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Xiang Q, Stryhanyuk H, Schmidt M, Kümmel S, Richnow HH, Zhu YG, Cui L, Musat N. Stable isotopes and nanoSIMS single-cell imaging reveals soil plastisphere colonizers able to assimilate sulfamethoxazole. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124197. [PMID: 38782163 DOI: 10.1016/j.envpol.2024.124197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The presence and accumulation of both, plastics and antibiotics in soils may lead to the colonization, selection, and propagation of soil bacteria with certain metabolic traits, e.g., antibiotic resistance, in the plastisphere. However, the impact of plastic-antibiotic tandem on the soil ecosystem functioning, particularly on microbial function and metabolism remains currently unexplored. Herein, we investigated the competence of soil bacteria to colonize plastics and degrade 13C-labeled sulfamethoxazole (SMX). Using single-cell imaging, isotope tracers, soil respiration and SMX mineralization bulk measurements we show that microbial colonization of polyethylene (PE) and polystyrene (PS) surfaces takes place within the first 30 days of incubation. Morphologically diverse microorganisms were colonizing both plastic types, with a slight preference for PE substrate. CARD-FISH bacterial cell counts on PE and PS surfaces formed under SMX amendment ranged from 5.36 × 103 to 2.06 × 104, and 2.06 × 103 to 3.43 × 103 hybridized cells mm-2, respectively. Nano-scale Secondary Ion Mass Spectrometry measurements show that 13C enrichment was highest at 130 days with values up to 1.29 atom%, similar to those of the 13CO2 pool (up to 1.26 atom%, or 22.55 ‰). Independent Mann-Whitney U test showed a significant difference between the control plastisphere samples incubated without SMX and those in 13C-SMX incubations (P < 0.001). Our results provide direct evidence demonstrating, at single-cell level, the capacity of bacterial colonizers of plastics to assimilate 13C-SMX from contaminated soils. These findings expand our knowledge on the role of soil-seeded plastisphere microbiota in the ecological functioning of soils impacted by anthropogenic stressors.
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Affiliation(s)
- Qian Xiang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Niculina Musat
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany; Department of Biology, Section for Microbiology, Aarhus University, 8000, Aarhus C, Denmark.
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Klimov PB, Hubert J, Erban T, Alejandra Perotti M, Braig HR, Flynt A, He Q, Cui Y. Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q). Int J Parasitol 2024:S0020-7519(24)00138-3. [PMID: 38992783 DOI: 10.1016/j.ijpara.2024.07.001] [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: 04/18/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.
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Affiliation(s)
- Pavel B Klimov
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA; Tyumen State University, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen, Russia.
| | - Jan Hubert
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia; Czech University of Life Science, Faculty of Microbiology Nutrient and Dietics, Prague, Czechia
| | - Tomas Erban
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia
| | - M Alejandra Perotti
- University of Reading, Ecology and Evolutionary Biology Section, School of Biological Sciences, Reading RG6 6AS, United Kingdom
| | - Henk R Braig
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, San Juan, J5400 DNQ, Argentina
| | - Alex Flynt
- University of Southern Mississippi, School of Biological, Environmental, and Earth Sciences, Hattiesburg, MS, USA
| | - Qixin He
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA.
| | - Yubao Cui
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University.Wuxi, PR Chin.
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Sarfatis A, Wang Y, Twumasi-Ankrah N, Moffitt JR. Highly Multiplexed Spatial Transcriptomics in Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601034. [PMID: 38979245 PMCID: PMC11230453 DOI: 10.1101/2024.06.27.601034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensal B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.
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Affiliation(s)
- Ari Sarfatis
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Yuanyou Wang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Nana Twumasi-Ankrah
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Jeffrey R. Moffitt
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
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Nisar MA, Ross KE, Brown MH, Bentham R, Best G, Eyre NS, Leterme SC, Whiley H. Increased flushing frequency of a model plumbing system initially promoted the formation of viable but non culturable cells but ultimately reduced the concentration of culturable and total Legionella DNA. Heliyon 2024; 10:e32334. [PMID: 38933949 PMCID: PMC11200333 DOI: 10.1016/j.heliyon.2024.e32334] [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: 06/08/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
Legionella is the causative agent of Legionnaires' disease, and its prevalence in potable water is a significant public health issue. Water stagnation within buildings increases the risk of Legionella. However, there are limited studies investigating how stagnation arising through intermittent usage affects Legionella proliferation and the studies that are available do not consider viable but non culturable (VBNC) Legionella. This study used a model plumbing system to examine how intermittent water stagnation affects both VBNC and culturable Legionella. The model plumbing system contained a water tank supplying two biofilm reactors. The model was initially left stagnant for ≈5 months (147 days), after which one reactor was flushed daily, and the other weekly. Biofilm coupons, and water samples were collected for analysis at days 0, 14 and 28. These samples were analysed for culturable and VBNC Legionella, free-living amoebae, and heterotrophic bacteria. After 28 days, once-a-day flushing significantly (p < 0.001) reduced the amount of biofilm-associated culturable Legionella (1.5 log10 reduction) compared with weekly flushing. However, higher counts of biofilm-associated VBNC Legionella (1 log10 higher) were recovered from the reactor with once-a-day flushing compared with weekly flushing. Likewise, once-a-day flushing increased the population of biofilm-associated Vermamoeba vermiformis (approximately 3 log10 higher) compared with weekly flushing, which indicated a positive relationship between VBNC Legionella and V. vermiformis. This is the first study to investigate the influence of stagnation on VBNC Legionella under environmental conditions. Overall, this study showed that a reduction in water stagnation decreased culturable Legionella but not VBNC Legionella.
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Affiliation(s)
- Muhammad Atif Nisar
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Kirstin E. Ross
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, 5042, Australia
| | - Richard Bentham
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Giles Best
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
- Flow Cytometry Facility, Flinders University, Bedford Park, SA, 5042, Australia
| | - Nicholas S. Eyre
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Sophie C. Leterme
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, 5042, Australia
- Institute for Nanoscience and Technology, Flinders University, Bedford Park, SA, 5042, Australia
| | - Harriet Whiley
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, 5042, Australia
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Snaidr L, Mühlhahn P, Beimfohr C, Kreuzer C, Richly C, Snaidr J. Specific cultivation-independent enumeration of viable cells in probiotic products using a combination of fluorescence in situ hybridization and flow cytometry. Front Microbiol 2024; 15:1410709. [PMID: 38933029 PMCID: PMC11199854 DOI: 10.3389/fmicb.2024.1410709] [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: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This study introduces an optimized integration of flow cytometry and fluorescence in situ hybridization (Flow-FISH) as an approach for the specific enumeration of gram-positive bacteria in probiotic products, overcoming the limitations of conventional methods. The enhanced Flow-FISH technique synergizes the rapid and automated capabilities of flow cytometry with the high specificity of FISH, facilitating the differentiation of viable cells at the species level within probiotic blends. By analyzing lyophilized samples of Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Bifidobacterium animalis subsp. lactis, and a commercial product, the study highlights the optimized Flow-FISH protocol's advantages, including reduced hybridization times to 1.5 h and elimination of centrifugation steps. Comparative evaluations with the widely accepted enumeration methods plate count and Live/Dead (L/D) staining were conducted. The study revealed that Flow-FISH produces higher viable cell counts than plate count, thereby challenging the traditional "gold standard" by highlighting its predisposition to underestimate actual viable cell numbers. Against L/D staining, Flow-FISH achieved comparable results, which, despite the different foundational premises of each technique, confirms the accuracy and reliability of our method. In conclusion, the optimized Flow-FISH protocol represents a significant leap forward in probiotic research and quality control. This method provides a rapid, robust, and highly specific alternative for the enumeration of probiotic bacteria, surpassing traditional methodologies. Its ability to enable a more detailed and reliable analysis of probiotic products paves the way for precise quality control and research insights, underscoring its potential to improve the field significantly.
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Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MDC, Azevedo NF. Oligonucleotide probes for imaging and diagnosis of bacterial infections. Crit Rev Biotechnol 2024:1-20. [PMID: 38830823 DOI: 10.1080/07388551.2024.2344574] [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: 02/15/2023] [Accepted: 06/17/2023] [Indexed: 06/05/2024]
Abstract
The rise of infectious diseases as a public health concern has necessitated the development of rapid and precise diagnostic methods. Imaging techniques like nuclear and optical imaging provide the ability to diagnose infectious diseases within the body, eliminating delays caused by sampling and pre-enrichments of clinical samples and offering spatial information that can aid in a more informed diagnosis. Traditional molecular probes are typically created to image infected tissue without accurately identifying the pathogen. In contrast, oligonucleotides can be tailored to target specific RNA sequences, allowing for the identification of pathogens, and even generating antibiotic susceptibility profiles by focusing on drug resistance genes. Despite the benefits that nucleic acid mimics (NAMs) have provided in terms of stabilizing oligonucleotides, the inadequate delivery of these relatively large molecules into the cytoplasm of bacteria remains a challenge for widespread use of this technology. This review summarizes the key advancements in the field of oligonucleotide probes for in vivo imaging, highlighting the most promising delivery systems described in the literature for developing optical imaging through in vivo hybridization.
