami HA, Chua AT, Corte TJ, Dalphin JC, Danoff SK, Diaz-Mendoza J, Duggal A, Egashira R, Ewing T, Gulati M, Inoue Y, Jenkins AR, Johannson KA, Johkoh T, Tamae-Kakazu M, Kitaichi M, Knight SL, Koschel D, Lederer DJ, Mageto Y, Maier LA, Matiz C, Morell F, Nicholson AG, Patolia S, Pereira CA, Renzoni EA, Salisbury ML, Selman M, Walsh SLF, Wuyts WA, Wilson KC. Diagnosis of Hypersensitivity Pneumonitis in Adults. An Official ATS/JRS/ALAT Clinical Practice Guideline. Am J Respir Crit Care Med 2020; 202:e36-e69. [PMID: 32706311 PMCID: PMC7397797 DOI: 10.1164/rccm.202005-2032st] [Citation(s) in RCA: 433] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: This guideline addresses the diagnosis of hypersensitivity pneumonitis (HP). It represents a collaborative effort among the American Thoracic Society, Japanese Respiratory Society, and Asociación Latinoamericana del Tórax.Methods: Systematic reviews were performed for six questions. The evidence was discussed, and then recommendations were formulated by a multidisciplinary committee of experts in the field of interstitial lung disease and HP using the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) approach.Results: The guideline committee defined HP, and clinical, radiographic, and pathological features were described. HP was classified into nonfibrotic and fibrotic phenotypes. There was limited evidence that was directly applicable to all questions. The need for a thorough history and a validated questionnaire to identify potential exposures was agreed on. Serum IgG testing against potential antigens associated with HP was suggested to identify potential exposures. For patients with nonfibrotic HP, a recommendation was made in favor of obtaining bronchoalveolar lavage (BAL) fluid for lymphocyte cellular analysis, and suggestions for transbronchial lung biopsy and surgical lung biopsy were also made. For patients with fibrotic HP, suggestions were made in favor of obtaining BAL for lymphocyte cellular analysis, transbronchial lung cryobiopsy, and surgical lung biopsy. Diagnostic criteria were established, and a diagnostic algorithm was created by expert consensus. Knowledge gaps were identified as future research directions.Conclusions: The guideline committee developed a systematic approach to the diagnosis of HP. The approach should be reevaluated as new evidence accumulates.
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Bellanger AP, Reboux G, Rouzet A, Barrera C, Rocchi S, Scherer E, Millon L. Hypersensitivity pneumonitis: A new strategy for serodiagnosis and environmental surveys. Respir Med 2019; 150:101-106. [PMID: 30961934 DOI: 10.1016/j.rmed.2019.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 01/08/2023]
Abstract
We propose a strategy for serodiagnosis of hypersensitivity pneumonitis (HP): 1) question patients about their private or occupational activity, or visit him on site; 2) select panels of six somatic specific antigens appropriate for each type of exposure; 3) and use ELISA to test concomitantly two recombinant antigens highly specific to Farmer's lung, Metalworking-fluid HP, and for Bird fancier's lung. The serodiagnosis provides an immunological argument that may complete radiological, functional lung exploration and clinical features; 4) If the serodiagnosis is negative but the suspicion of HP is strong, a microbial analysis of the patient's specific exposure is conducted; 5) "A la carte" antigens are produced from the microorganisms isolated in the patient's environment sample and tested; 6) Finally, the patient may be asked to undergo a specific inhalation challenge with the offending antigens in a safety cabin, or to avoid his usual environment for a few days.
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Affiliation(s)
- Anne-Pauline Bellanger
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Gabriel Reboux
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France.
