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Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nat Commun 2024; 15:6618. [PMID: 39103350 DOI: 10.1038/s41467-024-50124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron. From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D-glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.
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Affiliation(s)
- Yolanda Y Huang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Hung
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Omree Gal-Oz
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Christopher W Smith
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Davian Ho
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Héloïse Carion
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA.
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2
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Dreyer A, Masanta WO, Lugert R, Bohne W, Groß U, Leha A, Dakna M, Lenz C, Zautner AE. Proteome profiling of Campylobacter jejuni 81-176 at 37 °C and 42 °C by label-free mass spectrometry. BMC Microbiol 2024; 24:191. [PMID: 38822261 PMCID: PMC11140963 DOI: 10.1186/s12866-024-03348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND The main natural reservoir for Campylobacter jejuni is the avian intestinal tract. There, C. jejuni multiplies optimally at 42 °C - the avian body temperature. After infecting humans through oral intake, the bacterium encounters the lower temperature of 37 °C in the human intestinal tract. Proteome profiling by label-free mass spectrometry (DIA-MS) was performed to examine the processes which enable C. jejuni 81-176 to thrive at 37 °C in comparison to 42 °C. In total, four states were compared with each other: incubation for 12 h at 37 °C, for 24 h at 37 °C, for 12 h at 42 °C and 24 h at 42 °C. RESULTS It was shown that the proteomic changes not only according to the different incubation temperature but also to the length of the incubation period were evident when comparing 37 °C and 42 °C as well as 12 h and 24 h of incubation. Altogether, the expression of 957 proteins was quantifiable. 37.1 - 47.3% of the proteins analyzed showed significant differential regulation, with at least a 1.5-fold change in either direction (i.e. log2 FC ≥ 0.585 or log2 FC ≤ -0.585) and an FDR-adjusted p-value of less than 0.05. The significantly differentially expressed proteins could be arranged in 4 different clusters and 16 functional categories. CONCLUSIONS The C. jejuni proteome at 42 °C is better adapted to high replication rates than that at 37 °C, which was in particular indicated by the up-regulation of proteins belonging to the functional categories "replication" (e.g. Obg, ParABS, and NapL), "DNA synthesis and repair factors" (e.g. DNA-polymerase III, DnaB, and DnaE), "lipid and carbohydrate biosynthesis" (e.g. capsular biosynthesis sugar kinase, PrsA, AccA, and AccP) and "vitamin synthesis, metabolism, cofactor biosynthesis" (e.g. MobB, BioA, and ThiE). The relative up-regulation of proteins with chaperone function (GroL, DnaK, ClpB, HslU, GroS, DnaJ, DnaJ-1, and NapD) at 37 °C in comparison to 42 °C after 12 h incubation indicates a temporary lower-temperature proteomic response. Additionally the up-regulation of factors for DNA uptake (ComEA and RecA) at 37 °C compared to 42 °C indicate a higher competence for the acquisition of extraneous DNA at human body temperature.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Wycliffe O Masanta
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
- Department of Medical Microbiology, Maseno University Medical School, Private Bag, Maseno, 40105, Kenya
| | - Raimond Lugert
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Andreas Leha
- Department of Medical Statistics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Mohammed Dakna
- Department of Medical Statistics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Andreas E Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, 37075, Göttingen, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Germany.
- CHaMP, Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, 39120, Magdeburg, Germany.