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Affiliation(s)
- Luís Moreira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno Miguel Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Rita Sobral Santos
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Joana Angélica Loureiro
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Maria do Carmo Pereira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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Barbosa A, Azevedo NF, Goeres DM, Cerqueira L. Ecology of Legionella pneumophila biofilms: The link between transcriptional activity and the biphasic cycle. Biofilm 2024; 7:100196. [PMID: 38601816 PMCID: PMC11004079 DOI: 10.1016/j.bioflm.2024.100196] [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: 12/29/2023] [Revised: 03/10/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
There has been considerable discussion regarding the environmental life cycle of Legionella pneumophila and its virulence potential in natural and man-made water systems. On the other hand, the bacterium's morphogenetic mechanisms within host cells (amoeba and macrophages) have been well documented and are linked to its ability to transition from a non-virulent, replicative state to an infectious, transmissive state. Although the morphogenetic mechanisms associated with the formation and detachment of the L. pneumophila biofilm have also been described, the capacity of the bacteria to multiply extracellularly is not generally accepted. However, several studies have shown genetic pathways within the biofilm that resemble intracellular mechanisms. Understanding the functionality of L. pneumophila cells within a biofilm is fundamental for assessing the ecology and evaluating how the biofilm architecture influences L. pneumophila survival and persistence in water systems. This manuscript provides an overview of the biphasic cycle of L. pneumophila and its implications in associated intracellular mechanisms in amoeba. It also examines the molecular pathways and gene regulation involved in L. pneumophila biofilm formation and dissemination. A holistic analysis of the transcriptional activities in L. pneumophila biofilms is provided, combining the information of intracellular mechanisms in a comprehensive outline. Furthermore, this review discusses the techniques that can be used to study the morphogenetic states of the bacteria within biofilms, at the single cell and population levels.
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Affiliation(s)
- Ana Barbosa
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Darla M. Goeres
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- The Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Laura Cerqueira
- LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- ALiCE – Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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Bransfield RC, Goud Gadila SK, Kursawe LJ, Dwork AJ, Rosoklija G, Horn EJ, Cook MJ, Embers ME. Late-stage borreliosis and substance abuse. Heliyon 2024; 10:e31159. [PMID: 38779029 PMCID: PMC11108998 DOI: 10.1016/j.heliyon.2024.e31159] [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] [Received: 11/30/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Background Infectious diseases can contribute to substance abuse. Here, a fatal case of borreliosis and substance abuse is reported. This patient had a history of multiple tick bites and increasing multisystem symptoms, yet diagnosis and treatment were delayed. He experimented with multiple substances including phencyclidine (PCP), an N-methyl-d-aspartate (NMDA) receptor antagonist that opposes NMDA agonism caused by Borrelia infection. During PCP withdrawal, he committed one homicide, two assaults, and suicide. Methods Brain tissue was obtained from autopsy and stained for microglial activation and quinolinic acid (QA). Immunoflouresence (IFA) and fluorescence in situ hybridization (FISH) were used to identify the presence of pathogens in autopsy tissue. Results Autopsy tissue evaluation demonstrated Borrelia in the pancreas by IFA and heart by IFA and FISH. Activated microglia and QA were found in the brain, indicating neuroinflammation. It is postulated that PCP withdrawal may exacerbate symptoms produced by Borrelia-induced biochemical imbalances in the brain. This combination may have greatly increased his acute homicidal and suicidal risk. Patient databases also demonstrated the risk of homicide or suicide in patients diagnosed with borreliosis and confirmed multiple symptoms in these patients, including chronic pain, anxiety, and anhedonia. Conclusions Late-stage borreliosis is associated with multiple symptoms that may contribute to an increased risk of substance abuse and addictive disorders. More effective diagnosis and treatment of borreliosis, and attention to substance abuse potential may help reduce associated morbidity and mortality in patients with borreliosis, particularly in endemic areas.
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Affiliation(s)
- Robert C. Bransfield
- Rutgers-RWJ Medical School, Piscataway, NJ, USA. Hackensack Meridian Health-School of Medicine, Nutley, NJ, USA
| | - Shiva Kumar Goud Gadila
- Division of Immunology, Tulane National Primate Research Center, Tulane University Health Sciences, Covington, LA, USA
| | - Laura J. Kursawe
- Charité – Universitatsmedizin Berlin, Corporate Member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andrew J. Dwork
- Department of Psychiatry, Columbia University, New York, NY, United States. Division of Molecular Imaging and Neuropathology, New York, USA
- State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gorazd Rosoklija
- State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | | | - Monica E. Embers
- Division of Immunology, Tulane National Primate Research Center, Tulane University Health Sciences, Covington, LA, USA
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Slobodianyk-Kolomoiets M, Khlebas S, Mazur I, Rudnieva K, Potochilova V, Iungin O, Kamyshnyi O, Kamyshna I, Potters G, Spiers AJ, Moshynets O. Extracellular host DNA contributes to pathogenic biofilm formation during periodontitis. Front Cell Infect Microbiol 2024; 14:1374817. [PMID: 38779563 PMCID: PMC11109387 DOI: 10.3389/fcimb.2024.1374817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Periodontal diseases are known to be associated with polymicrobial biofilms and inflammasome activation. A deeper understanding of the subgingival cytological (micro) landscape, the role of extracellular DNA (eDNA) during periodontitis, and contribution of the host immune eDNA to inflammasome persistence, may improve our understanding of the mechanisms underlaying severe forms of periodontitis. Methods In this work, subgingival biolfilms developing on biologically neutral polyethylene terephthalate films placed in gingival cavities of patients with chronic periodontitis were investigated by confocal laser scanning microscopy (CLSM). This allowed examination of realistic cytological landscapes and visualization of extracellular polymeric substances (EPS) including amyloids, total proteins, carbohydrates and eDNA, as well as comparison with several single-strain in vitro model biofilms produced by oral pathogens such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus gordonii, S. sanguinis and S. mitis. Fluorescence in situ hybridization (FISH) analysis was also used to identify eDNA derived from eubacteria, streptococci and members of the Bacteroides-Porphyromonas-Prevotella (BPP) group associated with periodontitis. Results Analysis of subgingival biofilm EPS revealed low levels of amyloids and high levels of eDNA which appears to be the main matrix component. However, bacterial eDNA contributed less than a third of the total eDNA observed, suggesting that host-derived eDNA released in neutrophil extracellular traps may be of more importance in the development of biofilms causing periodontitis. Discussion eDNA derived from host immunocompetent cells activated at the onset of periodontitis may therefore be a major driver of bacterial persistence and pathogenesis.
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Affiliation(s)
| | - Svitlana Khlebas
- Department of Dentistry, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Iryna Mazur
- Department of Dentistry, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Kateryna Rudnieva
- Central Clinical Diagnostic Laboratory, Kyiv Regional Clinical Hospital, Kyiv, Ukraine
- Department of Microbiology, Virology and Immunology, Bogomolets National Medical Academy, Kyiv, Ukraine
| | | | - Olga Iungin
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Faculty of Chemical and Biopharmaceutical Technologies, Kyiv National University of Technologies and Design, Kyiv, Ukraine
| | - Olexandr Kamyshnyi
- Microbiology, Virology and Immunology Department, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Iryna Kamyshna
- Microbiology, Virology and Immunology Department, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Olena Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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11
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Brüwer JD, Sidhu C, Zhao Y, Eich A, Rößler L, Orellana LH, Fuchs BM. Globally occurring pelagiphage infections create ribosome-deprived cells. Nat Commun 2024; 15:3715. [PMID: 38698041 PMCID: PMC11066056 DOI: 10.1038/s41467-024-48172-w] [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: 02/09/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study. Up to 19% of SAR11 cells were phage-infected during a phytoplankton bloom, coinciding with a ~90% reduction in SAR11 cell abundance within 5 days. Frequently, a fraction of the infected SAR11 cells were devoid of detectable ribosomes, which appear to be a yet undescribed possible stage during pelagiphage infection. We dubbed such cells zombies and propose, among other possible explanations, a mechanism in which ribosomal RNA is used as a resource for the synthesis of new phage genomes. On a global scale, we detected phage-infected SAR11 and zombie cells in the Atlantic, Pacific, and Southern Oceans. Our findings illuminate the important impact of pelagiphages on SAR11 populations and unveil the presence of ribosome-deprived zombie cells as part of the infection cycle.
