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Sekeresova Kralova J, Donic C, Dassa B, Livyatan I, Jansen PM, Ben-Dor S, Fidel L, Trzebanski S, Narunsky-Haziza L, Asraf O, Brenner O, Dafni H, Jona G, Boura-Halfon S, Stettner N, Segal E, Brunke S, Pilpel Y, Straussman R, Zeevi D, Bacher P, Hube B, Shlezinger N, Jung S. Competitive fungal commensalism mitigates candidiasis pathology. J Exp Med 2024; 221:e20231686. [PMID: 38497819 PMCID: PMC10949073 DOI: 10.1084/jem.20231686] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/17/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. heterogenica or K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.
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Affiliation(s)
| | - Catalina Donic
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Livyatan
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Paul Mathias Jansen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Lena Fidel
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Trzebanski
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Omer Asraf
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Dafni
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ghil Jona
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Yitzhak Pilpel
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ravid Straussman
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Zeevi
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Petra Bacher
- Institute of Immunology, Christian-Albrecht-University of Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Kiel, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Neta Shlezinger
- The Robert H. Smith Faculty of Agriculture, Food and Environment The Hebrew University of Jerusalem, Rehovot, Israel
| | - Steffen Jung
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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2
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Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell 2022; 185:3789-3806.e17. [PMID: 36179670 PMCID: PMC9567272 DOI: 10.1016/j.cell.2022.09.005] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/13/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.
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Affiliation(s)
- Lian Narunsky-Haziza
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Micronoma Inc., San Diego, CA, USA
| | - Ilana Livyatan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Deborah Nejman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, USA
| | - Guy Amit
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel; Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Antonio González
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Gili Perry
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ruthie Ariel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arnon Meltser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Justin P Shaffer
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Nora Balint-Lahat
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dadiani
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Einav N Gal-Yam
- Breast Oncology Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Amir Bashan
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Haziza LN, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadian M, Gal-Yam EN, Pate SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R. Abstract 3054: Pan-cancer characterization of the tumor mycobiome and its clinical effects. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
While the study of the tumor microbiome and its effects on cancer biology has expanded considerably over the last few years, most of this research focused on bacteria and viruses, leaving behind the fungal kingdom. Recently, a few studies have demonstrated that specific fungi may promote tumor progression, stressing the importance of comprehensively studying the tumor mycobiome and its effects. To address this, we have characterized the mycobiome in 1,183 human tumors and their adjacent tissues, originating from eight major solid tumor types. Staining and imaging demonstrated the presence of fungi in both cancer and immune cells, with tumor-type specific distribution patterns. Quantitative PCR of the fungal 5.8s rDNA revealed the presence of fungal DNA in all tumor types. To characterize the tumor mycobiome and address potential contamination during tissue handling and processing, we subjected all samples, as well as 295 negative controls of different types, to sequencing of the ITS2 region that is situated between fungal rRNA genes. We found cancer-type specific mycobial signatures with relatively high similarity between tumors and their adjacent tissues. While the fungal mycobiome had a lower species richness as compared to the bacterial microbiome of the same tumors, fungi showed significant co-occurrences with specific bacteria, suggesting the existence of ecological niches within the tumors. We also found significant correlations with clinical parameters such as patient’s age, tumor stage, progression-free survival, overall survival, and response to immune checkpoint blockade therapy. Characterization of the tumor mycobiome may add a biologically relevant, previously overlooked, component to be considered in the study of cancer, including its effects on tumor initiation, progression, diagnosis, and response to therapy.
Citation Format: Lian Narunsky Haziza, Gregory D. Sepich-Poore, Ilana Livyatan, Omer Asraf, Cameron Martino, Deborah Nejman, Nancy Gavert, Jason E. Stajich, Guy Amit, Antonio González, Stephen Wandro, Gili Perry, Ruthie Ariel, Arnon Meltser, Justin P. Shaffer, Qiyun Zhu, Nora Balint-Lahat, Iris Barshack, Maya Dadian, Einav N. Gal-Yam, Sandip P. Pate, Amir Bashan, Austin D. Swafford, Yitzhak Pilpel, Rob Knight, Ravid Straussman. Pan-cancer characterization of the tumor mycobiome and its clinical effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3054.
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Affiliation(s)
| | | | | | - Omer Asraf
- 1Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Jason E. Stajich
- 3Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA
| | - Guy Amit
- 4Bar Ilan University, Ramat Gan, Israel
| | | | | | - Gili Perry
- 1Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Qiyun Zhu
- 6School of Life Sciences, Arizona State University, Tempe, AZ
| | | | - Iris Barshack
- 7Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Dadian
- 8Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Einav N. Gal-Yam
- 8Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Sandip P. Pate
- 9Breast Oncology Institute, Sheba Medical Center, Ramat Gan, Israel
| | | | - Austin D. Swafford
- 10Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | | | - Rob Knight
- 2University of California San Diego, La Jolla, CA
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Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene architectures that minimize cost of gene expression. Mol Cell 2021; 81:2494. [PMID: 34087180 DOI: 10.1016/j.molcel.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Slomka S, Françoise I, Hornung G, Asraf O, Biniashvili T, Pilpel Y, Dahan O. Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. Genetics 2020; 216:543-558. [PMID: 32847815 PMCID: PMC7536860 DOI: 10.1534/genetics.120.303401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 05/31/2020] [Accepted: 08/16/2020] [Indexed: 12/18/2022] Open
Abstract
Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.
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Affiliation(s)
- Shai Slomka
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itamar Françoise
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gil Hornung
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tammy Biniashvili
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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6
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Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y. Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity. Mol Cell 2019; 75:427-441.e5. [DOI: 10.1016/j.molcel.2019.06.041] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/05/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022]
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7
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Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Mol Cell 2016; 65:142-153. [PMID: 27989436 DOI: 10.1016/j.molcel.2016.11.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [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: 07/29/2016] [Revised: 10/10/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
Abstract
Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aviv Rotman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liron Zahavi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ernest Mordret
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Song Wu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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