| | - Adeline Rouzet
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Coralie Barrera
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Steffi Rocchi
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Emeline Scherer
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Laurence Millon
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
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Millon L, Rognon B, Valot B, Barrera C, Bellanger AP, Roussel S, Dalphin JC, Monod M, Reboux G. Common peptide epitopes induce cross-reactivity in hypersensitivity pneumonitis serodiagnosis. J Allergy Clin Immunol 2016; 138:1738-1741.e6. [DOI: 10.1016/j.jaci.2016.06.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/14/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022]
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Bellanger AP, Lignon T, Godet Y, Rognon B, Reboux G, Gbaguidi-Haore H, Borg C, Millon L. Fungal peptides from pneumonitis hypersensitivity etiologic agents are able to induce specific cellular immune response. J Immunol Methods 2016; 440:67-73. [PMID: 27876506 DOI: 10.1016/j.jim.2016.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 12/28/2022]
Abstract
PURPOSE Hypersensitivity pneumonitis (HP) is an immunoallergic disease due to chronic exposure to high quantities of different microorganisms such as Mycobacterium immunogenum (Mi), a mycobacterium, and Lichtheimia corymbifera (Lc), a filamentous fungus. It has recently been demonstrated that the protein DLDH (dihydrolipoyl dehydrogenase), is common to these microorganisms. This study aimed to investigate the immune potential of overlapping peptide pools covering the MiDLDH and LcDLDH. EXPERIMENTAL DESIGN A selection of 34 peptides, from the MiDLDH and LcDLDH, able to interact with Major Histocompatibility Complex (MHC) 1 and MHC 2, was obtained using three different epitope prediction websites. By means of ELISPOT assays, we compared the frequency of Interferon gamma (IFNγ) secreting peripheral blood mononuclear cells (PBMC) after stimulation with overlapping peptide pools. Tests were performed using cells from 35 healthy blood donors. RESULTS One peptide pool containing five peptides from MiDLDH and able to interact with MHC 2 induced a marked IFNγ specific immune response (Pool F, p<0.001, Wilcoxon signed-rank test). CONCLUSION This study demonstrated that peptides from microorganisms involved in HP were able to induce a high IFNγ specific immune response after stimulation of PBMCs from healthy blood donors which could be useful to develop an effective prevention strategy.
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Affiliation(s)
- Anne-Pauline Bellanger
- Chrono-Environnement CNRS 6249 Research Team, Franche-Comté University, Besançon, France; Parasitology-Mycology Department, Besançon University Hospital, Besançon, France.
| | - Thibaud Lignon
- Parasitology-Mycology Department, Besançon University Hospital, Besançon, France
| | - Yann Godet
- INSERM Unit 1098, University of Franche-Comté, Besançon, France
| | - Bénédicte Rognon
- Chrono-Environnement CNRS 6249 Research Team, Franche-Comté University, Besançon, France
| | - Gabriel Reboux
- Chrono-Environnement CNRS 6249 Research Team, Franche-Comté University, Besançon, France; Parasitology-Mycology Department, Besançon University Hospital, Besançon, France
| | | | - Christophe Borg
- INSERM Unit 1098, University of Franche-Comté, Besançon, France
| | - Laurence Millon
- Chrono-Environnement CNRS 6249 Research Team, Franche-Comté University, Besançon, France; Parasitology-Mycology Department, Besançon University Hospital, Besançon, France
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Identification of Antigenic Proteins from Lichtheimia corymbifera for Farmer's Lung Disease Diagnosis. PLoS One 2016; 11:e0160888. [PMID: 27490813 PMCID: PMC4973876 DOI: 10.1371/journal.pone.0160888] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022] Open
Abstract
The use of recombinant antigens has been shown to improve both the sensitivity and the standardization of the serological diagnosis of Farmer’s lung disease (FLD). The aim of this study was to complete the panel of recombinant antigens available for FLD serodiagnosis with antigens of Lichtheimia corymbifera, known to be involved in FLD. L. corymbifera proteins were thus separated by 2D electrophoresis and subjected to western blotting with sera from 7 patients with FLD and 9 healthy exposed controls (HEC). FLD-associated immunoreactive proteins were identified by mass spectrometry based on a protein database specifically created for this study and subsequently produced as recombinant antigens. The ability of recombinant antigens to discriminate patients with FLD from controls was assessed by ELISA performed with sera from FLD patients (n = 41) and controls (n = 43) recruited from five university hospital pneumology departments of France and Switzerland. Forty-one FLD-associated immunoreactive proteins from L. corymbifera were identified. Six of them were produced as recombinant antigens. With a sensitivity and specificity of 81.4 and 77.3% respectively, dihydrolipoyl dehydrogenase was the most effective antigen for discriminating FLD patients from HEC. ELISA performed with the putative proteasome subunit alpha type as an antigen was especially specific (88.6%) and could thus be used for FLD confirmation. The production of recombinant antigens from L. corymbifera represents an additional step towards the development of a standardized ELISA kit for FLD diagnosis.
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In-vitro-Serumdiagnostik. ALLERGOLOGIE 2016. [DOI: 10.1007/978-3-642-37203-2_51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Draft Genome Sequence of the Principal Etiological Agent of Farmer's Lung Disease, Saccharopolyspora rectivirgula. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01340-14. [PMID: 25523783 PMCID: PMC4271173 DOI: 10.1128/genomea.01340-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Saccharopolyspora rectivirgula is the main cause of farmer's lung disease. The development of recombinant antigens to standardize the serodiagnosis of the disease requires knowledge of the S. rectivirgula genome. We sequenced the genome of an environmental strain, S. rectivirgula DSM 43113. A total of 3,221 proteins were found to be encoded in a short 3.9-Mb genome.
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