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Affiliation(s)
- Jan D Brüwer
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Yanlin Zhao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Andreas Eich
- PSL Research University: EPHE-UPVD-CNRS,UAR 3278 CRIOBE, Moorea, French Polynesia
| | - Leonard Rößler
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Luis H Orellana
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
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12
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Knobloch S, Skirnisdóttir S, Dubois M, Mayolle L, Kolypczuk L, Leroi F, Leeper A, Passerini D, Marteinsson VÞ. The gut microbiome of farmed Arctic char ( Salvelinus alpinus) is shaped by feeding stage and nutrient presence. FEMS MICROBES 2024; 5:xtae011. [PMID: 38745980 PMCID: PMC11092275 DOI: 10.1093/femsmc/xtae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Food Technology, University of Applied Sciences Fulda, Leipziger Strasse 123, 36037 Fulda, Germany
| | | | - Marianne Dubois
- ESBS/University of Strasbourg, 300 Bd Sébastien Brant, 67085 Strasbourg, France
| | - Lucie Mayolle
- University of Technology of Compiègne, Rue Roger Couttolenc, 60203 Compiègne, France
| | - Laetitia Kolypczuk
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Françoise Leroi
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Alexandra Leeper
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, 1430 Ås, Norway
- Iceland Ocean Cluster, Department of Research and Innovation, Grandagarður 16, 101 Reykjavík, Iceland
| | - Delphine Passerini
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Viggó Þ Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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13
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Trznadel M, Holt CC, Livingston SJ, Kwong WK, Keeling PJ. Coral-infecting parasites in cold marine ecosystems. Curr Biol 2024; 34:1810-1816.e4. [PMID: 38608678 DOI: 10.1016/j.cub.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Coral reefs are a biodiversity hotspot,1,2 and the association between coral and intracellular dinoflagellates is a model for endosymbiosis.3,4 Recently, corals and related anthozoans have also been found to harbor another kind of endosymbiont, apicomplexans called corallicolids.5 Apicomplexans are a diverse lineage of obligate intracellular parasites6 that include human pathogens such as the malaria parasite, Plasmodium.7 Global environmental sequencing shows corallicolids are tightly associated with tropical and subtropical reef environments,5,8,9 where they infect diverse corals across a range of depths in many reef systems, and correlate with host mortality during bleaching events.10 All of this points to corallicolids being ecologically significant to coral reefs, but it is also possible they are even more widely distributed because most environmental sampling is biased against parasites that maintain a tight association with their hosts throughout their life cycle. We tested the global distribution of corallicolids using a more direct approach, by specifically targeting potential anthozoan host animals from cold/temperate marine waters outside the coral reef context. We found that corallicolids are in fact common in such hosts, in some cases at high frequency, and that they infect the same tissue as parasites from topical coral reefs. Parasite phylogeny suggests corallicolids move between hosts and habitats relatively frequently, but that biogeography is more conserved. Overall, these results greatly expand the range of corallicolids beyond coral reefs, suggesting they are globally distributed parasites of marine anthozoans, which also illustrates significant blind spots that result from strategies commonly used to sample microbial biodiversity.
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Affiliation(s)
- Morelia Trznadel
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Corey C Holt
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samuel J Livingston
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Waldan K Kwong
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
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14
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Gómez F, Rodríguez N, Rodríguez-Manfredi JA, Escudero C, Carrasco-Ropero I, Martínez JM, Ferrari M, De Angelis S, Frigeri A, Fernández-Sampedro M, Amils R. Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain. Microorganisms 2024; 12:829. [PMID: 38674771 PMCID: PMC11052175 DOI: 10.3390/microorganisms12040829] [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: 03/27/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.
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Affiliation(s)
- Felipe Gómez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - Cristina Escudero
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - José M. Martínez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
| | - Marco Ferrari
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Simone De Angelis
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Alessandro Frigeri
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Maite Fernández-Sampedro
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
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15
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Kendlbacher V, Winter TMR, Bright M. Zoothamnium mariella sp. nov., a marine, colonial ciliate with an atypcial growth pattern, and its ectosymbiont Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. PLoS One 2024; 19:e0300758. [PMID: 38557976 PMCID: PMC10984469 DOI: 10.1371/journal.pone.0300758] [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: 12/10/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Ciliates are unicellular eukaryotes, regularly involved in symbiotic associations. Symbionts may colonize the inside of their cells as well as their surface as ectosymbionts. Here, we report on a new ciliate species, designated as Zoothamnium mariella sp. nov. (Peritrichia, Sessilida), discovered in the northern Adriatic Sea (Mediterranean Sea) in 2021. We found this ciliate species to be monospecifically associated with a new genus of ectosymbiotic bacteria, here proposed as Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. To formally describe the new ciliate species, we investigated its morphology and sequenced its 18S rRNA gene. To demonstrate its association with a single species of bacterial ectosymbiont, we performed 16S rRNA gene sequencing, fluorescence in situ hybridization, and scanning electron microscopy. Additionally, we explored the two partners' cultivation requirements and ecology. Z. mariella sp. nov. was characterized by a colony length of up to 1 mm. A consistent number of either seven or eight long branches alternated on the stalk in close distance to each other. The colony developed three different types of zooids: microzooids ("trophic stage"), macrozooids ("telotroch stage"), and terminal zooids ("dividing stage"). Viewed from inside the cell, the microzooids' oral ciliature ran in 1 ¼ turns in a clockwise direction around the peristomial disc before entering the infundibulum, where it performed another ¾ turn. Phylogenetic analyses assigned Z. mariella sp. nov. to clade II of the family Zoothamnidae. The ectosymbiont formed a monophyletic clade within the Gammaproteobacteria along with two other ectosymbionts of peritrichous ciliates and a free-living vent bacterium. It colonized the entire surface of its ciliate host, except for the most basal stalk of large colonies, and exhibited a single, spindle-shaped morphotype. Furthermore, the two partners together appear to be generalists of temperate, oxic, marine shallow-water environments and were collectively cultivable in steady flow-through systems.
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Affiliation(s)
- Vincent Kendlbacher
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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16
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Peng S, Li JJ, Song W, Li Y, Zeng L, Liang Q, Wen X, Shang H, Liu K, Peng P, Xue W, Zou B, Yang L, Liang J, Zhang Z, Guo S, Chen T, Li W, Jin M, Xing XB, Wan P, Liu C, Lin H, Wei H, Lee RWJ, Zhang F, Wei L. CRB1-associated retinal degeneration is dependent on bacterial translocation from the gut. Cell 2024; 187:1387-1401.e13. [PMID: 38412859 DOI: 10.1016/j.cell.2024.01.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/07/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
The Crumbs homolog 1 (CRB1) gene is associated with retinal degeneration, most commonly Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP). Here, we demonstrate that murine retinas bearing the Rd8 mutation of Crb1 are characterized by the presence of intralesional bacteria. While normal CRB1 expression was enriched in the apical junctional complexes of retinal pigment epithelium and colonic enterocytes, Crb1 mutations dampened its expression at both sites. Consequent impairment of the outer blood retinal barrier and colonic intestinal epithelial barrier in Rd8 mice led to the translocation of intestinal bacteria from the lower gastrointestinal (GI) tract to the retina, resulting in secondary retinal degeneration. Either the depletion of bacteria systemically or the reintroduction of normal Crb1 expression colonically rescued Rd8-mutation-associated retinal degeneration without reversing the retinal barrier breach. Our data elucidate the pathogenesis of Crb1-mutation-associated retinal degenerations and suggest that antimicrobial agents have the potential to treat this devastating blinding disease.
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Affiliation(s)
- Shanzhen Peng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wanying Song
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Ye Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Lei Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qiaoxing Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Xiaofeng Wen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510000, China
| | - Haitao Shang
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Keli Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Peiyao Peng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wei Xue
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Liu Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Juanran Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhihui Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Tianjin Medical University Eye Hospital, Eye Institute & School of Optometry and Ophthalmology, Tianjin 300384, China
| | - Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Tingting Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wenxuan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Ming Jin
- Department of Ophthalmology, China-Japan Friendship Hospital, Beijing 10029, China
| | - Xiang-Bin Xing
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Pengxia Wan
- Department of Ophthalmology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Chunqiao Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Richard W J Lee
- UCL Institute of Ophthalmology and Moorfields Eye Hospital NHS Foundation Trust, London, UK.
| | - Feng Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China; The First Affiliated Hospital, Department of Ophthalmology, University of South China, Hengyang 421001, Hunan, China.
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17
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Bermudez C, Yao H, Widaningrum, Williams BA, Flanagan BM, Gidley MJ, Mikkelsen D. Biomass attachment and microbiota shifts during porcine faecal in vitro fermentation of almond and macadamia nuts differing in particle sizes. Food Funct 2024; 15:2406-2421. [PMID: 38265095 DOI: 10.1039/d3fo03612j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Nuts are highly nutritious and good sources of dietary fibre, when consumed as part of a healthy human diet. Upon consumption, nut particles of various sizes containing lipids entrapped by the plant cell walls enter the large intestine where they are fermented by the resident microbiota. This study investigated the microbial community shifts during in vitro fermentation of almond and macadamia substrates, of two particle sizes including fine particles (F = 250-500 μm) and cell clusters (CC = 710-1000 μm). The aim was to determine how particle size and biomass attachment altered the microbiota. Over the 48 h fermentation duration, short chain fatty acid concentrations increased due to particle size rather than nut type (almond or macadamia). However, nut type did change microbial population dynamics by stimulating specific genera. Tyzzerella, p253418B5 gut group, Lachnospiraceae UCG001, Geotrichum, Enterococcus, Amnipila and Acetitomaculum genera were unique for almonds. For macadamia, three unique genera including Prevotellaceae UCG004, Candidatus Methanomethylophilus and Alistipes were noted. Distinct shifts in the attached microbial biomass were noted due to nut particle size. Bacterial attachment to nut particles was visualised in situ during fermentation, revealing a decrease in lipids and an increase in attached bacteria over time. This interaction may be a pre-requisite for lipid breakdown during nut particle disappearance. Overall, this study provides insights into how nut fermentation alters the gut microbiota and the possible role that gut microbes have in lipid degradation.
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Affiliation(s)
- Cindy Bermudez
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, Australia.
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
| | - Hong Yao
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
| | - Widaningrum
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, Australia.
