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Häupl T, Sörensen T, Smiljanovic B, Darcy M, Scheder-Bieschin J, Steckhan N, Hartmann AM, Koppold DA, Stuhlmüller B, Skriner K, Walewska BM, Hoppe B, Bonin M, Burmester GR, Schendel P, Feist E, Liere K, Meixner M, Kessler C, Grützkau A, Michalsen A. Intestinal Microbiota Reduction Followed by Fasting Discloses Microbial Triggering of Inflammation in Rheumatoid Arthritis. J Clin Med 2023; 12:4359. [PMID: 37445394 DOI: 10.3390/jcm12134359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Rheumatoid arthritis (RA) synovitis is dominated by monocytes/macrophages with inflammatory patterns resembling microbial stimulation. In search of triggers, we reduced the intestinal microbiome in 20 RA patients (open label study DRKS00014097) by bowel cleansing and 7-day fasting (≤250 kcal/day) and performed immune monitoring and microbiome sequencing. Patients with metabolic syndrome (n = 10) served as a non-inflammatory control group. Scores of disease activity (DAS28/SDAI) declined within a few days and were improved in 19 of 20 RA patients after breaking the fast (median ∆DAS28 = -1.23; ∆SDAI = -43%) or even achieved remission (DAS28 < 2.6/n = 6; SDAI < 3.3/n = 3). Cytometric profiling with 46 different surface markers revealed the most pronounced phenomenon in RA to be an initially increased monocyte turnover, which improved within a few days after microbiota reduction and fasting. Serum levels of IL-6 and zonulin, an indicator of mucosal barrier disruption, decreased significantly. Endogenous cortisol levels increased during fasting but were insufficient to explain the marked improvement. Sequencing of the intestinal microbiota indicated that fasting reduced potentially arthritogenic bacteria and changed the microbial composition to species with broader metabolic capabilities. More eukaryotic, predominantly fungal colonizers were observed in RA, suggesting possible involvement. This study demonstrates a direct link between the intestinal microbiota and RA-specific inflammation that could be etiologically relevant and would support targeted nutritional interventions against gut dysbiosis as a causal therapeutic approach.
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Affiliation(s)
- Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Rheumatology, Helios Fachklinik Vogelsang-Gommern GmbH, 39245 Gommern, Germany
| | - Till Sörensen
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Biljana Smiljanovic
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Marine Darcy
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Justus Scheder-Bieschin
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Nico Steckhan
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Anika M Hartmann
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Dermatology, Venereology and Allergology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Daniela A Koppold
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Internal and Integrative Medicine, Immanuel Hospital Berlin, 14109 Berlin, Germany
- Department of Pediatrics, Division of Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Bruno Stuhlmüller
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Barbara M Walewska
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Berthold Hoppe
- Institute of Laboratory Medicine, Unfallkrankenhaus Berlin, 12683 Berlin, Germany
| | - Marc Bonin
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Gerd R Burmester
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Pascal Schendel
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
| | - Eugen Feist
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Rheumatology, Helios Fachklinik Vogelsang-Gommern GmbH, 39245 Gommern, Germany
| | - Karsten Liere
- Amedes Genetics, 10117 Berlin, Germany
- Services in Molecular Biology GmbH, 10115 Rüdersdorf, Germany
| | - Martin Meixner
- Amedes Genetics, 10117 Berlin, Germany
- Services in Molecular Biology GmbH, 10115 Rüdersdorf, Germany
| | - Christian Kessler
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Internal and Integrative Medicine, Immanuel Hospital Berlin, 14109 Berlin, Germany
| | | | - Andreas Michalsen
- Institute of Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, 10117 Berlin, Germany
- Department of Internal and Integrative Medicine, Immanuel Hospital Berlin, 14109 Berlin, Germany
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Gupta RK, Singh AK, Bajaj A, Khardenavis AA, Purohit HJ. Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior. J Basic Microbiol 2023; 63:359-376. [PMID: 36453555 DOI: 10.1002/jobm.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022]
Abstract
Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4 + -N, and NO3 - -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4 )2 SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.
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Affiliation(s)
- Rakesh K Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish K Singh
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
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More RP, Purohit HJ. The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. J Comput Biol 2016; 23:651-61. [PMID: 27104769 DOI: 10.1089/cmb.2016.0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classification of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a regular expression that is specific to each particular taxon. Our main goal was to identify discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We applied combined composite vector and multiple sequence alignment approaches to generate gene-specific signatures. Further, we mapped all the patterns into the different hypervariable regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as V3-V4 for targeted taxa. We also examined the evolution in discriminating patterns of signatures across taxonomic levels. We assessed the comparative classification accuracy of signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity close to 0.99. We developed signature-based software DNA Barcode Identification (DNA BarID) for taxonomic classification that is available at website http://www.neeri.res.in/DNA_BarID.htm . This pattern-based study provides a deeper understanding of taxon-specific discriminating patterns in 16S rRNA gene with respect to taxonomic classification.
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Affiliation(s)
- Ravi P More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
| | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
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Jia J, Chen Y, Jiang Y, Tang J, Yang L, Liang C, Jia Z, Zhao L. Visualized analysis of cellular fatty acid profiles of Vibrio parahaemolyticus strains under cold stress. FEMS Microbiol Lett 2014; 357:92-8. [PMID: 24910303 DOI: 10.1111/1574-6968.12498] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 12/01/2022] Open
Abstract
Vibrio parahaemolyticus is a common foodborne bacterial pathogen, which survives in cold environments and is sometimes difficult to culture. Fatty acid analysis under cold stress was conducted for several V. parahaemolyticus strains using gas chromatography/mass spectrometry, and the results were compared with those of the controls. All the fatty acid profiles obtained were visualized by multidimensional scaling (MDS) and self-organized map (SOM). It was observed that the fatty acid profiles of V. parahaemolyticus substantially changed under cold stress. The percentage of methyl palmitate remarkably decreased and that of methyl palmitoleate (except for two strains) and methyl oleate increased. These findings demonstrate the role of fatty acids in cold stress. The changes in the fatty acid profiles illustrated by MDS and SOM could differentiate strains under cold stress from the controls and can potentially lead to a method of detecting injured cold-stressed V. parahaemolyticus.
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Affiliation(s)
- Juntao Jia
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao, China
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Paliwal V, Puranik S, Purohit HJ. Integrated perspective for effective bioremediation. Appl Biochem Biotechnol 2011; 166:903-24. [PMID: 22198863 DOI: 10.1007/s12010-011-9479-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
Identification of factors which can influence the natural attenuation process with available microbial genetic capacities can support the bioremediation which has been viewed as the safest procedure to combat with anthropogenic compounds in ecosystems. With the advent of molecular techniques, assimilatory capacity of an ecosystem can be defined with changing community dynamics, and if required, the essential genetic potential can be met through bioaugmentation. At the same time, intensification of microbial processes with nutrient balancing, expressing and enhancing the degradative capacities, could reduce the time frame of restoration of the ecosystem. The new concept of ecosystems biology has added greatly to conceptualize the networking of the evolving microbiota of the niche that helps in effective application of bioremediation tools to manage pollutants as additional carbon source.
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Affiliation(s)
- Vasundhara Paliwal
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR, Nehru Marg, Nagpur 440020, India
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