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3
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Dreyer A, Lenz C, Groß U, Bohne W, Zautner AE. Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios. Front Microbiol 2023; 14:1247211. [PMID: 38029072 PMCID: PMC10666060 DOI: 10.3389/fmicb.2023.1247211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81-176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Wei D, Li Y, Che M, Li C, Wu Q, Sun C. Melatonin relieves hepatic lipid dysmetabolism caused by aging via modifying the secondary bile acid pattern of gut microbes. Cell Mol Life Sci 2022; 79:527. [PMID: 36151409 DOI: 10.1007/s00018-022-04412-0] [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: 02/28/2022] [Revised: 05/17/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
It has been reported that aging-generated gut microecosystem may promote host hepatic lipid dysmetabolism through shaping the pattern of secondary bile acids (BAs). Then as an oral drug, melatonin (Mel)-mediated beneficial efforts on the communication between gut microbiota and aging host are still not clearly. Here, we show that aging significantly shapes the pattern of gut microbiota and BAs, whereas Mel treatment reverses these phenotypes (P < 0.05), which is identified to depend on the existence of gut microbiota. Mechanistically, aging-triggered high-level expression of ileac farnesoid X receptor (FXR) is significantly decreased through Mel-mediated inhibition on Campylobacter jejuni (C. jejuni)-induced deconjugation of tauroursodeoxycholic acid (TUDCA) and glycoursodeoxycholic acid (GUDCA) (P < 0.05). The aging-induced high-level of serum taurine chenodeoxycholic acid (TCDCA) activate trimethylamine-N-oxide (TMAO)-triggered activating transcriptional factor 4 (ATF4) signaling via hepatic FXR, which further regulates hepatic BAs metabolism, whereas TUDCA inhibits aging-triggered high-level of hepatic ATF4. Overall, Mel reduces C. jejuni-mediated deconjugation of TUDCA to inhibit aging-triggered high-level expression of hepatic FXR, which further decreases hepatic TMAO production, to relieve hepatic lipid dysmetabolism.
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Affiliation(s)
- Dongqin Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yizhou Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Meng Che
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chaowei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Dieckmann AL, Riedel T, Bunk B, Spröer C, Overmann J, Groß U, Bader O, Bohne W, Morgenstern B, Hosseini M, Zautner AE. Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression. Microb Genom 2021; 7. [PMID: 34661518 PMCID: PMC8627207 DOI: 10.1099/mgen.0.000679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli/C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined ‘despeciation’. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli/C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C. coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni. The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1–9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli. Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.
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Affiliation(s)
- Anastasia-Lisa Dieckmann
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Thomas Riedel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF) Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF) Hannover-Braunschweig, Braunschweig, Germany
| | - Uwe Groß
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Oliver Bader
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Burkhard Morgenstern
- Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany
| | - Morteza Hosseini
- Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany.,IEETA/DETI, University of Aveiro, Aveiro, Portugal
| | - Andreas E Zautner
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
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Masanta WO, Zautner AE, Lugert R, Bohne W, Gross U, Leha A, Dakna M, Lenz C. Proteome Profiling by Label-Free Mass Spectrometry Reveals Differentiated Response of Campylobacter jejuni 81-176 to Sublethal Concentrations of Bile Acids. Proteomics Clin Appl 2018; 13:e1800083. [PMID: 30246935 PMCID: PMC6585709 DOI: 10.1002/prca.201800083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/27/2018] [Indexed: 11/18/2022]
Abstract
Purpose Bile acids are crucial components of the intestinal antimicrobial defense and represent a significant stress factor for enteric pathogens. Adaptation processes of Campylobacter jejuni to this hostile environment are analyzed in this study by a proteomic approach. Experimental design Proteome profiling by label‐free mass spectrometry (SWATH‐MS) has been used to characterize the adaptation of C. jejuni to sublethal concentrations of seven bile acids. Results The bile acids with the lowest inhibitory concentration (IC50), deoxycholic and chenodeoxycholic acid, induce the most significant proteome changes. Overall a downregulation of all basic biosynthetic pathways and a general decrease in the transcription machinery are found. Concurrently, an induction of factors involved in detoxification of reactive oxygen species, protein folding, and bile acid exporting efflux pumps is detected. Exposure to deoxycholic and chenodeoxycholic acid results in an increased expression of components of the more energy‐efficient aerobic respiration pathway, while the anaerobic branches of the electron transport chain are down‐expressed. Conclusions and clinical relevance The results show that C. jejuni has a differentiated system of adaptation to bile acid stresses. The findings enhance the understanding of the pathogenesis of campylobacteriosis, especially for survival of C. jejuni in the human intestine, and may provide clues to future medical treatment.
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Affiliation(s)
- Wycliffe O Masanta
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany.,Department of Medical Microbiology, Maseno University Medical School, Private Bag, 40105 Maseno, Kenya
| | - Andreas E Zautner
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Raimond Lugert
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Uwe Gross
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Andreas Leha
- Department of Medical Statistics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mohammed Dakna
- Department of Medical Statistics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, 37075 Göttingen, Germany
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