- Research Centre for Agroindustry, National Research and Innovation Agency (BRIN), Soekarno Integrated Science Center, Bogor, Indonesia
| | - Barbara A Williams
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
| | - Deirdre Mikkelsen
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, Australia.
- Centre for Nutrition and Food Sciences (CNAFS), Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
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18
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Fancy N, Nitin, Kniffen D, Melvin M, Kazemian N, Sadeghi J, Letef CA, D'Aloisio L, Copp AG, Inaba R, Hans G, Jafaripour S, Haskey N, Raman M, Daneshgar P, Chadee K, Ghosh S, Gibson DL, Pakpour S, Zandberg W, Bergstrom KSB. Fecal-adherent mucus is a non-invasive source of primary human MUC2 for structural and functional characterization in health and disease. J Biol Chem 2024; 300:105675. [PMID: 38272223 PMCID: PMC10891339 DOI: 10.1016/j.jbc.2024.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
The O-glycoprotein Mucin-2 (MUC2) forms the protective colon mucus layer. While animal models have demonstrated the importance of Muc2, few studies have explored human MUC2 in similar depth. Recent studies have revealed that secreted MUC2 is bound to human feces. We hypothesized human fecal MUC2 (HF-MUC2) was accessible for purification and downstream structural and functional characterization. We tested this via histologic and quantitative imaging on human fecal sections; extraction from feces for proteomic and O-glycomic characterization; and functional studies via growth and metabolic assays in vitro. Quantitative imaging of solid fecal sections showed a continuous mucus layer of varying thickness along human fecal sections with barrier functions intact. Lectin profiling showed HF-MUC2 bound several lectins but was weak to absent for Ulex europaeus 1 (α1,2 fucose-binding) and Sambucus nigra agglutinin (α2,6 sialic acid-binding), and did not have obvious b1/b2 barrier layers. HF-MUC2 separated by electrophoresis showed high molecular weight glycoprotein bands (∼1-2 MDa). Proteomics and Western analysis confirmed the enrichment of MUC2 and potential MUC2-associated proteins in HF-MUC2 extracts. MUC2 O-glycomics revealed diverse fucosylation, moderate sialylation, and little sulfation versus porcine colonic MUC2 and murine fecal Muc2. O-glycans were functional and supported the growth of Bacteroides thetaiotaomicron (B. theta) and short-chain fatty acid (SCFA) production in vitro. MUC2 could be similarly analyzed from inflammatory bowel disease stools, which displayed an altered glycomic profile and differential growth and SCFA production by B. theta versus healthy samples. These studies describe a new non-invasive platform for human MUC2 characterization in health and disease.
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Affiliation(s)
- Noah Fancy
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Nitin
- Chemistry, University of British Columbia-Okanagan, Kelowna, Canada
| | - Darrek Kniffen
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Mackenzie Melvin
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Negin Kazemian
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Javad Sadeghi
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Clara A Letef
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Leah D'Aloisio
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Amanda G Copp
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Rain Inaba
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Geetkamal Hans
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Simin Jafaripour
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Natasha Haskey
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Maitreyi Raman
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | | | - Kris Chadee
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sanjoy Ghosh
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Deanna L Gibson
- Biology, University of British Columbia-Okanagan, Kelowna, Canada
| | - Sepideh Pakpour
- School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada
| | - Wesley Zandberg
- Chemistry, University of British Columbia-Okanagan, Kelowna, Canada
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19
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Duan J, Kitamura K, Tsukamoto H, Van Phan H, Oba K, Hori T, Fujiwara T, Terada A. Enhanced granulation of activated sludge in an airlift reactor for organic carbon removal and ammonia retention from industrial fermentation wastewater: A comparative study. WATER RESEARCH 2024; 251:121091. [PMID: 38244299 DOI: 10.1016/j.watres.2023.121091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024]
Abstract
Ammonia retention and recovery from high-nitrogenous wastewater are new concepts being used for nitrogen management. A microaerophilic activated sludge system was developed to convert organic nitrogen into ammonia and retain it for its recovery; however, the settleability of activated sludge remains a challenge. Therefore, this study proposed an aerobic granular sludge system as a potential solution. Two types of sequencing batch reactors-airlift and upflow reactors-were operated to investigate the feasibility of fast granule formation, the performance of organic carbon removal and ammonia retention, and the dynamics of microbial community composition. The operation fed with industrial fermentation wastewater demonstrated that the airlift reactor ensured a more rapid granule formation than the upflow reactor because of the high shear force, and it maintained a superior ammonia retention stability of approximately 85 %. Throughout the operational period, changes in hydraulic retention time (HRT), settling time, and exchange ratio altered the granular particle sizes and microbial community compositions. Rhodocyclaceae were replaced with Comamonadaceae, Methylophilaceae, Xanthomonadaceae, and Chitinophagaceae as core taxa instrumental in granulation, likely because of their extracellular polymeric substance secretion. As the granulation process progressed, a significant decrease in the relative abundances of nitrifying bacteria-Nitrospiraceae and Nitrosomonadaceae-was observed. The reduction of settling time and HRT enhanced granulation and inhibited the activity of nitrifying bacteria. The success in granulation for ammonia conversion and retention in this study accelerates the paradigm shift from ammonia removal to ammonia recovery from industrial fermentation wastewater.
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Affiliation(s)
- Jingyu Duan
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Kotaro Kitamura
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Hiroki Tsukamoto
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Hop Van Phan
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Kohei Oba
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Taku Fujiwara
- Department of Global Ecology, Graduate School of Global Environmental Studies, Kyoto University, Kyoto 615-8540, Japan
| | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan; Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan.
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20
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Ouboter HT, Mesman R, Sleutels T, Postma J, Wissink M, Jetten MSM, Ter Heijne A, Berben T, Welte CU. Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea. Nat Commun 2024; 15:1477. [PMID: 38368447 PMCID: PMC10874420 DOI: 10.1038/s41467-024-45758-2] [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: 07/26/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.
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Affiliation(s)
- Heleen T Ouboter
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Rob Mesman
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, The Netherlands
- Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Jelle Postma
- Department of General Instrumentation, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Martijn Wissink
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
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21
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Roy R, Singh SK. The Microbiome Modulates the Immune System to Influence Cancer Therapy. Cancers (Basel) 2024; 16:779. [PMID: 38398170 PMCID: PMC10886470 DOI: 10.3390/cancers16040779] [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: 01/22/2024] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The gut microbiota composition can affect the tumor microenvironment and its interaction with the immune system, thereby having implications for treatment predictions. This article reviews the studies available to better understand how the gut microbiome helps the immune system fight cancer. To describe this fact, different mechanisms and approaches utilizing probiotics to improve advancements in cancer treatment will be discussed. Moreover, not only calorie intake but also the variety and quality of diet can influence cancer patients' immunotherapy treatment because dietary patterns can impair immunological activities either by stimulating or suppressing innate and adaptive immunity. Therefore, it is interesting and critical to understand gut microbiome composition as a biomarker to predict cancer immunotherapy outcomes and responses. Here, more emphasis will be given to the recent development in immunotherapies utilizing microbiota to improve cancer therapies, which is beneficial for cancer patients.
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Affiliation(s)
- Ruchi Roy
- UICentre for Drug Discovery, The University of Illinois, Chicago, IL 60612, USA
| | - Sunil Kumar Singh
- Department of Surgery, Division of Surgical Oncology, The University of Illinois at Chicago, Chicago, IL 60612, USA
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22
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Layunta E, Jäverfelt S, van de Koolwijk FC, Sivertsson M, Dolan B, Arike L, Thulin S, Vallance BA, Pelaseyed T. MUC17 is an essential small intestinal glycocalyx component that is disrupted in Crohn's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.578867. [PMID: 38405862 PMCID: PMC10888976 DOI: 10.1101/2024.02.08.578867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Crohn's disease (CD) is the chronic inflammation of the ileum and colon triggered by bacteria, but insights into molecular perturbations at the bacteria-epithelium interface are limited. We report that membrane mucin MUC17 protects small intestinal enterocytes against commensal and pathogenic bacteria. In non-inflamed CD ileum, reduced MUC17 levels correlated with a compromised glycocalyx, allowing bacterial contact with enterocytes. Muc17 deletion in mice rendered the small intestine prone to atypical infection while maintaining resistance to colitis. The loss of Muc17 resulted in spontaneous deterioration of epithelial homeostasis and extra-intestinal translocation of bacteria. Finally, Muc17-deficient mice harbored specific small intestinal bacterial taxa observed in CD. Our findings highlight MUC17 as an essential line of defense in the small intestine with relevance for early epithelial defects in CD.
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Affiliation(s)
- Elena Layunta
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Sofia Jäverfelt
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Fleur C van de Koolwijk
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Molly Sivertsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Brendan Dolan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Sara Thulin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Bruce A Vallance
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Thaher Pelaseyed
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
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23
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Kennedy JM, De Silva A, Walton GE, Poveda C, Gibson GR. Comparison of prebiotic candidates in ulcerative colitis using an in vitro fermentation model. J Appl Microbiol 2024; 135:lxae034. [PMID: 38337173 DOI: 10.1093/jambio/lxae034] [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: 09/03/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024]
Abstract
AIMS This study explored the effect of three different prebiotics, the human milk oligosaccharide 2'-fucosyllactose (2'-FL), an oligofructose-enriched inulin (fructo-oligosaccharide, or FOS), and a galacto-oligosaccaride (GOS) mixture, on the faecal microbiota from patients with ulcerative colitis (UC) using in vitro batch culture fermentation models. Changes in bacterial groups and short-chain fatty acid (SCFA) production were compared. METHODS AND RESULTS In vitro pH controlled batch culture fermentation was carried out over 48 h on samples from three healthy controls and three patients with active UC. Four vessels were run, one negative control and one for each of the prebiotic substrates. Bacterial enumeration was carried out using fluorescence in situ hybridization with flow cytometry. SCFA quantification was performed using gas chromatography mass spectrometry. All substrates had a positive effect on the gut microbiota and led to significant increases in total SCFA and propionate concentrations at 48 h. 2'-FL was the only substrate to significantly increase acetate and led to the greatest increase in total SCFA concentration at 48 h. 2'-FL best suppressed Desulfovibrio spp., a pathogen associated with UC. CONCLUSIONS 2'FL, FOS, and GOS all significantly improved the gut microbiota in this in vitro study and also led to increased SCFA.
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Affiliation(s)
- James M Kennedy
- Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
- Department of Gastroenterology, Royal Berkshire NHS Foundation Trust, Reading RG1 5AN, United Kingdom
| | - Aminda De Silva
- Department of Gastroenterology, Royal Berkshire NHS Foundation Trust, Reading RG1 5AN, United Kingdom
| | - Gemma E Walton
- Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
| | - Carlos Poveda
- Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, The University of Reading, Reading RG6 6AP, United Kingdom
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24
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Wang C, Liu S, Wang Z, Wang M, Pang H, Liu Y, Chang H, Sui Z. Rapid and Accurate Quantification of Viable Lactobacillus Cells in Infant Formula by Flow Cytometry Combined with Propidium Monoazide and Signal-Enhanced Fluorescence In Situ Hybridization. Anal Chem 2024; 96:1093-1101. [PMID: 38204177 DOI: 10.1021/acs.analchem.3c03742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Lactobacillus is an important member of the probiotic bacterial family for regulating human intestinal microflora and preserving its normalcy, and it has been widely used in infant formula. An appropriate and feasible method to quantify viable Lactobacilli cells is urgently required to evaluate the quality of probiotic-fortified infant formula. This study presents a rapid and accurate method to count viable Lactobacilli cells in infant formula using flow cytometry (FCM). First, Lactobacillus cells were specifically and rapidly stained by oligonucleotide probes based on a signal-enhanced fluorescence in situ hybridization (SEFISH) technique. A DNA-binding fluorescent probe, propidium monoazide (PMA), was then used to accurately recognize viable Lactobacillus cells. The entire process of this newly developed PMA-SEFISH-FCM method was accomplished within 2.5 h, which included pretreatment, dual staining, and FCM analysis; thus, this method showed considerably shorter time-to-results than other rapid methods. This method also demonstrated a good linear correlation (R2 = 0.9994) with the traditional plate-based method with a bacterial recovery rate of 91.24%. To the best of our knowledge, the present study is the first report of FCM combined with PMA and FISH for the specific detection of viable bacterial cells.
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Affiliation(s)
- Chenglong Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Siyuan Liu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
| | - Ziquan Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
| | - Meng Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
| | - Huimin Pang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
| | - Yingying Liu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
| | - Haiyan Chang
- College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhiwei Sui
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 10002, China
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25
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Pilliol V, Beye M, Terlier L, Balmelle J, Kacel I, Lan R, Aboudharam G, Grine G, Terrer E. Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis. Microorganisms 2024; 12:215. [PMID: 38276200 PMCID: PMC10819710 DOI: 10.3390/microorganisms12010215] [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: 12/20/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.
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Affiliation(s)
- Virginie Pilliol
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Mamadou Beye
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Laureline Terlier
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Julien Balmelle
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Idir Kacel
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Romain Lan
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
- CNRS, EFS, ADES, Aix-Marseille University, 13385 Marseille, France
| | - Gérard Aboudharam
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Ghiles Grine
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Elodie Terrer
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
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26
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Chen LM, Beck P, van Ede J, Pronk M, van Loosdrecht MCM, Lin Y. Anionic extracellular polymeric substances extracted from seawater-adapted aerobic granular sludge. Appl Microbiol Biotechnol 2024; 108:144. [PMID: 38231410 DOI: 10.1007/s00253-023-12954-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 01/18/2024]
Abstract
Anionic polymers, such as heparin, have been widely applied in the chemical and medical fields, particularly for binding proteins (e.g., fibroblast growth factor 2 (FGF-2) and histones). However, the current animal-based production of heparin brings great risks, including resource shortages and product contamination. Recently, anionic compounds, nonulosonic acids (NulOs), and sulfated glycoconjugates were discovered in the extracellular polymeric substances (EPS) of aerobic granular sludge (AGS). Given the prevalence of anionic polymers, in marine biofilms, it was hypothesized that the EPS from AGS grown under seawater condition could serve as a raw material for producing the alternatives to heparin. This study aimed to isolate and enrich the anionic fractions of EPS and evaluate their potential application in the chemical and medical fields. The AGS was grown in a lab-scale reactor fed with acetate, under the seawater condition (35 g/L sea salt). The EPS was extracted with an alkaline solution at 80 °C and fractionated by size exclusion chromatography. Its protein binding capacity was evaluated by native gel electrophoresis. It was found that the two highest molecular weight fractions (438- > 14,320 kDa) were enriched with NulO and sulfate-containing glycoconjugates. The enriched fractions can strongly bind the two histones involved in sepsis and a model protein used for purification by heparin-column. These findings demonstrated possibilities for the application of the extracted EPS and open up a novel strategy for resource recovery. KEY POINTS: • High MW EPS from seawater-adapted AGS are dominant with sulfated groups and NulOs • Fifty-eight percent of the EPS is high MW of 68-14,320 kDa • EPS and its fractions can bind histones and fibroblast growth factor 2.
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Affiliation(s)
- Le Min Chen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands.
| | - Paula Beck
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Jitske van Ede
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
- Royal HaskoningDHV, Laan 1914 35, Amersfoort, 3800, AL, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
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27
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Chen LM, Keisham S, Tateno H, van Ede J, Pronk M, van Loosdrecht MCM, Lin Y. Alterations of Glycan Composition in Aerobic Granular Sludge during the Adaptation to Seawater Conditions. ACS ES&T WATER 2024; 4:279-286. [PMID: 38229592 PMCID: PMC10788855 DOI: 10.1021/acsestwater.3c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024]
Abstract
Bacteria can synthesize a diverse array of glycans, being found attached to proteins and lipids or as loosely associated polysaccharides to the cells. The major challenge in glycan analysis in environmental samples lies in developing high-throughput and comprehensive characterization methodologies to elucidate the structure and monitor the change of the glycan profile, especially in protein glycosylation. To this end, in the current research, the dynamic change of the glycan profile of a few extracellular polymeric substance (EPS) samples was investigated by high-throughput lectin microarray and mass spectrometry, as well as sialylation and sulfation analysis. Those EPS were extracted from aerobic granular sludge collected at different stages during its adaptation to the seawater condition. It was found that there were glycoproteins in all of the EPS samples. In response to the exposure to seawater, the amount of glycoproteins and their glycan diversity displayed an increase during adaptation, followed by a decrease once the granules reached a stable state of adaptation. Information generated sheds light on the approaches to identify and monitor the diversity and dynamic alteration of the glycan profile of the EPS in response to environmental stimuli.
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Affiliation(s)
- Le Min Chen
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sunanda Keisham
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroaki Tateno
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Jitske van Ede
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mario Pronk
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Royal
HaskoningDHV, Laan 1914
35, Amersfoort 3800 AL, The Netherlands
| | - Mark C. M. van Loosdrecht
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Yuemei Lin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Coolen S, Rogowska-van der Molen MA, Kwakernaak I, van Pelt JA, Postma JL, van Alen T, Jansen RS, Welte CU. Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression. THE ISME JOURNAL 2024; 18:wrae097. [PMID: 38836495 PMCID: PMC11195473 DOI: 10.1093/ismejo/wrae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/22/2024] [Accepted: 06/03/2024] [Indexed: 06/06/2024]
Abstract
The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crop plants and poses a threat to global food production. Given that insects are known to live in a close relationship with microorganisms, our study provides insights into the community composition and function of the N. viridula-associated microbiota and its effect on host-plant interactions. We discovered that N. viridula hosts both vertically and horizontally transmitted microbiota throughout different developmental stages and their salivary glands harbor a thriving microbial community that is transmitted to the plant while feeding. The N. viridula microbiota was shown to aid its host with the detoxification of a plant metabolite, namely 3-nitropropionic acid, and repression of host plant defenses. Our results demonstrate that the N. viridula-associated microbiota plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies.
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Affiliation(s)
- Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Translational Plant Biology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ineke Kwakernaak
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Johan A van Pelt
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jelle L Postma
- Department of General Instrumentation, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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30
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Petriglieri F, Kondrotaite Z, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide. mSystems 2023; 8:e0066723. [PMID: 37992299 PMCID: PMC10746286 DOI: 10.1128/msystems.00667-23] [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: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 11/24/2023] Open
Abstract
IMPORTANCE Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.
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Affiliation(s)
- Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten K. D. Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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31
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Meziti A, Smeti E, Daniilides D, Spatharis S, Tsirtsis G, Kormas KA. Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems. PeerJ 2023; 11:e16655. [PMID: 38144191 PMCID: PMC10740597 DOI: 10.7717/peerj.16655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Background-Aim Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions. Methods Protistan community structure analysis was based on the diversity of the V2-V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis. Results It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage. Conclusion Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.
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Affiliation(s)
- Alexandra Meziti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
| | - Evangelia Smeti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, Greece
| | - Daniil Daniilides
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Athens, Greece
| | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
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32
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Jiang Y, Jia D, Sun Y, Ding N, Wang L. Microbiota: A key factor affecting and regulating the efficacy of immunotherapy. Clin Transl Med 2023; 13:e1508. [PMID: 38082435 PMCID: PMC10713876 DOI: 10.1002/ctm2.1508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Immunotherapy has made significant progress in cancer treatment; however, the responsiveness to immunotherapy varies widely among patients. Growing evidence has demonstrated the role of the gut microbiota in the efficacy of immunotherapy. MAIN BODY Herein, we summarise the changes in the microbiota in different cancers under various immunotherapies. The microbial-host signal transmission on immunotherapeutic responses and mechanisms associated with microbial translocation to tumours in the context of immunotherapy are also discussed. In addition, we have highlighted the clinical application value of methods for regulating the microbiota. Finally, we elaborate on the relationship between the microbiota, host and immunotherapy, and provide potential directions for future research. CONCLUSION Different microbiota cause changes in the tumour microenvironment through microbial signals thereby affecting immunotherapy efficacy. Translocation of gut microbiota and the role of extraintestinal microbiota in immunotherapy deserve attention. Microbiota regulation is a novel strategy for combination therapy with immunotherapy. Although there are several aspects that deserve further refinement and exploration with regard to administration and clinical translation. Nevertheless, it is foreseeable that the microbiota will become an integral part of cancer treatment.
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Affiliation(s)
- Yao Jiang
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Dingjiacheng Jia
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Yong Sun
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Ning Ding
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Liangjing Wang
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
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33
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Jackson PP, Wijeyesekera A, Williams CM, Theis S, van Harsselaar J, Rastall RA. Inulin-type fructans and 2'fucosyllactose alter both microbial composition and appear to alleviate stress-induced mood state in a working population compared to placebo (maltodextrin): the EFFICAD Trial, a randomized, controlled trial. Am J Clin Nutr 2023; 118:938-955. [PMID: 37657523 PMCID: PMC10636234 DOI: 10.1016/j.ajcnut.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND There is increasing interest in the bidirectional relationship existing between the gut and brain and the effects of both oligofructose and 2'fucosyllactose to alter microbial composition and mood state. Yet, much remains unknown about the ability of oligofructose and 2'fucosyllactose to improve mood state via targeted manipulation of the gut microbiota. OBJECTIVES We aimed to compare the effects of oligofructose and 2'fucosyllactose alone and in combination against maltodextrin (comparator) on microbial composition and mood state in a working population. METHODS We conducted a 5-wk, 4-arm, parallel, double-blind, randomized, placebo-controlled trial in 92 healthy adults with mild-to-moderate levels of anxiety and depression. Subjects were randomized to oligofructose 8 g/d (plus 2 g/d maltodextrin); maltodextrin 10 g/d; oligofructose 8 g/d plus 2'fucosyllactose (2 g/d) or 2'fucosyllactose 2 g/d (plus 8 g/d maltodextrin). Changes in microbial load (fluorescence in situ hybridization-flow cytometry) and composition (16S ribosomal RNA sequencing) were the primary outcomes. Secondary outcomes included gastrointestinal sensations, bowel habits, and mood state parameters. RESULTS There were significant increases in several bacterial taxa including Bifidobacterium, Bacteroides, Roseburia, and Faecalibacterium prausnitzii in both the oligofructose and oligofructose/2'fucosyllactose interventions (all P ≤ 0.05). Changes in bacterial taxa were highly heterogenous upon 2'fuscoyllactose supplementation. Significant improvements in Beck Depression Inventory, State Trait Anxiety Inventory Y1 and Y2, and Positive and Negative Affect Schedule scores and cortisol awakening response were detected across oligofructose, 2'fucosyllactose, and oligofructose/2'fucosyllactose combination interventions (all P ≤ 0.05). Both sole oligofructose and oligofructose/2'fuscosyllactose combination interventions outperformed both sole 2'fucosyllactose and maltodextrin in improvements in several mood state parameters (all P ≤ 0.05). CONCLUSION The results of this study indicate that oligofructose and combination of oligofructose/2'fucosyllactose can beneficially alter microbial composition along with improving mood state parameters. Future work is needed to understand key microbial differences separating individual responses to 2'fucosyllactose supplementation. This trial was registered at clinicaltrials.gov as NCT05212545.
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Affiliation(s)
- Peter Pj Jackson
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Anisha Wijeyesekera
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Claire M Williams
- University of Reading, School of Psychology and Clinical Language Science, Reading, United Kingdom
| | | | | | - Robert A Rastall
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom.
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Candry P, Chadwick GL, Caravajal-Arroyo JM, Lacoere T, Winkler MKH, Ganigué R, Orphan VJ, Rabaey K. Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities. THE ISME JOURNAL 2023; 17:2014-2022. [PMID: 37715042 PMCID: PMC10579388 DOI: 10.1038/s41396-023-01508-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.
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Affiliation(s)
- Pieter Candry
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - José Maria Caravajal-Arroyo
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tim Lacoere
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | | | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium.
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Zhang X, Joyce GH, Leu AO, Zhao J, Rabiee H, Virdis B, Tyson GW, Yuan Z, McIlroy SJ, Hu S. Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens'. Nat Commun 2023; 14:6118. [PMID: 37777538 PMCID: PMC10542353 DOI: 10.1038/s41467-023-41847-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023] Open
Abstract
Anaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by 'Candidatus Methanoperedens nitroreducens', an ANME acclimated to nitrate reduction. Ferrous iron-targeted fluorescent assays, metatranscriptomics, and single-cell imaging suggest that 'Ca. M. nitroreducens' uses surface-localized redox-active cytochromes for metal reduction. Electrochemical and Raman spectroscopic analyses also support the involvement of c-type cytochrome-mediated EET for electrode reduction. Furthermore, several genes encoding menaquinone cytochrome type-c oxidoreductases and extracellular MHCs are differentially expressed when different electron acceptors are used.
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Affiliation(s)
- Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Georgina H Joyce
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Jing Zhao
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- Ecological Engineering of Mine Wastes, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hesamoddin Rabiee
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, Australia
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia.
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Tsukamoto H, Phan HV, Suenaga T, Yasuda S, Kuroiwa M, Riya S, Ogata A, Hori T, Terada A. Microaerophilic Activated Sludge System for Ammonia Retention toward Recovery from High-Strength Nitrogenous Wastewater: Performance and Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13874-13886. [PMID: 37676844 DOI: 10.1021/acs.est.3c03002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
A transition to ammonia recovery from wastewater has started; however, a technology for sustainable nitrogen retention in the form of ammonia and organic carbon removal is still in development. This study validated a microaerophilic activated sludge (MAS) system to efficiently retain ammonia from high-strength nitrogenous wastewater. The MAS is based on conventional activated sludge (CAS) with aerobic and settling compartments. Low dissolved oxygen (DO) concentrations (<0.2 mg/L) and short solids retention times (SRTs) (<5 days) eliminated nitrifying bacteria. The two parallel MASs were successfully operated for 300 days and had ammonia retention of 101.7 ± 24.9% and organic carbon removal of 85.5 ± 8.9%. The MASs mitigated N2O emissions with an emission factor of <0.23%, much lower than the default value of CAS (1.6%). A short-term step-change test demonstrated that N2O indicated the initiation of nitrification and the completion of denitrification in the MAS. The parallel MASs had comparable microbial diversity, promoting organic carbon oxidation while inhibiting ammonia-oxidizing microorganisms (AOMs), as revealed by 16S rRNA gene amplicon sequencing, the quantitative polymerase chain reaction of functional genes, and fluorescence in situ hybridization of β-proteobacteria AOB. The microbial analyses also uncovered that filamentous bacteria were positively correlated with effluent turbidity. Together, controlling DO and SRT achieved organic carbon removal and successful ammonia retention, mainly by suppressing AOM activity. This process represents a new nitrogen management paradigm.
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Affiliation(s)
- Hiroki Tsukamoto
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Hop V Phan
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Toshikazu Suenaga
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
- Department of Chemical Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi- Hiroshima, Hiroshima 739-8527, Japan
| | - Shohei Yasuda
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
| | - Megumi Kuroiwa
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Shohei Riya
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
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Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Commun Biol 2023; 6:948. [PMID: 37723238 PMCID: PMC10507103 DOI: 10.1038/s42003-023-05299-8] [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: 03/10/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023] Open
Abstract
Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
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Affiliation(s)
- Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Julian A Liber
- Department of Biology, Duke University, Durham, NC, 27704, USA
| | - Abigail E Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Alan Kuo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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Bharathi SD, Dilshani A, Rishivanthi S, Khaitan P, Vamsidhar A, Jacob S. Resource Recycling, Recovery, and Xenobiotic Remediation from E-wastes Through Biofilm Technology: A Review. Appl Biochem Biotechnol 2023; 195:5669-5692. [PMID: 35796946 DOI: 10.1007/s12010-022-04055-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 11/02/2022]
Abstract
Around 50 million tonnes of electronic waste has been generated globally per year, causing an environmental hazard and negative effects on human health, such as infertility and thyroid disorders in adults, endocrine and neurological damage in both animals and humans, and impaired mental and physical development in children. Out of that, only 15% is recycled each year and the remaining is disposed of in a landfill, illegally traded or burned, and treated in a sub-standard way. The processes of recycling are challenged by the presence of brominated flame retardants. The different recycling technologies such as the chemical and mechanical methods have been well studied, while the most promising approach is the biological method. The process of utilizing microbes to decontaminate and degrade a wide range of pollutants into harmless products is known as bioremediation and it is an eco-friendly, cost-effective, and sustainable method. The bioremediation process is significantly aided by biofilm communities attached to electronic waste because they promote substrate bioavailability, metabolite transfer, and cell viability, all of which accelerate bioleaching and biodegradation. Microbes existing in biofilm mode relatable to free-floating planktonic cells are advantageous of bioremediation due to their tolerant ability to environmental stress and pollutants through diverse catabolic pathways. This article discusses the harmful effects of electronic waste and its management using biological strategies especially biofilm-forming communities for resource recovery.
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Affiliation(s)
- Sundaram Deepika Bharathi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Aswin Dilshani
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Srinivasan Rishivanthi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Pratham Khaitan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Adhinarayan Vamsidhar
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu Dist., 603203, Tamil Nadu, India.
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Pfisterer N, Ammer-Herrmenau C, Antweiler K, Küffer S, Ellenrieder V, Neesse A. Dynamics of intestinal and intratumoral microbiome signatures in genetically engineered mice and human pancreatic ductal adenocarcinoma. Pancreatology 2023; 23:663-673. [PMID: 37541802 DOI: 10.1016/j.pan.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Emerging evidence has recently revealed a prominent role of the microbiome in pancreatic ductal adenocarcinoma (PDAC). However, while most observations were made in patients, mouse models still require a precise characterization of their disease-related microbiome to employ them for mechanistic and interventional preclinical studies. METHODS To investigate the fecal and tumoral microbiome of LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx-1-Cre (KPC) and control (CTRL) mice, Oxford Nanopore sequencing was applied. Feces were collected from 10 KPC mice and 10 CTRLs at 3 timepoints (6 weeks, 12 weeks, and when tumor-bearing (KPC) or 6 months (CTRL), respectively). Metagenomic sequencing was performed on feces DNA. KPC tumor and healthy pancreas DNA samples were subjected to 16S rRNA gene sequencing. Bacterial marker components were detected in KPC tumor tissue over time by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC). RESULTS Murine fecal samples showed a significantly different microbiome compared to age-matched healthy CTRLs regarding beta diversity (p = 0.001, R2 = 0.2-0.25 for Bray-Curtis). Adjusted human PDAC classifiers predicted disease status from feces of KPC mice achieving area under the receiver operating characteristic (AUROC) values of 80%. Furthermore, KPC tumors harbored significantly more bacterial components than healthy pancreas. Also the microbial composition differs significantly between KPC tumors and healthy pancreas tissue (p = 0.042 for Bray-Curtis). Microbiota found highly abundant in human PDAC samples were considerably more abundant in KPC tumors as compared to healthy pancreas samples (p-value <0.001). CONCLUSION KPC fecal samples show similarities with the microbial composition of stool samples from human PDAC patients.
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Affiliation(s)
- Nina Pfisterer
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, 37075, Goettingen, Germany; Clinical Research Unit KFO5002, University Medical Center Goettingen, 37075, Goettingen, Germany
| | - Christoph Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, 37075, Goettingen, Germany; Clinical Research Unit KFO5002, University Medical Center Goettingen, 37075, Goettingen, Germany
| | - Kai Antweiler
- Institute of Medical Statistics, University Medical Center Goettingen, 37073, Goettingen, Germany
| | - Stefan Küffer
- Institute of Pathology, University Medical Center Goettingen, 37075, Goettingen, Germany
| | - Volker Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, 37075, Goettingen, Germany; Clinical Research Unit KFO5002, University Medical Center Goettingen, 37075, Goettingen, Germany
| | - Albrecht Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, 37075, Goettingen, Germany; Clinical Research Unit KFO5002, University Medical Center Goettingen, 37075, Goettingen, Germany.
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Fusi M, Ngugi DK, Marasco R, Booth JM, Cardinale M, Sacchi L, Clementi E, Yang X, Garuglieri E, Fodelianakis S, Michoud G, Daffonchio D. Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation. MICROBIOME 2023; 11:189. [PMID: 37612775 PMCID: PMC10463870 DOI: 10.1186/s40168-023-01629-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND The transition from water to air is a key event in the evolution of many marine organisms to access new food sources, escape water hypoxia, and exploit the higher and temperature-independent oxygen concentration of air. Despite the importance of microorganisms in host adaptation, their contribution to overcoming the challenges posed by the lifestyle changes from water to land is not well understood. To address this, we examined how microbial association with a key multifunctional organ, the gill, is involved in the intertidal adaptation of fiddler crabs, a dual-breathing organism. RESULTS Electron microscopy revealed a rod-shaped bacterial layer tightly connected to the gill lamellae of the five crab species sampled across a latitudinal gradient from the central Red Sea to the southern Indian Ocean. The gill bacterial community diversity assessed with 16S rRNA gene amplicon sequencing was consistently low across crab species, and the same actinobacterial group, namely Ilumatobacter, was dominant regardless of the geographic location of the host. Using metagenomics and metatranscriptomics, we detected that these members of actinobacteria are potentially able to convert ammonia to amino acids and may help eliminate toxic sulphur compounds and carbon monoxide to which crabs are constantly exposed. CONCLUSIONS These results indicate that bacteria selected on gills can play a role in the adaptation of animals in dynamic intertidal ecosystems. Hence, this relationship is likely to be important in the ecological and evolutionary processes of the transition from water to air and deserves further attention, including the ontogenetic onset of this association. Video Abstract.
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Affiliation(s)
- Marco Fusi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK.
| | - David K Ngugi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Ramona Marasco
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jenny Marie Booth
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Massimiliano Cardinale
- Institute of Applied Microbiology Research Center for BioSystems, Land Use, and Nutrition (IFZ) Justus-Liebig-University Giessen, D-35392, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Lecce-Monteroni, I-73100, Lecce, Italy
| | - Luciano Sacchi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Emanuela Clementi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Xinyuan Yang
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Stilianos Fodelianakis
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Jackson PPJ, Wijeyesekera A, Rastall RA. Oligofructose alone and in combination with 2'fucosyllactose induces physiologically relevant changes in γ-aminobutyric acid and organic acid production compared to sole 2'fucosyllactose supplementation: an in vitro study. FEMS Microbiol Ecol 2023; 99:fiad100. [PMID: 37653466 PMCID: PMC10481994 DOI: 10.1093/femsec/fiad100] [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: 03/10/2023] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
We explored the potential for the prebiotic oligofructose and prebiotic candidate 2'fucosyllactose, alone and in combination (50:50 blend) to induce physiologically relevant increases in neurotransmitter (γ-aminobutyric acid, serotonin, tryptophan, and dopamine) and organic acid (acetate, propionate, butyrate, lactate, and succinate) production as well as microbiome changes using anaerobic pH-controlled in vitro batch culture fermentations over 48 h. Changes in organic acid and neurotransmitter production were assessed by gas chromatography and liquid chromatography and, bacterial enumeration using fluorescence in situ hybridization, respectively. Both oligofructose and oligofructose/2'fucosyllactose combination fermentations induced physiologically relevant concentrations of γ-aminobutyric acid, acetate, propionate, butyrate, and succinate at completion (all P ≤ .05). A high degree of heterogeneity was seen amongst donors in both neurotransmitter and organic acid production in sole 2'FL fermentations suggesting a large responder/nonresponder status exists. Large increases in Bifidobacterium, Lactobacillus, and Bacteroides numbers were detected in oligofructose fermentation, smallest increases being detected in 2'fucosyllactose fermentation. Bacterial numbers in the combined oligofructose/2'fucosyllactose fermentation were closer to that of sole oligofructose. Our results indicate that oligofructose and oligofructose/2'fucosyllactose in combination have the potential to induce physiologically relevant increases in γ-aminobutyric and organic acid production along with offsetting the heterogenicity seen in response to sole 2'fucosyllactose supplementation.
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Affiliation(s)
- Peter Philip James Jackson
- Department of Food and Nutritional Sciences, University of Reading, Harry Nursten Building, Pepper Lane, Whiteknights, Reading RG6 6DZ, United Kingdom
| | - Anisha Wijeyesekera
- Department of Food and Nutritional Sciences, University of Reading, Harry Nursten Building, Pepper Lane, Whiteknights, Reading RG6 6DZ, United Kingdom
| | - Robert Adrian Rastall
- Department of Food and Nutritional Sciences, University of Reading, Harry Nursten Building, Pepper Lane, Whiteknights, Reading RG6 6DZ, United Kingdom
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Tesson SVM, Barbato M, Rosati B. Aerosolization flux, bio-products, and dispersal capacities in the freshwater microalga Limnomonas gaiensis (Chlorophyceae). Commun Biol 2023; 6:809. [PMID: 37537210 PMCID: PMC10400582 DOI: 10.1038/s42003-023-05183-5] [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: 02/27/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Little is known on the spreading capacities of Limnomonas gaiensis across freshwater lakes in Northern Europe. In this study, we show that the species could successfully be aerosolized from water sources by bubble bursting (2-40 particles.cm-3), irrespectively of its density in the water source or of the jet velocity used to simulate wave breaking. The species viability was impacted by both water turbulences and aerosolization. The survival rate of emitted cells was low, strain-specific, and differently impacted by bubble busting processes. The entity "microalga and bionts" could produce ethanol, and actively nucleate ice (principally ≤-18 °C) mediated soluble ice nucleation active proteins, thereby potentially impacting smog and cloud formation. Moreover, smallest strains could better cope with applied stressors. Survival to short-term exposure to temperatures down to -21 °C and freezing events further suggest that L. gaiensis could be air dispersed and contribute to their deposition.
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Affiliation(s)
- Sylvie V M Tesson
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
- Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Marta Barbato
- Department of Biology, Aarhus University, Aarhus, Denmark
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
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Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
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Fokin SI, Lebedeva NA, Potekhin A, Gammuto L, Petroni G, Serra V. Holospora-like bacteria "Candidatus Gortzia yakutica" and Preeria caryophila: Ultrastructure, promiscuity, and biogeography of the symbionts. Eur J Protistol 2023; 90:125998. [PMID: 37356197 DOI: 10.1016/j.ejop.2023.125998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
Two already known representatives of Holospora-like bacteria, "Candidatus Gortzia yakutica" from Paramecium putrinum and Preeria caryophila, originally retrieved from the Paramecium aurelia complex, were found in new hosts: Paramecium nephridiatum and Paramecium polycaryum, respectively. In the present study, these bacteria were investigated using morphological and molecular methods. For "Ca. G. yakutica", the first details of the electron microscopic structure in the main and new hosts were provided. Regarding Pr. caryophila, the ultrastructural description of this species was implemented by several features previously unknown, such as the so called "membrane cluster" dividing periplasm from cytoplasm and fine composition of infectious forms before and during its releasing from the infected macronucleus. The new combinations of these Holospora-like bacteria with ciliate hosts were discussed from biogeographical and ecological points of view. Host specificity of symbionts as a general paradigm was critically reviewed as well.
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Affiliation(s)
| | - Natalia A Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Russia
| | - Alexey Potekhin
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia; Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | | | - Giulio Petroni
- Department of Biology, University of Pisa, Italy; CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy; CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, Italy
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45
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Guo XK, Wang J, van Hensbergen VP, Liu J, Xu H, Hu X. Interactions between host and intestinal crypt-resided biofilms are controlled by epithelial fucosylation. Cell Rep 2023; 42:112754. [PMID: 37405914 DOI: 10.1016/j.celrep.2023.112754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/30/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
As highly organized consortia of bacteria, biofilms have long been implicated in aggravating inflammation. However, our understanding regarding in vivo host-biofilm interactions in the complex tissue environments remains limited. Here, we show a unique pattern of crypt occupation by mucus-associated biofilms during the early stage of colitis, which is genetically dependent on bacterial biofilm-forming capacity and restricted by host epithelial α1,2-fucosylation. α1,2-Fucosylation deficiency leads to markedly augmented crypt occupation by biofilms originated from pathogenic Salmonella Typhimurium or indigenous Escherichia coli, resulting in exacerbated intestinal inflammation. Mechanistically, α1,2-fucosylation-mediated restriction of biofilms relies on interactions between bacteria and liberated fucose from biofilm-occupied mucus. Fucose represses biofilm formation and biofilm-related genes in vitro and in vivo. Finally, fucose administration ameliorates experimental colitis, suggesting therapeutic potential of fucose for biofilm-related disorders. This work illustrates host-biofilm interactions during gut inflammation and identifies fucosylation as a physiological strategy for restraining biofilm formation.
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Affiliation(s)
- Xue-Kun Guo
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China.
| | - Jiali Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China
| | - Vincent P van Hensbergen
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China
| | - Jintao Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 10084, China
| | - Huji Xu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Clinical Medicine and School of Medicine, Tsinghua University, Beijing 100084, China; Department of Rheumatology and Immunology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China.
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Hidalgo-Villeda F, Million M, Defoort C, Vannier T, Svilar L, Lagier M, Wagner C, Arroyo-Portilla C, Chasson L, Luciani C, Bossi V, Gorvel JP, Lelouard H, Tomas J. Prolonged dysbiosis and altered immunity under nutritional intervention in a physiological mouse model of severe acute malnutrition. iScience 2023; 26:106910. [PMID: 37378323 PMCID: PMC10291336 DOI: 10.1016/j.isci.2023.106910] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/03/2023] [Accepted: 05/12/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute malnutrition (SAM) is a multifactorial disease affecting millions of children worldwide. It is associated with changes in intestinal physiology, microbiota, and mucosal immunity, emphasizing the need for multidisciplinary studies to unravel its full pathogenesis. We established an experimental model in which weanling mice fed a high-deficiency diet mimic key anthropometric and physiological features of SAM in children. This diet alters the intestinal microbiota (less segmented filamentous bacteria, spatial proximity to epithelium), metabolism (decreased butyrate), and immune cell populations (depletion of LysoDC in Peyer's patches and intestinal Th17 cells). A nutritional intervention leads to a fast zoometric and intestinal physiology recovery but to an incomplete restoration of the intestinal microbiota, metabolism, and immune system. Altogether, we provide a preclinical model of SAM and have identified key markers to target with future interventions during the education of the immune system to improve SAM whole defects.
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Affiliation(s)
- Fanny Hidalgo-Villeda
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
- Escuela de Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
- IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France
- Ap-HM, Marseille, France
| | - Catherine Defoort
- C2VN, INRA, INSERM, Aix Marseille University, CriBioM, Marseille, France
| | - Thomas Vannier
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Ljubica Svilar
- C2VN, INRA, INSERM, Aix Marseille University, CriBioM, Marseille, France
| | - Margaux Lagier
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Camille Wagner
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Cynthia Arroyo-Portilla
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
- Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Lionel Chasson
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Cécilia Luciani
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | | | - Jean-Pierre Gorvel
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Hugues Lelouard
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
| | - Julie Tomas
- Aix Marseille University, CNRS, INSERM, CIML, Turing Centre for Living Systems, Marseille, France
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47
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Džunková M, La Clair JJ, Tyml T, Doud D, Schulz F, Piquer-Esteban S, Porcel Sanchis D, Osborn A, Robinson D, Louie KB, Bowen BP, Bowers RM, Lee J, Arnau V, Díaz-Villanueva W, Stepanauskas R, Gosliner T, Date SV, Northen TR, Cheng JF, Burkart MD, Woyke T. Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium. MICROBIOME 2023; 11:130. [PMID: 37312139 DOI: 10.1186/s40168-023-01560-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. RESULTS We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. CONCLUSIONS Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo. Video Abstract.
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Affiliation(s)
- Mária Džunková
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain.
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Tomáš Tyml
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Devin Doud
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Piquer-Esteban
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Dafne Porcel Sanchis
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Andrew Osborn
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Robinson
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ben P Bowen
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert M Bowers
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Janey Lee
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vicente Arnau
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), Valencia, Spain
| | - Wladimiro Díaz-Villanueva
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), Valencia, Spain
| | | | | | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA
- University of California San Francisco, San Francisco, CA, USA
- San Francisco State University, San Francisco, CA, USA
| | - Trent R Northen
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA.
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48
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Wicaksono WA, Semler B, Pöltl M, Berg C, Berg G, Cernava T. The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts. ENVIRONMENTAL MICROBIOME 2023; 18:46. [PMID: 37264474 DOI: 10.1186/s40793-023-00501-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy. RESULTS Riccia spec. div. was colonized by a very high abundance of bacteria (1010 16S rRNA gene copies per g of thallus) as well as archaea and fungi (108 ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens. CONCLUSIONS Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Bettina Semler
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Martina Pöltl
- Institute of Biology, University of Graz, Graz, 8010, Austria
| | - Christian Berg
- Institute of Biology, University of Graz, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- Graz University of Technology, Graz, Austria.
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49
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Baltar F, Martínez-Pérez C, Amano C, Vial M, Robaina-Estévez S, Reinthaler T, Herndl GJ, Zhao Z, Logares R, Morales SE, González JM. A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean. Nat Microbiol 2023; 8:1137-1148. [PMID: 37095175 DOI: 10.1038/s41564-023-01374-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023]
Abstract
The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the 'Tara Oceans' and 'Malaspina' expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean.
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Affiliation(s)
- Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
| | - Clara Martínez-Pérez
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Marion Vial
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain.
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50
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Zvi-Kedem T, Vintila S, Kleiner M, Tchernov D, Rubin-Blum M. Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels. ISME COMMUNICATIONS 2023; 3:48. [PMID: 37210404 PMCID: PMC10199937 DOI: 10.1038/s43705-023-00254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
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Affiliation(s)
- Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel.
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